[GEN-834] Disable data guide generation (#537)

* comment out data guide generation --------- Co-authored-by: Rixing Xu <[email protected]>
Sage-Bionetworks · Sep 26, 2023 · c2ba7db · c2ba7db
1 parent db442a2
commit c2ba7db
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Showing 2 changed files with 30 additions and 28 deletions.
diff --git a/bin/consortium_to_public.py b/bin/consortium_to_public.py
@@ -204,22 +204,23 @@ def main(args):
         logger.info("DASHBOARD UPDATE COMPLETE")
         logger.info("AUTO GENERATE DATA GUIDE")
 
-    onco_link = databaseSynIdMappingDf["Id"][
-        databaseSynIdMappingDf["Database"] == "oncotreeLink"
-    ].values[0]
-    onco_link_ent = syn.get(onco_link)
-    oncotree_link = onco_link_ent.externalURL
-    oncotree_version = oncotree_link.split("=")[1]
-
-    data_guide_pdf = generate_data_guide(
-        args.genieVersion,
-        oncotree_version=oncotree_version,
-        database_mapping=databaseSynIdMappingId,
-    )
-    data_guide_ent = synapseclient.File(
-        data_guide_pdf, parent=folders["release_folder"]
-    )
-    syn.store(data_guide_ent)
+    # TODO: remove data guide code
+    # onco_link = databaseSynIdMappingDf["Id"][
+    #    databaseSynIdMappingDf["Database"] == "oncotreeLink"
+    # ].values[0]
+    # onco_link_ent = syn.get(onco_link)
+    # oncotree_link = onco_link_ent.externalURL
+    # oncotree_version = oncotree_link.split("=")[1]
+
+    # data_guide_pdf = generate_data_guide(
+    #    args.genieVersion,
+    #    oncotree_version=oncotree_version,
+    #    database_mapping=databaseSynIdMappingId,
+    # )
+    # data_guide_ent = synapseclient.File(
+    #    data_guide_pdf, parent=folders["release_folder"]
+    # )
+    # syn.store(data_guide_ent)
     logger.info("COMPLETED CONSORTIUM TO PUBLIC")
 
 

diff --git a/bin/database_to_staging.py b/bin/database_to_staging.py
@@ -295,18 +295,19 @@ def main(
         logger.info("DASHBOARD UPDATE COMPLETE")
         logger.info("AUTO GENERATE DATA GUIDE")
 
-    oncotree_version = oncotree_link.split("=")[1]
-    data_guide_pdf = generate_data_guide(
-        genie_version,
-        oncotree_version=oncotree_version,
-        database_mapping=databaseSynIdMappingId,
-    )
-    load.store_file(
-        syn=syn,
-        filepath=data_guide_pdf,
-        version_comment=genie_version,
-        parentid=folders["release_folder"],
-    )
+    # TODO: remove data guide code
+    # oncotree_version = oncotree_link.split("=")[1]
+    # data_guide_pdf = generate_data_guide(
+    #    genie_version,
+    #    oncotree_version=oncotree_version,
+    #    database_mapping=databaseSynIdMappingId,
+    # )
+    # load.store_file(
+    #    syn=syn,
+    #    filepath=data_guide_pdf,
+    #    version_comment=genie_version,
+    #    parentid=folders["release_folder"],
+    # )
     logger.info("COMPLETED DATABASE TO STAGING")