Fixed bladderpdo. Fixed schema issue. Added model type to schema

Author: jjacobson95

build/bladderpdo/00_createBladderPDOSampleFile.py

@@ -29,11 +29,11 @@ def _parse_model_type(sample_id):
     """Derive model_type from Sample ID."""
     low = sample_id.lower()
     if "_xenoorganoid" in low:
-        return "xdo"
+        return "xenograft derived organoid"
     if "_organoid" in low:
         return "organoid"
     if "_xenograft" in low:
-        return "xenograft"
+        return "patient derived xenograft"
     if "_parental" in low:
         return "tumor"
     return "unknown"

build/bladderpdo/01_createBladderPDOOmicsFiles.py

@@ -153,7 +153,7 @@ def get_bladder_pdo_copynumber(synObject, samples, genes):
     samples = pd.read_csv(args.samples)
 
     if args.expression:
-        get_bladder_pdo_transcriptomics(args.geolink, samples, genes).to_csv("bladderpdo_transcriptomics.csv", index=False)
+        get_bladder_pdo_transcriptomics(args.geolink, samples, genes).to_csv("/tmp/bladderpdo_transcriptomics.csv", index=False)
 
     if args.mutation:
         get_bladder_pdo_mutations(synObject, samples, genes).to_csv('/tmp/bladderpdo_mutations.csv', index=False)

build/improve_drug_mapping.json

@@ -4,10 +4,6 @@
       {
         "build_date": "01_24_25",
         "version": "2.0.0"
-      },
-      {
-        "build_date": "2025-04-18",
-        "version": "2.1.0"
       }
     ]
   },
@@ -223587,78 +223583,6 @@
     {
       "stable_id": "SMI_56600",
       "canSMILES": "COCCOC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC=CC(=C3)C"
-    },
-    {
-      "stable_id": "SMI_56601",
-      "canSMILES": "C1=CN=C(N=C1)C2=NN(N=N2)CC3=C(C=C(C=C3F)C(=O)NO)F"
-    },
-    {
-      "stable_id": "SMI_56602",
-      "canSMILES": "CC1(C2CC3C(C(=O)C(=C(C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)NCN5CCCC5)N(C)C)O.Cl"
-    },
-    {
-      "stable_id": "SMI_56603",
-      "canSMILES": "C1=CC=C2C(=C1)C=CC(=C2O)N=NC3=C4C=CC(=CC4=C(C=C3O)S(=O)(=O)O)[N+](=O)[O-].[Na+]"
-    },
-    {
-      "stable_id": "SMI_56604",
-      "canSMILES": "CC1=CC=C(C=C1)S(=O)(=O)O.CNC(=O)C1=NC=CC(=C1)OC2=CC=C(C=C2)NC(=O)NC3=CC(=C(C=C3)Cl)C(F)(F)F"
-    },
-    {
-      "stable_id": "SMI_56605",
-      "canSMILES": "C1=CC=C2C(=C1)C(=C(C(=O)C2=O)CC=C(Cl)Cl)O.[Na+]"
-    },
-    {
-      "stable_id": "SMI_56606",
-      "canSMILES": "CC(C1C2CC(=C(N2C1=O)C(=O)O)SCCN=CN)O"
-    },
-    {
-      "stable_id": "SMI_56607",
-      "canSMILES": "Oc1ccc2ccccc2c1N=Nc3ccc(cc3)N=Nc4ccccc4"
-    },
-    {
-      "stable_id": "SMI_56608",
-      "canSMILES": "CN1CC2(C=C)C3CC4OCC3C1C2C45C(=O)Nc6ccccc56"
-    },
-    {
-      "stable_id": "SMI_56609",
-      "canSMILES": "COc1ccc2nc3cc(Cl)ccc3c(Nc4ccc(O)c(CN5CCN(C)CC5)c4)c2c1"
-    },
-    {
-      "stable_id": "SMI_56610",
-      "canSMILES": "NC(=O)c1ncn(C2OC(CO)C(O)C2O)c1N"
-    },
-    {
-      "stable_id": "SMI_56611",
-      "canSMILES": "[Na+].ON=Nc1cnccn1"
-    },
-    {
-      "stable_id": "SMI_56612",
-      "canSMILES": "NC1=NC(=S)c2ncn(C3CC(O)C(CO)O3)c2N1"
-    },
-    {
-      "stable_id": "SMI_56613",
-      "canSMILES": "CCC(C)C(N)C(=O)N\\C(=C\\C)\\C(=O)NC1CSCC(NC(=O)C(CC(C)C)NC(=O)C(=C)NC(=O)C(NC1=O)C(C)CC)C(=O)NC2C(C)SCC(NC(=O)CNC(=O)C3CCCN3C2=O)C(=O)NC(CCCCN)C(=O)NC4C(C)SCC(NC(=O)CNC(=O)C(CCSC)NC(=O)C(CC(C)C)NC(=O)C(C)NC(=O)CNC4=O)C(=O)NC(CC(=O)N)C(=O)NC(CCSC)C(=O)NC(CCCCN)C(=O)NC5C(C)SCC6NC(=O)C(NC(=O)C(C)NC5=O)C(C)SCC(NC(=O)C(Cc7c[nH]cn7)NC6=O)C(=O)NC(CO)C(=O)NC(C(C)CC)C(=O)NC(Cc8c[nH]cn8)C(=O)NC(C(C)C)C(=O)NC(=C)C(=O)NC(CCCCN)C(=O)O"
-    },
-    {
-      "stable_id": "SMI_56614",
-      "canSMILES": "CC(=O)[O-].CC(=O)[O-].C1CCC(CC1)N.N.[Cl-].[Cl-].[Pt]"
-    },
-    {
-      "stable_id": "SMI_56615",
-      "canSMILES": "CC1(C2=C(C3=CC=CC=C3C(=O)C2=O)NC1=O)C"
-    },
-    {
-      "stable_id": "SMI_56616",
-      "canSMILES": "CC(C)(C)C(=O)NC1=CC2=C(C=C1)C3=CC=CC=C3C(=O)C2=O"
-    },
-    {
-      "stable_id": "SMI_56617",
-      "canSMILES": "COC1=CC(=C(C=C1NCC(=O)N2CCC(CC2)NS(=O)(=O)C=C)I)Cl"
-    },
-    {
-      "stable_id": "SMI_56618",
-      "canSMILES": "C1=CC=C(C(=C1)C2=CC=C(C=C2)C3=CSC4=C3C(=C(C(=O)N4)C#N)O)O"
     }
   ]
 }