update-project-details API

app/routes/main.py

@@ -1,7 +1,15 @@
-from fastapi import APIRouter
+from fastapi import APIRouter, Depends
+from sqlalchemy import select, update
+
+from app.models.dbsequence import DBSequence
+from app.models.peptideevidence import PeptideEvidence
+from app.models.spectrumidentification import SpectrumIdentification
+from app.models.upload import Upload
 from process_dataset import convert_pxd_accession_from_pride
+from sqlalchemy.orm import Session
+from app.routes.index import get_session
 import os
-
+import requests
 
 main_router = APIRouter()
 
@@ -18,3 +26,55 @@ async def parse(px_accession: str, temp_dir: str | None = None, dont_delete: boo
 @main_router.get("/health-test", tags=["Main"])
 async def health():
     return "OK"
+
+
+@main_router.get("/update-project-details", tags=["Maintenance"])
+async def update_project_details(session: Session = Depends(get_session)):
+    uploads = session.execute(select(Upload)).all()
+    projectListToUpdate = []
+    for upload in uploads:
+        isNeedToUpdate = False
+        # get project details from PRIDE API
+        # TODO: need to move URL to a configuration variable
+        px_url = 'https://www.ebi.ac.uk/pride/ws/archive/v2/projects/' + upload[0].project_id
+        print('GET request to PRIDE API: ' + px_url)
+        pride_response = requests.get(px_url)
+        r = requests.get(px_url)
+        if r.status_code == 200:
+            print('PRIDE API returned status code 200')
+            pride_json = pride_response.json()
+            pubmedId = ''
+            if len(pride_json['references']) > 0:
+                pubmedId = pride_json['references'][0]['pubmedId']
+            if pride_json is not None:
+                if upload[0].title is None or upload[0].title != pride_json['title']:
+                    isNeedToUpdate = True
+                    upload[0].title = pride_json['title']
+                if upload[0].description is None or upload[0].description != pride_json['projectDescription']:
+                    isNeedToUpdate = True
+                    upload[0].description = pride_json['projectDescription']
+                if (upload[0].pubmed_id is None and pubmedId != '') or upload[0].pubmed_id != pubmedId:
+                    isNeedToUpdate = True
+                    upload[0].pubmed_id = pubmedId
+
+                if isNeedToUpdate:
+                    projectListToUpdate.append(upload[0])
+
+    for upload in projectListToUpdate:
+        stmt = update(Upload).where(Upload.id == upload.id).values(title=upload.title, description=upload.description,
+                                                                   pubmed_id=upload.pubmed_id)
+        session.execute(stmt)
+    session.commit()
+
+
+@main_router.get("/calculate-stats", tags=["Maintenance"])
+async def calculate_stats(session: Session = Depends(get_session)):
+    rows = session.query(Upload).all()
+    for row in rows:
+        number_of_proteins = session.query(DBSequence).filter(DBSequence.upload_id == row.id).count()
+        print(f"Number of proteins: {number_of_proteins}")
+        number_of_peptides = session.query(PeptideEvidence).filter(PeptideEvidence.upload_id == row.id).count()
+        print(f"Number of peptides: {number_of_peptides}")
+        number_of_spectra = session.query(SpectrumIdentification).filter(SpectrumIdentification.upload_id == row.id).count()
+        print(f"Number of Spectra: {number_of_spectra}")
+        print(".......................................")