update

src/pif_compiler/services/__init__.py

@@ -14,30 +14,6 @@ Modules:
 """
 
 # ECHA Services
-from pif_compiler.services.echa_find import (
-    search_dossier,
-)
-
-from pif_compiler.services.echa_process import (
-    echaExtract,
-    echaExtract_multi,
-    echaExtract_specific,
-    echaExtract_local,
-    echa_noael_ld50,
-    echa_noael_ld50_multi,
-    echaPage_to_md,
-    openEchaPage,
-    markdown_to_json_raw,
-    clean_json,
-    json_to_dataframe,
-    filter_dataframe_by_dict,
-)
-
-from pif_compiler.services.echa_pdf import (
-    generate_pdf_with_header_and_cleanup,
-    search_generate_pdfs,
-    svg_to_data_uri,
-)
 
 # COSING Service
 from pif_compiler.services.cosing_service import (
@@ -62,25 +38,6 @@ from pif_compiler.services.db_utils import get_client
 
 
 __all__ = [
-    # ECHA Find
-    "search_dossier",
-    # ECHA Process
-    "echaExtract",
-    "echaExtract_multi",
-    "echaExtract_specific",
-    "echaExtract_local",
-    "echa_noael_ld50",
-    "echa_noael_ld50_multi",
-    "echaPage_to_md",
-    "openEchaPage",
-    "markdown_to_json_raw",
-    "clean_json",
-    "json_to_dataframe",
-    "filter_dataframe_by_dict",
-    # ECHA PDF
-    "generate_pdf_with_header_and_cleanup",
-    "search_generate_pdfs",
-    "svg_to_data_uri",
     # COSING Service
     "cosing_search",
     "clean_cosing",

src/pif_compiler/services/db_utils.py

@@ -1,4 +1,5 @@
 import os
+from urllib.parse import quote_plus
 
 from dotenv import load_dotenv
 from pymongo import MongoClient
@@ -15,6 +16,9 @@ def get_client():
     MONGO_HOST = os.getenv("MONGO_HOST")
     MONGO_PORT = os.getenv("MONGO_PORT")
 
+    MONGO_PORT = MONGO_PORT
+    ADMIN_PASSWORD = quote_plus(ADMIN_PASSWORD)
+
     client = MongoClient(
         f"mongodb://{ADMIN_USER}:{ADMIN_PASSWORD}@{MONGO_HOST}:{MONGO_PORT}/?authSource=admin",
         serverSelectionTimeoutMS=5000
@@ -34,4 +38,11 @@ def db_connect(db_name : str = 'toxinfo', collection_name : str = 'substance_ind
         logger.error(f"Error connecting to MongoDB: {e}")
         return None
 
-    return client, db, collection
+    return collection
+
+if __name__ == "__main__":
+    coll = db_connect()
+    if coll:
+        logger.info("Database connection successful.")
+    else:
+        logger.error("Database connection failed.")

src/pif_compiler/services/srv_echa.py

@@ -46,8 +46,9 @@ def search_substance(cas : str) -> dict:
                         "rmlName": result["substanceIndex"]["rmlName"],
                         "rmlId": result["substanceIndex"]["rmlId"]
                     }
+                    log.info(f"Substance found for CAS {cas}: {substance['rmlName']}")
                     return substance
-    log.error(f"Something went wrong")
+    log.error(f"Something went wrong searching the substance for CAS {cas}")
     return {}
 
 
@@ -69,6 +70,7 @@ def get_dossier_info(rmlId: str) -> dict:
         "assetExternalId": response_dossier_json['items'][0]['assetExternalId'],
         "rootKey": response_dossier_json['items'][0]['rootKey']
     }
+    log.info(f"Dossier info retrieved for RML ID {rmlId}")
     return dossier_info
 
 
@@ -105,6 +107,8 @@ def get_substance_index(assetExternalId : str) -> dict:
     at_href = at_link['href']
     index_data['acute_toxicity_link'] = LINK_DOSSIER + at_href + '.html'
 
+    log.info(f"Substance index retrieved for Asset External ID {assetExternalId}")
+
     return index_data
 
 #endregion
@@ -303,6 +307,12 @@ def generate_pdf_from_toxicology_info(index: dict):
         page.goto(index['toxicological_information_link'])
         page.pdf(path=f'pdfs/{index["substance"]["rmlCas"]}.pdf')
         browser.close()
+    if os.path.exists(f'pdfs/{index["substance"]["rmlCas"]}.pdf'):
+        log.info(f"PDF generated for CAS {index['substance']['rmlCas']}")
+        return True
+    else:
+        log.error(f"PDF generation failed for CAS {index['substance']['rmlCas']}")
+        return False
         
 #endregion
 
@@ -326,6 +336,8 @@ def echa_flow(cas) -> dict:
         "repeated_dose_toxicity": {}
     }
 
+    log.debug(f"ECHA flow intermediate result")
+
     # Fetch and parse toxicological information
     txi_link = index.get('toxicological_information_link')
     if txi_link:
@@ -349,7 +361,9 @@ def echa_flow(cas) -> dict:
 
     for key, value in result.items():
         if value is None or value == "" or value == [] or value == {}:
-            return False
+            log.warning(f"Missing data for key: {key} in CAS {cas}")
+        else:
+            log.info(f"Data retrieved for key: {key} in CAS {cas}")
     return result
 
 def cas_validation(cas: str) -> str:
@@ -367,9 +381,9 @@ def cas_validation(cas: str) -> str:
         return None
 
 def check_local(cas: str) -> bool:
-    client, db, collection = db_connect()
+    collection = db_connect()
 
-    if not collection:
+    if collection is None:
         log.error("No MongoDB collection available.")
         return None
 
@@ -383,9 +397,9 @@ def check_local(cas: str) -> bool:
         return None
     
 def add_to_local(data: dict) -> bool:
-    client, db, collection = db_connect()
+    collection = db_connect()
 
-    if not collection:
+    if collection is None:
         log.error("No MongoDB collection available.")
         return False
 
@@ -397,17 +411,22 @@ def add_to_local(data: dict) -> bool:
         log.error(f"Error inserting data into MongoDB: {e}")
         return False
     
-def search_substance(cas: str) -> dict:
+def orchestrator(cas: str) -> dict:
+    log.debug(f"Initiating search for CAS {cas} in ECHA service.")
     cas_validated = cas_validation(cas)
     if not cas_validated:
         return None
     else:
+        log.info(f"CAS {cas} validated successfully.")
         local_record = check_local(cas_validated)
         if local_record:
+            log.info(f"Returning local record for CAS {cas}.")
             return local_record
         else:
+            log.info(f"No local record, starting echa flow")
             echa_data = echa_flow(cas_validated)
             if echa_data:
+                log.info(f"Echa flow successful")
                 add_to_local(echa_data)
                 return echa_data
             else:
@@ -417,3 +436,8 @@ def search_substance(cas: str) -> dict:
 # to do: check if document is complete
 # to do: check lastupdate
 #endregion
+
+if __name__ == "__main__":
+    cas_test = "50-00-0"
+    result = orchestrator(cas_test)
+    print(result)