Merge pull request #137 from Sage-Bionetworks/GEN-1174-remove-tempora…

…ry-retraction [GEN-1174] Don't use temporary retraction table
Sage-Bionetworks · May 3, 2024 · b088810 · b088810
2 parents ef9e3cb + a1d28fe
commit b088810
Showing 1 changed file with 12 additions and 12 deletions.
diff --git a/geniesp/bpc_redcap_export_mapping.py b/geniesp/bpc_redcap_export_mapping.py
@@ -538,7 +538,7 @@ class BpcProjectRunner(metaclass=ABCMeta):
     _sample_retraction_synid = "syn25779833"
     _patient_retraction_synid = "syn25998970"
     _retraction_at_release_synid = "syn52915299"
-    _temporary_patient_retraction_synid = "syn29266682"
+    # _temporary_patient_retraction_synid = "syn29266682"
     # main GENIE assay information table
     _ASSAY_SYNID = "syn17009222"
     # exclude files to be created for cbioportal
@@ -606,11 +606,11 @@ def genie_clinicaldf(self) -> pd.DataFrame:
         )
         bpc_patient_retraction_df = bpc_patient_retraction_db.asDataFrame()
 
-        bpc_temp_patient_retraction_db = self.syn.tableQuery(
-            f"select patient_id from {self._temporary_patient_retraction_synid} where "
-            f"cohort like '{self._SPONSORED_PROJECT}%'"
-        )
-        bpc_temp_patient_retraction_df = bpc_temp_patient_retraction_db.asDataFrame()
+        # bpc_temp_patient_retraction_db = self.syn.tableQuery(
+        #     f"select patient_id from {self._temporary_patient_retraction_synid} where "
+        #     f"cohort like '{self._SPONSORED_PROJECT}%'"
+        # )
+        # bpc_temp_patient_retraction_df = bpc_temp_patient_retraction_db.asDataFrame()
 
         retraction_at_release = self.syn.tableQuery(
             f"select patient_id from {self._retraction_at_release_synid} where "
@@ -629,12 +629,12 @@ def genie_clinicaldf(self) -> pd.DataFrame:
         keep_clinicaldf = keep_clinicaldf[
             ~keep_clinicaldf["PATIENT_ID"].isin(retraction_at_release_df["patient_id"])
         ]
-        # Retract patients from temporary patient retraction db
-        keep_clinicaldf = keep_clinicaldf[
-            ~keep_clinicaldf["PATIENT_ID"].isin(
-                bpc_temp_patient_retraction_df["patient_id"]
-            )
-        ]
+        # # Retract patients from temporary patient retraction db
+        # keep_clinicaldf = keep_clinicaldf[
+        #     ~keep_clinicaldf["PATIENT_ID"].isin(
+        #         bpc_temp_patient_retraction_df["patient_id"]
+        #     )
+        # ]
         return keep_clinicaldf
 
     @cached_property