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/ADKP/dca_config.json b/ADKP/dca_config.json index bfe252b..b9b3b09 100644 --- a/ADKP/dca_config.json +++ b/ADKP/dca_config.json @@ -7,8 +7,8 @@ "template_menu_config_file": "https://raw.githubusercontent.com/adknowledgeportal/data-models/main/dca-template-config.json", "logo_location": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/ADKP/ADKnowledgePortal.png", "logo_link": "https://adknowledgeportal.synapse.org", - "dcc_help_link": "", - "portal_help_link": "" + "dcc_help_link": "https://dca-docs.scrollhelp.site/DCA/Working-version/Project-Agnostic/", + "portal_help_link": "https://help.adknowledgeportal.org/apd/" }, "dca": { "use_compliance_dashboard": false, @@ -25,7 +25,8 @@ "use_annotations": true }, "model_validate": { - "restrict_rules": false + "restrict_rules": false, + "enable_cross_manifest_validation": true }, "model_submit": { "table_column_names": "display_label", diff --git a/EL/dca_config.json b/EL/dca_config.json index bab7dce..33f51a8 100644 --- a/EL/dca_config.json +++ b/EL/dca_config.json @@ -27,7 +27,7 @@ "model_submit": { "use_schema_labels": true, "table_manipulation": "replace", - "manifest_record_type": "table_and_file", + "manifest_record_type": "file_only", "hide_blanks": false } } diff --git a/HTAN/dca_config.json b/HTAN/dca_config.json index dbbfafa..603a437 100644 --- a/HTAN/dca_config.json +++ b/HTAN/dca_config.json @@ -1,14 +1,14 @@ { "dcc": { - "name": "HTAN All Projects", + "name": "HTAN Phase 1 All Projects", "synapse_asset_view": "syn20446927", - "data_model_url": "https://raw.githubusercontent.com/ncihtan/data-models/v24.5.2/HTAN.model.jsonld", + "data_model_url": "https://raw.githubusercontent.com/ncihtan/data-models/v24.9.1/HTAN.model.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/ncihtan/data-models/v24.5.2/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/ncihtan/data-models/v24.9.1/dca-template-config.json", "logo_location": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/HTAN/HTAN_text_logo.png", "logo_link": "https://humantumoratlas.org", - "dcc_help_link": "", - "portal_help_link": "" + "dcc_help_link": 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"portal_help_link": "https://docs.humantumoratlas.org/" + }, + "dca": { + "use_compliance_dashboard": false, + "primary_col": "#605ca8", + "secondary_col": "#5F008C", + "sidebar_col": "#191919" + }, + "schematic": { + "manifest_generate": { + "output_format": "google_sheet", + "use_annotations": false + }, + "model_validate": { + "restrict_rules": false + }, + "model_submit": { + "use_schema_labels": true, + "table_manipulation": "replace", + "manifest_record_type": "file_only", + "hide_blanks": false + } + } +} diff --git a/MC2/dca_config.json b/MC2/dca_config.json index bdc6d60..844d8bb 100644 --- a/MC2/dca_config.json +++ b/MC2/dca_config.json @@ -2,9 +2,9 @@ "dcc": { "name": "Cancer Complexity Knowledge Portal - Database", "synapse_asset_view": "syn27210848", - "data_model_url": "https://raw.githubusercontent.com/mc2-center/data-models/v5.1.2/mc2.model.jsonld", + "data_model_url": "https://raw.githubusercontent.com/mc2-center/data-models/v7.1.0/mc2.model.jsonld", "data_model_info": 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100644 --- a/NF-OSI/dca_config.json +++ b/NF-OSI/dca_config.json @@ -2,9 +2,9 @@ "dcc": { "name": "NF-OSI", "synapse_asset_view": "syn16858331", - "data_model_url": "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v9.3.0/NF.jsonld", + "data_model_url": "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v9.9.0/NF.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v9.3.0/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v9.9.0/dca-template-config.json", "logo_location": "", "logo_link": "", "dcc_help_link": "", @@ -17,6 +17,9 @@ "sidebar_col": "#191919" }, "schematic": { + "global": { + "data_model_labels": "class_label" + }, "manifest_generate": { "output_format": "google_sheet", "use_annotations": true @@ -25,7 +28,6 @@ "restrict_rules": false }, "model_submit": { - "use_schema_labels": true, "table_manipulation": "replace", "manifest_record_type": "table_and_file", "hide_blanks": true, diff --git a/README.md b/README.md index e2fb731..6e35caa 100644 --- a/README.md +++ b/README.md @@ -43,6 +43,7 @@ Each DCC will have its own directory to store configuration files. At minimum it - `model_validate` - `restrict_rules`: `TRUE` or `FALSE`. [Schematic model validate and submit option](https://sage-schematic.readthedocs.io/en/develop/cli_reference.html#schematic-model-validate). + - `enable_cross_manifest_validation`: `TRUE` or `FALSE`. Use cross manifest validation. - `model_submit` 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 diff --git a/demo/dca-template-config.json b/demo/dca-template-config.json index 2963c67..911e337 100644 --- a/demo/dca-template-config.json +++ b/demo/dca-template-config.json @@ -18,9 +18,14 @@ { "display_name": "Other Assay", "schema_name": "OtherAssay", + "type": "file" + }, + { + "display_name": "MockComponent", + "schema_name": "MockComponent", "type": "record" } ], - "service_version": "v23.1.1", + "service_version": "v24.7.2", "schema_version": "" -} +} \ No newline at end of file diff --git a/tenants.json b/tenants.json index 6d22b4b..9c22549 100644 --- a/tenants.json +++ b/tenants.json @@ -26,7 +26,7 @@ "config_location":"BTC/dca_config.json" }, { - "name":"HTAN All Projects", + "name":"HTAN Phase 1 All Projects", "synapse_asset_view":"syn20446927", "config_location":"HTAN/dca_config.json" }, @@ -49,6 +49,11 @@ "name":"DCA Demo Upsert", "synapse_asset_view":"syn51489635", "config_location":"demo_upsert/dca_config.json" + }, + { + "name":"HTAN Phase 2 All Projects", + "synapse_asset_view":"syn63714258", + "config_location":"HTAN2/dca_config.json" } ] }