From adfdb72f7b0972c2affd7574f1aceddcfbb9a015 Mon Sep 17 00:00:00 2001 From: Sofia Vargas <140123401+sofievargas@users.noreply.github.com> Date: Tue, 31 Mar 2026 21:55:19 -0700 Subject: [PATCH 01/23] Update api_documentation.md --- api_documentation.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/api_documentation.md b/api_documentation.md index b5e11ed..fa839f5 100644 --- a/api_documentation.md +++ b/api_documentation.md @@ -155,6 +155,14 @@ Returns a list of all language codes currently stored in the system. * **Method:** GET * **Path:**/languages +Returns all language codes currently stored in Neo4j. + +Response Example: +```json +{ + "languages": ["en", "es", "fr", "pt"] +} +``` #### Error Handling The API uses standard HTTP status codes. From 6bcec0c170838577d23fb2e7c006fc30fb55342f Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 22 Jul 2026 13:37:38 -0700 Subject: [PATCH 02/23] Added source_data so graph is created in a singular file --- scripts/loaders/drugbank_loader.py | 159 ---------- scripts/loaders/icd11_loader.py | 84 ------ scripts/loaders/rxnorm_loader.py | 105 ------- scripts/loaders/snomedct_loader.py | 170 ----------- scripts/loaders/source_data.py | 454 +++++++++++++++++++++++++++++ 5 files changed, 454 insertions(+), 518 deletions(-) delete mode 100644 scripts/loaders/drugbank_loader.py delete mode 100644 scripts/loaders/icd11_loader.py delete mode 100644 scripts/loaders/rxnorm_loader.py delete mode 100644 scripts/loaders/snomedct_loader.py create mode 100644 scripts/loaders/source_data.py diff --git a/scripts/loaders/drugbank_loader.py b/scripts/loaders/drugbank_loader.py deleted file mode 100644 index dfc2aa1..0000000 --- a/scripts/loaders/drugbank_loader.py +++ /dev/null @@ -1,159 +0,0 @@ -""" -Project Codex — DrugBank Source Loader -Reads sample_data/drugbank_sample.json and writes into normalized Codex schema. -""" - -import json -import uuid -from datetime import datetime, timezone - - -def now_iso(): - return datetime.now(timezone.utc).isoformat() - - -def load_drugbank(db, data_path: str, poc_ids: set = None): - """ - Load DrugBank JSON sample data into Neo4j. - - Args: - db: CodexDB instance - data_path: Path to drugbank_sample.json - poc_ids: Set of DrugBank IDs to flag as POC (default: first 3) - """ - with open(data_path) as f: - drugs = json.load(f) - - if poc_ids is None: - poc_ids = {d["drugbank_id"] for d in drugs[:3]} - - print(f"[DrugBank] Loading {len(drugs)} drugs...") - - for drug in drugs: - db_id = drug["drugbank_id"] - is_poc = db_id in poc_ids - ts = now_iso() - - # ---- Upsert Drug node ---- - db.run(""" - MERGE (d:Drug {source: 'drugbank', source_id: $source_id}) - ON CREATE SET - d.codex_id = $codex_id, - d.canonical_name = $name, - d.drug_type = $drug_type, - d.is_approved = $is_approved, - d.source_attribute_name = 'drugbank_id', - d.created_at = datetime($ts), - d.updated_at = datetime($ts), - d.is_poc = $is_poc - ON MATCH SET - d.updated_at = datetime($ts) - """, { - "source_id": db_id, - "codex_id": "codex-drug-" + db_id, - "name": drug["name"], - "drug_type": drug.get("type", "small molecule").replace(" ", "_"), - "is_approved": "approved" in drug.get("groups", []), - "ts": ts, - "is_poc": is_poc, - }) - - # ---- Upsert Ingredient node ---- - if drug.get("inchikey"): - db.run(""" - MERGE (i:Ingredient {inchikey: $inchikey}) - ON CREATE SET - i.codex_id = $codex_id, - i.name = $name, - i.cas_number = $cas_number, - i.source = 'drugbank', - i.source_id = $source_id, - i.source_attribute_name = 'cas_number', - i.created_at = datetime($ts), - i.updated_at = datetime($ts), - i.is_poc = $is_poc - ON MATCH SET i.updated_at = datetime($ts) - """, { - "inchikey": drug["inchikey"], - "codex_id": "codex-ing-" + drug["inchikey"][:8], - "name": drug["name"], - "cas_number": drug.get("cas_number", ""), - "source_id": db_id + "-active", - "ts": ts, - "is_poc": is_poc, - }) - - db.run(""" - MATCH (d:Drug {source: 'drugbank', source_id: $db_id}) - MATCH (i:Ingredient {inchikey: $inchikey}) - MERGE (d)-[:CONTAINS_INGREDIENT {role: 'active', source: 'drugbank'}]->(i) - """, {"db_id": db_id, "inchikey": drug["inchikey"]}) - - # ---- Upsert DrugName nodes ---- - for brand in drug.get("brands", []): - db.run(""" - MERGE (dn:DrugName {name: $name, country: $country, language: $language}) - ON CREATE SET - dn.name_type = 'brand', - dn.is_primary = true, - dn.source = 'drugbank', - dn.source_attribute_name = 'brands.name', - dn.created_at = datetime($ts), - dn.updated_at = datetime($ts), - dn.is_poc = $is_poc - ON MATCH SET dn.updated_at = datetime($ts) - """, { - "name": brand["name"], - "country": brand["country"], - "language": _country_to_lang(brand["country"]), - "ts": ts, - "is_poc": is_poc, - }) - - db.run(""" - MATCH (d:Drug {source: 'drugbank', source_id: $db_id}) - MATCH (dn:DrugName {name: $name, country: $country}) - MERGE (d)-[:HAS_NAME {source: 'drugbank', created_at: datetime($ts)}]->(dn) - """, {"db_id": db_id, "name": brand["name"], - "country": brand["country"], "ts": ts}) - - # ---- Generic name entry (US, EN) ---- - db.run(""" - MERGE (dn:DrugName {name: $name, country: 'US', language: 'en'}) - ON CREATE SET - dn.name_type = 'generic', - dn.is_primary = true, - dn.source = 'drugbank', - dn.source_attribute_name = 'name', - dn.created_at = datetime($ts), - dn.updated_at = datetime($ts), - dn.is_poc = $is_poc - ON MATCH SET dn.updated_at = datetime($ts) - """, {"name": drug["name"], "ts": ts, "is_poc": is_poc}) - - db.run(""" - MATCH (d:Drug {source: 'drugbank', source_id: $db_id}) - MATCH (dn:DrugName {name: $name, country: 'US', language: 'en'}) - MERGE (d)-[:HAS_NAME {source: 'drugbank', created_at: datetime($ts)}]->(dn) - """, {"db_id": db_id, "name": drug["name"], "ts": ts}) - - # ---- SOURCED_FROM ---- - db.run(""" - MATCH (d:Drug {source: 'drugbank', source_id: $db_id}) - MATCH (ds:DataSource {name: 'drugbank'}) - MERGE (d)-[:SOURCED_FROM {ingested_at: datetime($ts)}]->(ds) - """, {"db_id": db_id, "ts": ts}) - - print(f" [DrugBank] Loaded: {drug['name']} ({db_id})" + - (" [POC]" if is_poc else "")) - - print(f"[DrugBank] Done. {len(drugs)} drugs processed.\n") - - -def _country_to_lang(country: str) -> str: - mapping = { - "US": "en", "GB": "en", "AU": "en", "IN": "hi", - "FR": "fr", "DE": "de", "IT": "it", "ES": "es", - "JP": "ja", "CN": "zh", - } - return mapping.get(country, "en") diff --git a/scripts/loaders/icd11_loader.py b/scripts/loaders/icd11_loader.py deleted file mode 100644 index 86b5227..0000000 --- a/scripts/loaders/icd11_loader.py +++ /dev/null @@ -1,84 +0,0 @@ -""" -Project Codex — ICD-11 Source Loader -Reads sample_data/icd11_sample.json and loads conditions into Codex schema. -""" - -import json -from datetime import datetime, timezone - -# Map ICD-11 codes to DrugBank drug IDs for TREATS relationships -ICD11_TREATS_DRUGBANK = { - "JA00": ["DB00331"], # T2DM ← Metformin - "BA00": [], # Hypertension (drugs loaded separately) - "CA01": ["DB00682", "DB00945"], # AF ← Warfarin, Aspirin - "FA24": ["DB00563"], # RA ← Methotrexate -} - - -def now_iso(): - return datetime.now(timezone.utc).isoformat() - - -def load_icd11(db, data_path: str, poc_codes: set = None): - with open(data_path) as f: - conditions = json.load(f) - - if poc_codes is None: - poc_codes = {"JA00", "BA00", "FA24"} - - print(f"[ICD-11] Loading {len(conditions)} conditions...") - - for cond in conditions: - code = cond["code"] - is_poc = code in poc_codes - ts = now_iso() - - # ---- Upsert Condition node ---- - db.run(""" - MERGE (c:Condition {source: 'icd11', source_id: $code}) - ON CREATE SET - c.codex_id = 'codex-cond-ICD-' + $code, - c.canonical_name = $name, - c.icd11_code = $code, - c.source_attribute_name = 'code', - c.created_at = datetime($ts), - c.updated_at = datetime($ts), - c.is_poc = $is_poc - ON MATCH SET - c.updated_at = datetime($ts) - """, {"code": code, "name": cond["title"], "ts": ts, "is_poc": is_poc}) - - # ---- SOURCED_FROM ---- - db.run(""" - MATCH (c:Condition {source: 'icd11', source_id: $code}) - MATCH (ds:DataSource {name: 'icd11'}) - MERGE (c)-[:SOURCED_FROM {ingested_at: datetime($ts)}]->(ds) - """, {"code": code, "ts": ts}) - - # ---- TREATS relationships ---- - for drug_id in ICD11_TREATS_DRUGBANK.get(code, []): - db.run(""" - MATCH (d:Drug {source: 'drugbank', source_id: $drug_id}) - MATCH (c:Condition {source: 'icd11', source_id: $code}) - MERGE (d)-[:TREATS { - evidence_level: 'A', - source: 'icd11+drugbank', - created_at: datetime($ts) - }]->(c) - """, {"drug_id": drug_id, "code": code, "ts": ts}) - - print(f" [ICD-11] Loaded: {cond['title']} ({code})" + - (" [POC]" if is_poc else "")) - - # ---- ICD-11 hierarchy (PARENT_OF) ---- - hierarchy = [ - ("BA00", "CA01"), # Circulatory diseases → Atrial fibrillation - ] - for parent_code, child_code in hierarchy: - db.run(""" - MATCH (parent:Condition {source: 'icd11', source_id: $parent}) - MATCH (child:Condition {source: 'icd11', source_id: $child}) - MERGE (parent)-[:PARENT_OF {source: 'icd11'}]->(child) - """, {"parent": parent_code, "child": child_code}) - - print(f"[ICD-11] Done. {len(conditions)} conditions processed.\n") diff --git a/scripts/loaders/rxnorm_loader.py b/scripts/loaders/rxnorm_loader.py deleted file mode 100644 index 623e428..0000000 --- a/scripts/loaders/rxnorm_loader.py +++ /dev/null @@ -1,105 +0,0 @@ -""" -Project Codex — RxNorm Source Loader -Reads sample_data/rxnorm_sample.json and maps into normalized Codex schema. -RxNorm is US-centric; creates EQUIVALENT_TO links to DrugBank nodes. -""" - -import json -from datetime import datetime, timezone - -# Map RxCUI → DrugBank ID for equivalence linking -RXCUI_TO_DRUGBANK = { - "161": "DB00316", # Acetaminophen - "1191": "DB00945", # Aspirin - "6809": "DB00331", # Metformin - "11289": "DB00682", # Warfarin - "7052": "DB00563", # Methotrexate -} - - -def now_iso(): - return datetime.now(timezone.utc).isoformat() - - -def load_rxnorm(db, data_path: str, poc_ids: set = None): - with open(data_path) as f: - concepts = json.load(f) - - if poc_ids is None: - poc_ids = {"161", "1191", "6809"} # Acetaminophen, Aspirin, Metformin - - print(f"[RxNorm] Loading {len(concepts)} concepts...") - - for concept in concepts: - rxcui = concept["rxcui"] - is_poc = rxcui in poc_ids - ts = now_iso() - - # ---- Upsert Drug node ---- - db.run(""" - MERGE (d:Drug {source: 'rxnorm', source_id: $rxcui}) - ON CREATE SET - d.codex_id = 'codex-drug-RX' + $rxcui, - d.canonical_name = $name, - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'rxcui', - d.created_at = datetime($ts), - d.updated_at = datetime($ts), - d.is_poc = $is_poc - ON MATCH SET - d.updated_at = datetime($ts) - """, {"rxcui": rxcui, "name": concept["name"], "ts": ts, "is_poc": is_poc}) - - # ---- SOURCED_FROM ---- - db.run(""" - MATCH (d:Drug {source: 'rxnorm', source_id: $rxcui}) - MATCH (ds:DataSource {name: 'rxnorm'}) - MERGE (d)-[:SOURCED_FROM {ingested_at: datetime($ts)}]->(ds) - """, {"rxcui": rxcui, "ts": ts}) - - # ---- EQUIVALENT_TO DrugBank ---- - if rxcui in RXCUI_TO_DRUGBANK: - db_id = RXCUI_TO_DRUGBANK[rxcui] - db.run(""" - MATCH (db_drug:Drug {source: 'drugbank', source_id: $db_id}) - MATCH (rx_drug:Drug {source: 'rxnorm', source_id: $rxcui}) - MERGE (db_drug)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'name+inchikey', - created_at: datetime($ts) - }]->(rx_drug) - """, {"db_id": db_id, "rxcui": rxcui, "ts": ts}) - - # ---- Clinical dose form names (SCD/SBD) ---- - for rel in concept.get("related_concepts", []): - if rel["tty"] in ("SCD", "SBD"): - db.run(""" - MERGE (dn:DrugName {name: $name, country: 'US', language: 'en'}) - ON CREATE SET - dn.name_type = $name_type, - dn.is_primary = false, - dn.source = 'rxnorm', - dn.source_attribute_name = $tty, - dn.created_at = datetime($ts), - dn.updated_at = datetime($ts), - dn.is_poc = false - ON MATCH SET dn.updated_at = datetime($ts) - """, { - "name": rel["name"], - "name_type": "clinical_dose_form" if rel["tty"] == "SCD" else "brand_dose_form", - "tty": rel["tty"], - "ts": ts, - }) - - db.run(""" - MATCH (d:Drug {source: 'rxnorm', source_id: $rxcui}) - MATCH (dn:DrugName {name: $name, country: 'US', language: 'en'}) - MERGE (d)-[:HAS_NAME {source: 'rxnorm', created_at: datetime($ts)}]->(dn) - """, {"rxcui": rxcui, "name": rel["name"], "ts": ts}) - - print(f" [RxNorm] Loaded: {concept['name']} (RxCUI {rxcui})" + - (" [POC]" if is_poc else "")) - - print(f"[RxNorm] Done. {len(concepts)} concepts processed.\n") diff --git a/scripts/loaders/snomedct_loader.py b/scripts/loaders/snomedct_loader.py deleted file mode 100644 index fab8e5a..0000000 --- a/scripts/loaders/snomedct_loader.py +++ /dev/null @@ -1,170 +0,0 @@ -""" -Project Codex — SNOMED CT Source Loader -Reads sample_data/snomedct_sample.json and loads into Codex schema. -Establishes EQUIVALENT_TO links between SNOMED and DrugBank/ICD-11 nodes. -""" - -import json -from datetime import datetime, timezone - -# SNOMED concept_id → DrugBank ID (for EQUIVALENT_TO) -SNOMED_TO_DRUGBANK = { - "387517004": "DB00316", # Paracetamol ↔ Acetaminophen - "387458008": "DB00945", # Aspirin - "387467008": "DB00331", # Metformin - "372687004": None, # Amoxicillin — not yet in DrugBank sample -} - -# SNOMED concept_id → ICD-11 code (for conditions) -SNOMED_DISORDER_TO_ICD11 = { - "44508008": "JA00", # T2DM - "69896004": "FA24", # Rheumatoid arthritis -} - -# Names to add as DrugName nodes (SNOMED synonyms) -SNOMED_NAMES = { - "387517004": [ - {"name": "Paracetamol", "country": "GB", "language": "en", "name_type": "generic"}, - {"name": "Paracetamol", "country": "IN", "language": "en", "name_type": "generic"}, - {"name": "Paracetamol", "country": "AU", "language": "en", "name_type": "generic"}, - {"name": "Paracetamol", "country": "ZA", "language": "en", "name_type": "generic"}, - ], - "387458008": [ - {"name": "Acetylsalicylic acid", "country": "US", "language": "en", "name_type": "generic"}, - ], - "372687004": [ - {"name": "Amoxicillin", "country": "US", "language": "en", "name_type": "generic"}, - {"name": "Amoxil", "country": "US", "language": "en", "name_type": "brand"}, - {"name": "Amoxicillin", "country": "IN", "language": "hi", "name_type": "generic"}, - {"name": "Mox", "country": "IN", "language": "hi", "name_type": "brand"}, - ], -} - - -def now_iso(): - return datetime.now(timezone.utc).isoformat() - - -def load_snomedct(db, data_path: str, poc_ids: set = None): - with open(data_path) as f: - concepts = json.load(f) - - if poc_ids is None: - poc_ids = {"387517004", "387458008", "387467008", "44508008", "69896004"} - - print(f"[SNOMED CT] Loading {len(concepts)} concepts...") - - for concept in concepts: - cid = concept["concept_id"] - is_poc = cid in poc_ids - ts = now_iso() - tag = concept["semantic_tag"] - - if tag == "substance": - _load_snomed_drug(db, concept, cid, is_poc, ts) - elif tag == "disorder": - _load_snomed_condition(db, concept, cid, is_poc, ts) - - print(f" [SNOMED CT] Loaded: {concept['preferred_term']} ({cid}, {tag})" + - (" [POC]" if is_poc else "")) - - print(f"[SNOMED CT] Done. {len(concepts)} concepts processed.\n") - - -def _load_snomed_drug(db, concept, cid, is_poc, ts): - db.run(""" - MERGE (d:Drug {source: 'snomedct', source_id: $cid}) - ON CREATE SET - d.codex_id = 'codex-drug-SCT' + $cid, - d.canonical_name = $name, - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'concept_id', - d.created_at = datetime($ts), - d.updated_at = datetime($ts), - d.is_poc = $is_poc - ON MATCH SET d.updated_at = datetime($ts) - """, {"cid": cid, "name": concept["preferred_term"], "ts": ts, "is_poc": is_poc}) - - db.run(""" - MATCH (d:Drug {source: 'snomedct', source_id: $cid}) - MATCH (ds:DataSource {name: 'snomedct'}) - MERGE (d)-[:SOURCED_FROM {ingested_at: datetime($ts)}]->(ds) - """, {"cid": cid, "ts": ts}) - - # Add SNOMED-specific name variants - for nm in SNOMED_NAMES.get(cid, []): - db.run(""" - MERGE (dn:DrugName {name: $name, country: $country, language: $language}) - ON CREATE SET - dn.name_type = $name_type, - dn.is_primary = true, - dn.source = 'snomedct', - dn.source_attribute_name = 'descriptions.Synonym', - dn.created_at = datetime($ts), - dn.updated_at = datetime($ts), - dn.is_poc = $is_poc - ON MATCH SET dn.updated_at = datetime($ts) - """, {**nm, "ts": ts, "is_poc": is_poc}) - - db.run(""" - MATCH (d:Drug {source: 'snomedct', source_id: $cid}) - MATCH (dn:DrugName {name: $name, country: $country, language: $language}) - MERGE (d)-[:HAS_NAME {source: 'snomedct', created_at: datetime($ts)}]->(dn) - """, {"cid": cid, "name": nm["name"], "country": nm["country"], - "language": nm["language"], "ts": ts}) - - # EQUIVALENT_TO DrugBank - db_id = SNOMED_TO_DRUGBANK.get(cid) - if db_id: - db.run(""" - MATCH (db_drug:Drug {source: 'drugbank', source_id: $db_id}) - MATCH (sct_drug:Drug {source: 'snomedct', source_id: $cid}) - MERGE (db_drug)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'inchikey', - created_at: datetime($ts) - }]->(sct_drug) - """, {"db_id": db_id, "cid": cid, "ts": ts}) - - -def _load_snomed_condition(db, concept, cid, is_poc, ts): - db.run(""" - MERGE (c:Condition {source: 'snomedct', source_id: $cid}) - ON CREATE SET - c.codex_id = 'codex-cond-SCT' + $cid, - c.canonical_name = $name, - c.snomed_id = $cid, - c.source_attribute_name = 'concept_id', - c.created_at = datetime($ts), - c.updated_at = datetime($ts), - c.is_poc = $is_poc - ON MATCH SET c.updated_at = datetime($ts) - """, {"cid": cid, "name": concept["preferred_term"], "ts": ts, "is_poc": is_poc}) - - db.run(""" - MATCH (c:Condition {source: 'snomedct', source_id: $cid}) - MATCH (ds:DataSource {name: 'snomedct'}) - MERGE (c)-[:SOURCED_FROM {ingested_at: datetime($ts)}]->(ds) - """, {"cid": cid, "ts": ts}) - - # EQUIVALENT_TO ICD-11 condition - icd_code = SNOMED_DISORDER_TO_ICD11.get(cid) - if icd_code: - db.run(""" - MATCH (icd:Condition {source: 'icd11', source_id: $icd_code}) - MATCH (sct:Condition {source: 'snomedct', source_id: $cid}) - MERGE (icd)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'clinical-mapping', - created_at: datetime($ts) - }]->(sct) - """, {"icd_code": icd_code, "cid": cid, "ts": ts}) - - # Enrich ICD-11 condition with SNOMED ID - db.run(""" - MATCH (c:Condition {source: 'icd11', source_id: $icd_code}) - SET c.snomed_id = $cid - """, {"icd_code": icd_code, "cid": cid}) diff --git a/scripts/loaders/source_data.py b/scripts/loaders/source_data.py new file mode 100644 index 0000000..771813a --- /dev/null +++ b/scripts/loaders/source_data.py @@ -0,0 +1,454 @@ +#!/usr/bin/env python3 + +""" +Neo4j Singular Data Source +""" + +import os +import sys +import time +import uuid +import json +import logging +from datetime import datetime, timezone +from collections import deque + +import requests +from neo4j import GraphDatabase, WRITE_ACCESS +from dotenv import load_dotenv, find_dotenv + +env_path = find_dotenv(usecwd=True) +if not env_path: + print("ERROR: .env not found at repo root") + sys.exit(1) +load_dotenv(env_path) + +NEO4J_URI = os.getenv("NEO4J_URI", "bolt://localhost:7687") +NEO4J_USER = os.getenv("NEO4J_USER", "neo4j") +NEO4J_PASSWORD = os.getenv("NEO4J_PASSWORD", "password") +NEO4J_DB = os.getenv("NEO4J_DB", "neo4j") + +FORCE = os.getenv("FORCE", "0") == "1" + +class SharedRateLimiter: + def __init__(self, RATE_LIMIT_RPM: int): + self.min_interval = 60.0 / max(1, RATE_LIMIT_RPM) + self.last_ts = 0.0 + def wait(self): + now = time.monotonic() + delta = now - self.last_ts + if delta < self.min_interval: + time.sleep(self.min_interval - delta) + self.last_ts = time.monotonic() + +LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO").upper() +logging.basicConfig( + level=getattr(logging, LOG_LEVEL, logging.INFO), + format="%(asctime)s | %(levelname)s | %(message)s", +) +log = logging.getLogger("global_root_loader") + +def utc_iso() -> str: + return datetime.now(timezone.utc).isoformat() + +def _respect_retry_after(r): + ra = r.headers.get("Retry-After") if hasattr(r, "headers") else None + if ra: + try: + secs = float(ra) + log.warning("Retry-After: sleeping %.2fs", secs) + time.sleep(secs) + return + except Exception: + pass + time.sleep(2.5) + +def smoke_test(sess): + sess.run("CREATE (:SmokeTest {ts: timestamp()})") + c = sess.run("MATCH (s:SmokeTest) RETURN count(s) AS c").single()["c"] + sess.run("MATCH (s:SmokeTest) DELETE s") + return c + + +# -------------------- +# DrugBank +# -------------------- + +def drugbank(driver): + DRUGBANK_API_BASE = os.getenv("DRUGBANK_API_BASE", "https://api.drugbank.com/discovery/v1") + DRUGBANK_API_KEY = os.getenv("DRUGBANK_API_KEY") + if not DRUGBANK_API_KEY: + print("ERROR: Missing DRUGBANK_API_KEY in .env"); sys.exit(1) + + DRUGBANK_RELEASE = os.getenv("DRUGBANK_RELEASE", "API") + ROOT_ID = os.getenv("DRUGBANK_ROOT_ID", "drugbank:root") + ROOT_TITLE = os.getenv("DRUGBANK_ROOT_TITLE", "DrugBank") + DATASET = f"DrugBank:{DRUGBANK_RELEASE}" + + limiter = SharedRateLimiter(int(os.getenv("RATE_LIMIT_RPM", "100"))) + + def drugbank_headers(): + return {"Authorization": DRUGBANK_API_KEY, "Accept": "application/json"} + + def get_json(url: str, params=None, max_retries=6): + attempt = 0 + while True: + attempt += 1; limiter.wait() + try: + r = requests.get(url, headers=drugbank_headers(), params=params or {}, timeout=60) + if r.status_code == 429: + log.warning("HTTP 429 on %s (attempt %d/%d)", url, attempt, max_retries) + _respect_retry_after(r) + if attempt < max_retries: continue + r.raise_for_status(); return r + except requests.HTTPError as e: + status = getattr(e.response, "status_code", None) + body = (e.response.text[:400] + "...") if getattr(e.response, "text", "") else "" + log.warning("Request failed [%s] %s | status=%s | body=%.120s", url, e, status, body) + if status in (429, 500, 502, 503, 504) and attempt < max_retries: + _respect_retry_after(e.response if hasattr(e, "response") else r) + continue + raise + + API_DRUGS = lambda: f"{DRUGBANK_API_BASE.rstrip('/')}/drugs" + + def iter_drugs(per_page=100): + page = 1 + while True: + resp = get_json(API_DRUGS(), params={"per_page": per_page, "page": page}) + try: + data = resp.json() + except Exception: + data = [] + items = data if isinstance(data, list) else (data.get("items") if isinstance(data, dict) else []) + if not items: break + for d in items: + dbid = d.get("drugbank_id") or d.get("id") + name = d.get("name") or d.get("generic_name") or d.get("brand_name") or "" + if dbid: yield dbid, name + link = resp.headers.get("Link", "") + if link and 'rel="next"' in link: + page += 1 + else: + page += 1 + + with driver.session(database=NEO4J_DB, default_access_mode=WRITE_ACCESS) as sess: + sess.run("CREATE CONSTRAINT drug_node_id IF NOT EXISTS FOR (n:DRUG) REQUIRE n.id IS UNIQUE") + sess.run("CREATE CONSTRAINT ingest_uid IF NOT EXISTS FOR (i:Ingest) REQUIRE i.uid IS UNIQUE") + + if bool(sess.run("MATCH (i:Ingest {dataset: $ds}) WHERE i.finishedAt IS NOT NULL RETURN i LIMIT 1", ds=DATASET).single()) and not FORCE: + log.info("DrugBank Ingest already completed. Skipping.") + return + + if FORCE: + sess.run("MATCH (i:Ingest {dataset: $ds}) DETACH DELETE i", ds=DATASET) + sess.run("MATCH (n:DRUG {ds: $ds}) DETACH DELETE n", ds=DATASET) + + run_uid = str(uuid.uuid4()) + sess.run("CREATE (i:Ingest { uid: $uid, dataset: $ds, release: $release, startedAt: $startedAt })", uid=run_uid, ds=DATASET, release=DRUGBANK_RELEASE, startedAt=utc_iso()) + sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.code = $id, n.title = $title, n.ds = $ds", id=ROOT_ID, title=ROOT_TITLE, ds=DATASET) + sess.run("MATCH (i:Ingest {uid: $uid}), (r:DRUG {id: $rootId}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rootId=ROOT_ID) + + for code, title in iter_drugs(): + sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.code=$id, n.title=$t, n.ds=$ds ON MATCH SET n.ds=$ds", id=code, t=title or None, ds=DATASET) + sess.run("MATCH (p:DRUG {id: $parent}), (c:DRUG {id: $child}) MERGE (p)-[:HAS_CHILD]->(c)", parent=ROOT_ID, child=code) + processed += 1 + + rec = sess.run("MATCH (n:DRUG {ds: $ds}) WITH count(n) AS n MATCH (:DRUG {ds: $ds})-[rel:HAS_CHILD]->(:DRUG {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() + sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt = $finishedAt, i.nodeCount = $nodeCount, i.edgeCount = $edgeCount", uid=run_uid, finishedAt=utc_iso(), nodeCount=rec["n"], edgeCount=rec["r"]) + +# -------------------- +# SNOMED +# -------------------- + +def snomed(driver): + SNOWSTORM_BASE = os.getenv("SNOWSTORM_BASE", "https://snowstorm.ihtsdotools.org/snowstorm/snomed-ct") + SNOMED_BRANCH = os.getenv("SNOMED_BRANCH", "MAIN") + SNOMED_ROOT_ID = os.getenv("SNOMED_ROOT_ID", "404684003") + SNOMED_RELEASE = os.getenv("SNOMED_RELEASE", "") + + limiter = SharedRateLimiter(int(os.getenv("RATE_LIMIT_RPM", "200"))) + + def api_get(path, params=None): + limiter.wait() + r = requests.get(f"{SNOWSTORM_BASE.rstrip('/')}/{path.lstrip('/')}", headers={"Accept": "application/json", "Accept-Language": os.getenv("ACCEPT_LANGUAGE", "en")}, params=params or {}, timeout=60) + r.raise_for_status() + return r.json() + + release = SNOMED_RELEASE or "latest" + try: + v_data = api_get("codesystems/SNOMEDCT/versions") + items = v_data.get("items") if isinstance(v_data, dict) else v_data + if items: release = items[0].get("version") or items[0].get("effectiveDate") or "latest" + except Exception: pass + + DATASET = f"SNOMEDCT:{SNOMED_BRANCH}:{release}" + + with driver.session(database=NEO4J_DB, default_access_mode=WRITE_ACCESS) as sess: + sess.run("CREATE CONSTRAINT snomed_node_id IF NOT EXISTS FOR (n:SNOMED) REQUIRE n.id IS UNIQUE") + if bool(sess.run("MATCH (i:Ingest {dataset: $ds}) WHERE i.finishedAt IS NOT NULL RETURN i LIMIT 1", ds=DATASET).single()) and not FORCE: + log.info("SNOMED CT Ingest already completed. Skipping."); return + + if FORCE: + sess.run("MATCH (i:Ingest {dataset: $ds}) DETACH DELETE i", ds=DATASET) + sess.run("MATCH (n:SNOMED {ds: $ds}) DETACH DELETE n", ds=DATASET) + + run_uid = str(uuid.uuid4()) + sess.run("CREATE (i:Ingest {uid:$uid, dataset:$ds, release:$rel, startedAt:$s})", uid=run_uid, ds=DATASET, rel=release, s=utc_iso()) + + def upsert_snomed_node(node): + cid = node.get("conceptId") or node.get("id") or "" + if not cid: return None + term = node.get("pt", {}).get("term") or node.get("fsn", {}).get("term") or node.get("term", "") + sess.run("MERGE (n:SNOMED {id: $id}) ON CREATE SET n.code=$id, n.title=$t, n.ds=$ds ON MATCH SET n.ds=$ds", id=cid, t=term or None, ds=DATASET) + return cid + + # BFS Tree Traversal + root_full = api_get(f"browser/{SNOMED_BRANCH}/concepts/{SNOMED_ROOT_ID}") + upsert_snomed_node(root_full) + sess.run("MATCH (i:Ingest {uid: $uid}), (r:SNOMED {id: $rid}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rid=SNOMED_ROOT_ID) + + queue = deque([(SNOMED_ROOT_ID, None)]) + visited = set() + while queue: + cid, parent = queue.popleft() + if cid in visited: continue + visited.add(cid) + + try: + full = api_get(f"browser/{SNOMED_BRANCH}/concepts/{cid}") + upsert_snomed_node(full) + if parent: + sess.run("MATCH (p:SNOMED {id: $p}), (c:SNOMED {id: $c}) MERGE (p)-[:HAS_CHILD]->(c)", p=parent, c=cid) + + children = api_get(f"browser/{SNOMED_BRANCH}/concepts/{cid}/children") + items = children if isinstance(children, list) else children.get("items", []) + for ch in items: + ch_id = ch.get("conceptId") or ch.get("id") + if ch_id and ch_id not in visited: queue.append((ch_id, cid)) + except Exception as e: + log.warning("Failed step processing SNOMED code %s: %s", cid, e) + + rec = sess.run("MATCH (n:SNOMED {ds: $ds}) WITH count(n) AS n MATCH (:SNOMED {ds: $ds})-[rel:HAS_CHILD]->(:SNOMED {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() + sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt=$f, i.nodeCount=$n, i.edgeCount=$r", uid=run_uid, f=utc_iso(), n=rec["n"], r=rec["r"]) + +# -------------------- +# RXNORM +# -------------------- + +def rxnorm(driver): + PRESCRIBABLE_ONLY = os.getenv("RXN_PRESCRIBABLE", "1") == "1" + RXN_RELEASE_ID = os.getenv("RXN_RELEASE_ID", "current") + DATASET = f"RxNorm:{'prescribable' if PRESCRIBABLE_ONLY else 'all'}:{RXN_RELEASE_ID}" + FORCE_RX = os.getenv("RXFORCE", "0") == "1" or FORCE + + limiter = SharedRateLimiter(int(os.getenv("RATE_LIMIT_RPM", "120"))) + ROOT_TTYS = [t.strip() for t in os.getenv("RXN_ROOT_TTYS", "IN,MIN,PIN").split(",") if t.strip()] + CHILD_TTYS = [t.strip() for t in os.getenv("RXN_CHILD_TTYS", "SCD,SBD,GPCK,BPCK,SCDF,SBDF,SCDC,SBDC,BN").split(",") if t.strip()] + + def rx_get(path, params=None): + limiter.wait() + prefix = "/Prescribe" if PRESCRIBABLE_ONLY else "" + r = requests.get(f"https://rxnav.nlm.nih.gov/REST{prefix}{path}", params=params or {}, timeout=60) + r.raise_for_status() + return r.json() + + with driver.session(database=NEO4J_DB) as sess: + sess.run("CREATE CONSTRAINT rxn_node_rxcui IF NOT EXISTS FOR (n:RXN) REQUIRE n.rxcui IS UNIQUE") + if bool(sess.run("MATCH (i:Ingest {dataset: $ds}) WHERE i.finishedAt IS NOT NULL RETURN i LIMIT 1", ds=DATASET).single()) and not FORCE_RX: + log.info("RxNorm Ingest already completed. Skipping."); return + + if FORCE_RX: + sess.run("MATCH (i:Ingest {dataset: $ds}) DETACH DELETE i", ds=DATASET) + sess.run("MATCH (n:RXN {ds: $ds}) DETACH DELETE n", ds=DATASET) + + run_uid = str(uuid.uuid4()) + sess.run("CREATE (i:Ingest {uid:$uid, dataset:$ds, release:$rel, startedAt:$s})", uid=run_uid, ds=DATASET, rel=RXN_RELEASE_ID, s=utc_iso()) + sess.run("MERGE (n:RXN {rxcui: 'ROOT'}) ON CREATE SET n.name='RxNorm', n.tty='ROOT', n.ds=$ds", ds=DATASET) + sess.run("MATCH (i:Ingest {uid: $uid}), (r:RXN {rxcui: 'ROOT'}) MERGE (i)-[:ROOT]->(r)", uid=run_uid) + + # Get top-level concepts + js = rx_get("/allconcepts.json", params={"tty": " ".join(ROOT_TTYS)}) + roots = [{"rxcui": m.get("rxcui"), "name": m.get("name"), "tty": m.get("tty")} for m in js.get("minConceptGroup", {}).get("minConcept", []) if m.get("rxcui")] + + for m in roots: + sess.run("MERGE (n:RXN {rxcui: $rxcui}) ON CREATE SET n.name=$name, n.tty=$tty, n.ds=$ds", rxcui=m["rxcui"], name=m["name"], tty=m["tty"], ds=DATASET) + sess.run("MATCH (p:RXN {rxcui: 'ROOT'}), (c:RXN {rxcui: $c}) MERGE (p)-[:HAS_CHILD]->(c)", c=m["rxcui"]) + + for idx, m in enumerate(roots): + if idx % 250 == 0: log.info("RxNorm build processing roots: %d / %d", idx, len(roots)) + try: + rel_js = rx_get(f"/rxcui/{m['rxcui']}/allrelated.json") + groups = rel_js.get("allRelatedGroup", {}).get("conceptGroup", []) + for g in groups: + tty = g.get("tty") + if tty not in CHILD_TTYS: continue + props = g.get("conceptProperties", []) + if isinstance(props, dict): props = [props] + for p in props: + if p.get("rxcui"): + sess.run("MERGE (n:RXN {rxcui: $rxcui}) ON CREATE SET n.name=$name, n.tty=$tty, n.ds=$ds ON MATCH SET n.ds=$ds", rxcui=p["rxcui"], name=p["name"], tty=p["tty"], ds=DATASET) + sess.run("MATCH (p:RXN {rxcui: $p}), (c:RXN {rxcui: $c}) MERGE (p)-[:HAS_CHILD]->(c)", p=m["rxcui"], c=p["rxcui"]) + except Exception as e: log.debug("Skipped paths on CUI %s: %s", m["rxcui"], e) + + rec = sess.run("MATCH (n:RXN {ds: $ds}) WITH count(n) AS n MATCH (:RXN {ds: $ds})-[rel:HAS_CHILD]->(:RXN {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() + sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt=$f, i.nodeCount=$n, i.edgeCount=$r", uid=run_uid, f=utc_iso(), n=rec["n"], r=rec["r"]) + +# -------------------- +# ICD-11 +# -------------------- + +def icd11(driver): + ICD_CLIENT_ID = os.getenv("ICD_CLIENT_ID") + ICD_CLIENT_SECRET = os.getenv("ICD_CLIENT_SECRET") + if not ICD_CLIENT_ID or not ICD_CLIENT_SECRET: + log.error("Missing ICD credentials. Skipping ICD-11."); return + + ICD_RELEASE_ID = os.getenv("ICD_RELEASE_ID", "2024-01") + DATASET = f"ICD11-21:{ICD_RELEASE_ID}" + limiter = SharedRateLimiter(int(os.getenv("RATE_LIMIT_RPM", "200"))) + + limiter.wait() + tok_r = requests.post("https://icdaccessmanagement.who.int/connect/token", data={"grant_type": "client_credentials", "scope": "icdapi_access"}, auth=(ICD_CLIENT_ID, ICD_CLIENT_SECRET), timeout=30) + tok_r.raise_for_status() + token = tok_r.json()["access_token"] + + def icd_get(url, params=None, max_retries=6): + attempt = 0 + while True: + attempt += 1; limiter.wait() + try: + r = requests.get(url, headers={"Authorization": f"Bearer {token}", "Accept": "application/json", "API-Version": "v2", "Accept-Language": "en"}, params=params or {}, timeout=60) + if r.status_code == 429: + _respect_retry_after(r); + if attempt < max_retries: + continue + r.raise_for_status(); return r.json() + except requests.HTTPError as e: + if getattr(e.response, "status_code", None) in (429, 500, 502, 503, 504) and attempt < max_retries: + _respect_retry_after(e.response); continue + raise + + def get_node_details(item): + if isinstance(item, str): + res = icd_get(item, params={"properties": "code,title"}) + t = res.get("title", "") + return item, res.get("code") or res.get("theCode") or "", t.get("@value", "") if isinstance(t, dict) else t + return item.get("@id"), item.get("code") or item.get("theCode") or "", item.get("title", {}).get("@value", "") if isinstance(item.get("title"), dict) else item.get("title", "") + + # Look up Chapter 21 Root + root_res = icd_get(f"https://id.who.int/icd/release/11/{ICD_RELEASE_ID}/mms", params={"flat": "true"}) + ch21_id = None + for child in root_res.get("child", []): + nid, code, title = get_node_details(child) + if code == "21" or "Symptoms, signs" in str(title): ch21_id = nid; break + + if not ch21_id: log.error("Could not find ICD-11 Chapter 21 node. Skipping."); return + + with driver.session(database=NEO4J_DB) as sess: + sess.run("CREATE CONSTRAINT icd_node_id IF NOT EXISTS FOR (n:ICD) REQUIRE n.id IS UNIQUE") + if bool(sess.run("MATCH (i:Ingest {dataset: $ds}) WHERE i.finishedAt IS NOT NULL RETURN i LIMIT 1", ds=DATASET).single()) and not FORCE: + log.info("ICD-11 Ingest already completed. Skipping."); return + + if FORCE: + sess.run("MATCH (i:Ingest {dataset: $ds}) DETACH DELETE i", ds=DATASET) + sess.run("MATCH (n:ICD {ds: $ds}) DETACH DELETE n", ds=DATASET) + + run_uid = str(uuid.uuid4()) + sess.run("CREATE (i:Ingest {uid:$uid, dataset:$ds, release:$rel, startedAt:$s})", uid=run_uid, ds=DATASET, rel=ICD_RELEASE_ID, s=utc_iso()) + + full_root = icd_get(ch21_id) + sess.run("MERGE (n:ICD {id: $id}) ON CREATE SET n.code=$c, n.title=$t, n.ds=$ds", id=ch21_id, c=full_root.get("code"), t=full_root.get("title", {}).get("@value"), ds=DATASET) + sess.run("MATCH (i:Ingest {uid: $uid}), (r:ICD {id: $rid}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rid=ch21_id) + + queue = deque([(ch21_id, None)]) + visited = set() + while queue: + nid, parent = queue.popleft() + if nid in visited: continue + visited.add(nid) + + full = icd_get(nid) + t_val = full.get("title", {}) + title_str = t_val.get("@value") if isinstance(t_val, dict) else t_val + sess.run("MERGE (n:ICD {id: $id}) ON CREATE SET n.code=$c, n.title=$t, n.ds=$ds ON MATCH SET n.ds=$ds", id=nid, c=full.get("code") or full.get("theCode"), t=title_str, ds=DATASET) + if parent: + sess.run("MATCH (p:ICD {id: $p}), (c:ICD {id: $c}) MERGE (p)-[:HAS_CHILD]->(c)", p=parent, c=nid) + + subtree = icd_get(nid, params={"include": "descendant", "depth": "1", "properties": "code,title"}) + children = subtree.get("child", []) or subtree.get("descendant", []) + for child in children: + cid, _, _ = get_node_details(child) + if cid and cid not in visited: queue.append((cid, nid)) + + rec = sess.run("MATCH (n:ICD {ds: $ds}) WITH count(n) AS n MATCH (:ICD {ds: $ds})-[rel:HAS_CHILD]->(:ICD {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() + sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt=$f, i.nodeCount=$n, i.edgeCount=$r", uid=run_uid, f=utc_iso(), n=rec["n"], r=rec["r"]) + +# -------------------- +# Combining into Singular Data Source +# -------------------- + +def unify_graph(driver): + log.info(">>> Combining graphes into a singular source...") + + with driver.session(database=NEO4J_DB) as sess: + # Secondary label (:Concept) applied to every medical node + log.info("Creating global structural indexes...") + sess.run("CREATE INDEX global_concept_code IF NOT EXISTS FOR (n:Concept) REQUIRE n.code") + + log.info("Applying global :Concept labels...") + sess.run("MATCH (n:DRUG) SET n:Concept") + sess.run("MATCH (n:SNOMED) SET n:Concept") + sess.run("MATCH (n:RXN) SET n:Concept") + sess.run("MATCH (n:ICD) SET n:Concept") + + log.info("Creating connections between RxNorm and DrugBank...") + sess.run(""" + MATCH (r:RXN), (d:DRUG) + WHERE r.name = d.title OR r.rxcui = d.code + MERGE (r)-[:SAME_AS {derivedBy: 'property_match'}]->(d) + """) + + log.info("Creating connections between SNOMED CT and ICD-11...") + sess.run(""" + MATCH (s:SNOMED), (i:ICD) + WHERE s.code = i.code OR s.title = i.title + MERGE (s)-[:MAPS_TO {derivedBy: 'exact_string_match'}]->(i) + """) + + log.info("<<< Graph combination complete. All sources are now connected.") + +def main(): + log.info("=" * 60) + log.info("Creating Singular Medical Knowledge Graph") + log.info("=" * 60) + + t0 = time.time() + driver = GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USER, NEO4J_PASSWORD)) + + try: + with driver.session(database=NEO4J_DB) as check_session: + sc = smoke_test(check_session) + log.info("Graph connection smoke test passed.") + + # Ingest separate sources into the single database + drugbank(driver) + snomed(driver) + rxnorm(driver) + icd11(driver) + + # Link them together to make a singular source + unify_graph(driver) + + except Exception as e: + log.critical("Pipeline was terminated prematurely: %s", e) + sys.exit(2) + finally: + driver.close() + + log.info("=" * 60) + log.info("All pipelines executed | Total duration: %.2f seconds", time.time() - t0) + log.info("=" * 60) + +if __name__ == "__main__": + main() \ No newline at end of file From afa8ff22d932027a9827332eb8adc53af7c9d92f Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Tue, 28 Jul 2026 20:26:57 -0700 Subject: [PATCH 03/23] Source loader has been tested to ensure it works In the process of integrating it with the UI --- .env | 16 +- {scripts => backend/neo4j_sources}/.DS_Store | Bin .../__pycache__/config.cpython-313.pyc | Bin .../__pycache__/config.cpython-314.pyc | Bin 0 -> 1044 bytes .../__pycache__/db.cpython-313.pyc | Bin .../__pycache__/db.cpython-314.pyc | Bin 0 -> 3368 bytes {scripts => backend/neo4j_sources}/config.py | 2 +- .../neo4j_sources}/source_data.py | 86 ++++++++-- .../codex => backend/translation}/__init__.py | 0 .../__pycache__/__init__.cpython-314.pyc | Bin 0 -> 183 bytes .../__pycache__/neo4j_driver.cpython-314.pyc | Bin 0 -> 7274 bytes .../translation}/config/fallbacks.json | 0 .../language_packs/english_pack.json | 0 .../language_packs/french_pack.json | 0 .../language_packs/russian_pack.json | 0 .../language_packs/spanish_pack.json | 0 .../language_packs/ukrainian_pack.json | 0 .../translation}/neo4j_driver.py | 0 .../translation}/services/__init__.py | 0 .../__pycache__/__init__.cpython-314.pyc | Bin 0 -> 192 bytes .../translation_service.cpython-314.pyc | Bin 0 -> 7836 bytes .../services/translation_service.py | 2 +- .../translation}/utils/__init__.py | 0 codex-build/__pycache__/api.cpython-314.pyc | Bin 0 -> 23950 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 0 -> 173 bytes .../__pycache__/neo4j_driver.cpython-314.pyc | Bin 0 -> 18165 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 0 -> 182 bytes .../translation_service.cpython-314.pyc | Bin 0 -> 1489 bytes .../__pycache__/api.cpython-314.pyc | Bin 0 -> 15698 bytes cypher/00_setup_constraints.cypher | 77 --------- cypher/01_load_drugbank.cypher | 162 ------------------ cypher/02_load_rxnorm.cypher | 112 ------------ cypher/03_load_icd11.cypher | 108 ------------ cypher/04_load_snomedct.cypher | 160 ----------------- cypher/05_demo_queries.cypher | 116 ------------- docker-compose.yml | 51 ++++++ sample_data/drugbank_sample.json | 104 ----------- sample_data/icd11_sample.json | 67 -------- sample_data/rxnorm_sample.json | 80 --------- sample_data/snomedct_sample.json | 104 ----------- scripts/db.py | 42 ----- scripts/dry_run.py | 122 ------------- scripts/loaders/.DS_Store | Bin 6148 -> 0 bytes scripts/loaders/__init__.py | 0 .../__pycache__/__init__.cpython-313.pyc | Bin 166 -> 0 bytes .../drugbank_loader.cpython-313.pyc | Bin 7107 -> 0 bytes .../__pycache__/icd11_loader.cpython-313.pyc | Bin 3636 -> 0 bytes .../__pycache__/rxnorm_loader.cpython-313.pyc | Bin 4748 -> 0 bytes .../snomedct_loader.cpython-313.pyc | Bin 7114 -> 0 bytes scripts/run_etl.py | 90 ---------- 50 files changed, 133 insertions(+), 1368 deletions(-) rename {scripts => backend/neo4j_sources}/.DS_Store (100%) rename {scripts => backend/neo4j_sources}/__pycache__/config.cpython-313.pyc (100%) create mode 100644 backend/neo4j_sources/__pycache__/config.cpython-314.pyc rename {scripts => backend/neo4j_sources}/__pycache__/db.cpython-313.pyc (100%) create mode 100644 backend/neo4j_sources/__pycache__/db.cpython-314.pyc rename {scripts => backend/neo4j_sources}/config.py (87%) rename {scripts/loaders => backend/neo4j_sources}/source_data.py (85%) rename {codex-main-test-build/codex => backend/translation}/__init__.py (100%) create mode 100644 backend/translation/__pycache__/__init__.cpython-314.pyc create mode 100644 backend/translation/__pycache__/neo4j_driver.cpython-314.pyc rename {codex-main-test-build/codex => backend/translation}/config/fallbacks.json (100%) rename {codex-main-test-build/codex => backend/translation}/language_packs/english_pack.json (100%) rename {codex-main-test-build/codex => backend/translation}/language_packs/french_pack.json (100%) rename {codex-main-test-build/codex => backend/translation}/language_packs/russian_pack.json (100%) rename {codex-main-test-build/codex => backend/translation}/language_packs/spanish_pack.json (100%) rename {codex-main-test-build/codex => backend/translation}/language_packs/ukrainian_pack.json (100%) rename {codex-main-test-build/codex => backend/translation}/neo4j_driver.py (100%) rename {codex-main-test-build/codex => backend/translation}/services/__init__.py (100%) create mode 100644 backend/translation/services/__pycache__/__init__.cpython-314.pyc create mode 100644 backend/translation/services/__pycache__/translation_service.cpython-314.pyc rename {codex-main-test-build/codex => backend/translation}/services/translation_service.py (97%) rename {codex-main-test-build/codex => backend/translation}/utils/__init__.py (100%) create mode 100644 codex-build/__pycache__/api.cpython-314.pyc create mode 100644 codex-build/codex/__pycache__/__init__.cpython-314.pyc create mode 100644 codex-build/codex/__pycache__/neo4j_driver.cpython-314.pyc create mode 100644 codex-build/codex/services/__pycache__/__init__.cpython-314.pyc create mode 100644 codex-build/codex/services/__pycache__/translation_service.cpython-314.pyc create mode 100644 codex-main-test-build/__pycache__/api.cpython-314.pyc delete mode 100644 cypher/00_setup_constraints.cypher delete mode 100644 cypher/01_load_drugbank.cypher delete mode 100644 cypher/02_load_rxnorm.cypher delete mode 100644 cypher/03_load_icd11.cypher delete mode 100644 cypher/04_load_snomedct.cypher delete mode 100644 cypher/05_demo_queries.cypher create mode 100644 docker-compose.yml delete mode 100644 sample_data/drugbank_sample.json delete mode 100644 sample_data/icd11_sample.json delete mode 100644 sample_data/rxnorm_sample.json delete mode 100644 sample_data/snomedct_sample.json delete mode 100644 scripts/db.py delete mode 100644 scripts/dry_run.py delete mode 100644 scripts/loaders/.DS_Store delete mode 100644 scripts/loaders/__init__.py delete mode 100644 scripts/loaders/__pycache__/__init__.cpython-313.pyc delete mode 100644 scripts/loaders/__pycache__/drugbank_loader.cpython-313.pyc delete mode 100644 scripts/loaders/__pycache__/icd11_loader.cpython-313.pyc delete mode 100644 scripts/loaders/__pycache__/rxnorm_loader.cpython-313.pyc delete mode 100644 scripts/loaders/__pycache__/snomedct_loader.cpython-313.pyc delete mode 100644 scripts/run_etl.py diff --git a/.env b/.env index 4d77ff8..68e01a6 100644 --- a/.env +++ b/.env @@ -1,6 +1,16 @@ # Project Codex — environment variables -# Copy this file to .env and fill in your values. +DRUGBANK_API_KEY= +DRUGBANK_API_BASE=https://api.drugbank.com/discovery/v1 +DRUGBANK_RELEASE=API -NEO4J_URI=bolt://127.0.0.1:7687 +ICD_CLIENT_ID= +ICD_CLIENT_SECRET= + +NEO4J_URI=bolt://localhost:7687 NEO4J_USER=neo4j -NEO4J_PASSWORD=codexpassword +NEO4J_PASSWORD=changeme +NEO4J_DB=neo4j + +RATE_LIMIT_RPM=100 +LOG_LEVEL=INFO +FORCE=1 \ No newline at end of file diff --git a/scripts/.DS_Store b/backend/neo4j_sources/.DS_Store similarity index 100% rename from scripts/.DS_Store rename to backend/neo4j_sources/.DS_Store diff --git 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t=full_root.get("title", {}).get("@value"), ds=DATASET) + # sess.run("MERGE (n:ICD {id: $id}) ON CREATE SET n.code=$c, n.title=$t, n.ds=$ds", id=ch21_id, c=full_root.get("code"), t=full_root.get("title", {}).get("@value"), ds=DATASET) + sess.run("MERGE (n:ICD {id: $id}) ON CREATE SET n.code=$c, n.title='ICD 11', n.ds=$ds", id=ch21_id, c=full_root.get("code"), ds=DATASET) sess.run("MATCH (i:Ingest {uid: $uid}), (r:ICD {id: $rid}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rid=ch21_id) queue = deque([(ch21_id, None)]) @@ -392,29 +417,44 @@ def unify_graph(driver): log.info(">>> Combining graphes into a singular source...") with driver.session(database=NEO4J_DB) as sess: + sess.run(""" + MERGE (g:G_ROOT {id: 'GLOBAL_ROOT'}) + ON CREATE SET g.title = 'Global Root', g.initializedAt = $ts + """, ts=utc_iso()) + # Secondary label (:Concept) applied to every medical node log.info("Creating global structural indexes...") - sess.run("CREATE INDEX global_concept_code IF NOT EXISTS FOR (n:Concept) REQUIRE n.code") + sess.run("CREATE INDEX global_concept_code IF NOT EXISTS FOR (n:Concept) ON n.code") + + sess.run(""" + MATCH (:Ingest)-[:ROOT]->(root) + SET root:Source + """) - log.info("Applying global :Concept labels...") - sess.run("MATCH (n:DRUG) SET n:Concept") - sess.run("MATCH (n:SNOMED) SET n:Concept") - sess.run("MATCH (n:RXN) SET n:Concept") - sess.run("MATCH (n:ICD) SET n:Concept") + log.info("Applying global :Concept labels to all internal medical entities...") + sess.run("MATCH (n:DRUG) WHERE NOT n:Source SET n:Concept") + sess.run("MATCH (n:SNOMED) WHERE NOT n:Source SET n:Concept") + sess.run("MATCH (n:RXN) WHERE NOT n:Source SET n:Concept") + sess.run("MATCH (n:ICD) WHERE NOT n:Source SET n:Concept") log.info("Creating connections between RxNorm and DrugBank...") sess.run(""" - MATCH (r:RXN), (d:DRUG) + MATCH (r:RXN:Concept), (d:DRUG:Concept) WHERE r.name = d.title OR r.rxcui = d.code MERGE (r)-[:SAME_AS {derivedBy: 'property_match'}]->(d) """) log.info("Creating connections between SNOMED CT and ICD-11...") sess.run(""" - MATCH (s:SNOMED), (i:ICD) + MATCH (s:SNOMED:Concept), (i:ICD:Concept) WHERE s.code = i.code OR s.title = i.title MERGE (s)-[:MAPS_TO {derivedBy: 'exact_string_match'}]->(i) """) + + sess.run(""" + MATCH (g:G_ROOT {id: 'GLOBAL_ROOT'}), (src:Source) + MERGE (g)-[:HAS_SOURCE]->(src) + """) log.info("<<< Graph combination complete. 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z%~ZbTM>RRIG*_`b=i8R^1m_#6yoZ%v^}!D&UmmfQ1aEav0XOEHZ--UE=wQ`{Yo2@s z#8yrechHjr;ZS8k@ z|JCf@6Eu-;0kIXiFjix7U5^pNi!KdfAhy!LiN5*ll2H4#SpExdU|xA=_Q$g~>u!%N zmh4>g?wae%naX7Qo#>LdFDH86I{o_TYwp|byW+=V%VN(%Hz(HpcI9a|=PH9T$CsiA zJQ=?fD;KH`f4px=Jjt4PeQ^F6s!4ZzeCh91n8n<^qjf_S+|MhVPkDr&*R?!l7yi55 Hj`;rtNhyWj literal 0 HcmV?d00001 diff --git a/cypher/00_setup_constraints.cypher b/cypher/00_setup_constraints.cypher deleted file mode 100644 index ea79fa3..0000000 --- a/cypher/00_setup_constraints.cypher +++ /dev/null @@ -1,77 +0,0 @@ -// ============================================================= -// Project Codex — Neo4j Schema Setup -// Step 0: Constraints and Indexes -// Run this FIRST before any data import -// ============================================================= - -// ---- Uniqueness Constraints ---- - -CREATE CONSTRAINT drug_codex_id IF NOT EXISTS -FOR (d:Drug) REQUIRE d.codex_id IS UNIQUE; - -CREATE CONSTRAINT drugname_unique IF NOT EXISTS -FOR (dn:DrugName) REQUIRE (dn.name, dn.country, dn.language) IS UNIQUE; - -CREATE CONSTRAINT condition_codex_id IF NOT EXISTS -FOR (c:Condition) REQUIRE c.codex_id IS UNIQUE; - -CREATE CONSTRAINT ingredient_codex_id IF NOT EXISTS -FOR (i:Ingredient) REQUIRE i.codex_id IS UNIQUE; - -CREATE CONSTRAINT datasource_name IF NOT EXISTS -FOR (ds:DataSource) REQUIRE ds.name IS UNIQUE; - -// ---- Indexes for fast lookups ---- - -CREATE INDEX drug_source_id IF NOT EXISTS -FOR (d:Drug) ON (d.source_id); - -CREATE INDEX drug_source IF NOT EXISTS -FOR (d:Drug) ON (d.source); - -CREATE INDEX drug_canonical_name IF NOT EXISTS -FOR (d:Drug) ON (d.canonical_name); - -CREATE INDEX drug_poc IF NOT EXISTS -FOR (d:Drug) ON (d.is_poc); - -CREATE INDEX drugname_country IF NOT EXISTS -FOR (dn:DrugName) ON (dn.country); - -CREATE INDEX drugname_language IF NOT EXISTS -FOR (dn:DrugName) ON (dn.language); - -CREATE INDEX condition_icd11 IF NOT EXISTS -FOR (c:Condition) ON (c.icd11_code); - -CREATE INDEX condition_snomed IF NOT EXISTS -FOR (c:Condition) ON (c.snomed_id); - -CREATE INDEX ingredient_inchikey IF NOT EXISTS -FOR (i:Ingredient) ON (i.inchikey); - -// ---- Register known data sources ---- - -MERGE (ds:DataSource {name: 'drugbank'}) -SET ds.url = 'https://go.drugbank.com/', - ds.license = 'Creative Commons Attribution-NonCommercial 4.0', - ds.version = '5.1.10', - ds.last_refreshed = datetime('2024-01-15T00:00:00Z'); - -MERGE (ds:DataSource {name: 'rxnorm'}) -SET ds.url = 'https://www.nlm.nih.gov/research/umls/rxnorm/', - ds.license = 'Public Domain (NLM)', - ds.version = '2024-01-02', - ds.last_refreshed = datetime('2024-01-10T00:00:00Z'); - -MERGE (ds:DataSource {name: 'icd11'}) -SET ds.url = 'https://icd.who.int/en', - ds.license = 'Creative Commons Attribution-NoDerivatives 3.0 IGO', - ds.version = '2024-01', - ds.last_refreshed = datetime('2024-01-08T00:00:00Z'); - -MERGE (ds:DataSource {name: 'snomedct'}) -SET ds.url = 'https://www.snomed.org/', - ds.license = 'SNOMED CT License', - ds.version = '2023-09-01', - ds.last_refreshed = datetime('2024-01-12T00:00:00Z'); diff --git a/cypher/01_load_drugbank.cypher b/cypher/01_load_drugbank.cypher deleted file mode 100644 index 950e2d1..0000000 --- a/cypher/01_load_drugbank.cypher +++ /dev/null @@ -1,162 +0,0 @@ -// ============================================================= -// Project Codex — DrugBank Source Loader -// Step 1: Load DrugBank data into normalized Codex schema -// Assumes: sample_data/drugbank_sample.json accessible via LOAD CSV -// or data passed as parameters from Python ETL -// ============================================================= - -// ---- Create Drug nodes from DrugBank ---- -// Note: In production, this runs per-record from the ETL pipeline. -// Below is the idiomatic Cypher using MERGE for upsert semantics. - -// Acetaminophen (Tylenol / Dolo / Panadol) -MERGE (d:Drug {source: 'drugbank', source_id: 'DB00316'}) -ON CREATE SET - d.codex_id = 'codex-drug-' + 'DB00316', - d.canonical_name = 'Acetaminophen', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'drugbank_id', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET - d.updated_at = datetime(); - -// DrugName nodes for Acetaminophen -MERGE (dn:DrugName {name: 'Acetaminophen', country: 'US', language: 'en'}) -ON CREATE SET dn.name_type = 'generic', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Tylenol', country: 'US', language: 'en'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = false, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Panadol', country: 'GB', language: 'en'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Dolo', country: 'IN', language: 'hi'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Dafalgan', country: 'FR', language: 'fr'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Ben-u-ron', country: 'DE', language: 'de'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -// Connect Drug → DrugNames -MATCH (d:Drug {source_id: 'DB00316'}) -MATCH (dn:DrugName) WHERE dn.name IN ['Acetaminophen','Tylenol','Panadol','Dolo','Dafalgan','Ben-u-ron'] -MERGE (d)-[:HAS_NAME {source: 'drugbank', created_at: datetime()}]->(dn); - -// Connect Drug → DataSource -MATCH (d:Drug {source_id: 'DB00316'}), (ds:DataSource {name: 'drugbank'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// Ingredient node for Acetaminophen -MERGE (i:Ingredient {source: 'drugbank', source_id: 'DB00316-active'}) -ON CREATE SET - i.codex_id = 'codex-ing-APAP', - i.name = 'Acetaminophen', - i.cas_number = '103-90-2', - i.inchikey = 'RZVAJINKPMORJF-UHFFFAOYSA-N', - i.source_attribute_name = 'cas_number', - i.created_at = datetime(), - i.updated_at = datetime(), - i.is_poc = true; - -MATCH (d:Drug {source_id: 'DB00316'}), (i:Ingredient {source_id: 'DB00316-active'}) -MERGE (d)-[:CONTAINS_INGREDIENT {role: 'active', source: 'drugbank'}]->(i); - -// ---- Aspirin ---- -MERGE (d:Drug {source: 'drugbank', source_id: 'DB00945'}) -ON CREATE SET - d.codex_id = 'codex-drug-DB00945', - d.canonical_name = 'Aspirin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'drugbank_id', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MERGE (dn:DrugName {name: 'Aspirin', country: 'US', language: 'en'}) -ON CREATE SET dn.name_type = 'generic', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Disprin', country: 'IN', language: 'hi'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Aspro', country: 'AU', language: 'en'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MATCH (d:Drug {source_id: 'DB00945'}) -MATCH (dn:DrugName) WHERE dn.name IN ['Aspirin','Disprin','Aspro'] -MERGE (d)-[:HAS_NAME {source: 'drugbank', created_at: datetime()}]->(dn); - -MATCH (d:Drug {source_id: 'DB00945'}), (ds:DataSource {name: 'drugbank'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// ---- Metformin ---- -MERGE (d:Drug {source: 'drugbank', source_id: 'DB00331'}) -ON CREATE SET - d.codex_id = 'codex-drug-DB00331', - d.canonical_name = 'Metformin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'drugbank_id', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MERGE (dn:DrugName {name: 'Glucophage', country: 'US', language: 'en'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Glycomet', country: 'IN', language: 'hi'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Metforal', country: 'IT', language: 'it'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Siofor', country: 'DE', language: 'de'}) -ON CREATE SET dn.name_type = 'brand', dn.is_primary = true, - dn.source = 'drugbank', dn.source_attribute_name = 'brands.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MATCH (d:Drug {source_id: 'DB00331'}) -MATCH (dn:DrugName) WHERE dn.name IN ['Glucophage','Glycomet','Metforal','Siofor'] -MERGE (d)-[:HAS_NAME {source: 'drugbank', created_at: datetime()}]->(dn); - -MATCH (d:Drug {source_id: 'DB00331'}), (ds:DataSource {name: 'drugbank'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// ---- Drug Interactions ---- -MATCH (d1:Drug {source_id: 'DB00316'}), (d2:Drug {source_id: 'DB00682'}) -MERGE (d1)-[:INTERACTS_WITH { - severity: 'moderate', - description: 'Warfarin anticoagulant effect may be increased', - source: 'drugbank' -}]->(d2); diff --git a/cypher/02_load_rxnorm.cypher b/cypher/02_load_rxnorm.cypher deleted file mode 100644 index 5ffd7ad..0000000 --- a/cypher/02_load_rxnorm.cypher +++ /dev/null @@ -1,112 +0,0 @@ -// ============================================================= -// Project Codex — RxNorm Source Loader -// Step 2: Map RxNorm concepts into the normalized Codex schema -// RxNorm is US-centric; maps to existing Drug nodes via InChIKey / name match -// ============================================================= - -// RxNorm uses MERGE ON MATCH to enrich existing Drug nodes with RxCUI, -// or creates new Drug nodes if the drug isn't in DrugBank yet. - -// ---- Acetaminophen (RxCUI 161) ---- -// Already in graph from DrugBank; enrich with RxNorm IDs -MERGE (d:Drug {source: 'rxnorm', source_id: '161'}) -ON CREATE SET - d.codex_id = 'codex-drug-RX161', - d.canonical_name = 'Acetaminophen', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'rxcui', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -// Link RxNorm entry to DataSource -MATCH (d:Drug {source: 'rxnorm', source_id: '161'}), (ds:DataSource {name: 'rxnorm'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// Establish EQUIVALENT_TO between DrugBank and RxNorm representations -MATCH (db:Drug {source: 'drugbank', source_id: 'DB00316'}) -MATCH (rx:Drug {source: 'rxnorm', source_id: '161'}) -MERGE (db)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'name+inchikey', - created_at: datetime() -}]->(rx); - -// Add RxNorm-specific name variants (clinical dose forms) -MERGE (dn:DrugName {name: 'Acetaminophen 325 MG Oral Tablet', country: 'US', language: 'en'}) -ON CREATE SET dn.name_type = 'clinical_dose_form', dn.is_primary = false, - dn.source = 'rxnorm', dn.source_attribute_name = 'SCD.name', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = false; - -MATCH (d:Drug {source: 'rxnorm', source_id: '161'}) -MATCH (dn:DrugName {name: 'Acetaminophen 325 MG Oral Tablet', country: 'US', language: 'en'}) -MERGE (d)-[:HAS_NAME {source: 'rxnorm', created_at: datetime()}]->(dn); - -// ---- Aspirin (RxCUI 1191) ---- -MERGE (d:Drug {source: 'rxnorm', source_id: '1191'}) -ON CREATE SET - d.codex_id = 'codex-drug-RX1191', - d.canonical_name = 'Aspirin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'rxcui', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MATCH (d:Drug {source: 'rxnorm', source_id: '1191'}), (ds:DataSource {name: 'rxnorm'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -MATCH (db:Drug {source: 'drugbank', source_id: 'DB00945'}) -MATCH (rx:Drug {source: 'rxnorm', source_id: '1191'}) -MERGE (db)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'name+inchikey', - created_at: datetime() -}]->(rx); - -// ---- Metformin (RxCUI 6809) ---- -MERGE (d:Drug {source: 'rxnorm', source_id: '6809'}) -ON CREATE SET - d.codex_id = 'codex-drug-RX6809', - d.canonical_name = 'Metformin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'rxcui', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MATCH (d:Drug {source: 'rxnorm', source_id: '6809'}), (ds:DataSource {name: 'rxnorm'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -MATCH (db:Drug {source: 'drugbank', source_id: 'DB00331'}) -MATCH (rx:Drug {source: 'rxnorm', source_id: '6809'}) -MERGE (db)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'name+inchikey', - created_at: datetime() -}]->(rx); - -// ---- Warfarin (RxCUI 11289) ---- -MERGE (d:Drug {source: 'rxnorm', source_id: '11289'}) -ON CREATE SET - d.codex_id = 'codex-drug-RX11289', - d.canonical_name = 'Warfarin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'rxcui', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = false -ON MATCH SET d.updated_at = datetime(); - -MATCH (d:Drug {source: 'rxnorm', source_id: '11289'}), (ds:DataSource {name: 'rxnorm'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); diff --git a/cypher/03_load_icd11.cypher b/cypher/03_load_icd11.cypher deleted file mode 100644 index 2d3d3fb..0000000 --- a/cypher/03_load_icd11.cypher +++ /dev/null @@ -1,108 +0,0 @@ -// ============================================================= -// Project Codex — ICD-11 Source Loader -// Step 3: Load ICD-11 conditions into the normalized Codex schema -// ============================================================= - -// ---- Type 2 Diabetes Mellitus (JA00) ---- -MERGE (c:Condition {source: 'icd11', source_id: 'JA00'}) -ON CREATE SET - c.codex_id = 'codex-cond-ICD-JA00', - c.canonical_name = 'Type 2 diabetes mellitus', - c.icd11_code = 'JA00', - c.source_attribute_name = 'code', - c.created_at = datetime(), - c.updated_at = datetime(), - c.is_poc = true -ON MATCH SET c.updated_at = datetime(); - -MATCH (c:Condition {source_id: 'JA00'}), (ds:DataSource {name: 'icd11'}) -MERGE (c)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// ---- Hypertensive diseases (BA00) ---- -MERGE (c:Condition {source: 'icd11', source_id: 'BA00'}) -ON CREATE SET - c.codex_id = 'codex-cond-ICD-BA00', - c.canonical_name = 'Hypertensive diseases', - c.icd11_code = 'BA00', - c.source_attribute_name = 'code', - c.created_at = datetime(), - c.updated_at = datetime(), - c.is_poc = true -ON MATCH SET c.updated_at = datetime(); - -MATCH (c:Condition {source_id: 'BA00'}), (ds:DataSource {name: 'icd11'}) -MERGE (c)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// ---- Atrial fibrillation (CA01) ---- -MERGE (c:Condition {source: 'icd11', source_id: 'CA01'}) -ON CREATE SET - c.codex_id = 'codex-cond-ICD-CA01', - c.canonical_name = 'Atrial fibrillation', - c.icd11_code = 'CA01', - c.source_attribute_name = 'code', - c.created_at = datetime(), - c.updated_at = datetime(), - c.is_poc = false -ON MATCH SET c.updated_at = datetime(); - -MATCH (c:Condition {source_id: 'CA01'}), (ds:DataSource {name: 'icd11'}) -MERGE (c)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// ---- Rheumatoid arthritis (FA24) ---- -MERGE (c:Condition {source: 'icd11', source_id: 'FA24'}) -ON CREATE SET - c.codex_id = 'codex-cond-ICD-FA24', - c.canonical_name = 'Rheumatoid arthritis', - c.icd11_code = 'FA24', - c.source_attribute_name = 'code', - c.created_at = datetime(), - c.updated_at = datetime(), - c.is_poc = true -ON MATCH SET c.updated_at = datetime(); - -MATCH (c:Condition {source_id: 'FA24'}), (ds:DataSource {name: 'icd11'}) -MERGE (c)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// ---- ICD-11 Chapter hierarchy (PARENT_OF) ---- -// Hypertensive diseases is a parent of Atrial fibrillation (both circulatory) -MATCH (parent:Condition {source_id: 'BA00'}) -MATCH (child:Condition {source_id: 'CA01'}) -MERGE (parent)-[:PARENT_OF {source: 'icd11'}]->(child); - -// ---- Drug → Condition TREATS relationships ---- -// Metformin treats Type 2 diabetes -MATCH (d:Drug {source: 'drugbank', source_id: 'DB00331'}) -MATCH (c:Condition {source_id: 'JA00'}) -MERGE (d)-[:TREATS { - evidence_level: 'A', - source: 'drugbank+icd11', - created_at: datetime() -}]->(c); - -// Warfarin treats Atrial fibrillation -MATCH (d:Drug {source: 'drugbank', source_id: 'DB00682'}) -MATCH (c:Condition {source_id: 'CA01'}) -MERGE (d)-[:TREATS { - evidence_level: 'A', - source: 'drugbank+icd11', - created_at: datetime() -}]->(c); - -// Methotrexate treats Rheumatoid arthritis -MATCH (d:Drug {source: 'drugbank', source_id: 'DB00563'}) -MATCH (c:Condition {source_id: 'FA24'}) -MERGE (d)-[:TREATS { - evidence_level: 'A', - source: 'drugbank+icd11', - created_at: datetime() -}]->(c); - -// Aspirin contraindicated for certain bleeding conditions (example) -MATCH (d:Drug {source: 'drugbank', source_id: 'DB00945'}) -MATCH (c:Condition {source_id: 'CA01'}) -MERGE (d)-[:TREATS { - evidence_level: 'B', - source: 'drugbank+icd11', - note: 'antiplatelet therapy for AF stroke prevention', - created_at: datetime() -}]->(c); diff --git a/cypher/04_load_snomedct.cypher b/cypher/04_load_snomedct.cypher deleted file mode 100644 index 9ea5532..0000000 --- a/cypher/04_load_snomedct.cypher +++ /dev/null @@ -1,160 +0,0 @@ -// ============================================================= -// Project Codex — SNOMED CT Source Loader -// Step 4: Load SNOMED CT concepts and link to existing nodes -// ============================================================= - -// ---- Paracetamol (SNOMED 387517004) — same as Acetaminophen ---- -// SNOMED uses "Paracetamol" (INN/WHO name) vs US "Acetaminophen" -// This demonstrates the core Codex translation use case - -MERGE (d:Drug {source: 'snomedct', source_id: '387517004'}) -ON CREATE SET - d.codex_id = 'codex-drug-SCT387517004', - d.canonical_name = 'Paracetamol', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'concept_id', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MATCH (d:Drug {source: 'snomedct', source_id: '387517004'}), (ds:DataSource {name: 'snomedct'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// SNOMED synonyms for Paracetamol -MERGE (dn:DrugName {name: 'Paracetamol', country: 'GB', language: 'en'}) -ON CREATE SET dn.name_type = 'generic', dn.is_primary = true, - dn.source = 'snomedct', dn.source_attribute_name = 'descriptions.FSN', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Paracetamol', country: 'IN', language: 'en'}) -ON CREATE SET dn.name_type = 'generic', dn.is_primary = false, - dn.source = 'snomedct', dn.source_attribute_name = 'descriptions.Synonym', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MERGE (dn:DrugName {name: 'Paracetamol', country: 'AU', language: 'en'}) -ON CREATE SET dn.name_type = 'generic', dn.is_primary = true, - dn.source = 'snomedct', dn.source_attribute_name = 'descriptions.Synonym', - dn.created_at = datetime(), dn.updated_at = datetime(), dn.is_poc = true; - -MATCH (d:Drug {source: 'snomedct', source_id: '387517004'}) -MATCH (dn:DrugName) WHERE dn.name = 'Paracetamol' -MERGE (d)-[:HAS_NAME {source: 'snomedct', created_at: datetime()}]->(dn); - -// Critical: EQUIVALENT_TO between DrugBank Acetaminophen and SNOMED Paracetamol -MATCH (db:Drug {source: 'drugbank', source_id: 'DB00316'}) -MATCH (sct:Drug {source: 'snomedct', source_id: '387517004'}) -MERGE (db)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'inchikey', - note: 'Same compound, different regional names', - created_at: datetime() -}]->(sct); - -// ---- Aspirin (SNOMED 387458008) ---- -MERGE (d:Drug {source: 'snomedct', source_id: '387458008'}) -ON CREATE SET - d.codex_id = 'codex-drug-SCT387458008', - d.canonical_name = 'Aspirin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'concept_id', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MATCH (d:Drug {source: 'snomedct', source_id: '387458008'}), (ds:DataSource {name: 'snomedct'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -MATCH (db:Drug {source: 'drugbank', source_id: 'DB00945'}) -MATCH (sct:Drug {source: 'snomedct', source_id: '387458008'}) -MERGE (db)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'name+inchikey', - created_at: datetime() -}]->(sct); - -// ---- Metformin (SNOMED 387467008) ---- -MERGE (d:Drug {source: 'snomedct', source_id: '387467008'}) -ON CREATE SET - d.codex_id = 'codex-drug-SCT387467008', - d.canonical_name = 'Metformin', - d.drug_type = 'small_molecule', - d.is_approved = true, - d.source_attribute_name = 'concept_id', - d.created_at = datetime(), - d.updated_at = datetime(), - d.is_poc = true -ON MATCH SET d.updated_at = datetime(); - -MATCH (d:Drug {source: 'snomedct', source_id: '387467008'}), (ds:DataSource {name: 'snomedct'}) -MERGE (d)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -MATCH (db:Drug {source: 'drugbank', source_id: 'DB00331'}) -MATCH (sct:Drug {source: 'snomedct', source_id: '387467008'}) -MERGE (db)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'name+inchikey', - created_at: datetime() -}]->(sct); - -// ---- SNOMED Condition: Type 2 Diabetes (44508008) ---- -MERGE (c:Condition {source: 'snomedct', source_id: '44508008'}) -ON CREATE SET - c.codex_id = 'codex-cond-SCT44508008', - c.canonical_name = 'Type 2 diabetes mellitus', - c.snomed_id = '44508008', - c.source_attribute_name = 'concept_id', - c.created_at = datetime(), - c.updated_at = datetime(), - c.is_poc = true -ON MATCH SET c.updated_at = datetime(); - -MATCH (c:Condition {source: 'snomedct', source_id: '44508008'}), (ds:DataSource {name: 'snomedct'}) -MERGE (c)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -// Link SNOMED condition to ICD-11 condition (same disorder) -MATCH (icd:Condition {source: 'icd11', source_id: 'JA00'}) -MATCH (sct:Condition {source: 'snomedct', source_id: '44508008'}) -MERGE (icd)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'clinical-mapping', - created_at: datetime() -}]->(sct); - -// Enrich ICD-11 condition with SNOMED ID -MATCH (c:Condition {source: 'icd11', source_id: 'JA00'}) -SET c.snomed_id = '44508008'; - -// ---- SNOMED Condition: Rheumatoid Arthritis (69896004) ---- -MERGE (c:Condition {source: 'snomedct', source_id: '69896004'}) -ON CREATE SET - c.codex_id = 'codex-cond-SCT69896004', - c.canonical_name = 'Rheumatoid arthritis', - c.snomed_id = '69896004', - c.source_attribute_name = 'concept_id', - c.created_at = datetime(), - c.updated_at = datetime(), - c.is_poc = true -ON MATCH SET c.updated_at = datetime(); - -MATCH (c:Condition {source: 'snomedct', source_id: '69896004'}), (ds:DataSource {name: 'snomedct'}) -MERGE (c)-[:SOURCED_FROM {ingested_at: datetime()}]->(ds); - -MATCH (icd:Condition {source: 'icd11', source_id: 'FA24'}) -MATCH (sct:Condition {source: 'snomedct', source_id: '69896004'}) -MERGE (icd)-[:EQUIVALENT_TO { - confidence: 1.0, - source: 'codex-normalization', - match_basis: 'clinical-mapping', - created_at: datetime() -}]->(sct); - -MATCH (c:Condition {source: 'icd11', source_id: 'FA24'}) -SET c.snomed_id = '69896004'; diff --git a/cypher/05_demo_queries.cypher b/cypher/05_demo_queries.cypher deleted file mode 100644 index c15c632..0000000 --- a/cypher/05_demo_queries.cypher +++ /dev/null @@ -1,116 +0,0 @@ -// ============================================================= -// Project Codex — Demo Queries -// Showcase the value of the normalized schema -// ============================================================= - -// ---- Query 1: Core Codex Use Case — Translate a medicine name ---- -// "What is Tylenol called in India, France, and Germany?" - -MATCH (d:Drug)-[:HAS_NAME]->(us_name:DrugName {name: 'Tylenol', country: 'US'}) -MATCH (d)-[:HAS_NAME]->(intl:DrugName) -WHERE intl.country <> 'US' -RETURN d.canonical_name AS drug, - intl.name AS international_name, - intl.country AS country, - intl.language AS language, - intl.name_type AS type -ORDER BY intl.country; - - -// ---- Query 2: Find all names for the same compound across all sources ---- -// "Show me everything we know about Acetaminophen/Paracetamol" - -MATCH (d:Drug) -WHERE d.canonical_name IN ['Acetaminophen', 'Paracetamol'] - OR d.source_id IN ['DB00316', '387517004', '161'] -OPTIONAL MATCH (d)-[:HAS_NAME]->(dn:DrugName) -OPTIONAL MATCH (d)-[:EQUIVALENT_TO]->(eq:Drug) -RETURN d.source AS source, - d.source_id AS source_id, - d.canonical_name AS canonical_name, - collect(DISTINCT dn.name + ' (' + dn.country + ')') AS names, - collect(DISTINCT eq.canonical_name + ' [' + eq.source + ']') AS equivalents; - - -// ---- Query 3: POC subset — all drugs with their translation names ---- - -MATCH (d:Drug {is_poc: true})-[:HAS_NAME]->(n:DrugName {is_poc: true}) -RETURN d.canonical_name AS drug, - d.source AS source, - collect(n.name + ' (' + n.country + ', ' + n.language + ')') AS names -ORDER BY d.canonical_name; - - -// ---- Query 4: Drug-Condition treatment graph ---- - -MATCH (d:Drug)-[t:TREATS]->(c:Condition) -RETURN d.canonical_name AS drug, - d.source AS drug_source, - c.canonical_name AS condition, - c.icd11_code AS icd11_code, - t.evidence_level AS evidence -ORDER BY d.canonical_name; - - -// ---- Query 5: Drug interaction safety check ---- - -MATCH (d1:Drug)-[i:INTERACTS_WITH]->(d2:Drug) -RETURN d1.canonical_name AS drug_1, - d2.canonical_name AS drug_2, - i.severity AS severity, - i.description AS description; - - -// ---- Query 6: Provenance — where did this data come from? ---- - -MATCH (d:Drug)-[:SOURCED_FROM]->(ds:DataSource) -RETURN d.canonical_name AS drug, - d.source AS source_system, - d.source_id AS original_id, - d.source_attribute_name AS original_field, - ds.version AS source_version, - ds.last_refreshed AS last_refreshed, - d.created_at AS ingested_at -ORDER BY d.canonical_name, d.source; - - -// ---- Query 7: Cross-source equivalence map ---- -// Show the full graph of equivalent drugs across all sources - -MATCH (d1:Drug)-[:EQUIVALENT_TO]->(d2:Drug) -RETURN d1.canonical_name AS name_a, - d1.source AS source_a, - d1.source_id AS id_a, - d2.canonical_name AS name_b, - d2.source AS source_b, - d2.source_id AS id_b; - - -// ---- Query 8: Data freshness audit ---- - -MATCH (ds:DataSource) -RETURN ds.name AS source, - ds.version AS version, - ds.last_refreshed AS last_refreshed, - ds.license AS license -ORDER BY ds.name; - - -// ---- Query 9: Find all brand names for a generic drug across countries ---- -// Given a generic INN name, show all brand names worldwide - -MATCH (d:Drug {canonical_name: 'Metformin', source: 'drugbank'}) -MATCH (d)-[:HAS_NAME]->(n:DrugName {name_type: 'brand'}) -RETURN n.name AS brand_name, - n.country AS country, - n.language AS language -ORDER BY n.country; - - -// ---- Query 10: Count records by source and POC flag ---- - -MATCH (d:Drug) -RETURN d.source AS source, - d.is_poc AS is_poc, - count(d) AS drug_count -ORDER BY d.source, d.is_poc; diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..46de4ca --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,51 @@ +services: + + frontend: + build: + context: ./frontend + containter_name: codex-frontend + ports: + - "9000:9000" + depends_on: + - api + volumes: + - ./frontend:/app + - /app/node_modules + + api: + build: + context: ./backend/translation + container_name: codex-api + ports: + - "8000:8000" + environment: + - NEO4J_URI=bolt://neo4j:7687 + - NEO4J_USER=neo4j + - NEO4J_PASSWORD=changeme + depends_on: + neo4j: + condition: service_healthy + volumes: + - ./backend/translation:/app + + neo4j: + image: neo4j:5.18 + container_name: codex-neo4j + environment: + NEO4J_AUTH: "neo4j/changeme" + NEO4J_PLUGINS: '["apoc"]' + NEO4J_dbms_security_procedures_unrestricted: "apoc.*" + ports: + - "7474:7474" # Neo4j Browser → http://localhost:7474 + - "7687:7687" # Bolt (used by the API) + volumes: + - neo4j_data:/data + healthcheck: + test: ["CMD-SHELL", "cypher-shell -u neo4j -p changeme 'RETURN 1' > /dev/null 2>&1"] + interval: 10s + timeout: 5s + retries: 15 + start_period: 30s + +volumes: + neo4j_data: \ No newline at end of file diff --git a/sample_data/drugbank_sample.json b/sample_data/drugbank_sample.json deleted file mode 100644 index cf32681..0000000 --- a/sample_data/drugbank_sample.json +++ /dev/null @@ -1,104 +0,0 @@ -[ - { - "drugbank_id": "DB00316", - "name": "Acetaminophen", - "type": "small molecule", - "groups": ["approved"], - "description": "Analgesic and antipyretic drug used to treat mild to moderate pain and fever.", - "cas_number": "103-90-2", - "inchikey": "RZVAJINKPMORJF-UHFFFAOYSA-N", - "brands": [ - { "name": "Tylenol", "country": "US" }, - { "name": "Panadol", "country": "GB" }, - { "name": "Dolo", "country": "IN" }, - { "name": "Dafalgan", "country": "FR" }, - { "name": "Ben-u-ron", "country": "DE" } - ], - "indication": "For the treatment of mild to moderate pain and fever.", - "mechanism_of_action": "Inhibits prostaglandin synthesis in the CNS.", - "affected_organisms": ["Humans"], - "interactions": [ - { "drugbank_id": "DB00682", "description": "Warfarin anticoagulant effect increased", "severity": "moderate" } - ] - }, - { - "drugbank_id": "DB00945", - "name": "Aspirin", - "type": "small molecule", - "groups": ["approved"], - "description": "Salicylate anti-inflammatory and analgesic drug.", - "cas_number": "50-78-2", - "inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N", - "brands": [ - { "name": "Aspirin", "country": "US" }, - { "name": "Ecotrin", "country": "US" }, - { "name": "Disprin", "country": "IN" }, - { "name": "Aspro", "country": "AU" }, - { "name": "ASS", "country": "DE" } - ], - "indication": "For mild to moderate pain, fever, and as antiplatelet therapy.", - "mechanism_of_action": "Irreversibly inhibits COX-1 and COX-2 enzymes.", - "affected_organisms": ["Humans"], - "interactions": [ - { "drugbank_id": "DB00682", "description": "Increased bleeding risk with warfarin", "severity": "major" } - ] - }, - { - "drugbank_id": "DB00331", - "name": "Metformin", - "type": "small molecule", - "groups": ["approved"], - "description": "Biguanide antidiabetic drug used to control blood glucose in type 2 diabetes.", - "cas_number": "657-24-9", - "inchikey": "XZWYZXLIPXDOLR-UHFFFAOYSA-N", - "brands": [ - { "name": "Glucophage", "country": "US" }, - { "name": "Glycomet", "country": "IN" }, - { "name": "Metforal", "country": "IT" }, - { "name": "Siofor", "country": "DE" }, - { "name": "Diabex", "country": "AU" } - ], - "indication": "First-line treatment for type 2 diabetes mellitus.", - "mechanism_of_action": "Activates AMP-activated protein kinase (AMPK), reducing hepatic gluconeogenesis.", - "affected_organisms": ["Humans"], - "interactions": [] - }, - { - "drugbank_id": "DB00682", - "name": "Warfarin", - "type": "small molecule", - "groups": ["approved"], - "description": "Anticoagulant used to prevent blood clot formation.", - "cas_number": "81-81-2", - "inchikey": "PJVWKTKQMONHTI-UHFFFAOYSA-N", - "brands": [ - { "name": "Coumadin", "country": "US" }, - { "name": "Warf", "country": "IN" }, - { "name": "Marevan", "country": "GB" }, - { "name": "Warfin", "country": "AU" } - ], - "indication": "Prevention and treatment of thromboembolic events.", - "mechanism_of_action": "Vitamin K antagonist; inhibits VKORC1.", - "affected_organisms": ["Humans"], - "interactions": [] - }, - { - "drugbank_id": "DB00563", - "name": "Methotrexate", - "type": "small molecule", - "groups": ["approved"], - "description": "Antimetabolite used in cancer and autoimmune disease treatment.", - "cas_number": "59-05-2", - "inchikey": "FBOZXECLQNJBKD-ZDUSSCGKSA-N", - "brands": [ - { "name": "Trexall", "country": "US" }, - { "name": "Folitrax", "country": "IN" }, - { "name": "Methofar", "country": "FR" }, - { "name": "Lantarel", "country": "DE" } - ], - "indication": "Treatment of certain cancers and autoimmune conditions including rheumatoid arthritis.", - "mechanism_of_action": "Inhibits dihydrofolate reductase (DHFR), blocking nucleotide synthesis.", - "affected_organisms": ["Humans"], - "interactions": [] - } -] diff --git a/sample_data/icd11_sample.json b/sample_data/icd11_sample.json deleted file mode 100644 index 602acbd..0000000 --- a/sample_data/icd11_sample.json +++ /dev/null @@ -1,67 +0,0 @@ -[ - { - "code": "JA00", - "title": "Type 2 diabetes mellitus", - "stem_id": "1780132783", - "chapter": "05", - "chapter_title": "Endocrine, nutritional or metabolic diseases", - "parent_code": "5A10-5A14.Z", - "linearization_uri": "http://id.who.int/icd/entity/1780132783", - "definition": "A metabolic disorder characterized by high blood sugar, insulin resistance, and relative lack of insulin.", - "synonyms": ["Adult-onset diabetes", "Non-insulin-dependent diabetes mellitus", "NIDDM"], - "inclusions": ["Diabetes mellitus due to insulin secretory defect"], - "exclusions": ["Type 1 diabetes mellitus (5A10)"] - }, - { - "code": "BA00", - "title": "Hypertensive diseases", - "stem_id": "1388325637", - "chapter": "11", - "chapter_title": "Diseases of the circulatory system", - "parent_code": "BA00-BA0Z", - "linearization_uri": "http://id.who.int/icd/entity/1388325637", - "definition": "Conditions characterized by persistently elevated blood pressure in the arteries.", - "synonyms": ["High blood pressure", "HTN"], - "inclusions": ["Essential hypertension", "Secondary hypertension"], - "exclusions": ["Hypertension complicating pregnancy (JA24)"] - }, - { - "code": "CA01", - "title": "Atrial fibrillation", - "stem_id": "230690328", - "chapter": "11", - "chapter_title": "Diseases of the circulatory system", - "parent_code": "CA01", - "linearization_uri": "http://id.who.int/icd/entity/230690328", - "definition": "Supraventricular arrhythmia characterized by uncoordinated atrial activation with consequent deterioration of atrial mechanical function.", - "synonyms": ["AF", "A-fib"], - "inclusions": ["Paroxysmal atrial fibrillation", "Persistent atrial fibrillation"], - "exclusions": [] - }, - { - "code": "FA24", - "title": "Rheumatoid arthritis", - "stem_id": "1068173526", - "chapter": "16", - "chapter_title": "Diseases of the musculoskeletal system or connective tissue", - "parent_code": "FA20-FA2Z", - "linearization_uri": "http://id.who.int/icd/entity/1068173526", - "definition": "Chronic inflammatory disorder affecting many joints, including those in the hands and feet.", - "synonyms": ["RA", "Rheumatoid disease"], - "inclusions": ["Seronegative rheumatoid arthritis", "Seropositive rheumatoid arthritis"], - "exclusions": ["Juvenile idiopathic arthritis (KA80)"] - }, - { - "code": "2C91.Z", - "title": "Malignant neoplasm of breast, unspecified", - "stem_id": "1162746685", - "chapter": "02", - "chapter_title": "Neoplasms", - "parent_code": "2C91", - "linearization_uri": "http://id.who.int/icd/entity/1162746685", - "definition": "Malignant tumour arising from epithelial cells of the breast.", - "synonyms": ["Breast cancer", "Carcinoma of breast"], - "inclusions": ["Ductal carcinoma in situ (DCIS)", "Lobular carcinoma"], - "exclusions": ["Benign neoplasm of breast (GA12)"] - } -] diff --git a/sample_data/rxnorm_sample.json b/sample_data/rxnorm_sample.json deleted file mode 100644 index 123a6dc..0000000 --- a/sample_data/rxnorm_sample.json +++ /dev/null @@ -1,80 +0,0 @@ -[ - { - "rxcui": "161", - "name": "Acetaminophen", - "tty": "IN", - "suppress": "N", - "umlscui": "C0000970", - "related_concepts": [ - { "rxcui": "209459", "name": "Acetaminophen 325 MG Oral Tablet", "tty": "SCD" }, - { "rxcui": "209387", "name": "Acetaminophen 500 MG Oral Tablet", "tty": "SCD" }, - { "rxcui": "198440", "name": "Tylenol 325 MG Oral Tablet", "tty": "SBD" } - ], - "attributes": [ - { "atv": "Drug", "atn": "SUBSTANCE_TYPE" }, - { "atv": "N", "atn": "OTC" } - ] - }, - { - "rxcui": "1191", - "name": "Aspirin", - "tty": "IN", - "suppress": "N", - "umlscui": "C0004057", - "related_concepts": [ - { "rxcui": "212033", "name": "Aspirin 325 MG Oral Tablet", "tty": "SCD" }, - { "rxcui": "437649", "name": "Ecotrin 325 MG Delayed Release Oral Tablet", "tty": "SBD" }, - { "rxcui": "308460", "name": "Aspirin 81 MG Oral Tablet", "tty": "SCD" } - ], - "attributes": [ - { "atv": "Drug", "atn": "SUBSTANCE_TYPE" }, - { "atv": "Y", "atn": "OTC" } - ] - }, - { - "rxcui": "6809", - "name": "Metformin", - "tty": "IN", - "suppress": "N", - "umlscui": "C0025598", - "related_concepts": [ - { "rxcui": "861007", "name": "Metformin hydrochloride 500 MG Oral Tablet", "tty": "SCD" }, - { "rxcui": "861025", "name": "Glucophage 500 MG Oral Tablet", "tty": "SBD" }, - { "rxcui": "861021", "name": "Metformin hydrochloride 1000 MG Oral Tablet", "tty": "SCD" } - ], - "attributes": [ - { "atv": "Drug", "atn": "SUBSTANCE_TYPE" }, - { "atv": "N", "atn": "OTC" } - ] - }, - { - "rxcui": "11289", - "name": "Warfarin", - "tty": "IN", - "suppress": "N", - "umlscui": "C0043031", - "related_concepts": [ - { "rxcui": "855295", "name": "Warfarin Sodium 5 MG Oral Tablet", "tty": "SCD" }, - { "rxcui": "855302", "name": "Coumadin 5 MG Oral Tablet", "tty": "SBD" } - ], - "attributes": [ - { "atv": "Drug", "atn": "SUBSTANCE_TYPE" }, - { "atv": "N", "atn": "OTC" } - ] - }, - { - "rxcui": "7052", - "name": "Methotrexate", - "tty": "IN", - "suppress": "N", - "umlscui": "C0025677", - "related_concepts": [ - { "rxcui": "105586", "name": "Methotrexate 2.5 MG Oral Tablet", "tty": "SCD" }, - { "rxcui": "573497", "name": "Trexall 5 MG Oral Tablet", "tty": "SBD" } - ], - "attributes": [ - { "atv": "Drug", "atn": "SUBSTANCE_TYPE" }, - { "atv": "N", "atn": "OTC" } - ] - } -] diff --git a/sample_data/snomedct_sample.json b/sample_data/snomedct_sample.json deleted file mode 100644 index 1a19eb3..0000000 --- a/sample_data/snomedct_sample.json +++ /dev/null @@ -1,104 +0,0 @@ -[ - { - "concept_id": "372687004", - "fsn": "Amoxicillin (substance)", - "preferred_term": "Amoxicillin", - "semantic_tag": "substance", - "active": true, - "module": "900000000000207008", - "descriptions": [ - { "type": "FSN", "term": "Amoxicillin (substance)", "language": "en" }, - { "type": "Synonym", "term": "Amoxil", "language": "en" }, - { "type": "Synonym", "term": "p-Hydroxyampicillin", "language": "en" } - ], - "relationships": [ - { "type": "Is a", "destination_id": "372687004", "destination_term": "Penicillin" }, - { "type": "Has dose form", "destination_id": "421026006", "destination_term": "Oral tablet" } - ] - }, - { - "concept_id": "387517004", - "fsn": "Paracetamol (substance)", - "preferred_term": "Paracetamol", - "semantic_tag": "substance", - "active": true, - "module": "900000000000207008", - "descriptions": [ - { "type": "FSN", "term": "Paracetamol (substance)", "language": "en" }, - { "type": "Synonym", "term": "Acetaminophen", "language": "en" }, - { "type": "Synonym", "term": "4'-hydroxyacetanilide", "language": "en" } - ], - "relationships": [ - { "type": "Is a", "destination_id": "372665008", "destination_term": "Analgesic" }, - { "type": "Is a", "destination_id": "372741007", "destination_term": "Antipyretic" } - ] - }, - { - "concept_id": "387467008", - "fsn": "Metformin (substance)", - "preferred_term": "Metformin", - "semantic_tag": "substance", - "active": true, - "module": "900000000000207008", - "descriptions": [ - { "type": "FSN", "term": "Metformin (substance)", "language": "en" }, - { "type": "Synonym", "term": "Dimethylbiguanide", "language": "en" } - ], - "relationships": [ - { "type": "Is a", "destination_id": "84524008", "destination_term": "Biguanide" }, - { "type": "Has therapeutic role", "destination_id": "67901000", "destination_term": "Antidiabetic" } - ] - }, - { - "concept_id": "44508008", - "fsn": "Type 2 diabetes mellitus (disorder)", - "preferred_term": "Type 2 diabetes mellitus", - "semantic_tag": "disorder", - "active": true, - "module": "900000000000207008", - "descriptions": [ - { "type": "FSN", "term": "Type 2 diabetes mellitus (disorder)", "language": "en" }, - { "type": "Synonym", "term": "NIDDM", "language": "en" }, - { "type": "Synonym", "term": "Non-insulin-dependent diabetes mellitus", "language": "en" }, - { "type": "Synonym", "term": "T2DM", "language": "en" } - ], - "relationships": [ - { "type": "Is a", "destination_id": "73211009", "destination_term": "Diabetes mellitus" }, - { "type": "Finding site", "destination_id": "113331007", "destination_term": "Endocrine system" } - ] - }, - { - "concept_id": "69896004", - "fsn": "Rheumatoid arthritis (disorder)", - "preferred_term": "Rheumatoid arthritis", - "semantic_tag": "disorder", - "active": true, - "module": "900000000000207008", - "descriptions": [ - { "type": "FSN", "term": "Rheumatoid arthritis (disorder)", "language": "en" }, - { "type": "Synonym", "term": "RA", "language": "en" }, - { "type": "Synonym", "term": "Atrophic arthritis", "language": "en" } - ], - "relationships": [ - { "type": "Is a", "destination_id": "3723001", "destination_term": "Arthritis" }, - { "type": "Associated morphology", "destination_id": "23583003", "destination_term": "Inflammation" } - ] - }, - { - "concept_id": "387458008", - "fsn": "Aspirin (substance)", - "preferred_term": "Aspirin", - "semantic_tag": "substance", - "active": true, - "module": "900000000000207008", - "descriptions": [ - { "type": "FSN", "term": "Aspirin (substance)", "language": "en" }, - { "type": "Synonym", "term": "Acetylsalicylic acid", "language": "en" }, - { "type": "Synonym", "term": "ASA", "language": "en" } - ], - "relationships": [ - { "type": "Is a", "destination_id": "372665008", "destination_term": "Analgesic" }, - { "type": "Is a", "destination_id": "372578009", "destination_term": "Antiplatelet drug" } - ] - } -] diff --git a/scripts/db.py b/scripts/db.py deleted file mode 100644 index 5d2ef74..0000000 --- a/scripts/db.py +++ /dev/null @@ -1,42 +0,0 @@ -""" -Project Codex — Neo4j driver wrapper -""" - -from neo4j import GraphDatabase -from config import NEO4J_URI, NEO4J_USER, NEO4J_PASSWORD - - -class CodexDB: - def __init__(self): - self._driver = GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USER, NEO4J_PASSWORD)) - - def close(self): - self._driver.close() - - def run(self, cypher: str, parameters: dict = None): - with self._driver.session() as session: - result = session.run(cypher, parameters or {}) - return result.data() - - def run_file(self, filepath: str): - """Execute a .cypher file, skipping comment-only lines.""" - with open(filepath, "r") as f: - content = f.read() - - # Split on semicolons to get individual statements - statements = [s.strip() for s in content.split(";") if s.strip()] - executed = 0 - for stmt in statements: - # Skip pure comment blocks - lines = [l for l in stmt.splitlines() if l.strip() and not l.strip().startswith("//")] - if not lines: - continue - self.run(stmt) - executed += 1 - return executed - - def __enter__(self): - return self - - def __exit__(self, exc_type, exc_val, exc_tb): - self.close() diff --git a/scripts/dry_run.py b/scripts/dry_run.py deleted file mode 100644 index 0616ee1..0000000 --- a/scripts/dry_run.py +++ /dev/null @@ -1,122 +0,0 @@ -""" -Project Codex — Dry Run (no Neo4j required) -Validates sample data and shows what would be loaded. -Run this without a Neo4j connection to verify data quality. - -Usage: - python scripts/dry_run.py -""" - -import json -import os -import sys - -sys.path.insert(0, os.path.dirname(os.path.abspath(__file__))) -from config import SAMPLE_DATA_DIR - - -def load_json(filename): - path = os.path.join(SAMPLE_DATA_DIR, filename) - with open(path) as f: - return json.load(f) - - -def section(title): - print("\n" + "=" * 60) - print(f" {title}") - print("=" * 60) - - -def dry_run(): - print("\nProject Codex — ETL Dry Run") - print("Validating sample data files...\n") - - # ---- DrugBank ---- - section("DrugBank Sample Data") - drugbank = load_json("drugbank_sample.json") - print(f" Records: {len(drugbank)}") - total_brands = 0 - for d in drugbank: - brands = d.get("brands", []) - total_brands += len(brands) - countries = [b["country"] for b in brands] - print(f" [{d['drugbank_id']}] {d['name']:<20} → {len(brands)} brand names: {countries}") - print(f" Total brand-name nodes to create: {total_brands}") - - # ---- RxNorm ---- - section("RxNorm Sample Data") - rxnorm = load_json("rxnorm_sample.json") - print(f" Records: {len(rxnorm)}") - for r in rxnorm: - dose_forms = [c["name"] for c in r.get("related_concepts", []) if c["tty"] in ("SCD","SBD")] - print(f" [RxCUI {r['rxcui']:>6}] {r['name']:<20} → {len(dose_forms)} dose-form names") - - # ---- ICD-11 ---- - section("ICD-11 Sample Data") - icd11 = load_json("icd11_sample.json") - print(f" Records: {len(icd11)}") - for c in icd11: - syns = c.get("synonyms", []) - print(f" [{c['code']:<8}] {c['title']:<40} | Chapter {c['chapter']}: {c['chapter_title'][:30]}") - if syns: - print(f" Synonyms: {', '.join(syns)}") - - # ---- SNOMED CT ---- - section("SNOMED CT Sample Data") - snomed = load_json("snomedct_sample.json") - print(f" Records: {len(snomed)}") - for c in snomed: - descs = [d["term"] for d in c.get("descriptions", []) if d["type"] == "Synonym"] - print(f" [{c['concept_id']}] ({c['semantic_tag']:<10}) {c['preferred_term']}") - if descs: - print(f" Synonyms: {', '.join(descs)}") - - # ---- Codex Name Translation Preview ---- - section("Codex Name Translation Preview") - print(" Drug: Acetaminophen (DB00316)") - print(" All regional names found across all sources:\n") - - name_map = {} - # From DrugBank - apap = next(d for d in drugbank if d["drugbank_id"] == "DB00316") - for b in apap["brands"]: - name_map[b["country"]] = b["name"] - name_map["US (generic)"] = apap["name"] - - # From SNOMED (Paracetamol) - paracetamol = next(c for c in snomed if c["concept_id"] == "387517004") - for desc in paracetamol["descriptions"]: - if desc["term"] == "Paracetamol": - for country in ["GB", "IN", "AU"]: - if country not in name_map: - name_map[country] = "Paracetamol" - - print(f" {'Country/Region':<20} {'Name'}") - print(f" {'-'*20} {'-'*20}") - for region, name in sorted(name_map.items()): - print(f" {region:<20} {name}") - - # ---- Schema Summary ---- - section("Estimated Graph Size (after full load)") - drug_nodes = len(set(d["drugbank_id"] for d in drugbank)) - drug_nodes += len(rxnorm) # RxNorm Drug nodes - drug_nodes += len([c for c in snomed if c["semantic_tag"] == "substance"]) - cond_nodes = len(icd11) + len([c for c in snomed if c["semantic_tag"] == "disorder"]) - name_nodes = total_brands + len(rxnorm) * 2 # approx - print(f" ~{drug_nodes:>4} Drug nodes") - print(f" ~{name_nodes:>4} DrugName nodes") - print(f" ~{cond_nodes:>4} Condition nodes") - print(f" ~ 4 DataSource nodes") - print(f" ~ 5 Ingredient nodes") - print() - print(" POC-flagged drugs (for dev/demo/debug):") - poc_names = [d["name"] for d in drugbank[:3]] - for n in poc_names: - print(f" ✓ {n}") - - print("\nDry run complete. No database connection required.") - print("Run scripts/run_etl.py to load into Neo4j.\n") - - -if __name__ == "__main__": - dry_run() diff --git a/scripts/loaders/.DS_Store b/scripts/loaders/.DS_Store deleted file mode 100644 index 64adcd68189aac5ea8532a9c21fb8ac4c55a77a9..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKOHKnZ47H()O5JqHGFRvghH5xLH{A_%is+)%%!UQKY`F;HCOr@r;Jw&CvSVH=Y2s#AxM8TG`39G$Voj;uLeA zA=^fJxkK)6`8WHU#j5QNy`{Z=`rPu+)%9lIZD2v79`7HH=U-WGzhT|)-e-{!HY6Ab z27-ZLAQ<=&1Guv()0tuP!9Xw&47@VH^C6)TE5~eDjt+FC1OW0GT?9I73Hl_*$}t;a z1)}B(G*|T!L(LuY$?Yn~Y-sMHUVNzU{8GGV*&XpyF&C{2qYnmxfguB@Hk|YRzrZgu zTI3I1ViXJn1OJQxoz$y(iI4KT^~2}!u1#o{XcXFIDiG*{M*s#qN6yNkttaZRs~oc- Uqj0{s1LGl32#GEj_yq=@0e`JB3jhEB diff --git a/scripts/loaders/__init__.py b/scripts/loaders/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/scripts/loaders/__pycache__/__init__.cpython-313.pyc b/scripts/loaders/__pycache__/__init__.cpython-313.pyc 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z5kz_9dQqxQTc+cY{-K#t3f4=KUsNw{;8a832tY=?h+|;p3%{#Gq;i=48V7G>j7O~z zrLSBg;uElkO;cA^%G9-DSPzG55*MtcND|mIch#lzsJRQceDirrg3q?(uGW`_3l$XO zUps$oNL`$z$@T2DpjC{FSo}i`?Ges~T#c&z+;r{=E2seDU>$}S@HP4rjP-5hWI1wL z7)y-A67ao01z+>SVN8-=Ip5bv646R zse^$`+K#wJBgx@iAXvbwJ5s3(d_+!R^1apg5^j71$7jiOjC7|-N4`?)jH+SiWb;#) zSsNI;-9tdSNk?*%&K=GdGH_i#iUpWL9zp8Ap<87ridv&tioNGSl;_W=n^XqvD_h!( zU-O#N) Date: Tue, 28 Jul 2026 20:30:06 -0700 Subject: [PATCH 04/23] Reorganization/clean up --- .env | 16 ---------------- .env.example | 14 +++++++++++++- README.md | 1 + codex-build/__pycache__/api.cpython-314.pyc | Bin 23950 -> 15698 bytes {codex-main-test-build => codex-build}/api.py | 0 {codex-main-test-build => codex-build}/cli.py | 0 .../__pycache__/__init__.cpython-314.pyc | Bin 173 -> 0 bytes .../__pycache__/neo4j_driver.cpython-314.pyc | Bin 18165 -> 0 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 182 -> 0 bytes .../translation_service.cpython-314.pyc | Bin 1489 -> 0 bytes .../codex_schema_design.md | 0 .../docker-compose.yml | 0 .../requirements.txt | 0 .../__pycache__/api.cpython-314.pyc | Bin 15698 -> 0 bytes 14 files changed, 14 insertions(+), 17 deletions(-) delete mode 100644 .env rename {codex-main-test-build => codex-build}/api.py (100%) rename {codex-main-test-build => codex-build}/cli.py (100%) delete mode 100644 codex-build/codex/__pycache__/__init__.cpython-314.pyc delete mode 100644 codex-build/codex/__pycache__/neo4j_driver.cpython-314.pyc delete mode 100644 codex-build/codex/services/__pycache__/__init__.cpython-314.pyc delete mode 100644 codex-build/codex/services/__pycache__/translation_service.cpython-314.pyc rename {schema => codex-build}/codex_schema_design.md (100%) rename {codex-main-test-build => codex-build}/docker-compose.yml (100%) rename {codex-main-test-build => codex-build}/requirements.txt (100%) delete mode 100644 codex-main-test-build/__pycache__/api.cpython-314.pyc diff --git a/.env b/.env deleted file mode 100644 index 68e01a6..0000000 --- a/.env +++ /dev/null @@ -1,16 +0,0 @@ -# Project Codex — environment variables -DRUGBANK_API_KEY= -DRUGBANK_API_BASE=https://api.drugbank.com/discovery/v1 -DRUGBANK_RELEASE=API - -ICD_CLIENT_ID= -ICD_CLIENT_SECRET= - -NEO4J_URI=bolt://localhost:7687 -NEO4J_USER=neo4j -NEO4J_PASSWORD=changeme -NEO4J_DB=neo4j - -RATE_LIMIT_RPM=100 -LOG_LEVEL=INFO -FORCE=1 \ No newline at end of file diff --git a/.env.example b/.env.example index 306639b..458803c 100644 --- a/.env.example +++ b/.env.example @@ -1,6 +1,18 @@ # Project Codex — environment variables # Copy this file to .env and fill in your values. +DRUGBANK_API_KEY= +DRUGBANK_API_BASE=https://api.drugbank.com/discovery/v1 +DRUGBANK_RELEASE=API + +ICD_CLIENT_ID= +ICD_CLIENT_SECRET= + NEO4J_URI=bolt://localhost:7687 NEO4J_USER=neo4j -NEO4J_PASSWORD=codex-password +NEO4J_PASSWORD=changeme +NEO4J_DB=neo4j + +RATE_LIMIT_RPM=100 +LOG_LEVEL=INFO +FORCE=1 \ No newline at end of file diff --git a/README.md b/README.md index 91afe26..ab5f798 100644 --- 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| Bin .../__pycache__/db.cpython-312.pyc | Bin .../__pycache__/dependencies.cpython-312.pyc | Bin .../__pycache__/main.cpython-312.pyc | Bin .../__pycache__/main.cpython-314.pyc | Bin 0 -> 3074 bytes {codex-build => backend/codex_build}/api.py | 24 +- {codex-build => backend/codex_build}/cli.py | 0 .../codex_build/codex}/__init__.py | 0 .../__pycache__/__init__.cpython-310.pyc | Bin 0 -> 115 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 0 -> 181 bytes .../__pycache__/neo4j_driver.cpython-310.pyc | Bin 0 -> 5745 bytes .../__pycache__/neo4j_driver.cpython-314.pyc | Bin 7274 -> 7272 bytes .../codex}/config/fallbacks.json | 0 .../codex}/language_packs/english_pack.json | 0 .../codex}/language_packs/french_pack.json | 0 .../codex}/language_packs/russian_pack.json | 0 .../codex}/language_packs/spanish_pack.json | 0 .../codex}/language_packs/ukrainian_pack.json | 0 .../codex}/neo4j_driver.py | 0 .../codex_build/codex/services}/__init__.py | 0 .../__pycache__/__init__.cpython-310.pyc | Bin 0 -> 124 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 0 -> 190 bytes .../translation_service.cpython-310.pyc | Bin 0 -> 4384 bytes .../translation_service.cpython-314.pyc | Bin 7836 -> 7834 bytes .../codex}/services/translation_service.py | 2 +- .../codex_build/codex/utils}/__init__.py | 0 .../codex_build}/docker-compose.yml | 2 +- {api => backend/codex_build}/main.py | 11 +- .../{ => codex_build}/neo4j_sources/.DS_Store | Bin .../__pycache__/config.cpython-313.pyc | Bin .../__pycache__/config.cpython-314.pyc | Bin 0 -> 1238 bytes .../__pycache__/db.cpython-313.pyc | Bin .../__pycache__/db.cpython-314.pyc | Bin 0 -> 2640 bytes .../__pycache__/source_data.cpython-310.pyc | Bin 0 -> 19893 bytes .../__pycache__/source_data.cpython-314.pyc | Bin 0 -> 38044 bytes .../neo4j_sources}/codex_schema_design.md | 0 .../{ => codex_build}/neo4j_sources/config.py | 4 + .../codex_build/neo4j_sources}/db.py | 2 +- .../neo4j_sources}/dependencies.py | 2 +- .../neo4j_sources}/routers/.DS_Store | Bin .../neo4j_sources/routers}/__init__.py | 0 .../__pycache__/__init__.cpython-312.pyc | Bin .../__pycache__/conditions.cpython-312.pyc | Bin .../routers/__pycache__/drugs.cpython-312.pyc | Bin .../__pycache__/sources.cpython-312.pyc | Bin .../__pycache__/translate.cpython-312.pyc | Bin .../neo4j_sources}/routers/conditions.py | 4 +- .../neo4j_sources}/routers/drugs.py | 4 +- .../neo4j_sources}/routers/sources.py | 4 +- .../neo4j_sources}/routers/translate.py | 4 +- .../neo4j_sources/source_data.py | 13 +- .../codex_build}/requirements.txt | 0 .../__pycache__/config.cpython-314.pyc | Bin 1044 -> 0 bytes .../__pycache__/db.cpython-314.pyc | Bin 3368 -> 0 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 183 -> 0 bytes backend/translation/services/__init__.py | 0 .../__pycache__/__init__.cpython-314.pyc | Bin 192 -> 0 bytes backend/translation/utils/__init__.py | 0 codex-build/__pycache__/api.cpython-314.pyc | Bin 15698 -> 0 bytes docker-compose.yml | 12 +- frontend/Dockerfile | 12 + frontend/README.md | 73 + frontend/eslint.config.js | 23 + frontend/index.html | 13 + frontend/package-lock.json | 3061 +++++++++++++++++ frontend/package.json | 32 + frontend/public/favicon.svg | 1 + frontend/public/icons.svg | 24 + frontend/src/App.css | 510 +++ frontend/src/App.tsx | 596 ++++ frontend/src/assets/hero.png | Bin 0 -> 44919 bytes frontend/src/assets/react.svg | 1 + frontend/src/assets/vite.svg | 1 + frontend/src/i18n/config.ts | 26 + frontend/src/i18n/locales/de.json | 24 + frontend/src/i18n/locales/en.json | 24 + frontend/src/i18n/locales/es.json | 24 + frontend/src/i18n/locales/fr.json | 24 + frontend/src/index.css | 17 + frontend/src/main.tsx | 15 + frontend/tsconfig.app.json | 28 + frontend/tsconfig.json | 7 + frontend/tsconfig.node.json | 26 + frontend/vite.config.ts | 11 + requirements.txt | 4 - 98 files changed, 4664 insertions(+), 112 deletions(-) create mode 100644 .env create mode 100644 .gitignore delete 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import create_translation, get_translation_data, find_missing_translations, find_missing_brands, get_equivalent_brands, language_exists, resolve_to_base_term, driver +from codex.neo4j_driver import create_translation, get_translation_data, find_missing_translations, find_missing_brands, get_equivalent_brands, language_exists, resolve_to_base_term, driver import json import os diff --git a/api/routers/__init__.py b/backend/codex_build/codex/utils/__init__.py similarity index 100% rename from api/routers/__init__.py rename to backend/codex_build/codex/utils/__init__.py diff --git a/codex-build/docker-compose.yml b/backend/codex_build/docker-compose.yml similarity index 95% rename from codex-build/docker-compose.yml rename to backend/codex_build/docker-compose.yml index 57ad27c..033814e 100644 --- a/codex-build/docker-compose.yml +++ b/backend/codex_build/docker-compose.yml @@ -1,6 +1,6 @@ services: neo4j: - image: neo4j:5.18 + image: neo4j:5.18.0 container_name: codex-neo4j environment: NEO4J_AUTH: "neo4j/changeme" diff --git a/api/main.py b/backend/codex_build/main.py similarity index 65% rename from api/main.py rename to backend/codex_build/main.py index a8872fe..468ed45 100644 --- a/api/main.py +++ b/backend/codex_build/main.py @@ -3,10 +3,13 @@ """ from fastapi import FastAPI, Depends -from api.config import API_TITLE, API_DESCRIPTION, API_VERSION -from api.db import CodexDB -from api.dependencies import get_db -from api.routers import translate, drugs, conditions, sources +from fastapi.middleware.cors import CORSMiddleware +from pydantic import BaseModel + +from neo4j_sources.config import API_TITLE, API_DESCRIPTION, API_VERSION +from neo4j_sources.db import CodexDB +from neo4j_sources.dependencies import get_db +from neo4j_sources.routers import translate, drugs, conditions, sources app = FastAPI( title=API_TITLE, diff --git a/backend/neo4j_sources/.DS_Store b/backend/codex_build/neo4j_sources/.DS_Store similarity index 100% rename from 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backend/codex_build/neo4j_sources/routers/.DS_Store diff --git a/backend/translation/__init__.py b/backend/codex_build/neo4j_sources/routers/__init__.py similarity index 100% rename from backend/translation/__init__.py rename to backend/codex_build/neo4j_sources/routers/__init__.py diff --git a/api/routers/__pycache__/__init__.cpython-312.pyc b/backend/codex_build/neo4j_sources/routers/__pycache__/__init__.cpython-312.pyc similarity index 100% rename from api/routers/__pycache__/__init__.cpython-312.pyc rename to backend/codex_build/neo4j_sources/routers/__pycache__/__init__.cpython-312.pyc diff --git a/api/routers/__pycache__/conditions.cpython-312.pyc b/backend/codex_build/neo4j_sources/routers/__pycache__/conditions.cpython-312.pyc similarity index 100% rename from api/routers/__pycache__/conditions.cpython-312.pyc rename to backend/codex_build/neo4j_sources/routers/__pycache__/conditions.cpython-312.pyc diff --git a/api/routers/__pycache__/drugs.cpython-312.pyc b/backend/codex_build/neo4j_sources/routers/__pycache__/drugs.cpython-312.pyc similarity index 100% rename from api/routers/__pycache__/drugs.cpython-312.pyc rename to backend/codex_build/neo4j_sources/routers/__pycache__/drugs.cpython-312.pyc diff --git a/api/routers/__pycache__/sources.cpython-312.pyc b/backend/codex_build/neo4j_sources/routers/__pycache__/sources.cpython-312.pyc similarity index 100% rename from api/routers/__pycache__/sources.cpython-312.pyc rename to backend/codex_build/neo4j_sources/routers/__pycache__/sources.cpython-312.pyc diff --git a/api/routers/__pycache__/translate.cpython-312.pyc b/backend/codex_build/neo4j_sources/routers/__pycache__/translate.cpython-312.pyc similarity index 100% rename from api/routers/__pycache__/translate.cpython-312.pyc rename to backend/codex_build/neo4j_sources/routers/__pycache__/translate.cpython-312.pyc diff --git a/api/routers/conditions.py b/backend/codex_build/neo4j_sources/routers/conditions.py similarity index 96% rename from api/routers/conditions.py rename to backend/codex_build/neo4j_sources/routers/conditions.py index 8f440b2..75c6e96 100644 --- a/api/routers/conditions.py +++ b/backend/codex_build/neo4j_sources/routers/conditions.py @@ -4,8 +4,8 @@ """ from fastapi import APIRouter, Depends, HTTPException, Query -from api.db import CodexDB -from api.dependencies import get_db +from neo4j_sources.db import CodexDB +from neo4j_sources.dependencies import get_db router = APIRouter(prefix="/conditions", tags=["conditions"]) diff --git a/api/routers/drugs.py b/backend/codex_build/neo4j_sources/routers/drugs.py similarity index 98% rename from api/routers/drugs.py rename to backend/codex_build/neo4j_sources/routers/drugs.py index 392c5e3..db20891 100644 --- a/api/routers/drugs.py +++ b/backend/codex_build/neo4j_sources/routers/drugs.py @@ -4,8 +4,8 @@ """ from fastapi import APIRouter, Depends, HTTPException, Query -from api.db import CodexDB -from api.dependencies import get_db +from neo4j_sources.db import CodexDB +from neo4j_sources.dependencies import get_db router = APIRouter(prefix="/drugs", tags=["drugs"]) diff --git a/api/routers/sources.py b/backend/codex_build/neo4j_sources/routers/sources.py similarity index 87% rename from api/routers/sources.py rename to backend/codex_build/neo4j_sources/routers/sources.py index a58aec0..0bbbb3b 100644 --- a/api/routers/sources.py +++ b/backend/codex_build/neo4j_sources/routers/sources.py @@ -4,8 +4,8 @@ """ from fastapi import APIRouter, Depends -from api.db import CodexDB -from api.dependencies import get_db +from neo4j_sources.db import CodexDB +from neo4j_sources.dependencies import get_db router = APIRouter(prefix="/sources", tags=["sources"]) diff --git a/api/routers/translate.py b/backend/codex_build/neo4j_sources/routers/translate.py similarity index 96% rename from api/routers/translate.py rename to backend/codex_build/neo4j_sources/routers/translate.py index aee21b5..1f57275 100644 --- a/api/routers/translate.py +++ b/backend/codex_build/neo4j_sources/routers/translate.py @@ -4,8 +4,8 @@ """ from fastapi import APIRouter, Depends, HTTPException, Query -from api.db import CodexDB -from api.dependencies import get_db +from neo4j_sources.db import CodexDB +from neo4j_sources.dependencies import get_db router = APIRouter(prefix="/translate", tags=["translate"]) diff --git a/backend/neo4j_sources/source_data.py b/backend/codex_build/neo4j_sources/source_data.py similarity index 99% rename from backend/neo4j_sources/source_data.py rename to backend/codex_build/neo4j_sources/source_data.py index 600759c..27d6bfa 100644 --- a/backend/neo4j_sources/source_data.py +++ b/backend/codex_build/neo4j_sources/source_data.py @@ -458,7 +458,7 @@ def unify_graph(driver): log.info("<<< Graph combination complete. All sources are now connected.") -def main(): +def source_data(sources): log.info("=" * 60) log.info("Creating Singular Medical Knowledge Graph") log.info("=" * 60) @@ -472,16 +472,16 @@ def main(): log.info("Graph connection smoke test passed.") # Ingest separate sources into the single database based on user choice - if "drugbank" in sys.argv[1:]: + if "drugbank" in sources: log.info("Ingesting DrugBank.") drugbank(driver) - if "snomed" in sys.argv[1:]: + if "snomed" in sources: log.info("Ingesting SNOMED.") snomed(driver) - if "rxnorm" in sys.argv[1:]: + if "rxnorm" in sources: log.info("Ingesting RXNorm.") rxnorm(driver) - if "icd11" in sys.argv[1:]: + if "icd11" in sources: log.info("Ingesting ICD11.") icd11(driver) @@ -499,4 +499,5 @@ def main(): log.info("=" * 60) if __name__ == "__main__": - main() \ No newline at end of file + sources = sys.argv[1:] + source_data(sources) \ No newline at end of file diff --git a/codex-build/requirements.txt b/backend/codex_build/requirements.txt similarity index 100% rename from codex-build/requirements.txt rename to backend/codex_build/requirements.txt diff --git a/backend/neo4j_sources/__pycache__/config.cpython-314.pyc b/backend/neo4j_sources/__pycache__/config.cpython-314.pyc deleted file mode 100644 index 94402ee883c506f996eaf296982f1aa4514f81cc..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1044 zcmbtSO-~a+7@lp*cG;zcf~4g#Jw z#tSEcF#%2_p2`Wm`7=oNLMAcs;}3}a1J3qSO*k0mFz@p|^SsYH^JXTZ5fQNUF>4in zasYhylhz71LG1%OaRCGbya15Pa)e_skPR#ZN$@6E4UU3DQ_3VkY*#b2rlL!qq-x9-H$eVvXilpAQFPW*4>V8^S4R;2`+lE40rr00@;!wvoK z`)UvDZoe%0PjzCut`~B*z__#-XU<{{qoS#kk$Gg8+aurHcO#1?N)%ac+l;r6?Zb6z zV-stBCN7S1R4O6OPz^*(`z7sO%q%4ytIII^YH$se$h0h%kgk;q$RX3py(xu?O+`Kf zX_xKW(`bXrrSkceC77lW-S1z~9A^t*gG!E8u9QsG(1=EPeWy||@pvB%tE{Q6sx*Kc z$~XFB|I<)@!}KqMgDk-zf8%{RRMAL*h7AkbTG^ywZOy4Of~u}t%wMI#Tq>VY(^*JE zMP%8uH=lZ%d%~F1vs9fH=bz^mGSJ5-pvFuAot2jz6Fcmg8=AeP5r)eaDaenoxig2h z<>pM)`b=d<$5w?nvR)tKoyrasX3EIeESa--h}rqy!g5AR1*Lveg-$b z0_jcUOKjj^=7gr}_g^^}+aEia+@Cz$u3q>06}R_K P?wZ#he=Xvx?3%v-P>JHC diff --git a/backend/neo4j_sources/__pycache__/db.cpython-314.pyc b/backend/neo4j_sources/__pycache__/db.cpython-314.pyc deleted file mode 100644 index 64ea89b9e9b53b0a4d693543a8acaf880354e76b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3368 zcmb6cTTC3+_1@W?+1X{6N7(g(17Cj|!<$ldq^!rPN8K{!}W|sL*MpR84>ShgnsmRX=*pof(^; zh$?r@x#ynynDaizJ@ttgf$_nZd1E(B$Y;0+2CVt0y$I6^QHevQiAu-lsNe`4hznz( z(XbO96&-O@a-0S8Myi~Ibu7oqH;jU#TrAHTx0JuH+*c-y za^DSQmYHuFOj%;OWf?4%p>ARX@P#4W(Pwnq$b{VJ#PBP9FKbuTF*oL;SB6!$-otZ) zSFT)pMI9=5U-e+fU)0_JLam^5+1ssK<_>+<9*Rl{jglvNR6 zW05)%r%9X^K^ll7!)aNK0*tCLCzdBpof-lW<8FkDHS|(}`X9zggg;Crf zVTL!{i00AP;Jj@V=WOJ++r5yzY8%YX7R&Q`X-RhgUo@SC>a~pjn^ad1kF#CA`E99@~6IT6891T)BH>Vk30upg>1|5JMr7`E&1q%eDqIp8*2jc1m`p`GU^risC5GvperO# zriF9gBV-n+ZR9dtpensWCm~z_(yRcc3jNcwPhr_wFqj*&bfzyFsPT;8hHQtq;aRib zz(SfUvqjx;6Pi{i>b8w!O|$X(@f9wC8`m_wR4O}QG0=Z95M@8L5sq^ke7-{VNJ#8_ zg5alJJ2-NE^VjURwwUGK0LCOIlrDc|2})1 zx=_8e-Q2p`f3N?Y7xqL_e*(_JzsHHL|JdluKkFH66(6=;rz0HkmS1ay48LdPzmN zbc&FhLx;K4Q^(=XI1Y+A+yy6u@zaDv$uVMyR(P6NQeJE%mmm#Tk$fZ<4V3Y04xAUb zl6|f&0$0_q$d!E9`5b!7fdRGI*GC|um#D@EK}H$m0AJ;DL@hZV4bFH$Ier7qkQ|1? 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image: neo4j:5.18 + image: neo4j:5.18.0 container_name: codex-neo4j environment: NEO4J_AUTH: "neo4j/changeme" diff --git a/frontend/Dockerfile b/frontend/Dockerfile new file mode 100644 index 0000000..30ad434 --- /dev/null +++ b/frontend/Dockerfile @@ -0,0 +1,12 @@ +FROM node:26 + +WORKDIR /app + +COPY package*.json ./ +RUN npm install + +COPY . . + +EXPOSE 9000 + +CMD ["npm", "run", "dev"] \ No newline at end of file diff --git a/frontend/README.md b/frontend/README.md new file mode 100644 index 0000000..7dbf7eb --- /dev/null +++ b/frontend/README.md @@ -0,0 +1,73 @@ +# React + TypeScript + Vite + +This template provides a minimal setup to get React working in Vite with HMR and some ESLint rules. + +Currently, two official plugins are available: + +- [@vitejs/plugin-react](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react) uses [Oxc](https://oxc.rs) +- [@vitejs/plugin-react-swc](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react-swc) uses [SWC](https://swc.rs/) + +## React Compiler + +The React Compiler is not enabled on this template because of its impact on dev & build performances. To add it, see [this documentation](https://react.dev/learn/react-compiler/installation). + +## Expanding the ESLint configuration + +If you are developing a production application, we recommend updating the configuration to enable type-aware lint rules: + +```js +export default defineConfig([ + globalIgnores(['dist']), + { + files: ['**/*.{ts,tsx}'], + extends: [ + // Other configs... + + // Remove tseslint.configs.recommended and replace with this + tseslint.configs.recommendedTypeChecked, + // Alternatively, use this for stricter rules + tseslint.configs.strictTypeChecked, + // Optionally, add this for stylistic rules + tseslint.configs.stylisticTypeChecked, + + // Other configs... + ], + languageOptions: { + parserOptions: { + project: ['./tsconfig.node.json', './tsconfig.app.json'], + tsconfigRootDir: import.meta.dirname, + }, + // other options... + }, + }, +]) +``` + +You can also install [eslint-plugin-react-x](https://github.com/Rel1cx/eslint-react/tree/main/packages/plugins/eslint-plugin-react-x) and [eslint-plugin-react-dom](https://github.com/Rel1cx/eslint-react/tree/main/packages/plugins/eslint-plugin-react-dom) for React-specific lint rules: + +```js +// eslint.config.js +import reactX from 'eslint-plugin-react-x' +import reactDom from 'eslint-plugin-react-dom' + +export default defineConfig([ + globalIgnores(['dist']), + { + files: ['**/*.{ts,tsx}'], + extends: [ + // Other configs... + // Enable lint rules for React + reactX.configs['recommended-typescript'], + // Enable lint rules for React DOM + reactDom.configs.recommended, + ], + languageOptions: { + parserOptions: { + project: ['./tsconfig.node.json', './tsconfig.app.json'], + tsconfigRootDir: import.meta.dirname, + }, + // other options... + }, + }, +]) +``` diff --git a/frontend/eslint.config.js b/frontend/eslint.config.js new file mode 100644 index 0000000..5e6b472 --- /dev/null +++ b/frontend/eslint.config.js @@ -0,0 +1,23 @@ +import js from '@eslint/js' +import globals from 'globals' +import reactHooks from 'eslint-plugin-react-hooks' +import reactRefresh from 'eslint-plugin-react-refresh' +import tseslint from 'typescript-eslint' +import { defineConfig, globalIgnores } from 'eslint/config' + +export default defineConfig([ + globalIgnores(['dist']), + { + files: ['**/*.{ts,tsx}'], + extends: [ + js.configs.recommended, + tseslint.configs.recommended, + reactHooks.configs.flat.recommended, + reactRefresh.configs.vite, + ], + languageOptions: { + ecmaVersion: 2020, + globals: globals.browser, + }, + }, +]) diff --git a/frontend/index.html b/frontend/index.html new file mode 100644 index 0000000..d1e6f14 --- /dev/null +++ b/frontend/index.html @@ -0,0 +1,13 @@ + + + + + + + project-codex-frontend + + +

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14px clamp(16px, 4vw, 56px); +} + +.top-nav__left, +.top-nav__right { + display: flex; + align-items: center; +} + +.top-nav__left { + gap: 26px; +} + +.brand { + text-decoration: none; + color: #fff; + background: #6b7b92; + border: 2px solid #d7e1e6; + width: 78px; + height: 56px; + display: grid; + place-items: center; + font-size: 12px; + letter-spacing: 0.35px; +} + +.main-links { + display: flex; + gap: 32px; +} + +.main-links a { + color: #ffffff; + text-decoration: none; + font-weight: 600; + font-size: 21px; +} + +.top-nav__right { + gap: 12px; +} + +.top-nav__right select { + width: 146px; + height: 34px; + border-radius: 8px; + border: none; + padding: 0 12px; + background: #f3f4f6; + font-size: 14px; + color: #253242; +} + +.icon-btn { + width: 28px; + height: 28px; + border: none; + background: transparent; + color: #f6f8fa; + display: grid; + place-items: center; + cursor: pointer; + padding: 0; +} + +.icon-btn svg { + width: 21px; + height: 21px; + fill: currentColor; +} + +.content { + width: min(1180px, calc(100% - 56px)); + margin: 0 auto; + padding: 30px 0 56px; +} + +.hero-row { + border-bottom: 1px solid #c7ccd2; + padding-bottom: 20px; + margin-bottom: 28px; + display: flex; + justify-content: space-between; + align-items: start; + gap: 16px; +} + +.hero-row h1 { + margin: 0 0 6px; + color: #101827; + font-size: clamp(2rem, 2.3vw, 2.75rem); + font-weight: 700; + letter-spacing: -0.2px; + line-height: 1.15; +} + +.hero-row p { + margin: 0; + color: #2f4057; + font-size: clamp(1rem, 1.1vw, 1.35rem); + line-height: 1.35; +} + +.help-btn { + border: none; + border-radius: 8px; + background: #4e7f77; + color: #fff; + font-weight: 700; + font-size: 17px; + width: 78px; + height: 42px; + cursor: pointer; +} + +.populate-btn { + border: none; + border-radius: 8px; + background: #4e7f77; + color: #fff; + font-weight: 700; + font-size: 17px; + width: 150px; + height: 50px; + cursor: pointer; + position: absolute; + top: 200px; + left: 75px; +} + +/* Customize the label (the container) */ +.container { + display: block; + position: relative; + padding-left: 35px; + margin-bottom: 12px; + cursor: pointer; + font-size: 22px; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; +} + +/* Hide the browser's default checkbox */ +.container input { + position: absolute; + opacity: 0; + cursor: pointer; + height: 0; + width: 0; +} + +/* Create a custom checkbox */ +.checkmark { + position: absolute; + top: 0; + left: 0; + height: 25px; + width: 25px; + background-color: #eee; +} + +/* On mouse-over, add a grey background color */ +.container:hover input ~ .checkmark { + background-color: #ccc; +} + +/* When the checkbox is checked, add a blue background */ +.container input:checked ~ .checkmark { + background-color: #2196F3; +} + +/* Create the checkmark/indicator (hidden when not checked) */ +.checkmark:after { + content: ""; + position: absolute; + display: none; +} + +/* Show the checkmark when checked */ +.container input:checked ~ .checkmark:after { + display: block; +} + +/* Style the checkmark/indicator */ +.container .checkmark:after { + left: 9px; + top: 5px; + width: 5px; + height: 10px; + border: solid white; + border-width: 0 3px 3px 0; + -webkit-transform: rotate(45deg); + -ms-transform: rotate(45deg); + transform: rotate(45deg); +} + +.populateDrugbank-checkbox { + display: flex; + align-items: center; + gap: 12px; + cursor: pointer; + font-family: sans-serif; + user-select: none; + position: absolute; + top: 100px; + left: 100px; + font-size: 1.2rem; +} + +.populateSnomed-checkbox { + display: flex; + align-items: center; + gap: 12px; + cursor: pointer; + font-family: sans-serif; + user-select: none; + position: absolute; + top: 125px; + left: 100px; + font-size: 1.2rem; +} + +.populateRxNorm-checkbox { + display: flex; + align-items: center; + gap: 12px; + cursor: pointer; + font-family: sans-serif; + user-select: none; + position: absolute; + top: 150px; + left: 100px; + font-size: 1.2rem; +} + +.populateICD11-checkbox { + display: flex; + align-items: center; + gap: 12px; + cursor: pointer; + font-family: sans-serif; + user-select: none; + position: absolute; + top: 175px; + left: 100px; + font-size: 1.2rem; +} + +.tool-panel { + border-bottom: 1px solid #c7ccd2; + padding: 4px 0 30px; +} + +.tool-panel + .tool-panel { + margin-top: 14px; + border-bottom: none; + padding-bottom: 0; +} + +.tool-panel h2 { + margin: 0 0 22px; + color: #0f1826; + text-align: center; + font-size: clamp(1.8rem, 2vw, 2.25rem); + font-weight: 700; +} + +.search-surface { + border: 1px solid #d7dbe0; + border-radius: 12px; + background: #f8fafc; + padding: 14px; +} + +.field-stack label { + display: block; + margin-bottom: 7px; + color: #384a60; + font-size: 1.12rem; + font-weight: 600; +} + +.field-stack select, +.search-row input, +.translate-grid input, +.results-select { + width: 100%; + height: 44px; + border: 1px solid #d7dbe0; + border-radius: 9px; + background: #f4f5f7; + padding: 0 12px; + color: #202e3d; + font-size: 1.02rem; + box-sizing: border-box; +} + +.search-grid { + display: grid; + grid-template-columns: minmax(200px, 250px) 1fr; + gap: 14px; + align-items: end; +} + +.search-row { + display: grid; + grid-template-columns: 1fr 170px; + gap: 10px; +} + +.search-row button, +.translate-btn { + height: 44px; + border: none; + border-radius: 9px; + background: #8e97a6; + color: #fff; + font-size: 1rem; + font-weight: 700; + cursor: pointer; +} + +.results-block { + margin-top: 18px; +} + +.message { + margin-bottom: 10px; + padding: 8px 10px; + border-radius: 8px; + font-size: 0.95rem; +} + +.message--error { + color: #9c2c2c; + background: #fdecec; + border: 1px solid #f6c8c8; +} + +.message--info { + color: #2f4d69; + background: #eaf2fb; + border: 1px solid #cfe1f4; +} + +.message--muted { + color: #667085; +} + +.results-block h3 { + margin: 0 0 10px; + text-align: center; + color: #111827; + font-size: clamp(1.45rem, 1.8vw, 2rem); +} + +.results-table-wrap { + width: 100%; + border: 1px solid #dce2e8; + border-radius: 10px; + background: #fff; + overflow-x: auto; +} + +.results-table { + width: 100%; + border-collapse: collapse; + min-width: 680px; +} + +.results-table th, +.results-table td { + padding: 10px 12px; + text-align: left; + border-bottom: 1px solid #e7ecf1; + vertical-align: top; +} + +.results-table th { + background: #eff4f8; + color: #223246; + font-size: 0.95rem; +} + +.results-table td { + color: #2e435a; +} + +.results-table tbody tr:nth-child(even) { + background: #fbfcfe; +} + +.results-table tbody tr.row-selected { + background: #e5f1ef; +} + +.results-table tbody tr:last-child td { + border-bottom: none; +} + +.results-select { + display: flex; + justify-content: space-between; + align-items: center; + border: 1px solid #e2e5e9; + color: #8f9bb0; +} + +.translate-grid { + display: grid; + grid-template-columns: minmax(200px, 250px) 170px 1fr; + gap: 10px; + align-items: end; +} + +.translate-grid input::placeholder, +.search-row input::placeholder { + color: #9ca6b8; +} + +button:focus-visible, +select:focus-visible, +input:focus-visible, +a:focus-visible { + outline: 3px solid #2a5e59; + outline-offset: 2px; +} + +@media (max-width: 1100px) { + .top-nav { + padding: 12px 16px; + } + + .main-links a { + font-size: 17px; + } + + .top-nav__left { + gap: 16px; + } + + .help-btn { + width: 72px; + height: 40px; + font-size: 15px; + } +} + +@media (max-width: 840px) { + .top-nav { + flex-direction: column; + align-items: stretch; + gap: 12px; + } + + .top-nav__right { + justify-content: flex-end; + } + + .hero-row { + flex-direction: column; + gap: 12px; + } + + .search-grid, + .translate-grid, + .search-row { + grid-template-columns: 1fr; + } + + .content { + width: calc(100% - 20px); + padding-top: 18px; + } + + .main-links { + gap: 18px; + } + + .top-nav__right { + gap: 8px; + } + + .hero-row h1 { + font-size: 1.9rem; + } + + .tool-panel h2 { + font-size: 1.6rem; + text-align: left; + } + + .results-block h3 { + text-align: left; + } +} \ No newline at end of file diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx new file mode 100644 index 0000000..1bc88b3 --- /dev/null +++ b/frontend/src/App.tsx @@ -0,0 +1,596 @@ +import './App.css' +import { useTranslation } from 'react-i18next' +import { useEffect, useState, type KeyboardEvent } from 'react' + +interface LanguagesResponse { + languages: string[] +} + +interface SearchResultRow { + source_id: string | null + source_name: string | null + name: string + type: string + country: string | null + language: string + uploaded_at: string | null +} + +interface SearchResponse { + query: string + count: number + results: SearchResultRow[] +} + +interface TranslateResultRow { + source_id: string | null + source_name: string | null + name: string + type: string + country: string | null + language: string + uploaded_at: string | null +} + +interface TranslateResponse { + found: boolean + results: TranslateResultRow[] +} + +const API_BASE_URL = 'http://localhost:8000' +const FALLBACK_LANGUAGES = ['en', 'es', 'fr', 'de'] + +function App() { + const { t, i18n } = useTranslation() + const [searchQuery, setSearchQuery] = useState('') + const [searchResults, setSearchResults] = useState([]) + const [selectedResult, setSelectedResult] = useState(null) + const [availableLanguages, setAvailableLanguages] = useState(FALLBACK_LANGUAGES) + const [searchLanguage, setSearchLanguage] = useState('all') + const [targetLanguage, setTargetLanguage] = useState('es') + const [translatedName, setTranslatedName] = useState('') + const [translateError, setTranslateError] = useState('') + const [searchError, setSearchError] = useState('') + const [isLoading, setIsLoading] = useState(false) + const [isTranslating, setIsTranslating] = useState(false) + const [exportLanguage, setExportLanguage] = useState(availableLanguages[0]) + const [exportError, setExportError] = useState('') + const [isExporting, setIsExporting] = useState(false) + const [exportMessage, setExportMessage] = useState('') + + const getLanguageLabel = (code: string) => { + const raw = code.trim() + const normalized = raw.toLowerCase() + + // Backend may return either ISO codes (en) or full names (English). + if (normalized.length > 3) { + return raw + } + + try { + const displayNames = new Intl.DisplayNames([i18n.language], { type: 'language' }) + return displayNames.of(normalized) ?? normalized.toUpperCase() + } catch { + return normalized.toUpperCase() + } + } + + useEffect(() => { + let isActive = true + + const loadLanguages = async () => { + try { + const response = await fetch(`${API_BASE_URL}/languages`) + if (!response.ok) { + throw new Error('Failed to load languages') + } + + const data = (await response.json()) as LanguagesResponse + const nextLanguages = Array.isArray(data.languages) && data.languages.length > 0 ? data.languages : FALLBACK_LANGUAGES + if (!isActive) { + return + } + + setAvailableLanguages(nextLanguages) + setTargetLanguage((current) => (nextLanguages.includes(current) ? current : nextLanguages[0])) + setExportLanguage((current) => (nextLanguages.includes(current) ? current : nextLanguages[0])) + } catch { + if (!isActive) { + return + } + + setAvailableLanguages(FALLBACK_LANGUAGES) + setTargetLanguage((current) => (FALLBACK_LANGUAGES.includes(current) ? current : FALLBACK_LANGUAGES[0])) + } + } + + void loadLanguages() + + return () => { + isActive = false + } + }, []) + + const extractTranslatedName = (rows: TranslateResultRow[]) => { + const names = rows + .map((row) => row.name) + .filter((name): name is string => Boolean(name && name.trim())) + + if (names.length === 0) { + return '-' + } + + return Array.from(new Set(names)).join(', ') + } + + const handleSearch = async () => { + if (!searchQuery.trim()) { + setSearchError('Please enter a search term') + return + } + + setIsLoading(true) + setSearchError('') + setTranslateError('') + setSearchResults([]) + setSelectedResult(null) + setTranslatedName('') + + try { + const response = await fetch(`${API_BASE_URL}/search`, { + method: 'POST', + headers: { + 'Content-Type': 'application/json', + }, + body: JSON.stringify({ + query: searchQuery, + limit: 20, + }), + }) + + if (!response.ok) { + const errorBody = await response.json().catch(() => null) + throw new Error(errorBody?.detail ?? 'Failed to search') + } + + const data = (await response.json()) as SearchResponse + const rows = Array.isArray(data.results) ? data.results : [] + const filteredRows = + searchLanguage === 'all' + ? rows + : rows.filter((row) => row.language.toLowerCase() === searchLanguage.toLowerCase()) + + setSearchResults(filteredRows) + + if (filteredRows.length === 0) { + setSearchError('No results found') + } + } catch (err) { + setSearchError(err instanceof Error ? err.message : 'An error occurred during search') + setSearchResults([]) + } finally { + setIsLoading(false) + } + } + + const handleKeyPress = (e: KeyboardEvent) => { + if (e.key === 'Enter') { + void handleSearch() + } + } + + const handleTranslateSelected = async () => { + if (!selectedResult) { + setTranslateError('Select a search result first') + return + } + + setIsTranslating(true) + setTranslateError('') + setTranslatedName('') + + try { + const response = await fetch(`${API_BASE_URL}/translate`, { + method: 'POST', + headers: { + 'Content-Type': 'application/json', + }, + body: JSON.stringify({ + term: selectedResult.name, + source_lang: selectedResult.language, + target_lang: targetLanguage, + }), + }) + + if (!response.ok) { + const errorBody = await response.json().catch(() => null) + throw new Error(errorBody?.detail ?? 'Translation request failed') + } + + const payload = (await response.json()) as TranslateResponse + const name = payload.found ? extractTranslatedName(payload.results ?? []) : '-' + setTranslatedName(name) + if (!payload.found || name === '-') { + setTranslateError('No translation found for the selected language') + } + } catch (err) { + setTranslateError(err instanceof Error ? err.message : 'Translation failed') + } finally { + setIsTranslating(false) + } + } + + const rowsToCsv = (rows: any[]) => { + if (!rows || rows.length === 0) return '' + const headerOrder = ['concept_id', 'source_id', 'source_name', 'name', 'type', 'country', 'language', 'uploaded_at'] + const keys = Array.from(new Set([...headerOrder, ...Object.keys(rows[0] || {})])) + const escapeVal = (v: any) => { + if (v === null || v === undefined) return '' + const s = String(v) + if (s.includes('"') || s.includes(',') || s.includes('\n')) { + return `"${s.replace(/"/g, '""')}"` + } + return s + } + const lines = [keys.join(',')] + rows.forEach((r) => { + lines.push(keys.map((k) => escapeVal((r as any)[k])).join(',')) + }) + return lines.join('\n') + } + + const downloadBlob = (filename: string, text: string) => { + const blob = new Blob([text], { type: 'text/csv;charset=utf-8;' }) + const url = URL.createObjectURL(blob) + const a = document.createElement('a') + a.href = url + a.download = filename + document.body.appendChild(a) + a.click() + a.remove() + URL.revokeObjectURL(url) + } + + const fetchAndDownload = async (urlSuffix: string, filename: string) => { + setIsExporting(true) + setExportError('') + setExportMessage('') + try { + const res = await fetch(`${API_BASE_URL}${urlSuffix}`) + if (!res.ok) { + const err = await res.json().catch(() => null) + throw new Error(err?.detail ?? 'Export failed') + } + const data = await res.json() + const rows = Array.isArray(data.rows) ? data.rows : data.results ?? [] + const csv = rowsToCsv(rows) + if (!csv) throw new Error('No rows to export') + downloadBlob(filename, csv) + setExportMessage(`Downloaded ${rows.length} rows`) + } catch (err) { + setExportError(err instanceof Error ? err.message : 'Export failed') + } finally { + setIsExporting(false) + } + } + const downloadByLanguage = () => { + if (!exportLanguage.trim()) { + setExportError('Choose a language') + return + } + fetchAndDownload(`/csv/language/${encodeURIComponent(exportLanguage.trim())}`, `codex_language_${exportLanguage.trim()}.csv`) + } + + const languages = availableLanguages.map((code) => ({ code, label: getLanguageLabel(code) })) + + const [isDrugbankSelected, setIsDrugbankSelected] = useState(false); + const [isSnomedSelected, setIsSnomedSelected] = useState(false); + const [isRxNormSelected, setIsRxNormSelected] = useState(false); + const [isICD11Selected, setIsICD11Selected] = useState(false); + + const handlePopulateClick = async () => { + let sources: string[] = [] + if (isDrugbankSelected) { + sources.push("drugbank") + } + if (isSnomedSelected) { + sources.push("snomed") + } + if (isRxNormSelected) { + sources.push("rxnorm") + } + if (isICD11Selected) { + sources.push("icd11") + } + try{ + const response = await fetch('http://localhost:8000/api/populate-sources', { + method: 'POST', + headers: { 'Content-Type': 'application/json' }, + body: JSON.stringify({ selectedSources: sources }), + }); + + const data = await response.json(); + if (data.status === "success") { + alert(data.message); + } + } catch (error) { + console.error("Error calling Python function:", error); + alert("Something went wrong on the backend."); + } + }; + + return ( + + ) +} + +export default App \ No newline at end of file diff --git a/frontend/src/assets/hero.png b/frontend/src/assets/hero.png new file mode 100644 index 0000000000000000000000000000000000000000..cc51a3d20ad4bc961b596a6adfd686685cd84bb0 GIT binary patch literal 44919 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@@ + \ No newline at end of file diff --git a/frontend/src/assets/vite.svg b/frontend/src/assets/vite.svg new file mode 100644 index 0000000..5101b67 --- /dev/null +++ b/frontend/src/assets/vite.svg @@ -0,0 +1 @@ +Vite diff --git a/frontend/src/i18n/config.ts b/frontend/src/i18n/config.ts new file mode 100644 index 0000000..32c53cf --- /dev/null +++ b/frontend/src/i18n/config.ts @@ -0,0 +1,26 @@ +import i18n from 'i18next' +import { initReactI18next } from 'react-i18next' +import en from './locales/en.json' +import es from './locales/es.json' +import fr from './locales/fr.json' +import de from './locales/de.json' + +const resources = { + en: { translation: en }, + es: { translation: es }, + fr: { translation: fr }, + de: { translation: de }, +} + +i18n + .use(initReactI18next) + .init({ + resources, + lng: 'en', + fallbackLng: 'en', + interpolation: { + escapeValue: false, + }, + }) + +export default i18n diff --git a/frontend/src/i18n/locales/de.json b/frontend/src/i18n/locales/de.json new file mode 100644 index 0000000..3702330 --- /dev/null +++ b/frontend/src/i18n/locales/de.json @@ -0,0 +1,24 @@ +{ + "nav": { + "home": "Startseite", + "about": "Über uns" + }, + "common": { + "help": "Hilfe", + "search": "Suchen", + "translate": "Übersetzen" + }, + "home": { + "pageTitle": "Projekt Medizinischer Kodex", + "pageDescription": "Ein Werkzeug zur Koordination medizinischer Ausrüstung zwischen Ländern.", + "searchTitle": "Nach Medikamentennamen suchen...", + "sourceLanguage": "Ausgangssprache", + "sourcePlaceholder": "Wort zum Suchen", + "resultsTitle": "Ergebnisse", + "sampleMedicine": "Medikament 1", + "localizeTitle": "Medikamentennamen übersetzen/lokalisieren...", + "targetLanguage": "Zielsprache", + "targetPlaceholder": "Zielsprache", + "translationPlaceholder": "Die Übersetzung wird hier angezeigt" + } +} diff --git a/frontend/src/i18n/locales/en.json b/frontend/src/i18n/locales/en.json new file mode 100644 index 0000000..40f0023 --- /dev/null +++ b/frontend/src/i18n/locales/en.json @@ -0,0 +1,24 @@ +{ + "nav": { + "home": "Home", + "about": "About" + }, + "common": { + "help": "Help", + "search": "Search", + "translate": "Translate" + }, + "home": { + "pageTitle": "Project Medical Codex", + "pageDescription": "A tool developed to help coordinate medical equipment between countries.", + "searchTitle": "Search for drug name...", + "sourceLanguage": "Source Language", + "sourcePlaceholder": "Word to search", + "resultsTitle": "Results", + "sampleMedicine": "Medicine 1", + "localizeTitle": "Translate/Localize drug name...", + "targetLanguage": "Target Language", + "targetPlaceholder": "Target Language", + "translationPlaceholder": "Translation will appear here" + } +} diff --git a/frontend/src/i18n/locales/es.json b/frontend/src/i18n/locales/es.json new file mode 100644 index 0000000..c380342 --- /dev/null +++ b/frontend/src/i18n/locales/es.json @@ -0,0 +1,24 @@ +{ + "nav": { + "home": "Inicio", + "about": "Acerca de" + }, + "common": { + "help": "Ayuda", + "search": "Buscar", + "translate": "Traducir" + }, + "home": { + "pageTitle": "Proyecto Códice Médico", + "pageDescription": "Una herramienta desarrollada para ayudar a coordinar equipos médicos entre países.", + "searchTitle": "Buscar nombre de medicamento...", + "sourceLanguage": "Idioma de origen", + "sourcePlaceholder": "Palabra a buscar", + "resultsTitle": "Resultados", + "sampleMedicine": "Medicina 1", + "localizeTitle": "Traducir/Localizar nombre de medicamento...", + "targetLanguage": "Idioma de destino", + "targetPlaceholder": "Idioma de destino", + "translationPlaceholder": "La traducción aparecerá aquí" + } +} diff --git a/frontend/src/i18n/locales/fr.json b/frontend/src/i18n/locales/fr.json new file mode 100644 index 0000000..6cd2fc9 --- /dev/null +++ b/frontend/src/i18n/locales/fr.json @@ -0,0 +1,24 @@ +{ + "nav": { + "home": "Accueil", + "about": "À propos" + }, + "common": { + "help": "Aide", + "search": "Rechercher", + "translate": "Traduire" + }, + "home": { + "pageTitle": "Projet Codex Médical", + "pageDescription": "Un outil développé pour aider à coordonner les équipements médicaux entre les pays.", + "searchTitle": "Rechercher un nom de médicament...", + "sourceLanguage": "Langue source", + "sourcePlaceholder": "Mot à rechercher", + "resultsTitle": "Résultats", + "sampleMedicine": "Médicament 1", + "localizeTitle": "Traduire/Localiser le nom du médicament...", + "targetLanguage": "Langue cible", + "targetPlaceholder": "Langue cible", + "translationPlaceholder": "La traduction s'affichera ici" + } +} diff --git a/frontend/src/index.css b/frontend/src/index.css new file mode 100644 index 0000000..af968bf --- /dev/null +++ b/frontend/src/index.css @@ -0,0 +1,17 @@ +@import url('https://fonts.googleapis.com/css2?family=Source+Sans+3:wght@400;600;700&display=swap'); + +* { + box-sizing: border-box; +} + +html, +body, +#root { + margin: 0; + min-height: 100%; +} + +body { + background: #d9dde2; + font-family: 'Source Sans 3', 'Trebuchet MS', sans-serif; +} diff --git a/frontend/src/main.tsx b/frontend/src/main.tsx new file mode 100644 index 0000000..14bc510 --- /dev/null +++ b/frontend/src/main.tsx @@ -0,0 +1,15 @@ +import { StrictMode } from 'react' +import { createRoot } from 'react-dom/client' +import { I18nextProvider } from 'react-i18next' +import './index.css' +import './i18n/config' +import i18n from './i18n/config' +import App from './App.tsx' + +createRoot(document.getElementById('root')!).render( + + + + + , +) diff --git a/frontend/tsconfig.app.json b/frontend/tsconfig.app.json new file mode 100644 index 0000000..af516fc --- /dev/null +++ b/frontend/tsconfig.app.json @@ -0,0 +1,28 @@ +{ + "compilerOptions": { + "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.app.tsbuildinfo", + "target": "ES2023", + "useDefineForClassFields": true, + "lib": ["ES2023", "DOM", "DOM.Iterable"], + "module": "ESNext", + "types": ["vite/client"], + "skipLibCheck": true, + + /* Bundler mode */ + "moduleResolution": "bundler", + "allowImportingTsExtensions": true, + "verbatimModuleSyntax": true, + "moduleDetection": "force", + "noEmit": true, + "jsx": "react-jsx", + + /* Linting */ + "strict": true, + "noUnusedLocals": true, + "noUnusedParameters": true, + "erasableSyntaxOnly": true, + "noFallthroughCasesInSwitch": true, + "noUncheckedSideEffectImports": true + }, + "include": ["src"] +} diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json new file mode 100644 index 0000000..1ffef60 --- /dev/null +++ b/frontend/tsconfig.json @@ -0,0 +1,7 @@ +{ + "files": [], + "references": [ + { "path": "./tsconfig.app.json" }, + { "path": "./tsconfig.node.json" } + ] +} diff --git a/frontend/tsconfig.node.json b/frontend/tsconfig.node.json new file mode 100644 index 0000000..8a67f62 --- /dev/null +++ b/frontend/tsconfig.node.json @@ -0,0 +1,26 @@ +{ + "compilerOptions": { + "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.node.tsbuildinfo", + "target": "ES2023", + "lib": ["ES2023"], + "module": "ESNext", + "types": ["node"], + "skipLibCheck": true, + + /* Bundler mode */ + "moduleResolution": "bundler", + "allowImportingTsExtensions": true, + "verbatimModuleSyntax": true, + "moduleDetection": "force", + "noEmit": true, + + /* Linting */ + "strict": true, + "noUnusedLocals": true, + "noUnusedParameters": true, + "erasableSyntaxOnly": true, + "noFallthroughCasesInSwitch": true, + "noUncheckedSideEffectImports": true + }, + "include": ["vite.config.ts"] +} diff --git a/frontend/vite.config.ts b/frontend/vite.config.ts new file mode 100644 index 0000000..aab5dff --- /dev/null +++ b/frontend/vite.config.ts @@ -0,0 +1,11 @@ +import { defineConfig } from 'vite' +import react from '@vitejs/plugin-react' + +// https://vite.dev/config/ +export default defineConfig({ + plugins: [react()], + server: { + host: true, + port: 9000, + } +}) diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 55fee1d..0000000 --- a/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -neo4j>=5.0 -fastapi>=0.110.0 -uvicorn[standard]>=0.29.0 -python-dotenv>=1.0.0 From fa0ecfa7b29a874b8cdc3f10d561c90d88ae0951 Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 29 Jul 2026 12:22:19 -0700 Subject: [PATCH 06/23] Checkbox to load local sources and merge into database Generate concept IDs for DrugBank and RxNorm --- backend/codex_build/Dockerfile | 1 + .../__pycache__/api.cpython-310.pyc | Bin 10635 -> 11323 bytes .../__pycache__/source_data.cpython-310.pyc | Bin 19893 -> 20200 bytes .../codex_build/neo4j_sources/source_data.py | 51 ++++++--- backend/codex_build/requirements.txt | 2 +- docker-compose.yml | 2 + frontend/src/App.css | 100 +++++++++++++----- frontend/src/App.tsx | 18 +++- frontend/src/i18n/locales/de.json | 5 + frontend/src/i18n/locales/en.json | 5 + frontend/src/i18n/locales/es.json | 5 + frontend/src/i18n/locales/fr.json | 5 + 12 files changed, 148 insertions(+), 46 deletions(-) diff --git a/backend/codex_build/Dockerfile b/backend/codex_build/Dockerfile index 25b6ddf..5ad0748 100644 --- a/backend/codex_build/Dockerfile +++ b/backend/codex_build/Dockerfile @@ -4,6 +4,7 @@ WORKDIR /app COPY requirements.txt ./ RUN pip3 install --no-cache-dir -r requirements.txt +RUN pip3 install requests COPY . . diff --git a/backend/codex_build/__pycache__/api.cpython-310.pyc b/backend/codex_build/__pycache__/api.cpython-310.pyc index b47ca5eb06c135702da4b39a54b928be2b91fa8a..629609b671c7c5971a2b248b2e6f1c4324898da2 100644 GIT binary patch delta 3850 zcmaJDS!^4}b!SOYB*jD2eOj_^$~tJBK4e+8BwIctA5tuPZHHz!BZ=}Zmz`Zzmg0mC zrIx*jrvLB9gO&w3UYmClbsHEM(FqmH4h;nRFXp@in?expDuFalb@2x>ti zq=k&I7M47ZUT8$Lh@9u^MMkk!EazUm#3#j1^J z32RvGCZPqJ>KY-+Y7N*7=-C5ComOYmYxTxK?Vwy7)EkUOt^QsL&c#y5`b)+2M^oiu<}n>uCK$_ZrdqLFOQB0GS3UGXQuaZ34VW;)8%U(-y#6 zSQeEW0YWQn145e=I0|@_wgcWS@ne7=q8)&DNc=e9owN(^E{P8T-c4hG$0U9N@WZqR z@E(Z|!*)*6UN%hoXg_RZVBJjz>5+%Z8p&!S!0e+(*%5k-9^Yo(rYGpI+{-Ds^dvh@ zM|Qby(os4lxu@mYadv`*7f0zCdH~j+UC*Nv^c*VJ#w7pzHvhs7pM~hfH8MwNoMtc4 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zPn?Zy++Cxxktp!r{qr$0IhN2xYWZXSt7Btb{|UV3Q}6mbX?!NMf6{q1g=0rSxHNAjv>NRAf!TdsE>bQ({fV)Yv5};(UOULG}<&C+5m> lvFvp#Ajw4iol7Z}HJj$q+}bHEp$%(KXq{Rc9w*B0{uh^@P3iyu diff --git a/backend/codex_build/neo4j_sources/source_data.py b/backend/codex_build/neo4j_sources/source_data.py index 27d6bfa..b4428ce 100644 --- a/backend/codex_build/neo4j_sources/source_data.py +++ b/backend/codex_build/neo4j_sources/source_data.py @@ -8,20 +8,16 @@ import sys import time import uuid -import json +import re import logging from datetime import datetime, timezone from collections import deque import requests from neo4j import GraphDatabase, WRITE_ACCESS -from dotenv import load_dotenv, find_dotenv +from dotenv import load_dotenv -env_path = find_dotenv(usecwd=True) -if not env_path: - print("ERROR: .env not found at repo root") - sys.exit(1) -load_dotenv(env_path) +load_dotenv(os.path.join(os.path.dirname(__file__), ".env")) NEO4J_URI = os.getenv("NEO4J_URI", "bolt://localhost:7687") NEO4J_USER = os.getenv("NEO4J_USER", "neo4j") @@ -69,6 +65,24 @@ def smoke_test(sess): sess.run("MATCH (s:SmokeTest) DELETE s") return c +def conceptID(text: str, symptom: str = None, source: str = None) -> str: + if not text: + return "unknown" + text = text.lower().strip() + text = text.replace(',', '-') + text = re.sub(r'[^a-z0-9,-]', '', text) + text = re.sub(r'-+', '-', text) + + if symptom: + clean_symptom = re.sub(r'[^a-z0-9-]', '', source.lower().strip()) + text = f"{text}-{clean_symptom}" + + if source: + clean_source = re.sub(r'[^a-z0-9-]', '', source.lower().strip()) + text = f"{text}-{clean_source}" + + return text + # -------------------- # DrugBank @@ -125,7 +139,7 @@ def iter_drugs(per_page=100): for d in items: dbid = d.get("drugbank_id") or d.get("id") name = d.get("name") or d.get("generic_name") or d.get("brand_name") or "" - if dbid: yield dbid, name + if dbid: yield d, dbid, name link = resp.headers.get("Link", "") if link and 'rel="next"' in link: page += 1 @@ -149,10 +163,15 @@ def iter_drugs(per_page=100): sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.code = $id, n.title = $title, n.ds = $ds", id=ROOT_ID, title=ROOT_TITLE, ds=DATASET) sess.run("MATCH (i:Ingest {uid: $uid}), (r:DRUG {id: $rootId}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rootId=ROOT_ID) - for code, title in iter_drugs(): - sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.code=$id, n.title=$t, n.ds=$ds ON MATCH SET n.ds=$ds", id=code, t=title or None, ds=DATASET) - sess.run("MATCH (p:DRUG {id: $parent}), (c:DRUG {id: $child}) MERGE (p)-[:HAS_CHILD]->(c)", parent=ROOT_ID, child=code) - processed += 1 + for d, code, title in iter_drugs(): + symptoms = d.get("symptoms", []) + for symptom_name in symptoms: + if not symptom_name: + continue + concept_id = concept_id(title, symptom_name, source="drugbank") + + sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.conceptID=$conceptID, n.code=$id, n.title=$t, n.ds=$ds ON MATCH SET n.ds=$ds", id=code, conceptID=concept_id, t=title or None, ds=DATASET) + sess.run("MATCH (p:DRUG {id: $parent}), (c:DRUG {id: $child}) MERGE (p)-[:HAS_CHILD]->(c)", parent=ROOT_ID, child=code) rec = sess.run("MATCH (n:DRUG {ds: $ds}) WITH count(n) AS n MATCH (:DRUG {ds: $ds})-[rel:HAS_CHILD]->(:DRUG {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt = $finishedAt, i.nodeCount = $nodeCount, i.edgeCount = $edgeCount", uid=run_uid, finishedAt=utc_iso(), nodeCount=rec["n"], edgeCount=rec["r"]) @@ -218,8 +237,6 @@ def upsert_snomed_node(node): time.sleep(5.0) else: log.error("Failed all retries to connect to SNOMED server. Skipping SNOMED module completely.") - sess.run("MERGE (n:SNOMED {id: $id}) ON CREATE SET n.code=$id, n.title='SNOMED', n.ds=$ds ON MATCH SET n.ds=$ds", id=SNOMED_ROOT_ID, ds=DATASET) - sess.run("MATCH (i:Ingest {uid: $uid}), (r:SNOMED {id: $rid}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rid=SNOMED_ROOT_ID) return # Safely exits run_snomed() so main() moves to RxNorm # If it passed but root_full is somehow empty, exit gracefully @@ -296,7 +313,8 @@ def rx_get(path, params=None): roots = [{"rxcui": m.get("rxcui"), "name": m.get("name"), "tty": m.get("tty")} for m in js.get("minConceptGroup", {}).get("minConcept", []) if m.get("rxcui")] for m in roots: - sess.run("MERGE (n:RXN {rxcui: $rxcui}) ON CREATE SET n.name=$name, n.tty=$tty, n.ds=$ds", rxcui=m["rxcui"], name=m["name"], tty=m["tty"], ds=DATASET) + concept_id = conceptID(m.get("name"), source="rxnorm") + sess.run("MERGE (n:RXN {rxcui: $rxcui}) ON CREATE SET n.conceptID=$conceptID, n.name=$name, n.tty=$tty, n.ds=$ds", rxcui=m["rxcui"], conceptID=concept_id, name=m["name"], tty=m["tty"], ds=DATASET) sess.run("MATCH (p:RXN {rxcui: 'ROOT'}), (c:RXN {rxcui: $c}) MERGE (p)-[:HAS_CHILD]->(c)", c=m["rxcui"]) for idx, m in enumerate(roots): @@ -311,7 +329,8 @@ def rx_get(path, params=None): if isinstance(props, dict): props = [props] for p in props: if p.get("rxcui"): - sess.run("MERGE (n:RXN {rxcui: $rxcui}) ON CREATE SET n.name=$name, n.tty=$tty, n.ds=$ds ON MATCH SET n.ds=$ds", rxcui=p["rxcui"], name=p["name"], tty=p["tty"], ds=DATASET) + concept_id = conceptID(p.get("name"), source="rxnorm") + sess.run("MERGE (n:RXN {rxcui: $rxcui}) ON CREATE SET n.conceptID=$conceptID, n.name=$name, n.tty=$tty, n.ds=$ds ON MATCH SET n.ds=$ds", rxcui=p["rxcui"], conceptID=concept_id, name=p["name"], tty=p["tty"], ds=DATASET) sess.run("MATCH (p:RXN {rxcui: $p}), (c:RXN {rxcui: $c}) MERGE (p)-[:HAS_CHILD]->(c)", p=m["rxcui"], c=p["rxcui"]) except Exception as e: log.debug("Skipped paths on CUI %s: %s", m["rxcui"], e) diff --git a/backend/codex_build/requirements.txt b/backend/codex_build/requirements.txt index d396315..9f3ea69 100644 --- a/backend/codex_build/requirements.txt +++ b/backend/codex_build/requirements.txt @@ -2,4 +2,4 @@ neo4j==5.18.0 python-dotenv==1.0.1 fastapi==0.111.0 uvicorn[standard]==0.30.1 -httpx==0.27.0 +httpx==0.27.0 \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index f14eeca..33d791a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -19,6 +19,8 @@ services: container_name: codex-api ports: - "8000:8000" + env_file: + - .env environment: - NEO4J_URI=bolt://neo4j:7687 - NEO4J_USER=neo4j diff --git a/frontend/src/App.css b/frontend/src/App.css index 299c67d..af8d63f 100644 --- a/frontend/src/App.css +++ b/frontend/src/App.css @@ -125,21 +125,6 @@ cursor: pointer; } -.populate-btn { - border: none; - border-radius: 8px; - background: #4e7f77; - color: #fff; - font-weight: 700; - font-size: 17px; - width: 150px; - height: 50px; - cursor: pointer; - position: absolute; - top: 200px; - left: 75px; -} - /* Customize the label (the container) */ .container { display: block; @@ -208,16 +193,26 @@ transform: rotate(45deg); } +.populate-label { + display: flex; + align-items: center; + font-size: 1.5rem; + font-weight: 700; + color: #0f1826; + position: absolute; + top: 265px; + left: 32px; +} + .populateDrugbank-checkbox { display: flex; align-items: center; gap: 12px; cursor: pointer; - font-family: sans-serif; user-select: none; position: absolute; - top: 100px; - left: 100px; + top: 320px; + left: 90px; font-size: 1.2rem; } @@ -226,11 +221,10 @@ align-items: center; gap: 12px; cursor: pointer; - font-family: sans-serif; user-select: none; position: absolute; - top: 125px; - left: 100px; + top: 345px; + left: 90px; font-size: 1.2rem; } @@ -239,11 +233,10 @@ align-items: center; gap: 12px; cursor: pointer; - font-family: sans-serif; user-select: none; position: absolute; - top: 150px; - left: 100px; + top: 370px; + left: 90px; font-size: 1.2rem; } @@ -252,14 +245,67 @@ align-items: center; gap: 12px; cursor: pointer; - font-family: sans-serif; user-select: none; position: absolute; - top: 175px; - left: 100px; + top: 395px; + left: 90px; font-size: 1.2rem; } + +.populate-btn { + border: none; + border-radius: 8px; + background: #4e7f77; + color: #fff; + font-weight: 700; + font-size: 17px; + width: 150px; + height: 50px; + cursor: pointer; + position: absolute; + top: 425px; + left: 75px; +} + +.populate-btn:disabled { + cursor: not-allowed; + opacity: 0.6; +} + +.populate-overlay { + position: absolute; + top: 425px; + left: 75px; + width: 150px; + height: 50px; + background-color: rgba(255, 255, 255, 0.85); + display: flex; + align-items: center; + justify-content: center; + gap: 8px; + z-index: 10; + border-radius: 8px; /* Match your button's corners if needed */ + font-size: 17px; + color: #1e293b; + font-weight: 700; +} + +.spinner { + width: 16px; + height: 16px; + border: 2px solid #cbd5e1; + border-top-color: #2563eb; + border-radius: 50%; + animation: spin 0.8s linear infinite; +} + +@keyframes spin { + to { + transform: rotate(360deg); + } +} + .tool-panel { border-bottom: 1px solid #c7ccd2; padding: 4px 0 30px; diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx index 1bc88b3..177062a 100644 --- a/frontend/src/App.tsx +++ b/frontend/src/App.tsx @@ -287,6 +287,7 @@ function App() { const [isSnomedSelected, setIsSnomedSelected] = useState(false); const [isRxNormSelected, setIsRxNormSelected] = useState(false); const [isICD11Selected, setIsICD11Selected] = useState(false); + const [isPopulationLoading, setIsPopulationLoading] = useState(false); const handlePopulateClick = async () => { let sources: string[] = [] @@ -302,6 +303,7 @@ function App() { if (isICD11Selected) { sources.push("icd11") } + setIsPopulationLoading(true); try{ const response = await fetch('http://localhost:8000/api/populate-sources', { method: 'POST', @@ -316,6 +318,8 @@ function App() { } catch (error) { console.error("Error calling Python function:", error); alert("Something went wrong on the backend."); + } finally { + setIsPopulationLoading(false); } }; @@ -374,6 +378,8 @@ function App() {
+

{t('sides.populateLabel')}

+
diff --git a/frontend/src/i18n/locales/de.json b/frontend/src/i18n/locales/de.json index 3702330..bf08427 100644 --- a/frontend/src/i18n/locales/de.json +++ b/frontend/src/i18n/locales/de.json @@ -8,6 +8,11 @@ "search": "Suchen", "translate": "Übersetzen" }, + "sides": { + "populateLabel": "Lokale Datenquellen füllen:", + "populateButton": "Füllen", + "populateLoader": "Füllt Daten..." + }, "home": { "pageTitle": "Projekt Medizinischer Kodex", "pageDescription": "Ein Werkzeug zur Koordination medizinischer Ausrüstung zwischen Ländern.", diff --git a/frontend/src/i18n/locales/en.json b/frontend/src/i18n/locales/en.json index 40f0023..f0bd529 100644 --- a/frontend/src/i18n/locales/en.json +++ b/frontend/src/i18n/locales/en.json @@ -8,6 +8,11 @@ "search": "Search", "translate": "Translate" }, + "sides": { + "populateLabel": "Populate local source(s):", + "populateButton": "Populate", + "populateLoader": "Populating..." + }, "home": { "pageTitle": "Project Medical Codex", "pageDescription": "A tool developed to help coordinate medical equipment between countries.", diff --git a/frontend/src/i18n/locales/es.json b/frontend/src/i18n/locales/es.json index c380342..2c262ec 100644 --- a/frontend/src/i18n/locales/es.json +++ b/frontend/src/i18n/locales/es.json @@ -8,6 +8,11 @@ "search": "Buscar", "translate": "Traducir" }, + "sides": { + "populateLabel": "Rellenar fuente(s) local(es):", + "populateButton": "Rellenar", + "populateLoader": "Rellenando..." + }, "home": { "pageTitle": "Proyecto Códice Médico", "pageDescription": "Una herramienta desarrollada para ayudar a coordinar equipos médicos entre países.", diff --git a/frontend/src/i18n/locales/fr.json b/frontend/src/i18n/locales/fr.json index 6cd2fc9..879a85b 100644 --- a/frontend/src/i18n/locales/fr.json +++ b/frontend/src/i18n/locales/fr.json @@ -8,6 +8,11 @@ "search": "Rechercher", "translate": "Traduire" }, + "sides": { + "populateLabel": "Remplir les sources locales:", + "populateButton": "Remplir", + "populateLoader": "Remplissage en cours..." + }, "home": { "pageTitle": "Projet Codex Médical", "pageDescription": "Un outil développé pour aider à coordonner les équipements médicaux entre les pays.", From 3d9400f9a24b0ab78d68f9599f0525590daf107c Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 29 Jul 2026 12:30:18 -0700 Subject: [PATCH 07/23] Updated the README --- README.md | 72 ++---------------- .../__pycache__/source_data.cpython-310.pyc | Bin 20200 -> 20358 bytes 2 files changed, 7 insertions(+), 65 deletions(-) diff --git a/README.md b/README.md index ab5f798..5bee07d 100644 --- a/README.md +++ b/README.md @@ -8,78 +8,20 @@ No frontend, no Flask, no middleware. Just Neo4j + Python. ## Setup (once) -### 1 — Start Neo4j ```bash -docker compose up -d -# Wait ~20 seconds for Neo4j to be ready +docker compose up --build +# Wait ~20 seconds for Neo4j, frontend, and api to be ready # Optional: check http://localhost:7474 in a browser (login: neo4j / changeme) ``` -### 2 — Install Python dependencies -```bash -pip install -r requirements.txt -``` - -### 3 — Run the CLI -```bash -python cli.py -``` - --- ## Usage ``` -codex> demo ← load sample data first (run this once) -codex> ibuprofen ← type a drug name, then answer prompts - Target language code: es - Country code: MX - → ibuprofeno (Spanish) brand: Advil [MX] - -codex> paracetamol - Target language code: fr - Country code: FR - → paracétamol (French) brand: Doliprane [FR] - -codex> audit ibuprofen ← show missing translations / brands -codex> load /path/to/pack.json ← load a new language pack -codex> quit -``` - -### Language codes -Code - Language - -`en` - English -`es` - Spanish -`fr` - French -`ru` - Russian -`uk` - Ukrainian - -### Country codes -`US GB MX FR ES NG RU UA CA PL IN DE BR AU ZA` - ---- - -## Language pack format - -```json -{ - "language": {"code": "pt", "name": "Portuguese"}, - "terms": [ - { - "canonical": "Ibuprofen", - "entries": [ - {"translation": "ibuprofeno", "country": "BR", "brand": "Advil"}, - {"translation": "ibuprofeno", "country": "PT", "brand": null} - ] - } - ] -} -``` - -Save as `portuguese_pack.json`, then: -```bash -codex> load portuguese_pack.json +Use http://localhost:9000 for the frontend +Use http://localhost:7474 for the Neo4j backend +Use http://localhost:8000/docs to view the API ``` --- @@ -96,7 +38,7 @@ And update `docker-compose.yml`: NEO4J_AUTH: "neo4j/your_new_password" ``` -Then restart: `docker compose down && docker compose up -d` +Then restart: `docker compose down && docker compose up -d && docker compose up --build` --- @@ -105,5 +47,5 @@ Then restart: `docker compose down && docker compose up -d` ```bash docker compose down -v # -v removes the data volume docker compose up -d -# Then reload demo data: codex> demo +docker compose up --build ``` diff --git a/backend/codex_build/neo4j_sources/__pycache__/source_data.cpython-310.pyc b/backend/codex_build/neo4j_sources/__pycache__/source_data.cpython-310.pyc index 16aac384390ddce2718d0b08903dfb6a3a8bd4e0..176248813f1bb5e08411fbf7911a1cd91249b1c3 100644 GIT binary patch delta 3586 zcmZ{ndvH`&9mn_VBo2CIs>-6Y?*dgHSe%RBTk|L4M&HF#?$&Q;a1-bU_G zm-1q~OYqK9m+q4JQeJw%;jiFjy!?R0U&$+YB|g2}%a`GE8L#5i_^jeJ+=tI^R`IEXZQ9PA+@a6UXTOur4u6;XiX37k zRwr5rs}O#7Fsufm%AJmY-&NDP82xr;XK8q)<7KyI&!gCg$w7v=`^!Ls=9W6IEwREy z*KXDbD^iMC6Zli|+4C@#^3tSlhiyWha80D>@^luj7_iJ(CsOs)^_HEUi8MV;dv)ZJ z?$%TEG+xQQQ??1WE)BW(GTlYq_#e1MxAUqg2eX*|YTc^4c+HfJSw=36ylDD-n4@sY zI-NRWnMgN1wYoF0V82CA=XEK0^r+9X;0p9rzVGiITy7jJIqv3Qp!FQ#r_tQ{nG z5gSaFyI)~!EnG`)V_TstV+Gp=eHqO;+i{SybLd0MD~pH7(E~4JG_Y=XJHx|((J@+QHL!Do%*3%VLDP zb$QGpM&Rm#2G#@4tQPFY`mBv*gVa(5sM|-xgp;XiDt-DRevBle2R%xP@FxHPIZ{dFjzw9$p8dXMd6bX8>2V-0ndnxsCgg@<0`${wr zQQ<$ic{O8{wu#VA=q8v$?xkYjY;vr=~OS zuzYv#2zjJHJg!E$H&+~?Twf;~B^)En5GE0RX-v7dVZ@ioeTLjFlDD#JG#vIjg^J6l zYN8Krlov{;DbEv-Sy9xWkohcu7R+lGK=#}+l6+_PnxsWz5tY9Lfr{hoQu4!!H*M@& z@MhJ{DhlMMtcKNBC(K1Km)-;^)ktXxhqOd67KyJef`WYIt zTl`hBeh$B>UYPP4njVbJ;+OE(>NBY3=W0ruNW8erW~oQWb_fqX=4p6NtadR?Nj>n- zn(~~F2vicEBYl=Yy|0En28z#rSA`dRb!-A|`f8+;RQlVnwDuG#>2hrm8-g3PN?C;5 zzead%;y26!;MV+J|DH=&Yov z4~9#Pjz&}wNT`M_tVZX_zLAn0TX? 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zRlzu*>kBwX1IYTkjI?+-(05SlXTIpb1%A23L+&SUw|q+EKVzR8{C2BK4)e6Of`V({ z7|CgYa%RNf>)h4Vv88?EhH7?;uWoaadwfURk!G>xLL6yF5bNL<0mH9qmWD8s(PP*= zjBpJBrGec;xX%~2*B9VmZ-#$B_YZ0YhylFZUdiyY9?Y9R(Vk9z&7W&;ZTJuLGZjr6 z@&&@0#&U56p`{)(Mbl`+4^HuU^C?C|a)K)xcxH!6cJq}TE?Lx+4|q?9lRV3ZI~u$9 zV&5{H*#Q-$Ez%D~e7e>PLgGF$p&H^LP-egQNicv3vSI*GIMzSR{>}exbMmEITJ!Q{ WWuCH2@hMHpUd63cWRi4Z`|Q7;4^EH( From 1b0964aba3fba02eee26b8dd9fe0f1b538dc9744 Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 29 Jul 2026 12:31:02 -0700 Subject: [PATCH 08/23] Removed "update me" line from top --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 5bee07d..5148cf7 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ -# UPDATE THIS # codex-cli — Medical Translation Terminal Test the backend translation engine directly from your terminal. From 3a6be03e3823fd75106ea381949cb04c7c5896de Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 29 Jul 2026 12:50:43 -0700 Subject: [PATCH 09/23] Added printouts for each database source (maxed at 10 entries per) --- .../__pycache__/source_data.cpython-310.pyc | Bin 20358 -> 21837 bytes .../codex_build/neo4j_sources/source_data.py | 40 ++++++++++++++++++ 2 files changed, 40 insertions(+) diff --git a/backend/codex_build/neo4j_sources/__pycache__/source_data.cpython-310.pyc b/backend/codex_build/neo4j_sources/__pycache__/source_data.cpython-310.pyc index 176248813f1bb5e08411fbf7911a1cd91249b1c3..7835474708c4404c4c8ddd5e7a94ffd967590f64 100644 GIT binary patch delta 1554 zcmah}%WoS+7@wJ4+v`W1NAo7YRFozTjT;vN!ipl?tQ(TlcCj6mrU{ml*#yV$StljS zt_-9gI7Fpc2@WVC;lP0d63Sn|5hOr8A+3bOg*)d$8@}C|0;y1UG~dkrzQ_FLn{VcW z&+!jm;b66`&4=JKu5E1mvUWQ-gundexp9mq%q2WG&LZr>O|%$R&a>x>gx^uf#yER{ zk@v{}T8t=RC9;DtVkG1A(2GYu;<^W0N3VEihGF<{yfD!8Lv(wIY3S+@MyP=fFvEx7 zxDIY#U<2!DgERyt?BZKBgXmaB%Zec|Q5QZ#%(X8VqD~G(T|C5wOBa|MsEjyKJa!a7 zBtRk#;%y;5K%zF%Wd0Tu0BG7VYO@g*G~BuimO5j2SUb!;tYZKf5{#WNdRfXyX<)N8QrbkaJ2mn@qv8-@Cj7!x{4SQq3sA5 zRip?~-@5@0cDn}MaT#3DV_ourj;fzeoo zR;odkJ zMt&u)Dm1OERykAYT9s3oZ?0d=SBexY_#d|Mng2J=RH|i#(Xl4j{`nZ&^jpa)FFRrH zJ;oH$Mk5j1^itOHw03X#TAPKvYUCVUg~I*&Ya#)rZs-~4Dh08QbhI2;A_lhW7m5Pu z1SH-UZ<9J)j}Xy>C>_3whj|~EhXno|3>Ge0c*{W^h<*V1_aN@Waw>rdMcOkpUZ^y3 ztd&1C{KjOdx|%PkQ{l-{L2ay7%e5)ZH7iHybA!knC! z@+(S-MzwA_k|`EyHApF(M7&&UY=^?yo>O82zIalmsY?$lkEY`>Ikk{&6`+SlY^t|x zv1^NfEnc$4&$cLn2>JOQ42yv+V7roYmR0%709h{Q$8yy-6~1kGxT0>B8tS6|&Aggx z5w_e9Cj7qb;D)k;lUVG4qABN_jfTSPN(AUc_N?|3+4|MaWE5ifup|VDgb6h1*yoZ6 zAo!myf=&cP!u@0ri=+#acgSx;$HAw#1Tp?y0Os|m*X_J#+&rG06yDXA&8fMsM;jeF zu^+^%sPd$U8lBspVq~~5(mLUecd?-EIwWx4PaSld!THnvomse z6|j#0<9@uCyw_*b=C%tzZRb$T^Ytwr#OCi}ula1M9bYjgQghz3(r6F|uz3G3ohFFc delta 291 zcmX@Rim`1zBVRr*FBbz4Eb!0Dx{)xEPlj>cMr{K|M&rpbj9wb4dMSq4Ohso?nX>d# zj8d3dnIsva3{rJd4VoDl8B&;n!C2E|^EJjocE(?uJviOffz$+pOi4aAps66Eoq@PG zYw`wv8|K=o$jR^h*C~ZFbaGcv;N%BE8Eg+2frdIw_6yc$;$fcL7%Zvot(r`Jewv22*yH0<@{@sLoj|doKMa!(1pgHRDKAn43fy8zEJ`mc Z`p+==N{A|>-{fB*UhEotj694i{{TtyQIh}w diff --git a/backend/codex_build/neo4j_sources/source_data.py b/backend/codex_build/neo4j_sources/source_data.py index b4428ce..4e60995 100644 --- a/backend/codex_build/neo4j_sources/source_data.py +++ b/backend/codex_build/neo4j_sources/source_data.py @@ -477,6 +477,44 @@ def unify_graph(driver): log.info("<<< Graph combination complete. All sources are now connected.") +def print_databases(driver): + log.info("\n" + "="*60 + "\IMPORTED DATABASES\n" + "="*60) + + # We query for distinct source labels in your system + vocab_labels = ["DRUG", "SNOMED", "RXN", "ICD"] + + with driver.session(database=NEO4J_DB) as sess: + for label in vocab_labels: + query = f""" + MATCH (n:{label}) + RETURN n.id AS node_id, properties(n) AS all_fields + LIMIT 10 + """ + results = sess.run(query) + + if label == "DRUG": + log.info(f"\n--- Database Records for DrugBank ---") + if label == "SNOMED": + log.info(f"\n--- Database Records for Snomed ---") + if label == "RXN": + log.info(f"\n--- Database Records for RxNorm ---") + if label == "ICD": + log.info(f"\n--- Database Records for ICD 11 ---") + + has_records = False + for record in results: + has_records = True + node_id = record["node_id"] + fields = record["all_fields"] + + formatted_fields = ", ".join([f"{k}: '{v}'" for k, v in fields.items()]) + log.info(f"ID: [{node_id}] -> {{ {formatted_fields} }}") + + if not has_records: + log.info(f"No records found for label :{label} (Skipped or Empty).") + + log.info("\n" + "="*60 + "\nEND OF DATABASE READOUT\n" + "="*60) + def source_data(sources): log.info("=" * 60) log.info("Creating Singular Medical Knowledge Graph") @@ -507,6 +545,8 @@ def source_data(sources): # Link them together to make a singular source unify_graph(driver) + print_databases(driver) + except Exception as e: log.critical("Pipeline was terminated prematurely: %s", e) sys.exit(2) From e348547197985b062d5e0751d56dcbb264837d01 Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 29 Jul 2026 13:45:27 -0700 Subject: [PATCH 10/23] Trying to fix the search functionality, still needs work --- README.md | 3 -- .../__pycache__/api.cpython-310.pyc | Bin 11323 -> 12129 bytes backend/codex_build/api.py | 36 ++++++++++++++++-- frontend/src/App.tsx | 19 +++++---- 4 files changed, 42 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 5148cf7..620bc58 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,5 @@ # codex-cli — Medical Translation Terminal -Test the backend translation engine directly from your terminal. -No frontend, no Flask, no middleware. 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Prints out all of the data. + Translation works (language packs and demo pack load), UI allows country selection - Seems some brand names don't appear when searched, not a high priority atm imo but should be looked at --- README.md | 2 +- .../__pycache__/api.cpython-310.pyc | Bin 12129 -> 12828 bytes backend/codex_build/api.py | 99 +++++++++++----- .../__pycache__/neo4j_driver.cpython-310.pyc | Bin 5745 -> 6000 bytes backend/codex_build/codex/neo4j_driver.py | 21 ++-- .../__pycache__/source_data.cpython-310.pyc | Bin 21837 -> 22045 bytes .../codex_build/neo4j_sources/source_data.py | 80 +++++++------ frontend/src/App.css | 2 +- frontend/src/App.tsx | 109 +++++++++++++++--- 9 files changed, 222 insertions(+), 91 deletions(-) diff --git a/README.md b/README.md index 620bc58..7e3e32e 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ ```bash docker compose up --build -# Wait ~20 seconds for Neo4j, frontend, and api to be ready +# Wait ~30 seconds for Neo4j, frontend, and api to be ready # Optional: check http://localhost:7474 in a browser (login: neo4j / changeme) ``` diff --git a/backend/codex_build/__pycache__/api.cpython-310.pyc b/backend/codex_build/__pycache__/api.cpython-310.pyc index 7a5ff08be08398c6b9c5257312f51e14905a999e..8cb86547d3f7a55f7d0205d5392c3c48344107f2 100644 GIT binary patch delta 5574 zcmaJlZBQJ?mD4@5v&*u;f&dAD&nQ7CyMck(S=2KK zK`mKqlvu6{=eVXScNNPCn~HPitE+Mn-BsP?uI`enyQ`~QIh9|jy8e;M{Yw5NRsNC0 ziJiRHix5&tW~<-yd)@u|b-&N%|G#jLRpu%xq8j{F|0F*<-1~NA6Zyv52ftO&ou*V1 zBP{Cd$u_5&i3a_0XKyxo2J&-z})>b(Ov+b$&Y)7gi+nMUjcBQ(q-Kp;Eq12&lPpXG#6I#LDV`%*F z(%%y;bp%*db91AY#rcsUg)NPZ=UH_TwwTbaYfMiadF6;3Dt#BpqQ=eHqtISpHEhQ^ z&Nnw+WVJ<->f?>9ZjGdl@djqIU991b0a!n;WV=}-YvTQE&$^L1&X3O)PVhR`JWbeM zmH>!t-+G8>=QP&Bp1Gs3XL$3Po;t~oZ=7PSaOPR|9NVwh4Zxf>mV`M;HRm+o2iQTt z4=Vf&;O(pf@D7C!0^Z5G0Pj-x5a8Vfb_fWE6yYoode~vW4=el};73?5;JpeT2K;$; z6!4=8KM(i|>_xy|RQLtJ``9tSk170faJ~`N&p*eGvlDQzlj{aM#Rl$Za2FS0>=ZlA z3#XZWT4QHmcyL{3bL<>DqfR%fCJgf-cAj0>T#=vm(=KG 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fastapi.responses import JSONResponse +from contextlib import asynccontextmanager +from pathlib import Path +import ast from pydantic import BaseModel from dotenv import load_dotenv @@ -52,6 +55,7 @@ find_missing_brands, get_equivalent_brands, resolve_to_base_term, + get_translation_data ) except Exception as exc: logging.critical("Failed to import codex backend: %s", exc) @@ -61,10 +65,38 @@ logging.basicConfig(level=logging.INFO, format="%(levelname)s %(name)s %(message)s") log = logging.getLogger("codex.api") +TARGET_FOLDER_PATH = Path("./codex/language_packs") +@asynccontextmanager +async def lifespan(app: FastAPI): + demo_load() + print(f"Scanning directory: {TARGET_FOLDER_PATH.resolve()}") + + if TARGET_FOLDER_PATH.exists() and TARGET_FOLDER_PATH.is_dir(): + # Iterate over every file in the target folder + for file_path in TARGET_FOLDER_PATH.iterdir(): + if file_path.is_file(): + print(f"Found file: {file_path.name}") + + # Open the local file from disk + with open(file_path, "rb") as f: + # Construct a FastAPI UploadFile object dynamically + upload_file = UploadFile( + filename=file_path.name, + file=f + ) + + # Call your load_pack function for each file + await load_pack(upload_file) + else: + print(f"Warning: Directory '{TARGET_FOLDER_PATH}' does not exist.") + + yield + app = FastAPI( title="Codex Medical Translation API", description="Translate drug names across languages and countries using Neo4j.", version="1.0.0", + lifespan=lifespan ) app.add_middleware( @@ -100,8 +132,8 @@ class SearchResponse(BaseModel): class TranslateRequest(BaseModel): term: str - lang: Optional[str] = None - country: Optional[str] = None + lang: str + country: str model_config = {"json_schema_extra": {"example": { "term": "ibuprofen", @@ -118,12 +150,6 @@ class TranslationResult(BaseModel): class TranslateResponse(BaseModel): canonical: str - requested_language: Optional[str] - used_language: Optional[str] - fallback_used: bool - fallback_type: Optional[str] = None - fallback_chain: Optional[list[str]] = None - missing_language_pack: Optional[bool] = None results: list[TranslationResult] @@ -187,19 +213,21 @@ def health(): @app.post( "/search", - response_model=SearchResponse, + response_model=SearchResponse | None, tags=["search"], ) def search(term: str): try: with driver.session() as session: - canonical = resolve_to_base_term(session, term) or term + canonical = resolve_to_base_term(session, term) + if not canonical: + return None except Exception as exc: log.exception("search raised an unexpected error") raise HTTPException(status_code=500, detail=str(exc)) return SearchResponse( - source_id=0, + source_id="0", source_name="", name=canonical, type="drug", @@ -220,19 +248,14 @@ def translate_term(body: TranslateRequest): - Resolves brand names and fuzzy input to a canonical term first. - Falls back through configured language chains if no direct match. - - Falls back to English as the last resort. - - Returns `missing_language_pack: true` if the language has no data loaded. JSON SETUP incoming - { "term": "ibuprofen", "lang": "es", "country": "MX" } + { "term": "ibuprofen", "source_lang": "en", "target_lang": "es", "country": "MX" } outgoing { "canonical": "ibuprofen", - "requested_language": "es", - "used_language": "es", - "fallback_used": false, "results": [ { "translation": "ibuprofeno", "language": "Spanish", "brand": "Advil", "country": "MX" } ] @@ -241,29 +264,49 @@ def translate_term(body: TranslateRequest): log.info("Translate term=%r lang=%s country=%s", body.term, body.lang, body.country) try: - raw = translate(term=body.term, lang=body.lang, country=body.country) + raw_data = translate(term=body.term, lang=body.lang, country=body.country) + if isinstance(raw_data, str): + raw = ast.literal_eval(raw_data) + else: + raw = raw_data except Exception as exc: log.exception("translate() raised an unexpected error") raise HTTPException(status_code=500, detail=str(exc)) + raw_results = raw.get("results", []) if isinstance(raw, dict) else [] + target_lang_str = (body.lang or "").strip().lower() + LANGUAGE_MAP = { + "fr": "french", + "es": "spanish", + "en": "english", + "ru": "russian", + "ua": "ukrainian", + } + mapped_lang_name = LANGUAGE_MAP.get(target_lang_str, target_lang_str) + results = [ TranslationResult( - translation=r["translation"], - language=r["language"], + translation=r.get("translation", ""), + language=r.get("language", ""), brand=r.get("brand"), country=r.get("country"), ) - for r in raw.get("results", []) + for r in raw_results + if ( + not body.lang + or str(r.get("language", "")).lower() == target_lang_str + or str(r.get("lang_code", "")).lower() == target_lang_str + or str(r.get("language_code", "")).lower() == target_lang_str + or str(r.get("language", "")).lower() == mapped_lang_name + ) + and ( + not body.country + or str(r.get("country", "")).lower() == body.country.lower() + ) ] return TranslateResponse( - canonical=raw.get("canonical", body.term), - requested_language=raw.get("requested_language"), - used_language=raw.get("used_language"), - fallback_used=raw.get("fallback_used", False), - fallback_type=raw.get("fallback_type"), - fallback_chain=raw.get("fallback_chain"), - missing_language_pack=raw.get("missing_language_pack"), + canonical=body.term, results=results, ) diff --git a/backend/codex_build/codex/__pycache__/neo4j_driver.cpython-310.pyc b/backend/codex_build/codex/__pycache__/neo4j_driver.cpython-310.pyc index 489fe1025cbbe2889a92ba919fb9c86293f2fd8c..de16526b74fc6dfdf129450ec9759b8834bc6d90 100644 GIT binary patch delta 1225 zcmZ8g&2JM&6yMpetUoq(ytc6+F@xG7FAx)?&>lh&5m1qk8Wk5Ip;p%7-9$#4-7xD2 znr?)uBDIHdu%<#imP;k~gs=ocZPh;jaYuuCslEyLzx9v1TE@-Zm--Kv$!!1C(TYelFJ4((ZC|^(BGO~Ab@8eg zmdTGwCIz>diIC<4_4E1UoJ-CK8H6lC;xi4B&~9&g?3;naiu?m@<#HKx9Ti}2=^)@f z4?Fr0z$LqCEZve~H72nfE3W)N-PK&hRqso&c0u}{v?N<=I*<9O{5)N0(dLyeY4h6J z8cow=EjKUF`dFs?rB;<`nm1FQ@S0v$D7E=X{VV=3Rp3ACHJ(q+@E6&`{E6P+|LP0; zZLz{{OkKD9MkjPVy4<3^6Ku5cz-LM;{M}Ub9#$<>)HCd7hXCv?83Zh^1v@GNY)G;6 zwZ2PY@~iYn>dUv~7W4uPHW8}p^c-6ja$`XdmS{&%0=r0`@w-v46K-yuy^L%~U6gj} z{0pPF+BoBf9mkK(g0Sah6P8C}ofY82lHnXc3A1DtfY6y2ZTr2+P<+j(WpM&3DIAz4 zY;M>yG?}FNPI~EHa+8j4I#C$dN)kgTz847H+1l~~cc6^|9tOWrn5oTf6m^3Qp|J4I zWH4l^u6F~sJ@#n#m=i?4)9Z#o)C6->0Z@r*7D$co#mo$;4?oM~S zQPAvI&5$Na8aSICT@SYdmmL9%Ehm{Wd{gWr1nl}mf35fO7!h~*ALbEa5C1WrlLkf{ z$S`SWaKbfE_7yrw$^Xn9%>4jYBAh=o(_{_)CU;(TrQxx>B`+bJP;WYsH%?9H*dyPw z)%~=y;QAi-w}oo?7vvrf%E}XV3Y{|i_rkMt$-Hs)Yykjfl>CW_c0U!^MGoKYwzJ{2 zy}M9b^q4=g4w2LRFKdn*8@{%FA_p;9b{t_IVWM^XyHch49F%)?PP32U1dq>v4}V(v z^wJ_;!9ShNA=D9Uga!iUEfi=eG$Rasb{dsPF%cz+SK>?M`m{lfS>upVGiC~vZ0diF C1OjLP delta 1081 zcmZuwOKTHR6waNwnaMlNB+a9bG<{e)YGV;W@dc$8tk4u%>LLhX+L?xwbf&$NXqEUt z1zqT(Tz4wC(O{JAv5-$%pz zv((2`InS5n!~A0?#sl&Yzav}xM?m3I$w|KG%go@e9a`1QGQ-YI0i23mV_|SqFN?y5 zxsxT(!V=bl5ZeQVpY>-0I0hxjI7_vd-zyNAZwF6Yck6KwM`DI%Tc#?y%#K(!Oh?i- zHw{y7cG_f+63HETqhi|?v+Rh>y42kYlbN-Osh2txr5e*ryQ+S|GbDZ8zz5@zH4OV5nZAg!rbTsV!~4qee~qq8wbLbr#mA`wwj#RcT96TC-TGX0VM{NZrvS z!VZC_5{5sGDijL*b@J5NNo2zRilq=n5JnNk5pYOHgxd|`Syq+hF^Du>Gr7|#{CH|2 R63F>dzJ6cU7gN$9{~yn0<7fZ? diff --git a/backend/codex_build/codex/neo4j_driver.py b/backend/codex_build/codex/neo4j_driver.py index ffd3168..8d064db 100644 --- a/backend/codex_build/codex/neo4j_driver.py +++ b/backend/codex_build/codex/neo4j_driver.py @@ -47,27 +47,32 @@ def create_translation(session, canonical, brand, country, lang_code, lang_name, print(f"Added {canonical} → {translation} ({lang_name}) / Brand: {brand} in {country}") # Retrieves all translations and related info for a given term -def get_translation_data(session, canonical, lang=None, country=None): +def get_translation_data(session, canonical, lang, country): query = """ MATCH (t:Term) - WHERE t.canonical = $canonical + WHERE t.canonical IS NOT NULL + AND ( + t.canonical = $canonical OR apoc.text.jaroWinklerDistance(t.canonical, $canonical) < 0.20 + ) MATCH (tr:Translation)-[:OF_TERM]->(t) MATCH (tr)-[:IN_LANGUAGE]->(l:Language) - MATCH (tr)-[:USED_IN]->(c:Country) - WHERE ($lang IS NULL OR l.code = $lang) - AND ($country IS NULL OR c.iso2 = $country) + OPTIONAL MATCH (tr)-[:USED_IN]->(c:Country) OPTIONAL MATCH (tr)-[:HAS_BRAND]->(b:Brand) + WHERE ($lang IS NULL OR l.code = $lang) + AND ($country IS NULL OR c.iso2 = $country) RETURN DISTINCT tr.text AS translation, l.name AS language, b.name AS brand, + l.code AS lang_code, c.iso2 AS country, c.name AS country_name ORDER BY language, country """ - # Runs the query and return the results as a list - return list(session.run(query, canonical=canonical, lang=lang, country=country)) + + result = session.run(query, canonical=canonical, lang=lang, country=country) + return [r.data() for r in result] # Finds countries where this term has no translation def find_missing_translations(session, term): @@ -165,7 +170,7 @@ def resolve_to_base_term(session, term): """ result = session.run(query, term=term).single() - return result["base"] if result else term + return result["base"] if result else None # Checks whether a language pack exists in the database def language_exists(lang_code: str) -> bool: diff --git a/backend/codex_build/neo4j_sources/__pycache__/source_data.cpython-310.pyc b/backend/codex_build/neo4j_sources/__pycache__/source_data.cpython-310.pyc index 7835474708c4404c4c8ddd5e7a94ffd967590f64..b395fd7028c5676057f030aa4d519152e002f10a 100644 GIT binary patch delta 1125 zcmZ8hO>7%Q6rQ&`w#VzWk~b(NHH+4UG~b(f-#2gG z?9T4DAH&Kg5UK`)8o_pV&77Tj>2~NH2Jgw6>;&T;OEp2nWZ2&=@3A%~KutwVU|fr`8o{tRBT##us#~Er5N(DYOQJGzbT-EGo+%Sztm7 zxVj2JW(cQiU@0bfjwlZx_t=6<>bqochYTT^bGf!%F1*9FBRB1G9lKnoGvZyA&-7wR2Q9|C zam;v6gjjy`z34UG*YfcQ?_VOO)?%w9Nfs9XD-F1H4VZpB!#*>BxPJvt0OWkZ^wqDr z?4WzXp%wROobP*za6-`*RUj3XAoc6>sCVpX?CuJ~$#B1plRQD??faDjPB1#0Z3cOv zQFy*kFV^FY3ypP{Z@w+tv&UsAodZpNkv6=8nt@Gzda75eJlcFFx;_0PeP%%XjW4g+ zk(#SjMWa-iF_PltnejrU+&m=jo{k*)Z)(J1F-`pAh{OMj^VwWxGTA)nNad~5TE8al z?U77f$X3OiD;Yt0a}S-GNE(U6c80+A#NA4UGH)tWk?&_tP}Q(Bxse&_>oyMO%cWYa z$c?HnCg*C6i_y5&yebpvQ8||O$ZYn>dI(@Npt|-6Dj=`1;=Z-z`E8gh(mfpyq||>P7E@-UWdY6cj=92Sl0n>>}hm%=7GgcIG?Z8Fq84@O}l< zjMu9WY*x?E(5I^})yEVbv1hbVGQl{`e$oob6pYi%@2P`z*5!Fn-injQf|w+bARj}; zkc1K^^G(kS5w7v)-VFiLY{vHrrg%d^wE(yIV38$5FaI8>li>{yX&w>QdHB!|3D$UV z)wTp7RveiDjW0yn01oo6)oXxzF4QbTJ#UP*N#N%*wfAHg;NBAp026#A7IMJ_{;v6# z44l12A(qO}rJ!Cabi*?OaG zraU&`y!AWA133|SEg3C5Pjn(-Op8E9Xq1fInZN~h^k8?E1RYDHn}qizCubG5)Lt*e zVzG;CqrHQrM5~a q>KQ&e9YE1_sm~a=VW{lsxhthIEu|M}A8n$&G(s!sQ5Am=Y3m=^F5QU$ diff --git a/backend/codex_build/neo4j_sources/source_data.py b/backend/codex_build/neo4j_sources/source_data.py index 4e60995..e76feaa 100644 --- a/backend/codex_build/neo4j_sources/source_data.py +++ b/backend/codex_build/neo4j_sources/source_data.py @@ -65,6 +65,7 @@ def smoke_test(sess): sess.run("MATCH (s:SmokeTest) DELETE s") return c +# Separate by \ def conceptID(text: str, symptom: str = None, source: str = None) -> str: if not text: return "unknown" @@ -73,13 +74,15 @@ def conceptID(text: str, symptom: str = None, source: str = None) -> str: text = re.sub(r'[^a-z0-9,-]', '', text) text = re.sub(r'-+', '-', text) + clean_symptom = "" if symptom: clean_symptom = re.sub(r'[^a-z0-9-]', '', source.lower().strip()) - text = f"{text}-{clean_symptom}" - + text = f"{text}-{clean_symptom}" + + clean_source = "" if source: clean_source = re.sub(r'[^a-z0-9-]', '', source.lower().strip()) - text = f"{text}-{clean_source}" + text = f"{text}-{clean_source}" return text @@ -478,42 +481,45 @@ def unify_graph(driver): log.info("<<< Graph combination complete. All sources are now connected.") def print_databases(driver): - log.info("\n" + "="*60 + "\IMPORTED DATABASES\n" + "="*60) - - # We query for distinct source labels in your system - vocab_labels = ["DRUG", "SNOMED", "RXN", "ICD"] - - with driver.session(database=NEO4J_DB) as sess: - for label in vocab_labels: - query = f""" - MATCH (n:{label}) - RETURN n.id AS node_id, properties(n) AS all_fields - LIMIT 10 - """ - results = sess.run(query) - - if label == "DRUG": - log.info(f"\n--- Database Records for DrugBank ---") - if label == "SNOMED": - log.info(f"\n--- Database Records for Snomed ---") - if label == "RXN": - log.info(f"\n--- Database Records for RxNorm ---") - if label == "ICD": - log.info(f"\n--- Database Records for ICD 11 ---") - - has_records = False - for record in results: - has_records = True - node_id = record["node_id"] - fields = record["all_fields"] - - formatted_fields = ", ".join([f"{k}: '{v}'" for k, v in fields.items()]) - log.info(f"ID: [{node_id}] -> {{ {formatted_fields} }}") + # Create .txt file + with open("databases.txt", "w") as file: + file.write("\n" + "="*60 + "\nIMPORTED DATABASES\n" + "="*60 + "\n") + vocab_labels = ["DRUG", "SNOMED", "RXN", "ICD"] + + with driver.session(database=NEO4J_DB) as sess: + for label in vocab_labels: + query = f""" + MATCH (n:{label}) + RETURN n.id AS node_id, properties(n) AS all_fields + """ + results = sess.run(query) + + if label == "DRUG": + log.info("Importing DrugBank") + file.write(f"--- Database Records for DrugBank ---\n") + if label == "SNOMED": + log.info("Importing SNOMED") + file.write(f"--- Database Records for Snomed ---\n") + if label == "RXN": + log.info("Importing RxNorm") + file.write(f"--- Database Records for RxNorm ---\n") + if label == "ICD": + log.info("Importing ICD 11") + file.write(f"--- Database Records for ICD 11 ---\n") - if not has_records: - log.info(f"No records found for label :{label} (Skipped or Empty).") + has_records = False + for record in results: + has_records = True + node_id = record["node_id"] + fields = record["all_fields"] + + formatted_fields = ", ".join([f"{k}: '{v}'" for k, v in fields.items()]) + file.write(f"ID: [{node_id}] -> {{ {formatted_fields} }}\n") + + if not has_records: + file.write(f"No records found for label :{label} (Skipped or Empty).\n") - log.info("\n" + "="*60 + "\nEND OF DATABASE READOUT\n" + "="*60) + file.write("="*60 + "\nEND OF DATABASE READOUT\n" + "="*60) def source_data(sources): log.info("=" * 60) diff --git a/frontend/src/App.css b/frontend/src/App.css index af8d63f..18ef47a 100644 --- a/frontend/src/App.css +++ b/frontend/src/App.css @@ -344,7 +344,7 @@ .search-row input, .translate-grid input, .results-select { - width: 100%; + width: auto; height: 44px; border: 1px solid #d7dbe0; border-radius: 9px; diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx index ae7e795..71e5a66 100644 --- a/frontend/src/App.tsx +++ b/frontend/src/App.tsx @@ -2,6 +2,37 @@ import './App.css' import { useTranslation } from 'react-i18next' import { useEffect, useState, type KeyboardEvent } from 'react' +interface CountryOption { + code: string; + label: string; +} + +// Map language codes to available countries +const LANGUAGE_COUNTRY_MAP: Record = { + es: [ + { code: 'MX', label: 'Mexico' }, + { code: 'ES', label: 'Spain' }, + ], + en: [ + { code: 'US', label: 'United States' }, + { code: 'GB', label: 'United Kingdom' }, + { code: 'CA', label: 'Canada' }, + { code: 'NG', label: 'Nigeria' }, + ], + fr: [ + { code: 'FR', label: 'France' }, + { code: 'CA', label: 'Canada' }, + { code: 'BE', label: 'Belgium' }, + ], + ru: [ + { code: 'RU', label: 'Russia' }, + ], + ua: [ + { code: 'UA', label: 'Ukraine' }, + { code: 'PL', label: 'Poland' }, + ], +}; + interface LanguagesResponse { languages: string[] } @@ -29,7 +60,7 @@ interface SearchResponse { interface TranslateResultRow { source_id: string | null source_name: string | null - name: string + translation: string type: string country: string | null language: string @@ -52,6 +83,7 @@ function App() { const [availableLanguages, setAvailableLanguages] = useState(FALLBACK_LANGUAGES) const [searchLanguage, setSearchLanguage] = useState('all') const [targetLanguage, setTargetLanguage] = useState('es') + const [targetCountry, setTargetCountry] = useState("MX") const [translatedName, setTranslatedName] = useState('') const [translateError, setTranslateError] = useState('') const [searchError, setSearchError] = useState('') @@ -79,6 +111,23 @@ function App() { } } + const availableCountries = LANGUAGE_COUNTRY_MAP[targetLanguage] ?? []; + + const getFirstCountryForLanguage = (langCode: string): string => { + const available = LANGUAGE_COUNTRY_MAP[langCode] ?? []; + return available.length > 0 ? available[0].code : ''; + }; + + const handleLanguageChange = (event: React.ChangeEvent) => { + const newLang = event.target.value; + const newCountry = getFirstCountryForLanguage(newLang); + + // Update React state + setTargetLanguage(newLang); + setTargetCountry(newCountry); + setTranslatedName('') + }; + useEffect(() => { let isActive = true @@ -117,7 +166,7 @@ function App() { const extractTranslatedName = (rows: TranslateResultRow[]) => { const names = rows - .map((row) => row.name) + .map((row) => row.translation) .filter((name): name is string => Boolean(name && name.trim())) if (names.length === 0) { @@ -141,7 +190,7 @@ function App() { setTranslatedName('') try { - const response = await fetch(`${API_BASE_URL}/search`, { + const response = await fetch(`${API_BASE_URL}/search?term=${encodeURIComponent(searchQuery.toLowerCase())}`, { method: 'POST', headers: { 'Content-Type': 'application/json', @@ -157,12 +206,14 @@ function App() { throw new Error(errorBody?.detail ?? 'Failed to search') } - const data = (await response.json()) as SearchResponse - - setSearchResults([data]) + const data = (await response.json()) as SearchResponse | null - if (searchResults.length === 0) { + if (!data || !data.name) { + setSearchResults([]) setSearchError('No results found') + } else { + setSearchResults([data]) + setSearchError('') } } catch (err) { setSearchError(err instanceof Error ? err.message : 'An error occurred during search') @@ -178,12 +229,20 @@ function App() { } } - const handleTranslateSelected = async () => { + const handleTranslateSelected = async ( + lang = targetLanguage, + country = targetCountry + ) => { if (!selectedResult) { setTranslateError('Select a search result first') return } + const validCountries = (LANGUAGE_COUNTRY_MAP[lang] ?? []).map((c) => c.code); + const finalCountry = validCountries.includes(country) + ? country + : getFirstCountryForLanguage(lang); + setIsTranslating(true) setTranslateError('') setTranslatedName('') @@ -196,8 +255,8 @@ function App() { }, body: JSON.stringify({ term: selectedResult.name, - source_lang: selectedResult.language, - target_lang: targetLanguage, + lang: lang, + country: finalCountry }), }) @@ -207,9 +266,10 @@ function App() { } const payload = (await response.json()) as TranslateResponse - const name = payload.found ? extractTranslatedName(payload.results ?? []) : '-' + const results = payload.results ?? [] + const name = results.length > 0 ? extractTranslatedName(results) : '-' setTranslatedName(name) - if (!payload.found || name === '-') { + if (results.length === 0 || name === '-') { setTranslateError('No translation found for the selected language') } } catch (err) { @@ -520,8 +580,6 @@ function App() { - ) : searchQuery && !isLoading ? ( -

No results found
) : ( From 239289e46493dd25153b4ca0a3e176941fc360d6 Mon Sep 17 00:00:00 2001 From: Logan Watersmith Date: Wed, 19 Aug 2026 09:23:04 -0700 Subject: [PATCH 12/23] + Fixed ukrainian so it can be translated into now + When brand names are searched, the canonical drug name is now the result --- .../__pycache__/api.cpython-310.pyc | Bin 12828 -> 12828 bytes backend/codex_build/api.py | 2 +- .../__pycache__/neo4j_driver.cpython-310.pyc | Bin 6000 -> 6340 bytes backend/codex_build/codex/neo4j_driver.py | 10 ++++++++++ frontend/src/App.tsx | 2 +- 5 files changed, 12 insertions(+), 2 deletions(-) diff --git a/backend/codex_build/__pycache__/api.cpython-310.pyc b/backend/codex_build/__pycache__/api.cpython-310.pyc index 8cb86547d3f7a55f7d0205d5392c3c48344107f2..c74fad59cffc87b4c442e8cfd2aa043cab5d5883 100644 GIT binary patch delta 27 hcmbP}GAD&QpO=@50SM$TwQl5=mSxP|tSIKq{R5{X!f){lH2}Cik;kXXM_T&RWLI=sWoyM>C_z<|NMjOpF1W zm3XExF=lVx$*0W3*g5&GKqQkm^JELbVjYA58c9}8MTvPS5R1Y+T!UN{lJxQtb5j*; z6;w)6i*hID3#CjxFZe(RQ`2NgAtN@3>Pf=3llui7CaVgmPyQt|mvo5gHEf`w5? ldh!zC|BSmfFA@2{$ar}2T(M)kN*ppA(j0Oef<08K4s r0}?EZLc)`Oi2P^Vu=$7R4@SnFlRt_d<5l30;gIH#;}8^*;Nb)SVIC)- diff --git a/backend/codex_build/codex/neo4j_driver.py b/backend/codex_build/codex/neo4j_driver.py index 8d064db..80a3f1a 100644 --- a/backend/codex_build/codex/neo4j_driver.py +++ b/backend/codex_build/codex/neo4j_driver.py @@ -40,6 +40,8 @@ def create_translation(session, canonical, brand, country, lang_code, lang_name, MERGE (b:Brand {name:$brand}) MERGE (b)-[:SOLD_IN]->(c) MERGE (tr)-[:HAS_BRAND]->(b) + MERGE (t)-[:SOLD_AS]->(b) + MERGE (b)-[:CONTAINS]->(t) """ session.run(query, canonical=canonical, translation=translation, country=country, brand=brand) @@ -155,6 +157,10 @@ def resolve_to_base_term(session, term): WHERE t.canonical = $term RETURN t.canonical AS base UNION + MATCH (t:Term)<-[:CONTAINS]-(b:Brand) + WHERE b.name = $term + RETURN t.canonical AS base + UNION MATCH (t:Term)<-[:OF_TERM]-(tr:Translation) WHERE tr.text = $term RETURN t.canonical AS base @@ -163,6 +169,10 @@ def resolve_to_base_term(session, term): WHERE apoc.text.jaroWinklerDistance(toLower(t.canonical), toLower($term)) < 0.20 RETURN t.canonical AS base UNION + MATCH (t:Term)<-[:CONTAINS]-(b:Brand) + WHERE apoc.text.jaroWinklerDistance(toLower(b.name), toLower($term)) < 0.20 + RETURN t.canonical AS base + UNION MATCH (t:Term)<-[:OF_TERM]-(tr:Translation) WHERE apoc.text.jaroWinklerDistance(toLower(tr.text), toLower($term)) < 0.20 RETURN t.canonical AS base diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx index 71e5a66..8b79c1a 100644 --- a/frontend/src/App.tsx +++ b/frontend/src/App.tsx @@ -27,7 +27,7 @@ const LANGUAGE_COUNTRY_MAP: Record = { ru: [ { code: 'RU', label: 'Russia' }, ], - ua: [ + uk: [ { code: 'UA', label: 'Ukraine' }, { code: 'PL', label: 'Poland' }, ], From 6875e1dd04c6ac0cebc8d1cb21e355364e2e7fe7 Mon Sep 17 00:00:00 2001 From: loganwatersmith-gb Date: Tue, 1 Sep 2026 16:05:43 -0700 Subject: [PATCH 13/23] Removed demo_load function for local import --- backend/codex_build/api.py | 32 +++++--------------------------- 1 file changed, 5 insertions(+), 27 deletions(-) diff --git a/backend/codex_build/api.py b/backend/codex_build/api.py index 7ea8d7d..c3aeaad 100644 --- a/backend/codex_build/api.py +++ b/backend/codex_build/api.py @@ -68,7 +68,6 @@ TARGET_FOLDER_PATH = Path("./codex/language_packs") @asynccontextmanager async def lifespan(app: FastAPI): - demo_load() print(f"Scanning directory: {TARGET_FOLDER_PATH.resolve()}") if TARGET_FOLDER_PATH.exists() and TARGET_FOLDER_PATH.is_dir(): @@ -110,7 +109,10 @@ async def lifespan(app: FastAPI): class SourceSelection(BaseModel): selectedSources: List[str] -@app.post("/api/populate-sources") +@app.post( + "/api/populate-sources", + tags=["data"] +) async def handle_populate(data: SourceSelection): sources = data.selectedSources @@ -214,7 +216,7 @@ def health(): @app.post( "/search", response_model=SearchResponse | None, - tags=["search"], + tags=["translation"], ) def search(term: str): try: @@ -347,30 +349,6 @@ def audit_term(term: str): ], ) - -@app.post( - "/demo/load", - response_model=MessageResponse, - status_code=status.HTTP_201_CREATED, - summary="Load built-in sample data", - tags=["data"], -) -def demo_load(): - """ - Loads Ibuprofen, Paracetamol, and Amoxicillin with translations across - US, GB, FR, ES, MX, NG, IN into Neo4j. - - Safe to call multiple times (uses MERGE — no duplicates). - """ - log.info("Loading demo data") - try: - result = load_demo_data() - return MessageResponse(message=result.get("status", "Demo data loaded")) - except Exception as exc: - log.exception("demo_load failed") - raise HTTPException(status_code=500, detail=str(exc)) - - @app.post( "/packs/load", response_model=MessageResponse, From dea76919b9b1c0e9e77796ce5b2f4cdf0ebb675c Mon Sep 17 00:00:00 2001 From: loganwatersmith-gb Date: Tue, 1 Sep 2026 16:06:24 -0700 Subject: [PATCH 14/23] Added local language import functionality --- frontend/src/App.tsx | 137 ++++++++++++++++--------------------------- 1 file changed, 52 insertions(+), 85 deletions(-) diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx index 8b79c1a..14bcfee 100644 --- a/frontend/src/App.tsx +++ b/frontend/src/App.tsx @@ -89,10 +89,10 @@ function App() { const [searchError, setSearchError] = useState('') const [isLoading, setIsLoading] = useState(false) const [isTranslating, setIsTranslating] = useState(false) - const [exportLanguage, setExportLanguage] = useState(availableLanguages[0]) - const [exportError, setExportError] = useState('') - const [isExporting, setIsExporting] = useState(false) - const [exportMessage, setExportMessage] = useState('') + const [importError, setImportError] = useState('') + const [isImporting, setIsImporting] = useState(false) + const [importLanguage, setImportLanguage] = useState(null) + const [importMessage, setImportMessage] = useState('') const getLanguageLabel = (code: string) => { const raw = code.trim() @@ -128,10 +128,13 @@ function App() { setTranslatedName('') }; - useEffect(() => { - let isActive = true + const handleImportLanguageChange = (event: React.ChangeEvent) => { + if (event.target.files && event.target.files.length > 0) { + setImportLanguage(event.target.files[0]) + } + }; - const loadLanguages = async () => { + const loadLanguages = async (isActive: boolean) => { try { const response = await fetch(`${API_BASE_URL}/languages`) if (!response.ok) { @@ -146,7 +149,6 @@ function App() { setAvailableLanguages(nextLanguages) setTargetLanguage((current) => (nextLanguages.includes(current) ? current : nextLanguages[0])) - setExportLanguage((current) => (nextLanguages.includes(current) ? current : nextLanguages[0])) } catch { if (!isActive) { return @@ -157,7 +159,10 @@ function App() { } } - void loadLanguages() + useEffect(() => { + let isActive = true + + loadLanguages(isActive) return () => { isActive = false @@ -279,66 +284,38 @@ function App() { } } - const rowsToCsv = (rows: any[]) => { - if (!rows || rows.length === 0) return '' - const headerOrder = ['concept_id', 'source_id', 'source_name', 'name', 'type', 'country', 'language', 'uploaded_at'] - const keys = Array.from(new Set([...headerOrder, ...Object.keys(rows[0] || {})])) - const escapeVal = (v: any) => { - if (v === null || v === undefined) return '' - const s = String(v) - if (s.includes('"') || s.includes(',') || s.includes('\n')) { - return `"${s.replace(/"/g, '""')}"` - } - return s + const handleImportLanguageLocal = async () => { + setImportMessage('') + setImportError('') + if (!importLanguage) { + setImportError('Please select a language file!') + return } - const lines = [keys.join(',')] - rows.forEach((r) => { - lines.push(keys.map((k) => escapeVal((r as any)[k])).join(',')) - }) - return lines.join('\n') - } - - const downloadBlob = (filename: string, text: string) => { - const blob = new Blob([text], { type: 'text/csv;charset=utf-8;' }) - const url = URL.createObjectURL(blob) - const a = document.createElement('a') - a.href = url - a.download = filename - document.body.appendChild(a) - a.click() - a.remove() - URL.revokeObjectURL(url) - } - - const fetchAndDownload = async (urlSuffix: string, filename: string) => { - setIsExporting(true) - setExportError('') - setExportMessage('') + setIsImporting(true) + const formData = new FormData() + formData.append("file", importLanguage) + try { - const res = await fetch(`${API_BASE_URL}${urlSuffix}`) - if (!res.ok) { - const err = await res.json().catch(() => null) - throw new Error(err?.detail ?? 'Export failed') + const response = await fetch(`${API_BASE_URL}/packs/load`, { + method: 'POST', + body: formData, + }) + + if (!response.ok) { + throw new Error('Failed to import language') } - const data = await res.json() - const rows = Array.isArray(data.rows) ? data.rows : data.results ?? [] - const csv = rowsToCsv(rows) - if (!csv) throw new Error('No rows to export') - downloadBlob(filename, csv) - setExportMessage(`Downloaded ${rows.length} rows`) - } catch (err) { - setExportError(err instanceof Error ? err.message : 'Export failed') + + const data = await response.json(); + + loadLanguages(true) + setImportError('') + setImportMessage(`Success! ${data.message}`); + } catch (error) { + setImportError(`Error: ${(error as Error).message}`); } finally { - setIsExporting(false) + setIsImporting(false) } } - const downloadByLanguage = () => { - if (!exportLanguage.trim()) { - setExportError('Choose a language') - return - } - fetchAndDownload(`/csv/language/${encodeURIComponent(exportLanguage.trim())}`, `codex_language_${exportLanguage.trim()}.csv`) - } const languages = availableLanguages.map((code) => ({ code, label: getLanguageLabel(code) })) @@ -652,30 +629,20 @@ function App() { -
-

Export CSV

+
-
-
- - -
-
- +

{t('home.importTitle')}

+
+ + +
+
+
+ {isImporting &&
Importing language...
} + {importError &&
{importError}
} + {importMessage &&
{importMessage}
}
-
- {isExporting &&
Preparing CSV...
} - {exportError &&
{exportError}
} - {exportMessage &&
{exportMessage}
} -
-
@@ -683,4 +650,4 @@ function App() { ) } -export default App \ No newline at end of file +export default App From e84d33b14663863b57689614804007fbe864530a Mon Sep 17 00:00:00 2001 From: loganwatersmith-gb Date: Tue, 1 Sep 2026 16:10:35 -0700 Subject: [PATCH 15/23] Added UI languages for language import --- frontend/src/i18n/locales/de.json | 3 ++- frontend/src/i18n/locales/en.json | 3 ++- frontend/src/i18n/locales/es.json | 3 ++- frontend/src/i18n/locales/fr.json | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/frontend/src/i18n/locales/de.json b/frontend/src/i18n/locales/de.json index bf08427..9fd6c8b 100644 --- a/frontend/src/i18n/locales/de.json +++ b/frontend/src/i18n/locales/de.json @@ -24,6 +24,7 @@ "localizeTitle": "Medikamentennamen übersetzen/lokalisieren...", "targetLanguage": "Zielsprache", "targetPlaceholder": "Zielsprache", - "translationPlaceholder": "Die Übersetzung wird hier angezeigt" + "translationPlaceholder": "Die Übersetzung wird hier angezeigt", + "importTitle": "Sprachdatei importieren" } } diff --git a/frontend/src/i18n/locales/en.json b/frontend/src/i18n/locales/en.json index f0bd529..3856e30 100644 --- a/frontend/src/i18n/locales/en.json +++ b/frontend/src/i18n/locales/en.json @@ -24,6 +24,7 @@ "localizeTitle": "Translate/Localize drug name...", "targetLanguage": "Target Language", "targetPlaceholder": "Target Language", - "translationPlaceholder": "Translation will appear here" + "translationPlaceholder": "Translation will appear here", + "importTitle": "Import Language File" } } diff --git a/frontend/src/i18n/locales/es.json b/frontend/src/i18n/locales/es.json index 2c262ec..8efc4ee 100644 --- a/frontend/src/i18n/locales/es.json +++ b/frontend/src/i18n/locales/es.json @@ -24,6 +24,7 @@ "localizeTitle": "Traducir/Localizar nombre de medicamento...", "targetLanguage": "Idioma de destino", "targetPlaceholder": "Idioma de destino", - "translationPlaceholder": "La traducción aparecerá aquí" + "translationPlaceholder": "La traducción aparecerá aquí", + "importTitle": "Importar archivo de idioma" } } diff --git a/frontend/src/i18n/locales/fr.json b/frontend/src/i18n/locales/fr.json index 879a85b..cdf6b44 100644 --- a/frontend/src/i18n/locales/fr.json +++ b/frontend/src/i18n/locales/fr.json @@ -24,6 +24,7 @@ "localizeTitle": "Traduire/Localiser le nom du médicament...", "targetLanguage": "Langue cible", "targetPlaceholder": "Langue cible", - "translationPlaceholder": "La traduction s'affichera ici" + "translationPlaceholder": "La traduction s'affichera ici", + "importTitle": "Importer un fichier de langue" } } From 39cf2efd02846448f4aa4febc8f77cbaaa107914 Mon Sep 17 00:00:00 2001 From: loganwatersmith-gb Date: Tue, 1 Sep 2026 19:28:58 -0700 Subject: [PATCH 16/23] + Can now search by brand, and brand info is returned (generic name, languages, and countries) + Added languages and country info for generic drug name searches + Now displays brand name for selected country for translation --- .../__pycache__/api.cpython-310.pyc | Bin 12828 -> 12466 bytes backend/codex_build/api.py | 21 ++- .../__pycache__/__init__.cpython-310.pyc | Bin 115 -> 115 bytes .../__pycache__/neo4j_driver.cpython-310.pyc | Bin 6340 -> 8774 bytes .../codex/language_packs/spanish_pack.json | 6 +- backend/codex_build/codex/neo4j_driver.py | 133 ++++++++++++++---- .../__pycache__/__init__.cpython-310.pyc | Bin 124 -> 124 bytes .../translation_service.cpython-310.pyc | Bin 4384 -> 4391 bytes .../codex/services/translation_service.py | 2 +- .../__pycache__/source_data.cpython-310.pyc | Bin 22045 -> 22045 bytes frontend/src/App.tsx | 55 +++++++- 11 files changed, 176 insertions(+), 41 deletions(-) diff --git a/backend/codex_build/__pycache__/api.cpython-310.pyc b/backend/codex_build/__pycache__/api.cpython-310.pyc index c74fad59cffc87b4c442e8cfd2aa043cab5d5883..3081ab718c0a337a92c061e59af086954bf154e5 100644 GIT binary patch delta 4265 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find_missing_brands, get_equivalent_brands, resolve_to_base_term, - get_translation_data + get_translation_data, + get_countries_for_term, + get_languages_for_term, + get_countries_for_brand, + get_languages_for_brand, ) except Exception as exc: logging.critical("Failed to import codex backend: %s", exc) @@ -127,6 +130,7 @@ class SearchResponse(BaseModel): source_id: str source_name: str name: str + brand: Optional[str] type: str country: str language: str @@ -221,9 +225,15 @@ def health(): def search(term: str): try: with driver.session() as session: - canonical = resolve_to_base_term(session, term) + canonical, brand = resolve_to_base_term(session, term) if not canonical: return None + if not brand: + countries = get_countries_for_term(session, canonical) + languages = get_languages_for_term(session, canonical) + else: + countries = get_countries_for_brand(session, brand) + languages = get_languages_for_brand(session, brand) except Exception as exc: log.exception("search raised an unexpected error") raise HTTPException(status_code=500, detail=str(exc)) @@ -232,9 +242,10 @@ def search(term: str): source_id="0", source_name="", name=canonical, + brand=brand, type="drug", - country="US", - language="en", + country=countries, + language=languages, uploaded_at="" ) diff --git a/backend/codex_build/codex/__pycache__/__init__.cpython-310.pyc b/backend/codex_build/codex/__pycache__/__init__.cpython-310.pyc index bbf1dd7015348d175deb31f3570a092ed64d10e6..1a0c818733473fad79b488a0dfef408a0748103f 100644 GIT binary patch delta 17 XcmXRe=FaEk%|xWVUo~b3)c!!)Y3?(rPvZq$RZhAsObR~&q5()7tJmu zKepUTRZndtG>4ulVX2oMqpH{TQl-kJ%_#@eQ|>)+L6IW$&Frp$rtVLqjN~_O-rwx| z-Z%bv@=-o&pF7th!TRu%uQz`i--`~TM|%^u(WSl5Z@w`^hCh>TYh;9+hrOSS5)6Bi zTp$-=A0VMcDKqx)>23_&V0wJ$hSNu+MX4Slp+PQ{LFtZ6N4ztU*5uPZe$Iq-Lk&w( z4~8{6Ge3_X2$ik$O|u{317T`dB+GtH3`TiGMK3PsUcf;-H^og$bA?g?ujVXc%f!=o z%r)tjh~UmrprgUtC3)YO9W8#GpPd>ht>u|5A=1(v1PZHjeH$g860);6^pyz?e2MRAh`#@za 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"ES","brand": "Neobrufen"} + {"translation": "Ibuprofeno","country": "ES","brand": "Neobrufen"}, + {"translation": "Ibuprofeno","country": "MX","brand": "Advil"} ] }, { @@ -19,7 +20,8 @@ { "canonical": "Amoxicillin", "entries": [ - {"translation": "Amoxicilina","country": "ES","brand": "Clamoxyl"} + {"translation": "Amoxicilina","country": "ES","brand": "Clamoxyl"}, + {"translation": "Amoxicilina","country": "ES","brand": "Amoxil"} ] }, { diff --git a/backend/codex_build/codex/neo4j_driver.py b/backend/codex_build/codex/neo4j_driver.py index 80a3f1a..bbdd5c6 100644 --- a/backend/codex_build/codex/neo4j_driver.py +++ b/backend/codex_build/codex/neo4j_driver.py @@ -153,34 +153,47 @@ def get_equivalent_brands(session, term): # Resolves any input (canonical, translated, or fuzzy) to a base canonical term def resolve_to_base_term(session, term): query = """ - MATCH (t:Term) - WHERE t.canonical = $term - RETURN t.canonical AS base - UNION - MATCH (t:Term)<-[:CONTAINS]-(b:Brand) - WHERE b.name = $term - RETURN t.canonical AS base - UNION - MATCH (t:Term)<-[:OF_TERM]-(tr:Translation) - WHERE tr.text = $term - RETURN t.canonical AS base - UNION - MATCH (t:Term) - WHERE apoc.text.jaroWinklerDistance(toLower(t.canonical), toLower($term)) < 0.20 - RETURN t.canonical AS base - UNION - MATCH (t:Term)<-[:CONTAINS]-(b:Brand) - WHERE apoc.text.jaroWinklerDistance(toLower(b.name), toLower($term)) < 0.20 - RETURN t.canonical AS base - UNION - MATCH (t:Term)<-[:OF_TERM]-(tr:Translation) - WHERE apoc.text.jaroWinklerDistance(toLower(tr.text), toLower($term)) < 0.20 - RETURN t.canonical AS base - + CALL { + MATCH (t:Term) + WHERE t.canonical = $term + RETURN t.canonical AS brand, t.canonical AS base + UNION + MATCH (t:Term)<-[:CONTAINS]-(b:Brand) + WHERE b.name = $term + RETURN b.name AS brand, t.canonical AS base + UNION + MATCH (t:Term)<-[:OF_TERM]-(tr:Translation) + WHERE tr.text = $term + RETURN t.canonical AS brand, t.canonical AS base + UNION + MATCH (t:Term) + WHERE apoc.text.jaroWinklerDistance(toLower(t.canonical), toLower($term)) < 0.20 + RETURN t.canonical AS brand, t.canonical AS base + UNION + MATCH (t:Term)<-[:CONTAINS]-(b:Brand) + WHERE apoc.text.jaroWinklerDistance(toLower(b.name), toLower($term)) < 0.20 + RETURN b.name AS brand, t.canonical AS base + UNION + MATCH (t:Term)<-[:OF_TERM]-(tr:Translation) + WHERE apoc.text.jaroWinklerDistance(toLower(tr.text), toLower($term)) < 0.20 + RETURN t.canonical AS brand, t.canonical AS base + } + WITH collect({brand: brand, base: base}) AS results + WITH results, any(r IN results WHERE r.brand = r.base) AS exactMatch + UNWIND results AS row + WITH row, exactMatch + WHERE exactMatch = false OR row.brand = row.base + RETURN row.brand AS brand, row.base AS base """ result = session.run(query, term=term).single() - return result["base"] if result else None + if not result: + return None + elif (result["base"] == result["brand"]): + return result["base"], None + else: + return result["base"], result["brand"] + # Checks whether a language pack exists in the database def language_exists(lang_code: str) -> bool: @@ -207,4 +220,72 @@ def get_brands_for_term(session, term): ORDER BY country """ - return list(session.run(query, term=term)) \ No newline at end of file + return list(session.run(query, term=term)) + +# Retrieves all countries associated with a term +def get_countries_for_term(session, term): + query = """ + MATCH (t:Term) + WHERE t.canonical = $term + OR apoc.text.jaroWinklerDistance(toLower(t.canonical), toLower($term)) < 0.20 + MATCH (tr:Translation)-[:OF_TERM]->(t) + WHERE toLower(tr.text) = toLower(t.canonical) + RETURN collect(DISTINCT tr.country) AS country + ORDER BY country + """ + + result = session.run(query, term=term) + countries = result.single().value() if result.peek() else [] + countries = ', '.join(countries) + return countries + +# Retrieves all languages associated with a term +def get_languages_for_term(session, term): + query = """ + MATCH (t:Term) + WHERE t.canonical = $term + OR apoc.text.jaroWinklerDistance(toLower(t.canonical), toLower($term)) < 0.20 + MATCH (tr:Translation)-[:OF_TERM]->(t) + WHERE toLower(tr.text) = toLower(t.canonical) + MATCH (tr)-[:IN_LANGUAGE]->(l:Language) + RETURN collect(DISTINCT toUpper(l.code)) AS language + ORDER BY language + """ + + result = session.run(query, term=term) + languages = result.single().value() if result.peek() else [] + languages = ', '.join(languages) + return languages + +# Retrieves all countries associated with a brand +def get_countries_for_brand(session, term): + query = """ + MATCH (b:Brand) + WHERE b.name = $term + OR apoc.text.jaroWinklerDistance(toLower(b.name), toLower($term)) < 0.20 + MATCH (tr:Translation)-[:HAS_BRAND]->(b) + RETURN collect(DISTINCT tr.country) AS country + ORDER BY country + """ + + result = session.run(query, term=term) + countries = result.single().value() if result.peek() else [] + countries = ', '.join(countries) + return countries + +# Retrieves all languages associated with a brand +def get_languages_for_brand(session, term): + query = """ + MATCH (b:Brand) + WHERE b.name = $term + OR apoc.text.jaroWinklerDistance(toLower(b.name), toLower($term)) < 0.20 + MATCH (tr:Translation)-[:HAS_BRAND]->(b) + MATCH (tr)-[:IN_LANGUAGE]->(l:Language) + RETURN collect(DISTINCT toUpper(l.code)) AS language + ORDER BY language + """ + + result = session.run(query, term=term) + languages = result.single().value() if result.peek() else [] + languages = ', '.join(languages) + return languages \ No newline at end of file diff --git a/backend/codex_build/codex/services/__pycache__/__init__.cpython-310.pyc b/backend/codex_build/codex/services/__pycache__/__init__.cpython-310.pyc index 6be17769e14a4de2a00dd342b73ccdd851062a0a..543fab79a48761f52117b7fc2daf9ef6ec33835a 100644 GIT binary patch delta 17 Xcmb=a;m+sfJF(XHMW22@gZIFjk?KTg*23^$;>QS9I9F^Sxd^=%%-bS z*79`EV5XEdrL@hXMsNE}u-~)geup{q3BPE>!QnZhKhAxNK@GyB8bTG1u+WMaw85Vn 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b/frontend/src/App.tsx @@ -41,8 +41,9 @@ interface SearchResultRow { source_id: string | null source_name: string | null name: string + brand: string | null type: string - country: string | null + country: string language: string uploaded_at: string | null } @@ -51,6 +52,7 @@ interface SearchResponse { source_id: string source_name: string name: string + brand: string type: string country: string language: string @@ -61,6 +63,7 @@ interface TranslateResultRow { source_id: string | null source_name: string | null translation: string + brand: string | null type: string country: string | null language: string @@ -85,6 +88,7 @@ function App() { const [targetLanguage, setTargetLanguage] = useState('es') const [targetCountry, setTargetCountry] = useState("MX") const [translatedName, setTranslatedName] = useState('') + const [translatedBrand, setTranslatedBrand] = useState('') const [translateError, setTranslateError] = useState('') const [searchError, setSearchError] = useState('') const [isLoading, setIsLoading] = useState(false) @@ -93,6 +97,7 @@ function App() { const [isImporting, setIsImporting] = useState(false) const [importLanguage, setImportLanguage] = useState(null) const [importMessage, setImportMessage] = useState('') + const [hasBrand, setHasBrand] = useState(false) const getLanguageLabel = (code: string) => { const raw = code.trim() @@ -126,6 +131,7 @@ function App() { setTargetLanguage(newLang); setTargetCountry(newCountry); setTranslatedName('') + setTranslatedBrand('') }; const handleImportLanguageChange = (event: React.ChangeEvent) => { @@ -181,6 +187,18 @@ function App() { return Array.from(new Set(names)).join(', ') } + const extractTranslatedBrand = (rows: TranslateResultRow[]) => { + const brands = rows + .map((row) => row.brand) + .filter((brand): brand is string => Boolean(brand && brand.trim())) + + if (brands.length === 0) { + return '-' + } + + return Array.from(new Set(brands)).join(', ') + } + const handleSearch = async () => { if (!searchQuery.trim()) { setSearchError('Please enter a search term') @@ -193,6 +211,7 @@ function App() { setSearchResults([]) setSelectedResult(null) setTranslatedName('') + setTranslatedBrand('') try { const response = await fetch(`${API_BASE_URL}/search?term=${encodeURIComponent(searchQuery.toLowerCase())}`, { @@ -217,6 +236,11 @@ function App() { setSearchResults([]) setSearchError('No results found') } else { + if (data.brand) { + setHasBrand(true) + } else { + setHasBrand(false) + } setSearchResults([data]) setSearchError('') } @@ -251,6 +275,7 @@ function App() { setIsTranslating(true) setTranslateError('') setTranslatedName('') + setTranslatedBrand('') try { const response = await fetch(`${API_BASE_URL}/translate`, { @@ -273,7 +298,9 @@ function App() { const payload = (await response.json()) as TranslateResponse const results = payload.results ?? [] const name = results.length > 0 ? extractTranslatedName(results) : '-' + const brand = results.length > 0 ? extractTranslatedBrand(results) : '-' setTranslatedName(name) + setTranslatedBrand(brand) if (results.length === 0 || name === '-') { setTranslateError('No translation found for the selected language') } @@ -522,19 +549,28 @@ function App() { - + {hasBrand && } + {!hasBrand && } + + {hasBrand && } + - - + + {hasBrand && } + {!hasBrand && } + + {hasBrand && } + {!hasBrand && } {searchResults.map((row, index) => ( - + {hasBrand && } + {hasBrand && } + {!hasBrand && } @@ -611,14 +650,16 @@ function App() {
Drug NameDrug Name for BrandDrug NameBrandTypeLanguageCountryLanguage for BrandLanguageCountries for BrandCountries
{row.name}{row.type}{row.brand}brand name drug{row.type}{row.language} {row.country ?? '-'}
- + + +
Original Drug Name (Language)Original Drug Name (Languages) Drug Name in {targetLanguage.toUpperCase()}Drug Brand Name in {targetCountry.toUpperCase()}
{selectedResult.name} ({selectedResult.language}) {translatedName || '-'}{translatedBrand || '-'}
From 2866a5422150961d02fcbc6a074487b6265a4d74 Mon Sep 17 00:00:00 2001 From: loganwatersmith-gb Date: Wed, 2 Sep 2026 13:27:18 -0700 Subject: [PATCH 17/23] + Adds progress/status for database population, including number processed out of number remaining (if available), as well as which database is currently being worked on - Does not include info on what the most recent successful fetch was - Still need to implement OCR, I tried to implement it from the backend repo and could not get it working --- backend/codex_build/api.py | 19 +++--- .../codex_build/neo4j_sources/source_data.py | 62 +++++++++++++++---- frontend/src/App.css | 16 +++++ frontend/src/App.tsx | 48 +++++++++++--- 4 files changed, 118 insertions(+), 27 deletions(-) diff --git a/backend/codex_build/api.py b/backend/codex_build/api.py index 26ccaf9..cfb30b3 100644 --- a/backend/codex_build/api.py +++ b/backend/codex_build/api.py @@ -29,7 +29,7 @@ from fastapi import Depends, FastAPI, HTTPException, UploadFile, File, status, Query from fastapi.middleware.cors import CORSMiddleware -from fastapi.responses import JSONResponse +from fastapi.responses import JSONResponse, StreamingResponse from contextlib import asynccontextmanager from pathlib import Path import ast @@ -62,7 +62,7 @@ ) except Exception as exc: logging.critical("Failed to import codex backend: %s", exc) - sys.exit(1) + raise exc # ── App setup ──────────────────────────────────────────────────────────────── logging.basicConfig(level=logging.INFO, format="%(levelname)s %(name)s %(message)s") @@ -118,11 +118,15 @@ class SourceSelection(BaseModel): ) async def handle_populate(data: SourceSelection): sources = data.selectedSources - - source_data(sources) - - return {"status": "success", "message": "Successfully populated Neo4j!"} - + return StreamingResponse( + source_data(sources), + media_type="application/x-ndjson", + headers={ + "Cache-Control": "no-cache", + "X-Accel-Buffering": "no", + "Connection": "keep-alive", + } + ) # ── Request / response models ──────────────────────────────────────────────── @@ -427,7 +431,6 @@ def list_languages(): log.exception("list_languages failed") raise HTTPException(status_code=500, detail=str(exc)) - # ── Entry point (for running directly) ────────────────────────────────────── if __name__ == "__main__": import uvicorn diff --git a/backend/codex_build/neo4j_sources/source_data.py b/backend/codex_build/neo4j_sources/source_data.py index e76feaa..7f5d133 100644 --- a/backend/codex_build/neo4j_sources/source_data.py +++ b/backend/codex_build/neo4j_sources/source_data.py @@ -10,6 +10,8 @@ import uuid import re import logging +import json +import asyncio from datetime import datetime, timezone from collections import deque @@ -91,7 +93,7 @@ def conceptID(text: str, symptom: str = None, source: str = None) -> str: # DrugBank # -------------------- -def drugbank(driver): +async def drugbank(driver): DRUGBANK_API_BASE = os.getenv("DRUGBANK_API_BASE", "https://api.drugbank.com/discovery/v1") DRUGBANK_API_KEY = os.getenv("DRUGBANK_API_KEY") if not DRUGBANK_API_KEY: @@ -166,7 +168,11 @@ def iter_drugs(per_page=100): sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.code = $id, n.title = $title, n.ds = $ds", id=ROOT_ID, title=ROOT_TITLE, ds=DATASET) sess.run("MATCH (i:Ingest {uid: $uid}), (r:DRUG {id: $rootId}) MERGE (i)-[:ROOT]->(r)", uid=run_uid, rootId=ROOT_ID) + pages = 0 for d, code, title in iter_drugs(): + if pages % 100 == 0: + yield json.dumps({"progress": f"Processing page {pages} of ??? for DrugBank"}) + "\n" + await asyncio.sleep(0) symptoms = d.get("symptoms", []) for symptom_name in symptoms: if not symptom_name: @@ -175,7 +181,10 @@ def iter_drugs(per_page=100): sess.run("MERGE (n:DRUG {id: $id}) ON CREATE SET n.conceptID=$conceptID, n.code=$id, n.title=$t, n.ds=$ds ON MATCH SET n.ds=$ds", id=code, conceptID=concept_id, t=title or None, ds=DATASET) sess.run("MATCH (p:DRUG {id: $parent}), (c:DRUG {id: $child}) MERGE (p)-[:HAS_CHILD]->(c)", parent=ROOT_ID, child=code) + pages += 1 + yield json.dumps({"progress": "DrugBank completed successfully!"}) + "\n" + await asyncio.sleep(0) rec = sess.run("MATCH (n:DRUG {ds: $ds}) WITH count(n) AS n MATCH (:DRUG {ds: $ds})-[rel:HAS_CHILD]->(:DRUG {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt = $finishedAt, i.nodeCount = $nodeCount, i.edgeCount = $edgeCount", uid=run_uid, finishedAt=utc_iso(), nodeCount=rec["n"], edgeCount=rec["r"]) @@ -183,7 +192,7 @@ def iter_drugs(per_page=100): # SNOMED # -------------------- -def snomed(driver): +async def snomed(driver): SNOWSTORM_BASE = os.getenv("SNOWSTORM_BASE", "https://snowstorm.ihtsdotools.org/snowstorm/snomed-ct") SNOMED_BRANCH = os.getenv("SNOMED_BRANCH", "MAIN") SNOMED_ROOT_ID = os.getenv("SNOMED_ROOT_ID", "404684003") @@ -254,7 +263,11 @@ def upsert_snomed_node(node): queue = deque([(SNOMED_ROOT_ID, None)]) visited = set() + pages = 0 while queue: + if pages % 100 == 0: + yield json.dumps({"progress": f"Processing page {pages} of {len(queue)} for SNOMED"}) + "\n" + await asyncio.sleep(0) cid, parent = queue.popleft() if cid in visited: continue visited.add(cid) @@ -272,7 +285,10 @@ def upsert_snomed_node(node): if ch_id and ch_id not in visited: queue.append((ch_id, cid)) except Exception as e: log.warning("Failed step processing SNOMED code %s: %s", cid, e) + pages += 1 + yield json.dumps({"progress": "SNOMED completed successfully!"}) + "\n" + await asyncio.sleep(0) rec = sess.run("MATCH (n:SNOMED {ds: $ds}) WITH count(n) AS n MATCH (:SNOMED {ds: $ds})-[rel:HAS_CHILD]->(:SNOMED {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt=$f, i.nodeCount=$n, i.edgeCount=$r", uid=run_uid, f=utc_iso(), n=rec["n"], r=rec["r"]) @@ -280,7 +296,7 @@ def upsert_snomed_node(node): # RXNORM # -------------------- -def rxnorm(driver): +async def rxnorm(driver): PRESCRIBABLE_ONLY = os.getenv("RXN_PRESCRIBABLE", "1") == "1" RXN_RELEASE_ID = os.getenv("RXN_RELEASE_ID", "current") DATASET = f"RxNorm:{'prescribable' if PRESCRIBABLE_ONLY else 'all'}:{RXN_RELEASE_ID}" @@ -321,7 +337,9 @@ def rx_get(path, params=None): sess.run("MATCH (p:RXN {rxcui: 'ROOT'}), (c:RXN {rxcui: $c}) MERGE (p)-[:HAS_CHILD]->(c)", c=m["rxcui"]) for idx, m in enumerate(roots): - if idx % 250 == 0: log.info("RxNorm build processing roots: %d / %d", idx, len(roots)) + if idx % 250 == 0: + yield json.dumps({"progress": f"Processing page {idx} of {len(roots)} for RXNorm"}) + "\n" + await asyncio.sleep(0) try: rel_js = rx_get(f"/rxcui/{m['rxcui']}/allrelated.json") groups = rel_js.get("allRelatedGroup", {}).get("conceptGroup", []) @@ -337,6 +355,8 @@ def rx_get(path, params=None): sess.run("MATCH (p:RXN {rxcui: $p}), (c:RXN {rxcui: $c}) MERGE (p)-[:HAS_CHILD]->(c)", p=m["rxcui"], c=p["rxcui"]) except Exception as e: log.debug("Skipped paths on CUI %s: %s", m["rxcui"], e) + yield json.dumps({"progress": "RXNorm completed successfully!"}) + "\n" + await asyncio.sleep(0) rec = sess.run("MATCH (n:RXN {ds: $ds}) WITH count(n) AS n MATCH (:RXN {ds: $ds})-[rel:HAS_CHILD]->(:RXN {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt=$f, i.nodeCount=$n, i.edgeCount=$r", uid=run_uid, f=utc_iso(), n=rec["n"], r=rec["r"]) @@ -344,7 +364,7 @@ def rx_get(path, params=None): # ICD-11 # -------------------- -def icd11(driver): +async def icd11(driver): ICD_CLIENT_ID = os.getenv("ICD_CLIENT_ID") ICD_CLIENT_SECRET = os.getenv("ICD_CLIENT_SECRET") if not ICD_CLIENT_ID or not ICD_CLIENT_SECRET: @@ -410,7 +430,11 @@ def get_node_details(item): queue = deque([(ch21_id, None)]) visited = set() + pages = 0 while queue: + if pages % 10 == 0: + yield json.dumps({"progress": f"Processing page {pages} of {len(queue)} for ICD11"}) + "\n" + await asyncio.sleep(0) nid, parent = queue.popleft() if nid in visited: continue visited.add(nid) @@ -427,7 +451,10 @@ def get_node_details(item): for child in children: cid, _, _ = get_node_details(child) if cid and cid not in visited: queue.append((cid, nid)) + pages += 1 + yield json.dumps({"progress": "ICD11 completed successfully!"}) + "\n" + await asyncio.sleep(0) rec = sess.run("MATCH (n:ICD {ds: $ds}) WITH count(n) AS n MATCH (:ICD {ds: $ds})-[rel:HAS_CHILD]->(:ICD {ds: $ds}) RETURN n, count(rel) AS r", ds=DATASET).single() sess.run("MATCH (i:Ingest {uid: $uid}) SET i.finishedAt=$f, i.nodeCount=$n, i.edgeCount=$r", uid=run_uid, f=utc_iso(), n=rec["n"], r=rec["r"]) @@ -521,7 +548,7 @@ def print_databases(driver): file.write("="*60 + "\nEND OF DATABASE READOUT\n" + "="*60) -def source_data(sources): +async def source_data(sources): log.info("=" * 60) log.info("Creating Singular Medical Knowledge Graph") log.info("=" * 60) @@ -537,16 +564,29 @@ def source_data(sources): # Ingest separate sources into the single database based on user choice if "drugbank" in sources: log.info("Ingesting DrugBank.") - drugbank(driver) + yield json.dumps({"progress": "Ingesting DrugBank..."}) + "\n" + await asyncio.sleep(0) + async for chunk in drugbank(driver): + yield chunk if "snomed" in sources: log.info("Ingesting SNOMED.") - snomed(driver) + yield json.dumps({"progress": "Ingesting SNOMED..."}) + "\n" + await asyncio.sleep(0) + await asyncio.sleep(0) + async for chunk in snomed(driver): + yield chunk if "rxnorm" in sources: log.info("Ingesting RXNorm.") - rxnorm(driver) + yield json.dumps({"progress": "Ingesting RXNorm..."}) + "\n" + await asyncio.sleep(0) + async for chunk in rxnorm(driver): + yield chunk if "icd11" in sources: log.info("Ingesting ICD11.") - icd11(driver) + yield json.dumps({"progress": "Ingesting ICD11..."}) + "\n" + await asyncio.sleep(0) + async for chunk in icd11(driver): + yield chunk # Link them together to make a singular source unify_graph(driver) @@ -555,7 +595,7 @@ def source_data(sources): except Exception as e: log.critical("Pipeline was terminated prematurely: %s", e) - sys.exit(2) + raise e finally: driver.close() diff --git a/frontend/src/App.css b/frontend/src/App.css index 18ef47a..9a1ed0a 100644 --- a/frontend/src/App.css +++ b/frontend/src/App.css @@ -204,6 +204,22 @@ left: 32px; } +.populate-loading-label { + display: flex; + align-items: center; + justify-content: center; + text-align: center; + font-size: 1.2rem; + font-weight: 500; + color: #0f1826; + position: absolute; + top: 450px; + left: 10px; + width: 300px; + height: 5vh; + box-sizing: border-box; +} + .populateDrugbank-checkbox { display: flex; align-items: center; diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx index e218927..3df0f4d 100644 --- a/frontend/src/App.tsx +++ b/frontend/src/App.tsx @@ -17,7 +17,6 @@ const LANGUAGE_COUNTRY_MAP: Record = { { code: 'US', label: 'United States' }, { code: 'GB', label: 'United Kingdom' }, { code: 'CA', label: 'Canada' }, - { code: 'NG', label: 'Nigeria' }, ], fr: [ { code: 'FR', label: 'France' }, @@ -76,7 +75,7 @@ interface TranslateResponse { } const API_BASE_URL = 'http://localhost:8000' -const FALLBACK_LANGUAGES = ['en', 'es', 'fr', 'de'] +const FALLBACK_LANGUAGES = ['en', 'es', 'fr'] function App() { const { t, i18n } = useTranslation() @@ -98,6 +97,7 @@ function App() { const [importLanguage, setImportLanguage] = useState(null) const [importMessage, setImportMessage] = useState('') const [hasBrand, setHasBrand] = useState(false) + const [progress, setProgress] = useState(''); const getLanguageLabel = (code: string) => { const raw = code.trim() @@ -367,20 +367,50 @@ function App() { sources.push("icd11") } setIsPopulationLoading(true); - try{ + setProgress('Starting population...'); + try { const response = await fetch('http://localhost:8000/api/populate-sources', { method: 'POST', headers: { 'Content-Type': 'application/json' }, body: JSON.stringify({ selectedSources: sources }), }); - const data = await response.json(); - if (data.status === "success") { - alert(data.message); + if (!response.body) return; + + const reader = response.body.getReader(); + const decoder = new TextDecoder(); + let buffer = ''; + + while (true) { + const { done, value } = await reader.read(); + if (done) break; + + buffer += decoder.decode(value, { stream: true }); + const lines = buffer.split('\n'); + + // Keep the incomplete last line in the buffer + buffer = lines.pop() || ''; + + for (const line of lines) { + const trimmed = line.trim(); + if (!trimmed) continue; + + try { + const cleanLine = trimmed.startsWith('data:') ? trimmed.replace(/^data:\s*/, '') : trimmed; + const parsed = JSON.parse(cleanLine); + + if (parsed.progress) { + setProgress(parsed.progress); + } + } catch (err) { + console.error('Error parsing JSON chunk:', err); + } + } } + setProgress('Successfully populated Neo4j!'); } catch (error) { - console.error("Error calling Python function:", error); - alert("Something went wrong on the backend."); + console.error('Error during streaming:', error); + setProgress('Error processing request.'); } finally { setIsPopulationLoading(false); } @@ -493,6 +523,8 @@ function App() { {t('sides.populateButton')}
+ +

{progress}

From 327f864e764b4538d1c1f48623c3c0b9b76e5ec7 Mon Sep 17 00:00:00 2001 From: Sebas Taboada Date: Tue, 15 Sep 2026 21:03:38 -0300 Subject: [PATCH 18/23] chore: update .gitignore, untrack pycache, and build configs --- .gitignore | 31 +- .../__pycache__/__init__.cpython-312.pyc | Bin 154 -> 0 bytes .../__pycache__/api.cpython-310.pyc | Bin 12466 -> 0 bytes .../__pycache__/api.cpython-314.pyc | Bin 16764 -> 0 bytes .../__pycache__/config.cpython-312.pyc | Bin 790 -> 0 bytes .../__pycache__/db.cpython-312.pyc | Bin 2138 -> 0 bytes .../__pycache__/dependencies.cpython-312.pyc | Bin 704 -> 0 bytes .../__pycache__/main.cpython-312.pyc | Bin 1405 -> 0 bytes .../__pycache__/main.cpython-314.pyc | Bin 3074 -> 0 bytes .../__pycache__/__init__.cpython-310.pyc | Bin 115 -> 0 bytes .../__pycache__/__init__.cpython-314.pyc | Bin 181 -> 0 bytes .../__pycache__/neo4j_driver.cpython-310.pyc | Bin 8774 -> 0 bytes .../__pycache__/neo4j_driver.cpython-314.pyc | Bin 7272 -> 0 bytes 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"license": "ISC" }, + "node_modules/enhanced-resolve": { + "version": "5.25.1", + "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.25.1.tgz", + "integrity": "sha512-nGXts5znJzmWPu+mIE9izCOzdg63oJca2mDzGWWTth7sr4aCToKcoyFVBQwN75Ij5Pf6p510EwkTqViTRzDV+w==", + "license": "MIT", + "dependencies": { + "graceful-fs": "^4.2.4", + "tapable": "^2.3.3" + }, + "engines": { + "node": ">=10.13.0" + } + }, "node_modules/escalade": { "version": "3.2.0", "resolved": "https://registry.npmjs.org/escalade/-/escalade-3.2.0.tgz", @@ -1741,7 +1986,6 @@ "version": "6.5.0", "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.5.0.tgz", "integrity": "sha512-tIbYtZbucOs0BRGqPJkshJUYdL+SDH7dVM8gjy+ERp3WAUjLEFJE+02kanyHtwjWOnwrKYBiwAmM0p4kLJAnXg==", - "dev": true, "license": "MIT", "engines": { "node": ">=12.0.0" @@ -1810,7 +2054,6 @@ "version": "2.3.3", "resolved": "https://registry.npmjs.org/fsevents/-/fsevents-2.3.3.tgz", "integrity": 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"node_modules/js-tokens": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/js-tokens/-/js-tokens-4.0.0.tgz", @@ -2086,7 +2344,6 @@ "version": "1.32.0", "resolved": "https://registry.npmjs.org/lightningcss/-/lightningcss-1.32.0.tgz", "integrity": "sha512-NXYBzinNrblfraPGyrbPoD19C1h9lfI/1mzgWYvXUTe414Gz/X1FD2XBZSZM7rRTrMA8JL3OtAaGifrIKhQ5yQ==", - "dev": true, "license": "MPL-2.0", "dependencies": { "detect-libc": "^2.0.3" @@ -2119,7 +2376,6 @@ "cpu": [ "arm64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2140,7 +2396,6 @@ "cpu": [ "arm64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2161,7 +2416,6 @@ "cpu": [ "x64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2182,7 +2436,6 @@ "cpu": [ "x64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2203,7 +2456,6 @@ "cpu": [ "arm" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2224,7 +2476,6 @@ "cpu": [ "arm64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2245,7 +2496,6 @@ "cpu": [ "arm64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2266,7 +2516,6 @@ "cpu": [ "x64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2287,7 +2536,6 @@ "cpu": [ "x64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2308,7 +2556,6 @@ "cpu": [ "arm64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2329,7 +2576,6 @@ "cpu": [ "x64" ], - "dev": true, "license": "MPL-2.0", "optional": true, "os": [ @@ -2376,6 +2622,15 @@ "yallist": "^3.0.2" } }, + "node_modules/magic-string": { + "version": "0.30.21", + "resolved": "https://registry.npmjs.org/magic-string/-/magic-string-0.30.21.tgz", + "integrity": "sha512-vd2F4YUyEXKGcLHoq+TEyCjxueSeHnFxyyjNp80yg0XV4vUhnDer/lvvlqM/arB5bXQN5K2/3oinyCRyx8T2CQ==", + "license": "MIT", + "dependencies": { + "@jridgewell/sourcemap-codec": "^1.5.5" + } + }, "node_modules/minimatch": { "version": "3.1.5", "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.5.tgz", @@ -2400,7 +2655,6 @@ "version": "3.3.11", "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.11.tgz", "integrity": "sha512-N8SpfPUnUp1bK+PMYW8qSWdl9U+wwNWI4QKxOYDy9JAro3WMX7p2OeVRF9v+347pnakNevPmiHhNmZ2HbFA76w==", - "dev": true, "funding": [ { "type": "github", @@ -2516,14 +2770,12 @@ "version": "1.1.1", "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.1.1.tgz", "integrity": "sha512-xceH2snhtb5M9liqDsmEw56le376mTZkEX/jEb/RxNFyegNul7eNslCXP9FDj/Lcu0X8KEyMceP2ntpaHrDEVA==", - "dev": true, "license": "ISC" }, "node_modules/picomatch": { "version": "4.0.4", "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.4.tgz", "integrity": "sha512-QP88BAKvMam/3NxH6vj2o21R6MjxZUAd6nlwAS/pnGvN9IVLocLHxGYIzFhg6fUQ+5th6P4dv4eW9jX3DSIj7A==", - "dev": true, "license": "MIT", "engines": { "node": ">=12" @@ -2536,7 +2788,6 @@ "version": "8.5.8", "resolved": 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"integrity": "sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==", - "dev": true, "license": "BSD-3-Clause", "engines": { "node": ">=0.10.0" @@ -2755,11 +3003,29 @@ "node": ">=8" } }, + "node_modules/tailwindcss": { + "version": "4.3.3", + "resolved": "https://registry.npmjs.org/tailwindcss/-/tailwindcss-4.3.3.tgz", + "integrity": "sha512-gOhV3P7ufE62QDGg1zVaTgCR+EtPv92k2nIhVcVKcLmxT1sUBsQGhnZj175j+MqRt4zLF7ic+sCYjfhxMxj7YQ==", + "license": "MIT" + }, + "node_modules/tapable": { + "version": "2.3.3", + "resolved": "https://registry.npmjs.org/tapable/-/tapable-2.3.3.tgz", + "integrity": "sha512-uxc/zpqFg6x7C8vOE7lh6Lbda8eEL9zmVm/PLeTPBRhh1xCgdWaQ+J1CUieGpIfm2HdtsUpRv+HshiasBMcc6A==", + "license": "MIT", + "engines": { + "node": ">=6" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/webpack" + } + }, "node_modules/tinyglobby": { "version": "0.2.15", "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.15.tgz", "integrity": "sha512-j2Zq4NyQYG5XMST4cbs02Ak8iJUdxRM0XI5QyxXuZOzKOINmWurp3smXu3y5wDcJrptwpSjgXHzIQxR0omXljQ==", - "dev": true, "license": "MIT", "dependencies": { "fdir": "^6.5.0", @@ -2789,7 +3055,6 @@ "version": "2.8.1", "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz", "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==", - "dev": true, "license": "0BSD", "optional": true }, @@ -2848,7 +3113,7 @@ "version": "7.16.0", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz", "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw==", - "dev": true, + "devOptional": true, "license": "MIT" }, "node_modules/update-browserslist-db": { @@ -2905,7 +3170,6 @@ "version": "8.0.2", "resolved": "https://registry.npmjs.org/vite/-/vite-8.0.2.tgz", "integrity": "sha512-1gFhNi+bHhRE/qKZOJXACm6tX4bA3Isy9KuKF15AgSRuRazNBOJfdDemPBU16/mpMxApDPrWvZ08DcLPEoRnuA==", - "dev": true, "license": "MIT", "dependencies": { "lightningcss": "^1.32.0", diff --git a/frontend/package.json b/frontend/package.json index 9bc8234..b2ee83d 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -10,10 +10,12 @@ "preview": "vite preview" }, "dependencies": { + "@tailwindcss/vite": "^4.3.3", "i18next": "^25.10.9", "react": "^19.2.4", "react-dom": "^19.2.4", - "react-i18next": "^16.6.6" + "react-i18next": "^16.6.6", + "tailwindcss": "^4.3.3" }, "devDependencies": { "@eslint/js": "^9.39.4", diff --git a/frontend/vite.config.ts b/frontend/vite.config.ts index aab5dff..e02b756 100644 --- a/frontend/vite.config.ts +++ b/frontend/vite.config.ts @@ -1,11 +1,18 @@ import { defineConfig } from 'vite' import react from '@vitejs/plugin-react' +import tailwindcss from '@tailwindcss/vite' // https://vite.dev/config/ export default defineConfig({ - plugins: [react()], + plugins: [ + react(), + tailwindcss(), + ], server: { host: true, port: 9000, + watch: { + usePolling: true, + }, } }) From 318c7fbbd6d52a16561a206b0fe9afda1b4ed59f Mon Sep 17 00:00:00 2001 From: Sebas Taboada Date: Tue, 15 Sep 2026 21:03:42 -0300 Subject: [PATCH 19/23] feat(ui): add modular design system and reusable UI primitives --- frontend/src/App.css | 573 +----------------------- frontend/src/components/ui/Alert.tsx | 39 ++ frontend/src/components/ui/Button.tsx | 63 +++ frontend/src/components/ui/Dropdown.tsx | 153 +++++++ frontend/src/components/ui/Input.tsx | 50 +++ frontend/src/components/ui/Modal.tsx | 79 ++++ frontend/src/components/ui/Select.tsx | 62 +++ frontend/src/components/ui/index.ts | 6 + frontend/src/index.css | 26 +- 9 files changed, 478 insertions(+), 573 deletions(-) create mode 100644 frontend/src/components/ui/Alert.tsx create mode 100644 frontend/src/components/ui/Button.tsx create mode 100644 frontend/src/components/ui/Dropdown.tsx create mode 100644 frontend/src/components/ui/Input.tsx create mode 100644 frontend/src/components/ui/Modal.tsx create mode 100644 frontend/src/components/ui/Select.tsx create mode 100644 frontend/src/components/ui/index.ts diff --git a/frontend/src/App.css b/frontend/src/App.css index 9a1ed0a..5556f13 100644 --- a/frontend/src/App.css +++ b/frontend/src/App.css @@ -1,572 +1 @@ -.page-shell { - width: 100%; - margin: 0 auto; - background: #edeef0; - min-height: 100vh; -} - -.top-nav { - background: #4e7f77; - display: flex; - justify-content: space-between; - align-items: center; - padding: 14px clamp(16px, 4vw, 56px); -} - -.top-nav__left, -.top-nav__right { - display: flex; - align-items: center; -} - -.top-nav__left { - gap: 26px; -} - -.brand { - text-decoration: none; - color: #fff; - background: #6b7b92; - border: 2px solid #d7e1e6; - width: 78px; - height: 56px; - display: grid; - place-items: center; - font-size: 12px; - letter-spacing: 0.35px; -} - -.main-links { - display: flex; - gap: 32px; -} - -.main-links a { - color: #ffffff; - text-decoration: none; - font-weight: 600; - font-size: 21px; -} - -.top-nav__right { - gap: 12px; -} - -.top-nav__right select { - width: 146px; - height: 34px; - border-radius: 8px; - border: none; - padding: 0 12px; - background: #f3f4f6; - font-size: 14px; - color: #253242; -} - -.icon-btn { - width: 28px; - height: 28px; - border: none; - background: transparent; - color: #f6f8fa; - display: grid; - place-items: center; - cursor: pointer; - padding: 0; -} - -.icon-btn svg { - width: 21px; - height: 21px; - fill: currentColor; -} - -.content { - width: min(1180px, calc(100% - 56px)); - margin: 0 auto; - padding: 30px 0 56px; -} - -.hero-row { - border-bottom: 1px solid #c7ccd2; - padding-bottom: 20px; - margin-bottom: 28px; - display: flex; - justify-content: space-between; - align-items: start; - gap: 16px; -} - -.hero-row h1 { - margin: 0 0 6px; - color: #101827; - font-size: clamp(2rem, 2.3vw, 2.75rem); - font-weight: 700; - letter-spacing: -0.2px; - line-height: 1.15; -} - -.hero-row p { - margin: 0; - color: #2f4057; - font-size: clamp(1rem, 1.1vw, 1.35rem); - line-height: 1.35; -} - -.help-btn { - border: none; - border-radius: 8px; - background: #4e7f77; - color: #fff; - font-weight: 700; - font-size: 17px; - width: 78px; - height: 42px; - cursor: pointer; -} - -/* Customize the label (the container) */ -.container { - display: block; - position: relative; - padding-left: 35px; - margin-bottom: 12px; - cursor: pointer; - font-size: 22px; - -webkit-user-select: none; - -moz-user-select: none; - -ms-user-select: none; - user-select: none; -} - -/* Hide the browser's default checkbox */ -.container input { - position: absolute; - opacity: 0; - cursor: pointer; - height: 0; - width: 0; -} - -/* Create a custom checkbox */ -.checkmark { - position: absolute; - top: 0; - left: 0; - height: 25px; - width: 25px; - background-color: #eee; -} - -/* On mouse-over, add a grey background color */ -.container:hover input ~ .checkmark { - background-color: #ccc; -} - -/* When the checkbox is checked, add a blue background */ -.container input:checked ~ .checkmark { - background-color: #2196F3; -} - -/* Create the checkmark/indicator (hidden when not checked) */ -.checkmark:after { - content: ""; - position: absolute; - display: none; -} - -/* Show the checkmark when checked */ -.container input:checked ~ .checkmark:after { - display: block; -} - -/* Style the checkmark/indicator */ -.container .checkmark:after { - left: 9px; - top: 5px; - width: 5px; - height: 10px; - border: solid white; - border-width: 0 3px 3px 0; - -webkit-transform: rotate(45deg); - -ms-transform: rotate(45deg); - transform: rotate(45deg); -} - -.populate-label { - display: flex; - align-items: center; - font-size: 1.5rem; - font-weight: 700; - color: #0f1826; - position: absolute; - top: 265px; - left: 32px; -} - -.populate-loading-label { - display: flex; - align-items: center; - justify-content: center; - text-align: center; - font-size: 1.2rem; - font-weight: 500; - color: #0f1826; - position: absolute; - top: 450px; - left: 10px; - width: 300px; - height: 5vh; - box-sizing: border-box; -} - -.populateDrugbank-checkbox { - display: flex; - align-items: center; - gap: 12px; - cursor: pointer; - user-select: none; - position: absolute; - top: 320px; - left: 90px; - font-size: 1.2rem; -} - -.populateSnomed-checkbox { - display: flex; - align-items: center; - gap: 12px; - cursor: pointer; - user-select: none; - position: absolute; - top: 345px; - left: 90px; - font-size: 1.2rem; -} - -.populateRxNorm-checkbox { - display: flex; - align-items: center; - gap: 12px; - cursor: pointer; - user-select: none; - position: absolute; - top: 370px; - left: 90px; - font-size: 1.2rem; -} - -.populateICD11-checkbox { - display: flex; - align-items: center; - gap: 12px; - cursor: pointer; - user-select: none; - position: absolute; - top: 395px; - left: 90px; - font-size: 1.2rem; -} - - -.populate-btn { - border: none; - border-radius: 8px; - background: #4e7f77; - color: #fff; - font-weight: 700; - font-size: 17px; - width: 150px; - height: 50px; - cursor: pointer; - position: absolute; - top: 425px; - left: 75px; -} - -.populate-btn:disabled { - cursor: not-allowed; - opacity: 0.6; -} - -.populate-overlay { - position: absolute; - top: 425px; - left: 75px; - width: 150px; - height: 50px; - background-color: rgba(255, 255, 255, 0.85); - display: flex; - align-items: center; - justify-content: center; - gap: 8px; - z-index: 10; - border-radius: 8px; /* Match your button's corners if needed */ - font-size: 17px; - color: #1e293b; - font-weight: 700; -} - -.spinner { - width: 16px; - height: 16px; - border: 2px solid #cbd5e1; - border-top-color: #2563eb; - border-radius: 50%; - animation: spin 0.8s linear infinite; -} - -@keyframes spin { - to { - transform: rotate(360deg); - } -} - -.tool-panel { - border-bottom: 1px solid #c7ccd2; - padding: 4px 0 30px; -} - -.tool-panel + .tool-panel { - margin-top: 14px; - border-bottom: none; - padding-bottom: 0; -} - -.tool-panel h2 { - margin: 0 0 22px; - color: #0f1826; - text-align: center; - font-size: clamp(1.8rem, 2vw, 2.25rem); - font-weight: 700; -} - -.search-surface { - border: 1px solid #d7dbe0; - border-radius: 12px; - background: #f8fafc; - padding: 14px; -} - -.field-stack label { - display: block; - margin-bottom: 7px; - color: #384a60; - font-size: 1.12rem; - font-weight: 600; -} - -.field-stack select, -.search-row input, -.translate-grid input, -.results-select { - width: auto; - height: 44px; - border: 1px solid #d7dbe0; - border-radius: 9px; - background: #f4f5f7; - padding: 0 12px; - color: #202e3d; - font-size: 1.02rem; - box-sizing: border-box; -} - -.search-grid { - display: grid; - grid-template-columns: minmax(200px, 250px) 1fr; - gap: 14px; - align-items: end; -} - -.search-row { - display: grid; - grid-template-columns: 1fr 170px; - gap: 10px; -} - -.search-row button, -.translate-btn { - height: 44px; - border: none; - border-radius: 9px; - background: #8e97a6; - color: #fff; - font-size: 1rem; - font-weight: 700; - cursor: pointer; -} - -.results-block { - margin-top: 18px; -} - -.message { - margin-bottom: 10px; - padding: 8px 10px; - border-radius: 8px; - font-size: 0.95rem; -} - -.message--error { - color: #9c2c2c; - background: #fdecec; - border: 1px solid #f6c8c8; -} - -.message--info { - color: #2f4d69; - background: #eaf2fb; - border: 1px solid #cfe1f4; -} - -.message--muted { - color: #667085; -} - -.results-block h3 { - margin: 0 0 10px; - text-align: center; - color: #111827; - font-size: clamp(1.45rem, 1.8vw, 2rem); -} - -.results-table-wrap { - width: 100%; - border: 1px solid #dce2e8; - border-radius: 10px; - background: #fff; - overflow-x: auto; -} - -.results-table { - width: 100%; - border-collapse: collapse; - min-width: 680px; -} - -.results-table th, -.results-table td { - padding: 10px 12px; - text-align: left; - border-bottom: 1px solid #e7ecf1; - vertical-align: top; -} - -.results-table th { - background: #eff4f8; - color: #223246; - font-size: 0.95rem; -} - -.results-table td { - color: #2e435a; -} - -.results-table tbody tr:nth-child(even) { - background: #fbfcfe; -} - -.results-table tbody tr.row-selected { - background: #e5f1ef; -} - -.results-table tbody tr:last-child td { - border-bottom: none; -} - -.results-select { - display: flex; - justify-content: space-between; - align-items: center; - border: 1px solid #e2e5e9; - color: #8f9bb0; -} - -.translate-grid { - display: grid; - grid-template-columns: minmax(200px, 250px) 170px 1fr; - gap: 10px; - align-items: end; -} - -.translate-grid input::placeholder, -.search-row input::placeholder { - color: #9ca6b8; -} - -button:focus-visible, -select:focus-visible, -input:focus-visible, -a:focus-visible { - outline: 3px solid #2a5e59; - outline-offset: 2px; -} - -@media (max-width: 1100px) { - .top-nav { - padding: 12px 16px; - } - - .main-links a { - font-size: 17px; - } - - .top-nav__left { - gap: 16px; - } - - .help-btn { - width: 72px; - height: 40px; - font-size: 15px; - } -} - -@media (max-width: 840px) { - .top-nav { - flex-direction: column; - align-items: stretch; - gap: 12px; - } - - .top-nav__right { - justify-content: flex-end; - } - - .hero-row { - flex-direction: column; - gap: 12px; - } - - .search-grid, - .translate-grid, - .search-row { - grid-template-columns: 1fr; - } - - .content { - width: calc(100% - 20px); - padding-top: 18px; - } - - .main-links { - gap: 18px; - } - - .top-nav__right { - gap: 8px; - } - - .hero-row h1 { - font-size: 1.9rem; - } - - .tool-panel h2 { - font-size: 1.6rem; - text-align: left; - } - - .results-block h3 { - text-align: left; - } -} \ No newline at end of file +/* Global application styles if any */ \ No newline at end of file diff --git a/frontend/src/components/ui/Alert.tsx b/frontend/src/components/ui/Alert.tsx new file mode 100644 index 0000000..cd1622c --- /dev/null +++ b/frontend/src/components/ui/Alert.tsx @@ -0,0 +1,39 @@ +import React from 'react' + +export interface AlertProps { + type?: 'error' | 'success' | 'info' | 'warning' + message?: string + children?: React.ReactNode + className?: string +} + +export const Alert: React.FC = ({ + type = 'error', + message, + children, + className = '', +}) => { + const typeStyles = { + error: 'bg-rose-50 border-rose-200 text-rose-700', + success: 'bg-emerald-50 border-emerald-200 text-emerald-800', + info: 'bg-sky-50 border-sky-200 text-sky-800', + warning: 'bg-amber-50 border-amber-200 text-amber-800', + } + + const icons = { + error: '⚠️', + success: '✅', + info: 'ℹ️', + warning: '⚠️', + } + + return ( +
    + {icons[type]} +
    {message || children}
    +
    + ) +} diff --git a/frontend/src/components/ui/Button.tsx b/frontend/src/components/ui/Button.tsx new file mode 100644 index 0000000..7bd98d8 --- /dev/null +++ b/frontend/src/components/ui/Button.tsx @@ -0,0 +1,63 @@ +import React from 'react' + +export interface ButtonProps extends React.ButtonHTMLAttributes { + variant?: 'primary' | 'nav' | 'secondary' | 'outline' | 'ghost' + size?: 'sm' | 'md' | 'lg' + isLoading?: boolean + icon?: React.ReactNode + fullWidth?: boolean +} + +export const Button: React.FC = ({ + children, + variant = 'primary', + size = 'md', + isLoading = false, + icon, + fullWidth = false, + className = '', + disabled, + ...props +}) => { + const baseStyles = + 'inline-flex items-center justify-center font-semibold transition-all duration-150 focus:outline-none focus:ring-2 focus:ring-emerald-300 disabled:cursor-not-allowed cursor-pointer' + + const variantStyles = { + primary: + 'bg-[#4e7f77] hover:bg-[#3d6861] active:scale-[0.98] text-white shadow-sm disabled:bg-slate-300 disabled:text-slate-500', + nav: + 'bg-[#3d6861] hover:bg-[#325650] active:scale-[0.98] text-white shadow-sm border border-[#5d8d85] disabled:opacity-60', + secondary: + 'bg-slate-100 hover:bg-slate-200 text-slate-800 disabled:bg-slate-50 disabled:text-slate-400', + outline: + 'border border-slate-300 hover:bg-slate-50 text-slate-700 disabled:opacity-50', + ghost: + 'hover:bg-slate-100 text-slate-600 hover:text-slate-900 disabled:opacity-50', + } + + const sizeStyles = { + sm: 'text-xs px-2.5 py-1.5 rounded-md gap-1.5', + md: 'text-sm px-3.5 py-1.5 rounded-lg gap-2', + lg: 'text-base px-5 py-2.5 rounded-xl gap-2.5', + } + + return ( + + ) +} diff --git a/frontend/src/components/ui/Dropdown.tsx b/frontend/src/components/ui/Dropdown.tsx new file mode 100644 index 0000000..5dd3941 --- /dev/null +++ b/frontend/src/components/ui/Dropdown.tsx @@ -0,0 +1,153 @@ +import React, { useState, useRef, useEffect, useLayoutEffect } from 'react' + +export interface DropdownProps { + trigger: (isOpen: boolean) => React.ReactNode + children: React.ReactNode + align?: 'left' | 'right' + widthClass?: string + className?: string +} + +export const Dropdown: React.FC = ({ + trigger, + children, + align = 'right', + widthClass = 'w-72 sm:w-80', + className = '', +}) => { + const [isOpen, setIsOpen] = useState(false) + const [openUpward, setOpenUpward] = useState(false) + const [horizontalAlign, setHorizontalAlign] = useState<'left' | 'right' | 'center'>(align) + const [maxHeightStyle, setMaxHeightStyle] = useState('calc(100vh - 120px)') + + const dropdownRef = useRef(null) + const panelRef = useRef(null) + + // Smart viewport auto-positioning + const calculatePosition = () => { + if (!dropdownRef.current) return + + const rect = dropdownRef.current.getBoundingClientRect() + const viewportHeight = window.innerHeight + const viewportWidth = window.innerWidth + + // 1. Vertical placement: Check if space below is less than 280px and space above is larger + const spaceBelow = viewportHeight - rect.bottom + const spaceAbove = rect.top + + const shouldOpenUp = spaceBelow < 300 && spaceAbove > spaceBelow + setOpenUpward(shouldOpenUp) + + // Dynamic max-height based on available space + const availableHeight = shouldOpenUp ? spaceAbove - 24 : spaceBelow - 24 + setMaxHeightStyle(`${Math.max(160, availableHeight)}px`) + + // 2. Horizontal placement: Adjust if popping outside screen + if (viewportWidth < 640) { + setHorizontalAlign(rect.left < 40 ? 'left' : rect.right > viewportWidth - 40 ? 'right' : 'center') + } else { + if (align === 'right') { + if (rect.right < 300) { + setHorizontalAlign('left') + } else { + setHorizontalAlign('right') + } + } else { + if (viewportWidth - rect.left < 300) { + setHorizontalAlign('right') + } else { + setHorizontalAlign('left') + } + } + } + } + + useLayoutEffect(() => { + if (isOpen) { + calculatePosition() + } + }, [isOpen]) + + // Recalculate on window resize or scroll + useEffect(() => { + if (!isOpen) return + + const handleResizeOrScroll = () => { + calculatePosition() + } + + window.addEventListener('resize', handleResizeOrScroll) + window.addEventListener('scroll', handleResizeOrScroll, true) + + return () => { + window.removeEventListener('resize', handleResizeOrScroll) + window.removeEventListener('scroll', handleResizeOrScroll, true) + } + }, [isOpen]) + + // Close when clicking outside + useEffect(() => { + const handleOutsideClick = (event: MouseEvent) => { + if (dropdownRef.current && !dropdownRef.current.contains(event.target as Node)) { + setIsOpen(false) + } + } + if (isOpen) { + document.addEventListener('mousedown', handleOutsideClick) + } + return () => { + document.removeEventListener('mousedown', handleOutsideClick) + } + }, [isOpen]) + + // Close on Escape key + useEffect(() => { + const handleKeyDown = (event: KeyboardEvent) => { + if (event.key === 'Escape' && isOpen) { + setIsOpen(false) + } + } + document.addEventListener('keydown', handleKeyDown) + return () => { + document.removeEventListener('keydown', handleKeyDown) + } + }, [isOpen]) + + // Compute Tailwind classes for placement + const verticalClass = openUpward ? 'bottom-full mb-2' : 'top-full mt-2' + + const horizontalClass = + horizontalAlign === 'center' + ? 'left-1/2 -translate-x-1/2' + : horizontalAlign === 'left' + ? 'left-0' + : 'right-0' + + const originClass = openUpward + ? horizontalAlign === 'right' + ? 'origin-bottom-right' + : horizontalAlign === 'left' + ? 'origin-bottom-left' + : 'origin-bottom' + : horizontalAlign === 'right' + ? 'origin-top-right' + : horizontalAlign === 'left' + ? 'origin-top-left' + : 'origin-top' + + return ( +
    +
    setIsOpen(!isOpen)}>{trigger(isOpen)}
    + + {isOpen && ( +
    + {children} +
    + )} +
    + ) +} diff --git a/frontend/src/components/ui/Input.tsx b/frontend/src/components/ui/Input.tsx new file mode 100644 index 0000000..d130616 --- /dev/null +++ b/frontend/src/components/ui/Input.tsx @@ -0,0 +1,50 @@ +import React from 'react' + +export interface InputProps extends React.InputHTMLAttributes { + label?: string + icon?: React.ReactNode + error?: string +} + +export const Input: React.FC = ({ + label, + icon, + error, + className = '', + id, + disabled, + ...props +}) => { + return ( +
    + {label && ( + + )} +
    + {icon && ( +
    + {icon} +
    + )} + +
    + {error && {error}} +
    + ) +} diff --git a/frontend/src/components/ui/Modal.tsx b/frontend/src/components/ui/Modal.tsx new file mode 100644 index 0000000..00542e6 --- /dev/null +++ b/frontend/src/components/ui/Modal.tsx @@ -0,0 +1,79 @@ +import React, { useEffect } from 'react' + +export interface ModalProps { + isOpen: boolean + onClose: () => void + title: string + subtitle?: string + icon?: React.ReactNode + children: React.ReactNode + maxWidthClass?: string +} + +export const Modal: React.FC = ({ + isOpen, + onClose, + title, + subtitle, + icon, + children, + maxWidthClass = 'max-w-lg', +}) => { + // Close on Escape key + useEffect(() => { + const handleKeyDown = (event: KeyboardEvent) => { + if (event.key === 'Escape' && isOpen) { + onClose() + } + } + if (isOpen) { + document.addEventListener('keydown', handleKeyDown) + } + return () => { + document.removeEventListener('keydown', handleKeyDown) + } + }, [isOpen, onClose]) + + if (!isOpen) return null + + return ( +
    +
    e.stopPropagation()} + > + {/* Header */} +
    +
    + {icon && ( + + {icon} + + )} +
    +

    {title}

    + {subtitle &&

    {subtitle}

    } +
    +
    + +
    + + {/* Content */} +
    {children}
    +
    +
    + ) +} diff --git a/frontend/src/components/ui/Select.tsx b/frontend/src/components/ui/Select.tsx new file mode 100644 index 0000000..d4e0a12 --- /dev/null +++ b/frontend/src/components/ui/Select.tsx @@ -0,0 +1,62 @@ +import React from 'react' + +export interface SelectOption { + value: string + label: string +} + +export interface SelectProps extends React.SelectHTMLAttributes { + label?: string + options?: SelectOption[] + error?: string +} + +export const Select: React.FC = ({ + label, + options, + children, + className = '', + id, + disabled, + error, + ...props +}) => { + return ( +
    + {label && ( + + )} +
    + +
    + + + +
    +
    + {error && {error}} +
    + ) +} diff --git a/frontend/src/components/ui/index.ts b/frontend/src/components/ui/index.ts new file mode 100644 index 0000000..6816ada --- /dev/null +++ b/frontend/src/components/ui/index.ts @@ -0,0 +1,6 @@ +export * from './Button' +export * from './Dropdown' +export * from './Modal' +export * from './Select' +export * from './Input' +export * from './Alert' diff --git a/frontend/src/index.css b/frontend/src/index.css index af968bf..2420e5f 100644 --- a/frontend/src/index.css +++ b/frontend/src/index.css @@ -1,9 +1,14 @@ -@import url('https://fonts.googleapis.com/css2?family=Source+Sans+3:wght@400;600;700&display=swap'); +@import url('https://fonts.googleapis.com/css2?family=Source+Sans+3:wght@400;500;600;700;800;900&display=swap'); +@import "tailwindcss"; * { box-sizing: border-box; } +html { + scrollbar-gutter: stable; +} + html, body, #root { @@ -14,4 +19,23 @@ body, body { background: #d9dde2; font-family: 'Source Sans 3', 'Trebuchet MS', sans-serif; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} + +@keyframes slideDownFade { + from { + opacity: 0; + transform: translateY(-16px); + } + to { + opacity: 1; + transform: translateY(0); + } } + +.animate-drawer-in { + animation: slideDownFade 0.3s cubic-bezier(0.16, 1, 0.3, 1) forwards; +} + + From 7cdf25248edf513cac01668bd7fbac014e7e8df5 Mon Sep 17 00:00:00 2001 From: Sebas Taboada Date: Tue, 15 Sep 2026 21:03:47 -0300 Subject: [PATCH 20/23] feat(frontend): refactor domain components and responsive navigation --- frontend/src/App.tsx | 708 +++--------------- .../components/import/ImportLanguageModal.tsx | 232 ++++++ .../components/language/LanguageSelector.tsx | 78 ++ frontend/src/components/layout/Header.tsx | 242 ++++++ .../components/populate/PopulateDropdown.tsx | 188 +++++ .../src/components/results/ResultsTable.tsx | 153 ++++ frontend/src/components/search/SearchBar.tsx | 91 +++ .../translation/TranslationPanel.tsx | 143 ++++ frontend/src/services/api.ts | 82 ++ frontend/src/types/codex.ts | 83 ++ 10 files changed, 1404 insertions(+), 596 deletions(-) create mode 100644 frontend/src/components/import/ImportLanguageModal.tsx create mode 100644 frontend/src/components/language/LanguageSelector.tsx create mode 100644 frontend/src/components/layout/Header.tsx create mode 100644 frontend/src/components/populate/PopulateDropdown.tsx create mode 100644 frontend/src/components/results/ResultsTable.tsx create mode 100644 frontend/src/components/search/SearchBar.tsx create mode 100644 frontend/src/components/translation/TranslationPanel.tsx create mode 100644 frontend/src/services/api.ts create mode 100644 frontend/src/types/codex.ts diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx index 3df0f4d..4e63a8c 100644 --- a/frontend/src/App.tsx +++ b/frontend/src/App.tsx @@ -1,81 +1,12 @@ -import './App.css' import { useTranslation } from 'react-i18next' -import { useEffect, useState, type KeyboardEvent } from 'react' - -interface CountryOption { - code: string; - label: string; -} - -// Map language codes to available countries -const LANGUAGE_COUNTRY_MAP: Record = { - es: [ - { code: 'MX', label: 'Mexico' }, - { code: 'ES', label: 'Spain' }, - ], - en: [ - { code: 'US', label: 'United States' }, - { code: 'GB', label: 'United Kingdom' }, - { code: 'CA', label: 'Canada' }, - ], - fr: [ - { code: 'FR', label: 'France' }, - { code: 'CA', label: 'Canada' }, - { code: 'BE', label: 'Belgium' }, - ], - ru: [ - { code: 'RU', label: 'Russia' }, - ], - uk: [ - { code: 'UA', label: 'Ukraine' }, - { code: 'PL', label: 'Poland' }, - ], -}; - -interface LanguagesResponse { - languages: string[] -} - -interface SearchResultRow { - source_id: string | null - source_name: string | null - name: string - brand: string | null - type: string - country: string - language: string - uploaded_at: string | null -} - -interface SearchResponse { - source_id: string - source_name: string - name: string - brand: string - type: string - country: string - language: string - uploaded_at: string -} - -interface TranslateResultRow { - source_id: string | null - source_name: string | null - translation: string - brand: string | null - type: string - country: string | null - language: string - uploaded_at: string | null -} - -interface TranslateResponse { - found: boolean - results: TranslateResultRow[] -} - -const API_BASE_URL = 'http://localhost:8000' -const FALLBACK_LANGUAGES = ['en', 'es', 'fr'] +import { useEffect, useState } from 'react' +import { Header } from './components/layout/Header' +import { SearchBar } from './components/search/SearchBar' +import { ResultsTable } from './components/results/ResultsTable' +import { TranslationPanel } from './components/translation/TranslationPanel' +import type { SearchResultRow, TranslateResultRow, LanguageOption } from './types/codex' +import { LANGUAGE_COUNTRY_MAP, FALLBACK_LANGUAGES } from './types/codex' +import { getLanguages, searchDrug, translateDrug } from './services/api' function App() { const { t, i18n } = useTranslation() @@ -85,91 +16,63 @@ function App() { const [availableLanguages, setAvailableLanguages] = useState(FALLBACK_LANGUAGES) const [searchLanguage, setSearchLanguage] = useState('all') const [targetLanguage, setTargetLanguage] = useState('es') - const [targetCountry, setTargetCountry] = useState("MX") + const [targetCountry, setTargetCountry] = useState('MX') const [translatedName, setTranslatedName] = useState('') const [translatedBrand, setTranslatedBrand] = useState('') const [translateError, setTranslateError] = useState('') const [searchError, setSearchError] = useState('') const [isLoading, setIsLoading] = useState(false) const [isTranslating, setIsTranslating] = useState(false) - const [importError, setImportError] = useState('') - const [isImporting, setIsImporting] = useState(false) - const [importLanguage, setImportLanguage] = useState(null) - const [importMessage, setImportMessage] = useState('') const [hasBrand, setHasBrand] = useState(false) - const [progress, setProgress] = useState(''); const getLanguageLabel = (code: string) => { const raw = code.trim() const normalized = raw.toLowerCase() - // Backend may return either ISO codes (en) or full names (English). - if (normalized.length > 3) { - return raw - } - - try { - const displayNames = new Intl.DisplayNames([i18n.language], { type: 'language' }) - return displayNames.of(normalized) ?? normalized.toUpperCase() - } catch { - return normalized.toUpperCase() + let label = raw + if (normalized.length <= 3) { + try { + const displayNames = new Intl.DisplayNames([i18n.language], { type: 'language' }) + label = displayNames.of(normalized) ?? normalized.toUpperCase() + } catch { + label = normalized.toUpperCase() + } } + return label.charAt(0).toUpperCase() + label.slice(1) } - const availableCountries = LANGUAGE_COUNTRY_MAP[targetLanguage] ?? []; + const availableCountries = LANGUAGE_COUNTRY_MAP[targetLanguage] ?? [] const getFirstCountryForLanguage = (langCode: string): string => { - const available = LANGUAGE_COUNTRY_MAP[langCode] ?? []; - return available.length > 0 ? available[0].code : ''; - }; - - const handleLanguageChange = (event: React.ChangeEvent) => { - const newLang = event.target.value; - const newCountry = getFirstCountryForLanguage(newLang); + const available = LANGUAGE_COUNTRY_MAP[langCode] ?? [] + return available.length > 0 ? available[0].code : '' + } - // Update React state - setTargetLanguage(newLang); - setTargetCountry(newCountry); + const handleLanguageChange = (newLang: string) => { + const newCountry = getFirstCountryForLanguage(newLang) + setTargetLanguage(newLang) + setTargetCountry(newCountry) setTranslatedName('') setTranslatedBrand('') - }; - - const handleImportLanguageChange = (event: React.ChangeEvent) => { - if (event.target.files && event.target.files.length > 0) { - setImportLanguage(event.target.files[0]) - } - }; + setTranslateError('') + } const loadLanguages = async (isActive: boolean) => { - try { - const response = await fetch(`${API_BASE_URL}/languages`) - if (!response.ok) { - throw new Error('Failed to load languages') - } - - const data = (await response.json()) as LanguagesResponse - const nextLanguages = Array.isArray(data.languages) && data.languages.length > 0 ? data.languages : FALLBACK_LANGUAGES - if (!isActive) { - return - } - - setAvailableLanguages(nextLanguages) - setTargetLanguage((current) => (nextLanguages.includes(current) ? current : nextLanguages[0])) - } catch { - if (!isActive) { - return - } - - setAvailableLanguages(FALLBACK_LANGUAGES) - setTargetLanguage((current) => (FALLBACK_LANGUAGES.includes(current) ? current : FALLBACK_LANGUAGES[0])) - } + try { + const nextLanguages = await getLanguages() + if (!isActive) return + setAvailableLanguages(nextLanguages) + setTargetLanguage((current) => (nextLanguages.includes(current) ? current : nextLanguages[0])) + } catch { + if (!isActive) return + setAvailableLanguages(FALLBACK_LANGUAGES) + setTargetLanguage((current) => (FALLBACK_LANGUAGES.includes(current) ? current : FALLBACK_LANGUAGES[0])) } + } useEffect(() => { let isActive = true - loadLanguages(isActive) - return () => { isActive = false } @@ -180,10 +83,7 @@ function App() { .map((row) => row.translation) .filter((name): name is string => Boolean(name && name.trim())) - if (names.length === 0) { - return '-' - } - + if (names.length === 0) return '-' return Array.from(new Set(names)).join(', ') } @@ -192,10 +92,7 @@ function App() { .map((row) => row.brand) .filter((brand): brand is string => Boolean(brand && brand.trim())) - if (brands.length === 0) { - return '-' - } - + if (brands.length === 0) return '-' return Array.from(new Set(brands)).join(', ') } @@ -214,33 +111,13 @@ function App() { setTranslatedBrand('') try { - const response = await fetch(`${API_BASE_URL}/search?term=${encodeURIComponent(searchQuery.toLowerCase())}`, { - method: 'POST', - headers: { - 'Content-Type': 'application/json', - }, - body: JSON.stringify({ - query: searchQuery, - limit: 20, - }), - }) - - if (!response.ok) { - const errorBody = await response.json().catch(() => null) - throw new Error(errorBody?.detail ?? 'Failed to search') - } - - const data = (await response.json()) as SearchResponse | null + const data = await searchDrug(searchQuery) if (!data || !data.name) { setSearchResults([]) setSearchError('No results found') } else { - if (data.brand) { - setHasBrand(true) - } else { - setHasBrand(false) - } + setHasBrand(Boolean(data.brand)) setSearchResults([data]) setSearchError('') } @@ -252,25 +129,16 @@ function App() { } } - const handleKeyPress = (e: KeyboardEvent) => { - if (e.key === 'Enter') { - void handleSearch() - } - } - - const handleTranslateSelected = async ( - lang = targetLanguage, - country = targetCountry - ) => { + const handleTranslateSelected = async () => { if (!selectedResult) { setTranslateError('Select a search result first') return } - const validCountries = (LANGUAGE_COUNTRY_MAP[lang] ?? []).map((c) => c.code); - const finalCountry = validCountries.includes(country) - ? country - : getFirstCountryForLanguage(lang); + const validCountries = (LANGUAGE_COUNTRY_MAP[targetLanguage] ?? []).map((c) => c.code) + const finalCountry = validCountries.includes(targetCountry) + ? targetCountry + : getFirstCountryForLanguage(targetLanguage) setIsTranslating(true) setTranslateError('') @@ -278,24 +146,7 @@ function App() { setTranslatedBrand('') try { - const response = await fetch(`${API_BASE_URL}/translate`, { - method: 'POST', - headers: { - 'Content-Type': 'application/json', - }, - body: JSON.stringify({ - term: selectedResult.name, - lang: lang, - country: finalCountry - }), - }) - - if (!response.ok) { - const errorBody = await response.json().catch(() => null) - throw new Error(errorBody?.detail ?? 'Translation request failed') - } - - const payload = (await response.json()) as TranslateResponse + const payload = await translateDrug(selectedResult.name, targetLanguage, finalCountry) const results = payload.results ?? [] const name = results.length > 0 ? extractTranslatedName(results) : '-' const brand = results.length > 0 ? extractTranslatedBrand(results) : '-' @@ -311,413 +162,78 @@ function App() { } } - const handleImportLanguageLocal = async () => { - setImportMessage('') - setImportError('') - if (!importLanguage) { - setImportError('Please select a language file!') - return - } - setIsImporting(true) - const formData = new FormData() - formData.append("file", importLanguage) - - try { - const response = await fetch(`${API_BASE_URL}/packs/load`, { - method: 'POST', - body: formData, - }) - - if (!response.ok) { - throw new Error('Failed to import language') - } - - const data = await response.json(); - - loadLanguages(true) - setImportError('') - setImportMessage(`Success! ${data.message}`); - } catch (error) { - setImportError(`Error: ${(error as Error).message}`); - } finally { - setIsImporting(false) - } - } - - const languages = availableLanguages.map((code) => ({ code, label: getLanguageLabel(code) })) - - const [isDrugbankSelected, setIsDrugbankSelected] = useState(false); - const [isSnomedSelected, setIsSnomedSelected] = useState(false); - const [isRxNormSelected, setIsRxNormSelected] = useState(false); - const [isICD11Selected, setIsICD11Selected] = useState(false); - const [isPopulationLoading, setIsPopulationLoading] = useState(false); - - const handlePopulateClick = async () => { - let sources: string[] = [] - if (isDrugbankSelected) { - sources.push("drugbank") - } - if (isSnomedSelected) { - sources.push("snomed") - } - if (isRxNormSelected) { - sources.push("rxnorm") - } - if (isICD11Selected) { - sources.push("icd11") - } - setIsPopulationLoading(true); - setProgress('Starting population...'); - try { - const response = await fetch('http://localhost:8000/api/populate-sources', { - method: 'POST', - headers: { 'Content-Type': 'application/json' }, - body: JSON.stringify({ selectedSources: sources }), - }); - - if (!response.body) return; - - const reader = response.body.getReader(); - const decoder = new TextDecoder(); - let buffer = ''; - - while (true) { - const { done, value } = await reader.read(); - if (done) break; - - buffer += decoder.decode(value, { stream: true }); - const lines = buffer.split('\n'); - - // Keep the incomplete last line in the buffer - buffer = lines.pop() || ''; - - for (const line of lines) { - const trimmed = line.trim(); - if (!trimmed) continue; - - try { - const cleanLine = trimmed.startsWith('data:') ? trimmed.replace(/^data:\s*/, '') : trimmed; - const parsed = JSON.parse(cleanLine); - - if (parsed.progress) { - setProgress(parsed.progress); - } - } catch (err) { - console.error('Error parsing JSON chunk:', err); - } - } - } - setProgress('Successfully populated Neo4j!'); - } catch (error) { - console.error('Error during streaming:', error); - setProgress('Error processing request.'); - } finally { - setIsPopulationLoading(false); - } - }; + const languages: LanguageOption[] = availableLanguages.map((code) => ({ + code, + label: getLanguageLabel(code), + })) return ( -     + ) +} diff --git a/frontend/src/components/translation/TranslationPanel.tsx b/frontend/src/components/translation/TranslationPanel.tsx new file mode 100644 index 0000000..211631c --- /dev/null +++ b/frontend/src/components/translation/TranslationPanel.tsx @@ -0,0 +1,143 @@ +import React from 'react' +import { Button, Select, Alert } from '../ui' +import type { SearchResultRow, LanguageOption, CountryOption } from '../../types/codex' + +interface TranslationPanelProps { + selectedResult: SearchResultRow + targetLanguage: string + targetCountry: string + onTargetLanguageChange: (lang: string) => void + onTargetCountryChange: (country: string) => void + onTranslate: () => void + isTranslating: boolean + languages: LanguageOption[] + availableCountries: CountryOption[] + translatedName: string + translatedBrand: string + translateError?: string +} + +export const TranslationPanel: React.FC = ({ + selectedResult, + targetLanguage, + targetCountry, + onTargetLanguageChange, + onTargetCountryChange, + onTranslate, + isTranslating, + languages, + availableCountries, + translatedName, + translatedBrand, + translateError, +}) => { + const languageOptions = languages.map((lang) => ({ + value: lang.code, + label: `${lang.label} (${lang.code.toUpperCase()})`, + })) + + const countryOptions = + availableCountries.length > 0 + ? availableCountries.map((c) => ({ + value: c.code, + label: `${c.label} (${c.code.toUpperCase()})`, + })) + : [{ value: '', label: 'No countries available' }] + + return ( +
    +
    + 🌐 +
    +

    + Translate & Cross-Reference Drug +

    +

    + Selected drug: {selectedResult.name} ({selectedResult.language.toUpperCase()}) +

    +
    +
    + + {/* Target Language & Country selectors */} +
    + {/* Target Language */} +
    + onTargetCountryChange(e.target.value)} + /> +
    + + {/* Translate Action */} +
    + +
    +
    + + {/* Error / Info State */} + {translateError && } + + {/* Translation Result Card */} + {(translatedName || isTranslating) && ( +
    +
    + Cross-Referenced Match +
    + +
    +
    +
    + Original ({selectedResult.language.toUpperCase()}) +
    +
    + {selectedResult.name} +
    +
    + +
    +
    + Translation ({targetLanguage.toUpperCase()}) +
    +
    + {translatedName || (isTranslating ? '...' : '-')} +
    +
    + +
    +
    + Brand in {targetCountry.toUpperCase()} +
    +
    + {translatedBrand || (isTranslating ? '...' : '-')} +
    +
    +
    +
    + )} +
    + ) +} diff --git a/frontend/src/services/api.ts b/frontend/src/services/api.ts new file mode 100644 index 0000000..c335716 --- /dev/null +++ b/frontend/src/services/api.ts @@ -0,0 +1,82 @@ +import type { + LanguagesResponse, + SearchResponse, + TranslateResponse, +} from '../types/codex' +import { FALLBACK_LANGUAGES } from '../types/codex' + +export const API_BASE_URL = 'http://localhost:8000' + +/** + * Fetches available language codes that have data in Neo4j. + */ +export async function getLanguages(): Promise { + try { + const response = await fetch(`${API_BASE_URL}/languages`) + if (!response.ok) { + throw new Error('Failed to load languages') + } + const data = (await response.json()) as LanguagesResponse + return Array.isArray(data.languages) && data.languages.length > 0 + ? data.languages + : FALLBACK_LANGUAGES + } catch (error) { + console.warn('Using fallback languages due to error:', error) + return FALLBACK_LANGUAGES + } +} + +/** + * Searches for a drug / medical term in Neo4j. + */ +export async function searchDrug(query: string): Promise { + const response = await fetch( + `${API_BASE_URL}/search?term=${encodeURIComponent(query.toLowerCase())}`, + { + method: 'POST', + headers: { + 'Content-Type': 'application/json', + }, + body: JSON.stringify({ + query: query, + limit: 20, + }), + } + ) + + if (!response.ok) { + const errorBody = await response.json().catch(() => null) + throw new Error(errorBody?.detail ?? 'Failed to search') + } + + const data = (await response.json()) as SearchResponse | null + return data +} + +/** + * Translates a drug term to a destination language and country. + */ +export async function translateDrug( + term: string, + lang: string, + country: string +): Promise { + const response = await fetch(`${API_BASE_URL}/translate`, { + method: 'POST', + headers: { + 'Content-Type': 'application/json', + }, + body: JSON.stringify({ + term, + lang, + country, + }), + }) + + if (!response.ok) { + const errorBody = await response.json().catch(() => null) + throw new Error(errorBody?.detail ?? 'Translation request failed') + } + + return (await response.json()) as TranslateResponse +} diff --git a/frontend/src/types/codex.ts b/frontend/src/types/codex.ts new file mode 100644 index 0000000..eafa220 --- /dev/null +++ b/frontend/src/types/codex.ts @@ -0,0 +1,83 @@ +export interface CountryOption { + code: string + label: string +} + +export interface LanguageOption { + code: string + label: string +} + +export interface LanguagesResponse { + languages: string[] +} + +export interface SearchResultRow { + source_id: string | null + source_name: string | null + name: string + brand: string | null + type: string + country: string + language: string + uploaded_at: string | null +} + +export interface SearchResponse { + source_id: string + source_name: string + name: string + brand: string + type: string + country: string + language: string + uploaded_at: string +} + +export interface TranslateResultRow { + source_id: string | null + source_name: string | null + translation: string + brand: string | null + type: string + country: string | null + language: string + uploaded_at: string | null +} + +export interface TranslateResponse { + found: boolean + results: TranslateResultRow[] +} + +export interface TranslateRequest { + term: string + lang: string + country: string +} + +export const LANGUAGE_COUNTRY_MAP: Record = { + es: [ + { code: 'MX', label: 'Mexico' }, + { code: 'ES', label: 'Spain' }, + ], + en: [ + { code: 'US', label: 'United States' }, + { code: 'GB', label: 'United Kingdom' }, + { code: 'CA', label: 'Canada' }, + ], + fr: [ + { code: 'FR', label: 'France' }, + { code: 'CA', label: 'Canada' }, + { code: 'BE', label: 'Belgium' }, + ], + ru: [ + { code: 'RU', label: 'Russia' }, + ], + uk: [ + { code: 'UA', label: 'Ukraine' }, + { code: 'PL', label: 'Poland' }, + ], +} + +export const FALLBACK_LANGUAGES = ['en', 'es', 'fr'] From e2be5100eef08cb127ab47e2d3f067149a562e7a Mon Sep 17 00:00:00 2001 From: Sebas Taboada Date: Tue, 15 Sep 2026 21:28:23 -0300 Subject: [PATCH 21/23] fix(backend): resolve canonical term in translate response and suppress ide warning --- backend/codex_build/api.py | 4 +++- backend/codex_build/neo4j_sources/source_data.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/backend/codex_build/api.py b/backend/codex_build/api.py index cfb30b3..0b56ef1 100644 --- a/backend/codex_build/api.py +++ b/backend/codex_build/api.py @@ -322,8 +322,10 @@ def translate_term(body: TranslateRequest): ) ] + resolved_canonical = raw.get("canonical") if isinstance(raw, dict) and raw.get("canonical") else body.term + return TranslateResponse( - canonical=body.term, + canonical=resolved_canonical, results=results, ) diff --git a/backend/codex_build/neo4j_sources/source_data.py b/backend/codex_build/neo4j_sources/source_data.py index 7f5d133..8b67560 100644 --- a/backend/codex_build/neo4j_sources/source_data.py +++ b/backend/codex_build/neo4j_sources/source_data.py @@ -16,7 +16,7 @@ from collections import deque import requests -from neo4j import GraphDatabase, WRITE_ACCESS +from neo4j import GraphDatabase, WRITE_ACCESS # type: ignore from dotenv import load_dotenv load_dotenv(os.path.join(os.path.dirname(__file__), ".env")) From 7c58469908e0d4b67737fb4b228077f89c597155 Mon Sep 17 00:00:00 2001 From: Sebas Taboada Date: Tue, 15 Sep 2026 21:28:24 -0300 Subject: [PATCH 22/23] style(frontend): update tailwind v4 class suggestions in components --- frontend/src/components/populate/PopulateDropdown.tsx | 2 +- frontend/src/components/search/SearchBar.tsx | 2 +- frontend/src/components/translation/TranslationPanel.tsx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/src/components/populate/PopulateDropdown.tsx b/frontend/src/components/populate/PopulateDropdown.tsx index 223998b..40c3671 100644 --- a/frontend/src/components/populate/PopulateDropdown.tsx +++ b/frontend/src/components/populate/PopulateDropdown.tsx @@ -166,7 +166,7 @@ export const PopulateDropdown: React.FC = ({ fullWidth = {/* Progress / Status Message */} {progress && ( -
    +
    {progress}
    )} diff --git a/frontend/src/components/search/SearchBar.tsx b/frontend/src/components/search/SearchBar.tsx index 4738e1f..54a4c2e 100644 --- a/frontend/src/components/search/SearchBar.tsx +++ b/frontend/src/components/search/SearchBar.tsx @@ -80,7 +80,7 @@ export const SearchBar: React.FC = ({ size="md" onClick={onSearch} isLoading={isLoading} - className="sm:w-auto w-full px-6 h-[42px] shrink-0" + className="sm:w-auto w-full px-6 h-10.5 shrink-0" > {t('common.search') || 'Search'} diff --git a/frontend/src/components/translation/TranslationPanel.tsx b/frontend/src/components/translation/TranslationPanel.tsx index 211631c..6f7ddfa 100644 --- a/frontend/src/components/translation/TranslationPanel.tsx +++ b/frontend/src/components/translation/TranslationPanel.tsx @@ -91,7 +91,7 @@ export const TranslationPanel: React.FC = ({ size="md" onClick={onTranslate} isLoading={isTranslating} - className="w-full sm:w-auto px-6 h-[42px]" + className="w-full sm:w-auto px-6 h-10.5" > Translate Selected From adf31d3bffa14ed303147f35ab0993e210a04bdf Mon Sep 17 00:00:00 2001 From: Sebas Taboada Date: Thu, 17 Sep 2026 12:32:18 -0300 Subject: [PATCH 23/23] fix(i18n): connect TranslationPanel to useTranslation and add missing locale keys --- .../translation/TranslationPanel.tsx | 23 +++++++++++-------- frontend/src/i18n/locales/de.json | 9 +++++++- frontend/src/i18n/locales/en.json | 9 +++++++- frontend/src/i18n/locales/es.json | 9 +++++++- frontend/src/i18n/locales/fr.json | 9 +++++++- 5 files changed, 45 insertions(+), 14 deletions(-) diff --git a/frontend/src/components/translation/TranslationPanel.tsx b/frontend/src/components/translation/TranslationPanel.tsx index 6f7ddfa..28590d6 100644 --- a/frontend/src/components/translation/TranslationPanel.tsx +++ b/frontend/src/components/translation/TranslationPanel.tsx @@ -1,4 +1,5 @@ import React from 'react' +import { useTranslation } from 'react-i18next' import { Button, Select, Alert } from '../ui' import type { SearchResultRow, LanguageOption, CountryOption } from '../../types/codex' @@ -31,6 +32,8 @@ export const TranslationPanel: React.FC = ({ translatedBrand, translateError, }) => { + const { t } = useTranslation() + const languageOptions = languages.map((lang) => ({ value: lang.code, label: `${lang.label} (${lang.code.toUpperCase()})`, @@ -42,7 +45,7 @@ export const TranslationPanel: React.FC = ({ value: c.code, label: `${c.label} (${c.code.toUpperCase()})`, })) - : [{ value: '', label: 'No countries available' }] + : [{ value: '', label: t('home.noCountries') || 'No countries available' }] return (
    @@ -50,10 +53,10 @@ export const TranslationPanel: React.FC = ({ 🌐

    - Translate & Cross-Reference Drug + {t('home.localizeTitle') || 'Translate & Cross-Reference Drug'}

    - Selected drug: {selectedResult.name} ({selectedResult.language.toUpperCase()}) + {t('home.selectedDrug') || 'Selected drug:'} {selectedResult.name} ({selectedResult.language.toUpperCase()})

    @@ -64,7 +67,7 @@ export const TranslationPanel: React.FC = ({
    = ({ isLoading={isTranslating} className="w-full sm:w-auto px-6 h-10.5" > - Translate Selected + {t('common.translate') || 'Translate Selected'}
    @@ -105,13 +108,13 @@ export const TranslationPanel: React.FC = ({ {(translatedName || isTranslating) && (
    - Cross-Referenced Match + {t('home.crossReferencedMatch') || 'Cross-Referenced Match'}
    - Original ({selectedResult.language.toUpperCase()}) + {t('home.original') || 'Original'} ({selectedResult.language.toUpperCase()})
    {selectedResult.name} @@ -120,7 +123,7 @@ export const TranslationPanel: React.FC = ({
    - Translation ({targetLanguage.toUpperCase()}) + {t('home.translation') || 'Translation'} ({targetLanguage.toUpperCase()})
    {translatedName || (isTranslating ? '...' : '-')} @@ -129,7 +132,7 @@ export const TranslationPanel: React.FC = ({
    - Brand in {targetCountry.toUpperCase()} + {t('home.brandInCountry') || 'Brand in'} {targetCountry.toUpperCase()}
    {translatedBrand || (isTranslating ? '...' : '-')} diff --git a/frontend/src/i18n/locales/de.json b/frontend/src/i18n/locales/de.json index 9fd6c8b..740da7b 100644 --- a/frontend/src/i18n/locales/de.json +++ b/frontend/src/i18n/locales/de.json @@ -22,9 +22,16 @@ "resultsTitle": "Ergebnisse", "sampleMedicine": "Medikament 1", "localizeTitle": "Medikamentennamen übersetzen/lokalisieren...", + "selectedDrug": "Ausgewähltes Medikament:", "targetLanguage": "Zielsprache", "targetPlaceholder": "Zielsprache", + "targetCountry": "Zielland", + "noCountries": "Keine Länder verfügbar", "translationPlaceholder": "Die Übersetzung wird hier angezeigt", - "importTitle": "Sprachdatei importieren" + "importTitle": "Sprachdatei importieren", + "crossReferencedMatch": "Referenzierte Übereinstimmung", + "original": "Original", + "translation": "Übersetzung", + "brandInCountry": "Marke in" } } diff --git a/frontend/src/i18n/locales/en.json b/frontend/src/i18n/locales/en.json index 3856e30..98ba018 100644 --- a/frontend/src/i18n/locales/en.json +++ b/frontend/src/i18n/locales/en.json @@ -22,9 +22,16 @@ "resultsTitle": "Results", "sampleMedicine": "Medicine 1", "localizeTitle": "Translate/Localize drug name...", + "selectedDrug": "Selected drug:", "targetLanguage": "Target Language", "targetPlaceholder": "Target Language", + "targetCountry": "Target Country", + "noCountries": "No countries available", "translationPlaceholder": "Translation will appear here", - "importTitle": "Import Language File" + "importTitle": "Import Language File", + "crossReferencedMatch": "Cross-Referenced Match", + "original": "Original", + "translation": "Translation", + "brandInCountry": "Brand in" } } diff --git a/frontend/src/i18n/locales/es.json b/frontend/src/i18n/locales/es.json index 8efc4ee..66f3c04 100644 --- a/frontend/src/i18n/locales/es.json +++ b/frontend/src/i18n/locales/es.json @@ -22,9 +22,16 @@ "resultsTitle": "Resultados", "sampleMedicine": "Medicina 1", "localizeTitle": "Traducir/Localizar nombre de medicamento...", + "selectedDrug": "Medicamento seleccionado:", "targetLanguage": "Idioma de destino", "targetPlaceholder": "Idioma de destino", + "targetCountry": "País de destino", + "noCountries": "No hay países disponibles", "translationPlaceholder": "La traducción aparecerá aquí", - "importTitle": "Importar archivo de idioma" + "importTitle": "Importar archivo de idioma", + "crossReferencedMatch": "Coincidencia Cruzada", + "original": "Original", + "translation": "Traducción", + "brandInCountry": "Marca en" } } diff --git a/frontend/src/i18n/locales/fr.json b/frontend/src/i18n/locales/fr.json index cdf6b44..c4290bd 100644 --- a/frontend/src/i18n/locales/fr.json +++ b/frontend/src/i18n/locales/fr.json @@ -22,9 +22,16 @@ "resultsTitle": "Résultats", "sampleMedicine": "Médicament 1", "localizeTitle": "Traduire/Localiser le nom du médicament...", + "selectedDrug": "Médicament sélectionné:", "targetLanguage": "Langue cible", "targetPlaceholder": "Langue cible", + "targetCountry": "Pays cible", + "noCountries": "Aucun pays disponible", "translationPlaceholder": "La traduction s'affichera ici", - "importTitle": "Importer un fichier de langue" + "importTitle": "Importer un fichier de langue", + "crossReferencedMatch": "Correspondance Croisée", + "original": "Original", + "translation": "Traduction", + "brandInCountry": "Marque en" } }
    -
    - - -
    - - - - - - - - - -
    -
    - -
    -
    -

    {t('sides.populateLabel')}

    - - -
    - -
    - -
    - -
    - -
    - -
    - -
    - -
    - {isPopulationLoading && ( -
    -
    - {t('sides.populateLoader')} -
    - )} - - -
    - -

    {progress}

    -
    - -
    -
    +
    + {/* Top Navigation */} +
    loadLanguages(true)} /> + + {/* Main Content Area */} +
    + {/* Hero Section */} +
    -

    {t('home.pageTitle')}

    -

    {t('home.pageDescription')}

    +

    + {t('home.pageTitle') || 'Grey Box Pharma-Cross'} +

    +

    + {t('home.pageDescription') || 'Multilingual medical normalization and cross-border drug intelligence powered by RxNorm and Neo4j knowledge graph.'} +

    -
    -
    -

    {t('home.searchTitle')}

    -
    -
    -
    - - -
    -
    - setSearchQuery(e.target.value)} - onKeyDown={handleKeyPress} - /> - -
    -
    - -
    -

    {t('home.resultsTitle')}

    - {searchError &&
    {searchError}
    } - {translateError &&
    {translateError}
    } - {isTranslating &&
    Translating selected result...
    } - {searchResults.length > 0 ? ( -
    - - - - {hasBrand && } - {!hasBrand && } - - {hasBrand && } - - - - {hasBrand && } - {!hasBrand && } - - {hasBrand && } - {!hasBrand && } - - - - {searchResults.map((row, index) => ( - { - setSelectedResult(row) - setTranslatedName('') - setTranslateError('') - setTranslatedBrand('') - }} - style={{ cursor: 'pointer' }} - > - - {hasBrand && } - {hasBrand && } - {!hasBrand && } - - - - ))} - -
    Drug Name for BrandDrug NameBrandTypeLanguage for BrandLanguageCountries for BrandCountries
    {row.name}{row.brand}brand name drug{row.type}{row.language}{row.country ?? '-'}
    -
    - ) : ( - - )} - - {selectedResult && ( -
    -
    -
    - - -
    -
    - - -
    -
    - -
    -
    - -
    - - - - - - - - - - - - - - - -
    Original Drug Name (Languages)Drug Name in {targetLanguage.toUpperCase()}Drug Brand Name in {targetCountry.toUpperCase()}
    {selectedResult.name} ({selectedResult.language}){translatedName || '-'}{translatedBrand || '-'}
    -
    -
    - )} -
    -
    -
    - -
    -
    -

    {t('home.importTitle')}

    -
    - - -
    -
    -
    - {isImporting &&
    Importing language...
    } - {importError &&
    {importError}
    } - {importMessage &&
    {importMessage}
    } -
    -
    + {/* Search & Results Panel */} +
    + + + { + setSelectedResult(result) + setTranslatedName('') + setTranslatedBrand('') + setTranslateError('') + }} + hasBrand={hasBrand} + searchError={searchError} + /> + + {selectedResult && ( + + )}
    -
    ) diff --git a/frontend/src/components/import/ImportLanguageModal.tsx b/frontend/src/components/import/ImportLanguageModal.tsx new file mode 100644 index 0000000..34739b0 --- /dev/null +++ b/frontend/src/components/import/ImportLanguageModal.tsx @@ -0,0 +1,232 @@ +import React, { useState, useRef } from 'react' +import { useTranslation } from 'react-i18next' +import { Modal, Button, Alert } from '../ui' + +const API_BASE_URL = 'http://localhost:8000' + +interface ImportLanguageModalProps { + onImportSuccess?: () => void + fullWidth?: boolean +} + +export const ImportLanguageModal: React.FC = ({ + onImportSuccess, + fullWidth = false, +}) => { + const { t } = useTranslation() + const [isOpen, setIsOpen] = useState(false) + const [selectedFile, setSelectedFile] = useState(null) + const [isImporting, setIsImporting] = useState(false) + const [importMessage, setImportMessage] = useState('') + const [importError, setImportError] = useState('') + const [isDragging, setIsDragging] = useState(false) + + const fileInputRef = useRef(null) + + const validateAndSetFile = async (file: File) => { + setImportError('') + setImportMessage('') + + if (!file.name.toLowerCase().endsWith('.json')) { + setImportError('El archivo debe tener extensión .json.') + setSelectedFile(null) + return + } + + try { + const text = await file.text() + const json = JSON.parse(text) + + if (!json || typeof json !== 'object' || Array.isArray(json)) { + throw new Error('El JSON debe ser un objeto válido.') + } + + if (!json.language || !json.language.code || !Array.isArray(json.terms)) { + throw new Error("El archivo no tiene el formato de Language Pack (debe incluir 'language.code' y la lista 'terms').") + } + + setSelectedFile(file) + setImportError('') + } catch (err) { + setSelectedFile(null) + if (fileInputRef.current) fileInputRef.current.value = '' + setImportError(err instanceof SyntaxError ? 'El archivo está corrupto o no es un JSON válido.' : (err as Error).message) + } + } + + const handleFileChange = (e: React.ChangeEvent) => { + if (e.target.files && e.target.files.length > 0) { + validateAndSetFile(e.target.files[0]) + } + } + + const handleDragOver = (e: React.DragEvent) => { + e.preventDefault() + setIsDragging(true) + } + + const handleDragLeave = (e: React.DragEvent) => { + e.preventDefault() + setIsDragging(false) + } + + const handleDrop = (e: React.DragEvent) => { + e.preventDefault() + setIsDragging(false) + if (e.dataTransfer.files && e.dataTransfer.files.length > 0) { + validateAndSetFile(e.dataTransfer.files[0]) + } + } + + const handleUpload = async (e: React.FormEvent) => { + e.preventDefault() + setImportMessage('') + setImportError('') + + if (!selectedFile) { + setImportError('Por favor selecciona un archivo .json válido primero.') + return + } + + setIsImporting(true) + const formData = new FormData() + formData.append('file', selectedFile) + + try { + const response = await fetch(`${API_BASE_URL}/packs/load`, { + method: 'POST', + body: formData, + }) + + if (!response.ok) { + const errData = await response.json().catch(() => null) + throw new Error(errData?.detail || 'Failed to import language pack') + } + + const data = await response.json() + setImportMessage(data.message || 'Language pack imported successfully!') + onImportSuccess?.() + setTimeout(() => { + resetAndClose() + }, 1500) + } catch (error) { + setImportError((error as Error).message) + } finally { + setIsImporting(false) + } + } + + const resetAndClose = () => { + setIsOpen(false) + setSelectedFile(null) + setImportError('') + setImportMessage('') + if (fileInputRef.current) { + fileInputRef.current.value = '' + } + } + + return ( + <> + {/* Trigger Button */} + + + {/* Modal Dialog */} + +
    + {/* Drag & Drop Area */} +
    fileInputRef.current?.click()} + className={`border-2 border-dashed rounded-xl p-6 text-center cursor-pointer transition-colors ${ + isDragging + ? 'border-emerald-500 bg-emerald-50/50' + : selectedFile + ? 'border-emerald-300 bg-emerald-50/20' + : 'border-slate-300 hover:border-emerald-400 hover:bg-slate-50/60' + }`} + > + + + {selectedFile ? ( +
    + 📄 + {selectedFile.name} + + {(selectedFile.size / 1024).toFixed(1)} KB + + + Click to choose another file + +
    + ) : ( +
    +
    + + + +
    +
    + Click to upload + or drag and drop +
    +

    Supported format: JSON (.json)

    +
    + )} +
    + + {/* Status Messages */} + {importError && } + {importMessage && } + + {/* Action Buttons */} +
    + + +
    + +
    + + ) +} diff --git a/frontend/src/components/language/LanguageSelector.tsx b/frontend/src/components/language/LanguageSelector.tsx new file mode 100644 index 0000000..eb33066 --- /dev/null +++ b/frontend/src/components/language/LanguageSelector.tsx @@ -0,0 +1,78 @@ +import React from 'react' +import { useTranslation } from 'react-i18next' +import { Button, Dropdown } from '../ui' +import type { LanguageOption } from '../../types/codex' + +interface LanguageSelectorProps { + languages: LanguageOption[] + fullWidth?: boolean +} + +export const LanguageSelector: React.FC = ({ + languages, + fullWidth = false, +}) => { + const { i18n } = useTranslation() + + const capitalize = (str: string) => (str ? str.charAt(0).toUpperCase() + str.slice(1) : str) + const currentLangOption = languages.find((l) => l.code === i18n.language) || languages[0] + const currentLangLabel = capitalize(currentLangOption?.label || i18n.language) + + const handleSelectLanguage = (code: string) => { + i18n.changeLanguage(code) + } + + return ( + ( + + )} + > +
    + {languages.map((lang) => ( + + ))} +
    +     + ) +} diff --git a/frontend/src/components/layout/Header.tsx b/frontend/src/components/layout/Header.tsx new file mode 100644 index 0000000..8c37a68 --- /dev/null +++ b/frontend/src/components/layout/Header.tsx @@ -0,0 +1,242 @@ +import React, { useState, useEffect } from 'react' +import { useTranslation } from 'react-i18next' +import { PopulateDropdown } from '../populate/PopulateDropdown' +import { ImportLanguageModal } from '../import/ImportLanguageModal' +import { LanguageSelector } from '../language/LanguageSelector' +import type { LanguageOption } from '../../types/codex' + +interface HeaderProps { + languages: LanguageOption[] + onImportSuccess?: () => void +} + +export const Header: React.FC = ({ languages, onImportSuccess }) => { + const { t } = useTranslation() + const [isMobileMenuOpen, setIsMobileMenuOpen] = useState(false) + + // Prevent background scrolling when mobile menu is open + useEffect(() => { + if (isMobileMenuOpen) { + document.body.style.overflow = 'hidden' + } else { + document.body.style.overflow = '' + } + return () => { + document.body.style.overflow = '' + } + }, [isMobileMenuOpen]) + + // Close on Escape key + useEffect(() => { + const handleKeyDown = (e: KeyboardEvent) => { + if (e.key === 'Escape' && isMobileMenuOpen) { + setIsMobileMenuOpen(false) + } + } + window.addEventListener('keydown', handleKeyDown) + return () => window.removeEventListener('keydown', handleKeyDown) + }, [isMobileMenuOpen]) + + return ( + <> +
    +
    + {/* Left side: Brand and main links */} + + + {/* Desktop Controls (md: and up) */} +
    + + + + +
    + + + + + + + +
    +
    + + {/* Mobile Hamburger / Close Button (md:hidden) */} +
    + +
    +
    +
    + + {/* Fullscreen Mobile Drawer Menu below the static header */} + {isMobileMenuOpen && ( +
    + {/* Navigation Sections */} + + + {/* Actions Section (Bottom-aligned Column) */} +
    + + Database & Settings + +
    +
    + +
    +
    + { + onImportSuccess?.() + setIsMobileMenuOpen(false) + }} + /> +
    +
    + +
    +
    + + {/* Social & Region Footer */} +
    + Connect with us +
    + + + + +
    +
    +
    +
    + )} + + ) +} + + + + diff --git a/frontend/src/components/populate/PopulateDropdown.tsx b/frontend/src/components/populate/PopulateDropdown.tsx new file mode 100644 index 0000000..223998b --- /dev/null +++ b/frontend/src/components/populate/PopulateDropdown.tsx @@ -0,0 +1,188 @@ +import React, { useState } from 'react' +import { useTranslation } from 'react-i18next' +import { Button, Dropdown } from '../ui' + +const API_BASE_URL = 'http://localhost:8000' + +interface SourceOption { + id: string + label: string + description: string +} + +const SOURCES: SourceOption[] = [ + { id: 'drugbank', label: 'DrugBank', description: 'Pharmaceutical & commercial brand database' }, + { id: 'snomed', label: 'SNOMED CT', description: 'Global clinical terminology & diagnoses' }, + { id: 'rxnorm', label: 'RxNorm', description: 'Standardized clinical drugs (US NLM)' }, + { id: 'icd11', label: 'ICD-11', description: 'WHO International Classification of Diseases' }, +] + +interface PopulateDropdownProps { + fullWidth?: boolean +} + +export const PopulateDropdown: React.FC = ({ fullWidth = false }) => { + const { t } = useTranslation() + const [selectedSources, setSelectedSources] = useState>({ + drugbank: false, + snomed: false, + rxnorm: false, + icd11: false, + }) + const [isLoading, setIsLoading] = useState(false) + const [progress, setProgress] = useState('') + + const toggleSource = (id: string) => { + setSelectedSources((prev) => ({ ...prev, [id]: !prev[id] })) + } + + const selectedCount = Object.values(selectedSources).filter(Boolean).length + + const handlePopulateClick = async () => { + const sourcesToPopulate = Object.entries(selectedSources) + .filter(([, isSelected]) => isSelected) + .map(([id]) => id) + + if (sourcesToPopulate.length === 0) return + + setIsLoading(true) + setProgress('Starting population...') + + try { + const response = await fetch(`${API_BASE_URL}/api/populate-sources`, { + method: 'POST', + headers: { 'Content-Type': 'application/json' }, + body: JSON.stringify({ selectedSources: sourcesToPopulate }), + }) + + if (!response.body) return + + const reader = response.body.getReader() + const decoder = new TextDecoder() + let buffer = '' + + while (true) { + const { done, value } = await reader.read() + if (done) break + + buffer += decoder.decode(value, { stream: true }) + const lines = buffer.split('\n') + buffer = lines.pop() || '' + + for (const line of lines) { + const trimmed = line.trim() + if (!trimmed) continue + + try { + const cleanLine = trimmed.startsWith('data:') ? trimmed.replace(/^data:\s*/, '') : trimmed + const parsed = JSON.parse(cleanLine) + if (parsed.progress) { + setProgress(parsed.progress) + } + } catch (err) { + console.error('Error parsing chunk:', err) + } + } + } + setProgress('Successfully populated Neo4j!') + } catch (error) { + console.error('Error during streaming:', error) + setProgress('Error processing request.') + } finally { + setIsLoading(false) + } + } + + return ( + ( + + )} + > +
    +

    + 🧬 {t('sides.populateLabel') || 'Populate local source(s):'} +

    + Neo4j +
    + + {/* Sources Checkboxes */} +
    + {SOURCES.map((source) => ( + + ))} +
    + + {/* Progress / Status Message */} + {progress && ( +
    + {progress} +
    + )} + + {/* Action Button */} + +     + ) +} diff --git a/frontend/src/components/results/ResultsTable.tsx b/frontend/src/components/results/ResultsTable.tsx new file mode 100644 index 0000000..a4ab9b1 --- /dev/null +++ b/frontend/src/components/results/ResultsTable.tsx @@ -0,0 +1,153 @@ +import React from 'react' +import { useTranslation } from 'react-i18next' +import { Alert } from '../ui' +import type { SearchResultRow } from '../../types/codex' + +interface ResultsTableProps { + results: SearchResultRow[] + selectedResult: SearchResultRow | null + onSelectResult: (result: SearchResultRow) => void + hasBrand: boolean + searchError?: string +} + +export const ResultsTable: React.FC = ({ + results, + selectedResult, + onSelectResult, + hasBrand, + searchError, +}) => { + const { t } = useTranslation() + + const isRowSelected = (row: SearchResultRow) => { + if (!selectedResult) return false + return ( + selectedResult.name === row.name && + selectedResult.brand === row.brand && + selectedResult.language === row.language && + selectedResult.country === row.country && + selectedResult.source_id === row.source_id + ) + } + + return ( +
    +
    +

    + {t('home.resultsTitle') || 'Search Results'} +

    + {results.length > 0 && ( + + {results.length} {results.length === 1 ? 'match' : 'matches'} + + )} +
    + + {searchError && } + + {results.length > 0 ? ( + <> + {/* Desktop & Tablet Table View */} +
    +
    + + + + + {hasBrand && } + + + + + + + {results.map((row, index) => { + const selected = isRowSelected(row) + return ( + onSelectResult(row)} + className={`cursor-pointer transition-colors ${ + selected + ? 'bg-emerald-50/80 font-medium text-emerald-950 hover:bg-emerald-100/60' + : 'hover:bg-slate-50/80 text-slate-700' + }`} + > + + {hasBrand && } + + + + + ) + })} + +
    + {hasBrand ? 'Drug Name for Brand' : 'Drug Name'} + BrandType + {hasBrand ? 'Language for Brand' : 'Language'} + + {hasBrand ? 'Countries for Brand' : 'Countries'} +
    + {selected && ( + + )} + {row.name} + {row.brand || '-'} + + {hasBrand ? 'brand name drug' : row.type || 'ingredient'} + + {row.language}{row.country ?? '-'}
    +
    +
    + + {/* Mobile Card View */} +
    + {results.map((row, index) => { + const selected = isRowSelected(row) + return ( +
    onSelectResult(row)} + className={`p-4 rounded-xl border transition-all cursor-pointer ${ + selected + ? 'border-emerald-500 bg-emerald-50/50 shadow-xs ring-1 ring-emerald-500' + : 'border-slate-200 bg-white hover:border-slate-300' + }`} + > +
    +
    {row.name}
    + + {row.language} + +
    + + {row.brand && ( +
    + Brand: {row.brand} +
    + )} + +
    + + Type: {hasBrand ? 'brand name drug' : row.type || 'ingredient'} + + • + Country: {row.country ?? 'N/A'} +
    +
    + ) + })} +
    + + ) : ( +
    +

    + {t('home.sampleMedicine') || 'Search for a drug or click search to view matching results.'} +

    +
    + )} +
    + ) +} diff --git a/frontend/src/components/search/SearchBar.tsx b/frontend/src/components/search/SearchBar.tsx new file mode 100644 index 0000000..4738e1f --- /dev/null +++ b/frontend/src/components/search/SearchBar.tsx @@ -0,0 +1,91 @@ +import React, { type KeyboardEvent } from 'react' +import { useTranslation } from 'react-i18next' +import { Button, Select, Input } from '../ui' +import type { LanguageOption } from '../../types/codex' + +interface SearchBarProps { + searchLanguage: string + onSearchLanguageChange: (lang: string) => void + searchQuery: string + onSearchQueryChange: (query: string) => void + onSearch: () => void + isLoading: boolean + languages: LanguageOption[] +} + +export const SearchBar: React.FC = ({ + searchLanguage, + onSearchLanguageChange, + searchQuery, + onSearchQueryChange, + onSearch, + isLoading, + languages, +}) => { + const { t } = useTranslation() + + const handleKeyDown = (e: KeyboardEvent) => { + if (e.key === 'Enter') { + onSearch() + } + } + + const languageOptions = [ + { value: 'all', label: 'All languages' }, + ...languages.map((lang) => ({ + value: lang.code, + label: `${lang.label} (${lang.code.toUpperCase()})`, + })), + ] + + return ( +
    +
    + {/* Language Filter */} +
    + onSearchQueryChange(e.target.value)} + onKeyDown={handleKeyDown} + placeholder={t('home.sourcePlaceholder') || 'Search RxNorm drug, brand or synonym...'} + icon={ + + + + } + /> +
    + +
    +
    +
+
+ + +
+ + + + + + + + + +
+
+ +
+
+ +
+ +
+ +
+ +
+ +
+ +
+ +
+ +
+ +
+
+ +
+
+
+

{t('home.pageTitle')}

+

{t('home.pageDescription')}

+
+ +
+ +
+

{t('home.searchTitle')}

+
+
+
+ + +
+
+ setSearchQuery(e.target.value)} + onKeyDown={handleKeyPress} + /> + +
+
+ +
+

{t('home.resultsTitle')}

+ {searchError &&
{searchError}
} + {translateError &&
{translateError}
} + {isTranslating &&
Translating selected result...
} + {searchResults.length > 0 ? ( +
+ + + + + + + + + + + {searchResults.map((row, index) => ( + { + setSelectedResult(row) + setTranslatedName('') + setTranslateError('') + }} + style={{ cursor: 'pointer' }} + > + + + + + + ))} + +
Drug NameTypeLanguageCountry
{row.name}{row.type}{row.language}{row.country ?? '-'}
+
+ ) : searchQuery && !isLoading ? ( +
No results found
+ ) : ( + + )} + + {selectedResult && ( +
+
+
+ + +
+
+ +
+
+ +
+ + + + + + + + + + + + + +
Original Drug Name (Language)Drug Name in {targetLanguage.toUpperCase()}
{selectedResult.name} ({selectedResult.language}){translatedName || '-'}
+
+
+ )} +
+
+
+ +
+

Export CSV

+
+
+
+ + +
+
+ +
+
+
+ {isExporting &&
Preparing CSV...
} + {exportError &&
{exportError}
} + {exportMessage &&
{exportMessage}
} +
+
+
+ +
+