remove sample_class_filter

genie/consortium_to_public.py

@@ -3,9 +3,8 @@
 import logging
 import os
 
-import synapseutils
 import pandas as pd
-
+import synapseutils
 from genie import (
     create_case_lists,
     database_to_staging,
@@ -119,8 +118,6 @@ def consortiumToPublic(
         clinicalDf, processingDate, publicReleaseCutOff
     )
     logger.info("SAMPLE CLASS FILTER")
-    remove_sc_samples = database_to_staging.sample_class_filter(clinical_df=clinicalDf)
-    removeForPublicSamples = list(set(removeForPublicSamples).union(remove_sc_samples))
     # comment back in when public release filter back on
     # publicReleaseSamples = publicReleaseSamples.append(keepForPublicSamples)
     # Make sure all null oncotree codes are removed

genie/database_to_staging.py

@@ -555,24 +555,6 @@ def seq_date_filter(clinicalDf, processingDate, consortiumReleaseCutOff):
     return removeSeqDateSamples
 
 
-def sample_class_filter(clinical_df: pd.DataFrame) -> list:
-    """Filter samples by SAMPLE_CLASS
-
-    Args:
-        clinical_df (pd.DataFrame): Clinical dataframe
-
-    Returns:
-        list: List of samples to filter out
-    """
-    if clinical_df.get("SAMPLE_CLASS") is not None:
-        remove_samples = clinical_df["SAMPLE_ID"][
-            clinical_df["SAMPLE_CLASS"] == "cfDNA"
-        ].tolist()
-    else:
-        remove_samples = []
-    return remove_samples
-
-
 # TODO: Add to transform.py
 def mutation_in_cis_filter(
     syn,