deprecate meta_fusions.txt

Author: rxu17

genie/consortium_to_public.py

@@ -5,7 +5,6 @@
 import sys
 
 import pandas as pd
-import synapseclient
 import synapseutils
 from genie import (
     create_case_lists,
@@ -14,15 +13,14 @@
     load,
     process_functions,
 )
+from genie.load import _copyRecursive
 
 logger = logging.getLogger(__name__)
 stdout_handler = logging.StreamHandler(stream=sys.stdout)
 stdout_handler.setLevel(logging.INFO)
 logger.addHandler(stdout_handler)
-from typing import Dict
-
-from genie.load import _copyRecursive
 
+DEPRECATED_PUBLIC_RELEASE_FILES = ["data_fusions.txt", "meta_fusions.txt"]
 
 # TODO: Add to transform.py
 def commonVariantFilter(mafDf):
@@ -213,7 +211,7 @@ def consortiumToPublic(
     )
     genePanelEntities = []
     for entName, entId in consortiumRelease[2]:
-        is_deprecated_file = entName in ["data_fusions.txt"]
+        is_deprecated_file = entName in DEPRECATED_PUBLIC_RELEASE_FILES
         # skip files to convert
         if (
             entName.startswith("data_linear")

genie/database_to_staging.py

@@ -102,6 +102,7 @@
     "mutationInCis_Flag",
 ]
 
+DEPRECATED_CONSORTIUM_RELEASE_FILES = ["data_fusions.txt", "meta_fusions.txt"]
 
 # TODO: Add to transform.py
 def _to_redact_interval(df_col: pd.Series) -> Tuple[pd.Series, pd.Series]:
@@ -1978,7 +1979,7 @@ def revise_metadata_files(syn, consortiumid, genie_version=None):
             i["id"], downloadLocation=GENIE_RELEASE_DIR, ifcollision="overwrite.local"
         )
         for i in release_files
-        if "meta" in i["name"] and i["name"] != "meta_fusions.txt"
+        if "meta" in i["name"] and i["name"] not in DEPRECATED_CONSORTIUM_RELEASE_FILES
     ]
 
     for meta_ent in meta_file_ents:
@@ -2091,7 +2092,7 @@ def create_link_version(
             release_file["name"] != "data_clinical.txt" or release_type == "consortium"
         )
         is_gene_panel = release_file["name"].startswith("data_gene_panel")
-        is_deprecated_file = release_file["name"] in ["data_fusions.txt"]
+        is_deprecated_file = release_file["name"] in DEPRECATED_CONSORTIUM_RELEASE_FILES
 
         if not_folder and not_public and not is_gene_panel and not is_deprecated_file:
             syn.store(