From 21dc0d54f2ba358b72e22d3e4d9d6a59a64ce2c3 Mon Sep 17 00:00:00 2001 From: "Jessica Vera, Ph.D." <56414911+jmvera255@users.noreply.github.com> Date: Wed, 18 Dec 2024 11:14:22 -0600 Subject: [PATCH] Implement VEOIBD testing config into production (#235) * 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 * update to match testing configs, add links to key resources in config, clean up template list * update with configs from testing branching * add missing closing curly bracket * add missing closing curly bracket * add missing model validation and submit params * use dca template in prod branch, copy-paste error --------- 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> --- VEOIBD/dca-template-config.json | 5 +++++ VEOIBD/dca_config.json | 18 ++++++++++++------ 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/VEOIBD/dca-template-config.json b/VEOIBD/dca-template-config.json index 9deb4cb..7659f82 100644 --- a/VEOIBD/dca-template-config.json +++ b/VEOIBD/dca-template-config.json @@ -5,6 +5,11 @@ "schema_name": "ClinicalMetadataTemplate", "type": "record" }, + { + "display_name": "Medication History Metadata Template", + "schema_name": "MedicationHistoryMetadataTemplate", + "type": "record" + }, { "display_name": "Biospecimen Metadata Template", "schema_name": "BiospecimenMetadataTemplate", diff --git a/VEOIBD/dca_config.json b/VEOIBD/dca_config.json index 76eabbf..63e99e6 100644 --- a/VEOIBD/dca_config.json +++ b/VEOIBD/dca_config.json @@ -3,12 +3,12 @@ "name": "VEOIBD", "synapse_asset_view": "syn51397378", "data_model_url": "https://raw.githubusercontent.com/VEOIBD/data_models/main/veoibd.data.model.jsonld", - "data_model_info": "", + "data_model_info": "https://veoibd.github.io/data_models/", "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/VEOIBD/dca-template-config.json", "logo_location": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/VEOIBD/VEOIBD Logo.png", "logo_link": "https://veoibd.org", - "dcc_help_link": "", - "portal_help_link": "" + "dcc_help_link": "https://dca-docs.scrollhelp.site/DCA/Working-version/VEOIBD/?l=en", + "portal_help_link": "https://www.synapse.org/Synapse:syn29377188/wiki/619107" }, "dca": { "use_compliance_dashboard": false, @@ -17,18 +17,24 @@ "sidebar_col": "#191920" }, "schematic": { + "global": { + "data_model_labels" : "class_label" + }, "manifest_generate": { "output_format": "excel", "use_annotations": false }, "model_validate": { - "restrict_rules": false + "restrict_rules": false, + "enable_cross_manifest_validation": false }, "model_submit": { - "use_schema_labels": true, + "table_column_names": "display_label", "table_manipulation": "replace", + "annotation_keys": "display_label", "manifest_record_type": "file_only", - "hide_blanks": false + "hide_blanks": false, + "file_annotations_upload": true } } } \ No newline at end of file