From ad26123b63002f6be30b66a9e4fecb020fc9402b Mon Sep 17 00:00:00 2001 From: "Jessica Vera, Ph.D" <56414911+jmvera255@users.noreply.github.com> Date: Mon, 8 Jul 2024 13:14:29 -0500 Subject: [PATCH] new DCA config for VEOIBD (#192) * Use google sheet for NF-OSI and GF (#71) Use google sheet for NF-OSI and GF * Veoibd config (#73) * update config file and logo * update the submit_manifest_record_type to file_entities to enable annotations on files and include most recent changes in template config * Update dcc_config.csv * Fix typo in config_schema.py (#75) * Update HTAN config file (#76) * Update dca-template-config.json * Update dca-template-config.json * Update dca-template-config.json * Update dca-template-config.json (#78) Added additional templates, "Study", "Metabolomics", "Whole Genome Sequencing", "bsSeq", "scRNAseq", "genotype assay", and "proteomics" * Update dca-template-config.json (#79) Updated names of templates * Update dcc_config.csv (#80) updated link to new EL data model * Update HTAN data model to v23.8.1 (#83) * Update HTAN data model to v23.8.1 * Update dca-template-config.json for HTAN v23.8.1 * Update production mtDCA with HTAN v23.8.2 data model and config (#86) * Update dca-template-config.json * Update dcc_config.csv * Updates to MC2 Center content for mtDCA (#89) * Update dcc_config.csv Update to MC2 data model v3.0.0 * [create-pull-request] automated change * Update dca-template-config.json Remove templates not intended for contributors from config * Replace templates with v3.0.0 versions Update templates for DatasetView, ToolView, PublicationView Add EducationalResource template Generated with schematic 23.8.1 using MC2 Data Model v3.0.0 --------- Co-authored-by: Bankso * AD model updates (#90) * update AD template menu * change AD data model URL * restore empty line * Update HTAN to v23.8.3 data model (#92) * Update dca-template-config.json (#93) * update file annotation template name (#96) changed name in data model, now need to change in config (display name hasn't changed) * Updated EL DCA configuration (#84) * Update dca-template-config.json Removed study schema for now * Update dcc_config.csv Changed data model location and name in the ELITE data model repo. * Update dca-template-config.json Changed records to record * Veoibd config (#97) * update config file and logo * update the submit_manifest_record_type to file_entities to enable annotations on files and include most recent changes in template config * Update dcc_config.csv * update submit_manifest_record_type and Submit_table_manipulation * Changed data model url for EL (#98) Updated the pointer for the EL data model. This change is because I have been consolidating the EL repositories into a central location. * Updated EL logo and site links (#99) * Changed data model url for EL Updated the pointer for the EL data model. This change is because I have been consolidating the EL repositories into a central location. * added EL logo * Delete EL/ELITE Logo.png * Added elite logo * updated EL links to logo and site * Update HTAN data model version (#101) * Revert HTAN to v23.8.2 (#103) * For EL logo, change path from ELITE to EL (#105) * Update dcc_config.csv (#112) * Update dcc_config.csv * Update dca-template-config.json * Update for HTAN v23.10.1 data model (#113) * Update config to HTAN v23.10.1 data model * Update HTAN config template for v23.10.1 data model * Bump HTAN data model to v23.10.2 (#115) * Return publication manifest to HTAN config (#116) * Update dca-template-config.json (#119) * Fix typo in dca-template-config.json (#120) * patch/table-file (#121) * Update dca-template-config.json * Update dcc_config.csv * added new template to dropdown menu and removed template folder (#124) * Fix typo in config_schema.py (#75) * Update HTAN config file (#76) * Update dca-template-config.json * Update dca-template-config.json * Update dca-template-config.json * Update dca-template-config.json (#78) Added additional templates, "Study", "Metabolomics", "Whole Genome Sequencing", "bsSeq", "scRNAseq", "genotype assay", and "proteomics" * Update dca-template-config.json (#79) Updated names of templates * Update HTAN data model to v23.8.1 (#83) * Update HTAN data model to v23.8.1 * Update dca-template-config.json for HTAN v23.8.1 * Update dca-template-config.json (#93) * Updated EL DCA configuration (#84) * Update dca-template-config.json Removed study schema for now * Update dcc_config.csv Changed data model location and name in the ELITE data model repo. * Update dca-template-config.json Changed records to record * Updated EL logo and site links (#99) * Changed data model url for EL Updated the pointer for the EL data model. This change is because I have been consolidating the EL repositories into a central location. * added EL logo * Delete EL/ELITE Logo.png * Added elite logo * updated EL links to logo and site * Update dcc_config.csv (#112) * Update dcc_config.csv * Update dca-template-config.json * Update for HTAN v23.10.1 data model (#113) * Update config to HTAN v23.10.1 data model * Update HTAN config template for v23.10.1 data model * Return publication manifest to HTAN config (#116) * Update dca-template-config.json (#119) * Fix typo in dca-template-config.json (#120) * added new template to dropdown menu and removed template folder (#124) * resolving merge conflicts and hopefully resolve template config validation action * sync with Sage prod branch * sync with Sage prod branch * new DCA config for VEOIBD --------- Co-authored-by: Anthony Williams Co-authored-by: Dan Lu <90745557+danlu1@users.noreply.github.com> Co-authored-by: Adam Taylor Co-authored-by: Nicholas Lee <126523251+nlee-sage@users.noreply.github.com> Co-authored-by: Orion Banks <49208907+Bankso@users.noreply.github.com> Co-authored-by: Bankso Co-authored-by: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Co-authored-by: Christina Conrad <114612268+cconrad8@users.noreply.github.com> --- .github/config_schema.py | 2 +- VEOIBD/dca-template-config.json | 25 ------------------------- VEOIBD/dca_config.json | 6 +++--- 3 files changed, 4 insertions(+), 29 deletions(-) diff --git a/.github/config_schema.py b/.github/config_schema.py index b268f63..46870da 100644 --- a/.github/config_schema.py +++ b/.github/config_schema.py @@ -11,7 +11,7 @@ def get_args(): """Set up command-line interface and get arguments.""" parser = argparse.ArgumentParser() parser.add_argument('-c', '--config_path', metavar="", - required=True, help='path to schematic config ymal file') + required=True, help='path to schematic config yaml file') parser.add_argument('-sr', '--service_repo', metavar="", help='repo path to service') parser.add_argument('-o', '--out_dir', default='www', metavar="", diff --git a/VEOIBD/dca-template-config.json b/VEOIBD/dca-template-config.json index 0b14089..9deb4cb 100644 --- a/VEOIBD/dca-template-config.json +++ b/VEOIBD/dca-template-config.json @@ -9,31 +9,6 @@ "display_name": "Biospecimen Metadata Template", "schema_name": "BiospecimenMetadataTemplate", "type": "record" - }, - { - "display_name": "Bulk RNAseq Assay Template", - "schema_name": "BulkRNAseqAssayTemplate", - "type": "record" - }, - { - "display_name": "scRNAseq Assay Template", - "schema_name": "ScRNAseqAssayTemplate", - "type": "record" - }, - { - "display_name": "Bulk RNAseq Raw File Annotations", - "schema_name": "BulkRNAseqRawFileAnnotations", - "type": "file" - }, - { - "display_name": "Bulk RNASeq Counts File Annotations", - "schema_name": "BulkRNASeqCountsFileAnnotations", - "type": "file" - }, - { - "display_name": "Metadata File Annotations", - "schema_name": "MetadataFileAnnotations", - "type": "file" } ], "service_version": "v23.1.1", diff --git a/VEOIBD/dca_config.json b/VEOIBD/dca_config.json index 70e8b4b..76eabbf 100644 --- a/VEOIBD/dca_config.json +++ b/VEOIBD/dca_config.json @@ -22,13 +22,13 @@ "use_annotations": false }, "model_validate": { - "restrict_rules": true + "restrict_rules": false }, "model_submit": { "use_schema_labels": true, - "table_manipulation": "upsert", + "table_manipulation": "replace", "manifest_record_type": "file_only", "hide_blanks": false } } -} +} \ No newline at end of file