revert changes in pipeline

Author: danlu1

genie_registry/bed.py

@@ -8,7 +8,6 @@
 
 from genie.example_filetype_format import FileTypeFormat
 from genie import load, process_functions, validate
-from synapseclient.models import query
 
 LOGGER = logging.getLogger(__name__)
 
@@ -513,6 +512,7 @@ def _process(self, beddf, seq_assay_id, newpath, parentid, create_panel=True):
         """
         seq_assay_id = seq_assay_id.upper()
         seq_assay_id = seq_assay_id.replace("_", "-")
+
         # Add in 6th column which is the clinicalReported
         if len(beddf.columns) > 5:
             if all(beddf[5].apply(lambda x: x in [True, False])):
@@ -548,8 +548,9 @@ def _process(self, beddf, seq_assay_id, newpath, parentid, create_panel=True):
         # Change all start and end to int
         beddf["Start_Position"] = beddf["Start_Position"].apply(int)
         beddf["End_Position"] = beddf["End_Position"].apply(int)
-        gene_position_table = query("SELECT * FROM syn11806563")
-        gene_positiondf = gene_position_table.convert_dtypes()
+
+        gene_position_table = self.syn.tableQuery("SELECT * FROM syn11806563")
+        gene_positiondf = gene_position_table.asDataFrame()
         beddf["ID"] = beddf["Hugo_Symbol"]
         # The apply function of a DataFrame is called twice on the first
         # row (known pandas behavior)
@@ -685,11 +686,12 @@ def _validate(self, beddf):
             total_error += error
 
             if to_validate_symbol:
-                gene_position_table = query("SELECT * FROM syn11806563")
-                gene_positiondf = gene_position_table.convert_dtypes()
+                gene_position_table = self.syn.tableQuery("SELECT * FROM syn11806563")
+                gene_positiondf = gene_position_table.asDataFrame()
                 # The apply function of a DataFrame is called twice on the first row (known
                 # pandas behavior)
                 beddf = beddf.apply(lambda x: remap_symbols(x, gene_positiondf), axis=1)
+
                 if any(beddf["Hugo_Symbol"].isnull()):
                     warning += (
                         "BED file: "

genie_registry/clinical.py

@@ -13,7 +13,6 @@
 from genie import extract, load, process_functions, validate
 from genie.database_to_staging import redact_phi
 from genie.example_filetype_format import FileTypeFormat
-from synapseclient.models import query
 
 logger = logging.getLogger(__name__)
 
@@ -474,10 +473,10 @@ def uploadMissingData(
             process_functions.SCRIPT_DIR, f"{self._fileType}_missing_{col}.csv"
         )
         # PLFM-7428 - there are limits on a "not in" function on Synapse tables
-        center_samples = query(
+        center_samples = self.syn.tableQuery(
             f"select {col} from {dbSynId} where " f"CENTER='{self.center}'"
         )
-        center_samples_df = center_samples.convert_dtypes()
+        center_samples_df = center_samples.asDataFrame()
         # Get all the samples that are in the database but missing from
         # the input file
         missing_df = center_samples_df[col][~center_samples_df[col].isin(df[col])]

genie_registry/cna.py

@@ -7,7 +7,6 @@
 
 from genie.example_filetype_format import FileTypeFormat
 from genie import process_functions
-from synapseclient.models import query
 
 logger = logging.getLogger(__name__)
 
@@ -132,10 +131,10 @@ def _process(self, cnaDf):
             del cnaDf[cnaDf.columns[index][0]]
 
         bedSynId = self.genie_config["bed"]
-        bed = query(
+        bed = self.syn.tableQuery(
             f"select Hugo_Symbol, ID from {bedSynId} where CENTER = '{self.center}'"
         )
-        bedDf = bed.convert_dtypes()
+        bedDf = bed.asDataFrame()
         cnaDf["Hugo_Symbol"] = cnaDf["Hugo_Symbol"].apply(
             lambda x: validateSymbol(x, bedDf)
         )
@@ -223,11 +222,11 @@ def _validate(self, cnvDF, nosymbol_check):
             cnvDF["HUGO_SYMBOL"] = keepSymbols
             if haveColumn and not nosymbol_check:
                 bedSynId = self.genie_config["bed"]
-                bed = query(
+                bed = self.syn.tableQuery(
                     f"select Hugo_Symbol, ID from {bedSynId} "
                     f"where CENTER = '{self.center}'"
                 )
-                bedDf = bed.convert_dtypes()
+                bedDf = bed.asDataFrame()
                 cnvDF["remapped"] = cnvDF["HUGO_SYMBOL"].apply(
                     lambda x: validateSymbol(x, bedDf)
                 )

genie_registry/mutationsInCis.py

@@ -5,7 +5,6 @@
 
 from genie.example_filetype_format import FileTypeFormat
 from genie import load, process_functions
-from synapseclient.models import query
 
 logger = logging.getLogger(__name__)
 
@@ -49,12 +48,12 @@ def process_steps(self, mutationInCis, newPath, databaseSynId):
     def _validate(self, mutationInCisDf):
         mutationInCisSynId = self.genie_config["mutationsInCis"]
         # Pull down the correct database
-        existingMergeCheck = query(
+        existingMergeCheck = self.syn.tableQuery(
             "select * from {} where Center = '{}'".format(
                 mutationInCisSynId, self.center
             )
         )
-        existingMergeCheckDf = existingMergeCheck.convert_dtypes()
+        existingMergeCheckDf = existingMergeCheck.asDataFrame()
 
         total_error = ""
         warning = ""