From c2ba7db94c80cef38004cdd4ab2df2c6a6875f6a Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Tue, 26 Sep 2023 15:44:38 -0700 Subject: [PATCH] [GEN-834] Disable data guide generation (#537) * comment out data guide generation --------- Co-authored-by: Rixing Xu --- bin/consortium_to_public.py | 33 +++++++++++++++++---------------- bin/database_to_staging.py | 25 +++++++++++++------------ 2 files changed, 30 insertions(+), 28 deletions(-) diff --git a/bin/consortium_to_public.py b/bin/consortium_to_public.py index c25b1312..688752f5 100644 --- 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 index fdc8e6f8..1cbc8644 100644 --- 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")