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 <[email protected]> * 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 <[email protected]> Co-authored-by: Dan Lu <[email protected]> Co-authored-by: Adam Taylor <[email protected]> Co-authored-by: Nicholas Lee <[email protected]> Co-authored-by: Orion Banks <[email protected]> Co-authored-by: Bankso <[email protected]> Co-authored-by: Abby Vander Linden <[email protected]> Co-authored-by: Christina Conrad <[email protected]>
Sage-Bionetworks · Jul 8, 2024 · ad26123 · ad26123
1 parent 3143349
commit ad26123
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Showing 3 changed files with 4 additions and 29 deletions.
diff --git 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
@@ -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
@@ -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
     }
   }
-}
+}