From 4210e8385d2783d587b126701fa230f6b3a5318f Mon Sep 17 00:00:00 2001 From: kdaily Date: Tue, 26 Nov 2019 11:34:19 -0800 Subject: [PATCH] remove collection 2458. This is the reference tissue project collection, and a submission (12098) has a genomics sample file that has tabs, not spaces. The corresponding issue in the ndasynapse Python package is https://github.com/bsmn/ndasynapse/issues/39. --- run-live-manifests.sh | 2 +- run-original-manifests.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/run-live-manifests.sh b/run-live-manifests.sh index efccaee..dc47bb5 100644 --- a/run-live-manifests.sh +++ b/run-live-manifests.sh @@ -10,4 +10,4 @@ aws ssm get-parameters --names nda-config --with-decryption --region us-east-1 - echo "Running ndasynapse" $(query-nda --version) > /dev/stderr -manifest_guid_data.py --config /root/ndaconfig.json --collection_id 2458 2960 2961 2962 2963 2964 2965 2966 2967 2968 --manifest_type ${manifest_type} > /tmp/nda-manifests-${manifest_type}-LIVE.csv && synapse store --noForceVersion --parentId syn20858271 /tmp/nda-manifests-${manifest_type}-LIVE.csv; +manifest_guid_data.py --config /root/ndaconfig.json --collection_id 2960 2961 2962 2963 2964 2965 2966 2967 2968 --manifest_type ${manifest_type} > /tmp/nda-manifests-${manifest_type}-LIVE.csv && synapse store --noForceVersion --parentId syn20858271 /tmp/nda-manifests-${manifest_type}-LIVE.csv; diff --git a/run-original-manifests.sh b/run-original-manifests.sh index 3d38228..375df5b 100755 --- a/run-original-manifests.sh +++ b/run-original-manifests.sh @@ -10,4 +10,4 @@ aws ssm get-parameters --names nda-config --with-decryption --region us-east-1 - echo "Running ndasynapse" $(query-nda --version) > /dev/stderr -query-nda --config /root/ndaconfig.json get-collection-manifests --collection_id 2458 2960 2961 2962 2963 2964 2965 2966 2967 2968 --manifest_type ${manifest_type} > /tmp/nda-manifests-${manifest_type}-ORIGINAL.csv && synapse store --noForceVersion --parentId syn20858272 /tmp/nda-manifests-${manifest_type}-ORIGINAL.csv +query-nda --config /root/ndaconfig.json get-collection-manifests --collection_id 2960 2961 2962 2963 2964 2965 2966 2967 2968 --manifest_type ${manifest_type} > /tmp/nda-manifests-${manifest_type}-ORIGINAL.csv && synapse store --noForceVersion --parentId syn20858272 /tmp/nda-manifests-${manifest_type}-ORIGINAL.csv