From f952102f1dfbfcc727d1f880f3c74602ddbde066 Mon Sep 17 00:00:00 2001 From: Will Date: Fri, 6 Aug 2021 10:46:52 -0500 Subject: [PATCH 01/11] chore(metadata): migrate agg MDS configs --- brh.data-commons.org/manifest.json | 4 + .../metadata/aggregate_config.json | 118 +++++++++ healdata.org/manifest.json | 4 + healdata.org/metadata/aggregate_config.json | 238 ++++++++++++++++++ preprod.healdata.org/manifest.json | 4 + .../metadata/aggregate_config.json | 238 ++++++++++++++++++ 6 files changed, 606 insertions(+) create mode 100644 brh.data-commons.org/metadata/aggregate_config.json create mode 100644 healdata.org/metadata/aggregate_config.json create mode 100644 preprod.healdata.org/metadata/aggregate_config.json diff --git a/brh.data-commons.org/manifest.json b/brh.data-commons.org/manifest.json index 8dab0bca6f..a4f9b23e72 100755 --- a/brh.data-commons.org/manifest.json +++ b/brh.data-commons.org/manifest.json @@ -46,6 +46,10 @@ "portal": { "GEN3_BUNDLE": "heal" }, + "metadata": { + 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a/brh.data-commons.org/metadata/aggregate_config.json +++ b/brh.data-commons.org/metadata/aggregate_config.json @@ -15,6 +15,7 @@ "Kids First": { "mds_url": "https://gen3.datacommons.io", "commons_url" : "https://kidsfirstdrc.org", + "study_data_field" : "gen3_discovery", "columns_to_fields": { "_subjects_count" : "subjects_count", "study_description" : "description", @@ -36,6 +37,7 @@ "MIDRC": { "mds_url": "https://data.midrc.org", "commons_url" : "data.midrc.org", + "study_data_field" : "discovery_metadata", "columns_to_fields": { "_subjects_count" : "cases_count", "study_description" : "research_description", From 247e563b0490ca84e958e3baff1dc95c44326462 Mon Sep 17 00:00:00 2001 From: Will Date: Wed, 11 Aug 2021 17:50:59 -0500 Subject: [PATCH 04/11] chore(configs): update mds configs --- brh.data-commons.org/metadata/aggregate_config.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/brh.data-commons.org/metadata/aggregate_config.json b/brh.data-commons.org/metadata/aggregate_config.json index 5d11649d3d..c244457d32 100644 --- a/brh.data-commons.org/metadata/aggregate_config.json +++ b/brh.data-commons.org/metadata/aggregate_config.json @@ -14,7 +14,7 @@ }, "Kids First": { "mds_url": "https://gen3.datacommons.io", - "commons_url" : "https://kidsfirstdrc.org", + "commons_url" : "kidsfirstdrc.org", "study_data_field" : "gen3_discovery", "columns_to_fields": { "_subjects_count" : "subjects_count", @@ -92,7 +92,7 @@ }, "Proteomic Data Commons": { "mds_url": "https://gen3.datacommons.io", - "commons_url": "portal.gdc.cancer.gov", + "commons_url": "proteomic.datacommons.cancer.gov/pdc", "columns_to_fields": { "_subjects_count" : "cases_count", "study_id" : "_unique_id", @@ -105,7 +105,7 @@ }, "Cancer Imaging Data Commons": { "mds_url": "https://gen3.datacommons.io", - "commons_url": "portal.gdc.cancer.gov", + "commons_url": "imaging.datacommons.cancer.gov/", "columns_to_fields": { "_subjects_count" : "cases_count", "study_id" : "_unique_id", From f224d260a581c8d66f13478764c131333ab07724 Mon Sep 17 00:00:00 2001 From: Will Date: Thu, 12 Aug 2021 13:23:49 -0500 Subject: [PATCH 05/11] chore(debug): use branch for cdis-jenkins-lib --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 23005e239a..ec2d94acee 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,5 +1,5 @@ #!groovy -@Library('cdis-jenkins-lib@master') _ +@Library('cdis-jenkins-lib@feat/metadata') _ testPipeline { MANIFEST = "True" } From 9db8cb88d8b10b5c717b67cd05af21aff5541b93 Mon Sep 17 00:00:00 2001 From: Will Date: Mon, 16 Aug 2021 12:46:12 -0500 Subject: [PATCH 06/11] chore: remove branch for Jenkinsfile --- Jenkinsfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index ec2d94acee..23005e239a 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,5 +1,5 @@ #!groovy -@Library('cdis-jenkins-lib@feat/metadata') _ +@Library('cdis-jenkins-lib@master') _ testPipeline { MANIFEST = "True" } From 417376d9155c92ca79453752cd833c1d74eca8f6 Mon Sep 17 00:00:00 2001 From: Will Date: Mon, 16 Aug 2021 15:50:47 -0500 Subject: [PATCH 07/11] fix(debug): remove multiple env configs --- brh.data-commons.org/manifest.json | 4 ---- healdata.org/manifest.json | 4 ---- 2 files changed, 8 deletions(-) diff --git a/brh.data-commons.org/manifest.json b/brh.data-commons.org/manifest.json index a4f9b23e72..8dab0bca6f 100755 --- a/brh.data-commons.org/manifest.json +++ b/brh.data-commons.org/manifest.json @@ -46,10 +46,6 @@ "portal": { "GEN3_BUNDLE": "heal" }, - "metadata": { - "USE_AGG_MDS": true, - "AGG_MDS_NAMESPACE": "brhdemo" - }, "canary": { "default": 0 }, diff --git a/healdata.org/manifest.json b/healdata.org/manifest.json index 1334caaed2..fbf9713869 100644 --- a/healdata.org/manifest.json +++ b/healdata.org/manifest.json @@ -33,10 +33,6 @@ "arborist": { "deployment_version": "2" }, - "metadata": { - "USE_AGG_MDS": true, - "AGG_MDS_NAMESPACE": "healprod" - }, "portal": { "GEN3_BUNDLE": "heal" }, From 4e1a4883ab1483ec751dd77fe171d26f15d06cf4 Mon Sep 17 00:00:00 2001 From: Will Date: Tue, 17 Aug 2021 08:31:03 -0500 Subject: [PATCH 08/11] chore(debug): remove all changes --- .../metadata/aggregate_config.json | 120 ----- healdata.org/metadata/aggregate_config.json | 488 ------------------ preprod.healdata.org/manifest.json | 6 +- .../metadata/aggregate_config.json | 365 ------------- 4 files changed, 1 insertion(+), 978 deletions(-) delete mode 100644 brh.data-commons.org/metadata/aggregate_config.json delete mode 100644 healdata.org/metadata/aggregate_config.json delete mode 100644 preprod.healdata.org/metadata/aggregate_config.json diff --git a/brh.data-commons.org/metadata/aggregate_config.json b/brh.data-commons.org/metadata/aggregate_config.json deleted file mode 100644 index c244457d32..0000000000 --- a/brh.data-commons.org/metadata/aggregate_config.json +++ /dev/null @@ -1,120 +0,0 @@ -{ - "gen3_commons": { - "IBD Commons": { - "mds_url": "https://ibdgc.datacommons.io", - "commons_url" : "ibdgc.datacommons.io", - "study_data_field" : "my_metadata", - "guid_type" : "my_metadata", - "columns_to_fields": { - "_subjects_count" : "subjects_count", - "study_description" : "brief_summary", - "short_name": "dataset_title", - "full_name": "dataset_title" - } - }, - "Kids First": { - "mds_url": "https://gen3.datacommons.io", - "commons_url" : "kidsfirstdrc.org", - "study_data_field" : "gen3_discovery", - "columns_to_fields": { - "_subjects_count" : "subjects_count", - "study_description" : "description", - "study_id" : "dbgap_accession_number" - }, - "select_field": { - "field_name" : "commons", - "field_value" : "Kids First" - } - }, - "BioData Catalyst": { - "mds_url": "https://gen3.biodatacatalyst.nhlbi.nih.gov", - "commons_url" : "gen3.biodatacatalyst.nhlbi.nih.gov", - "columns_to_fields": { - "short_name": "name", - "_unique_id" : "study_id" - } - }, - "MIDRC": { 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Aug 2021 10:59:02 -0500 Subject: [PATCH 10/11] chore(debug): enable agg mds --- preprod.healdata.org/manifest.json | 1 + 1 file changed, 1 insertion(+) diff --git a/preprod.healdata.org/manifest.json b/preprod.healdata.org/manifest.json index 2010621f73..8394ddf07a 100644 --- a/preprod.healdata.org/manifest.json +++ b/preprod.healdata.org/manifest.json @@ -34,6 +34,7 @@ "deployment_version": "2" }, "metadata": { + "USE_AGG_MDS": true, "AGG_MDS_NAMESPACE": "healpreprod" }, "portal": { From 6dcaf460e7361ef6a220e30a614d49c961c3e592 Mon Sep 17 00:00:00 2001 From: Will Date: Tue, 17 Aug 2021 12:54:24 -0500 Subject: [PATCH 11/11] chore(debug): add back single config file --- .../metadata/aggregate_config.json | 379 ++++++++++++++++++ 1 file changed, 379 insertions(+) create mode 100644 preprod.healdata.org/metadata/aggregate_config.json diff --git a/preprod.healdata.org/metadata/aggregate_config.json b/preprod.healdata.org/metadata/aggregate_config.json new file mode 100644 index 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