diff --git a/dcc/BTC/dca_config.json b/dcc/BTC/dca_config.json index 0aa7146..24cc361 100644 --- a/dcc/BTC/dca_config.json +++ b/dcc/BTC/dca_config.json @@ -4,7 +4,7 @@ "synapse_asset_view": "syn51407795", "data_model_url": "https://raw.githubusercontent.com/Sage-Bionetworks/btc-data-models/main/btc.model.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/BTC/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/BTC/dca-template-config.json", "logo_location": "", "logo_link": "", "dcc_help_link": "", diff --git a/dcc/EL/dca_config.json b/dcc/EL/dca_config.json index 47cf04a..e66e4d6 100644 --- a/dcc/EL/dca_config.json +++ b/dcc/EL/dca_config.json @@ -4,7 +4,7 @@ "synapse_asset_view": "syn51753858", "data_model_url": "https://raw.githubusercontent.com/Sage-Bionetworks/ELITE-data-models/main/example.model.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/EL/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/EL/dca-template-config.json", "logo_location": "", "logo_link": "", "dcc_help_link": "", diff --git a/dcc/GF/dca_config.json b/dcc/GF/dca_config.json index 4a9e5b8..9caadce 100644 --- a/dcc/GF/dca_config.json +++ b/dcc/GF/dca_config.json @@ -4,7 +4,7 @@ "synapse_asset_view": "syn28142805", "data_model_url": "https://raw.githubusercontent.com/gf-dcc/data-model/v1.1.0-rc/GF.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/GF/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/GF/dca-template-config.json", "logo_location": "", "logo_link": "", "dcc_help_link": "", diff --git a/dcc/MC2/dca_config.json b/dcc/MC2/dca_config.json index 81da481..cb70f1c 100644 --- a/dcc/MC2/dca_config.json +++ b/dcc/MC2/dca_config.json @@ -4,7 +4,7 @@ "synapse_asset_view": "syn27210848", "data_model_url": "https://raw.githubusercontent.com/mc2-center/data-models/main/mc2.model.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/MC2/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/mc2-center/data-models/v5.1.2/dca_config/dca-template-config.json", "logo_location": "dcc/MC2/cckp_logo.png", "logo_link": "https://cancercomplexity.synapse.org", "dcc_help_link": "", diff --git a/dcc/VEOIBD/dca_config.json b/dcc/VEOIBD/dca_config.json index d48e77e..e774bad 100644 --- a/dcc/VEOIBD/dca_config.json +++ b/dcc/VEOIBD/dca_config.json @@ -4,7 +4,7 @@ "synapse_asset_view": "syn51397378", "data_model_url": "https://raw.githubusercontent.com/VEOIBD/data_models/main/veoibd.data.model.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/VEOIBD/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/VEOIBD/dca-template-config.json", "logo_location": "dcc/VEOIBD/VEOIBD Logo.png", "logo_link": "https://veoibd.org", "dcc_help_link": "", diff --git a/dcc/demo_upsert/dca_config.json b/dcc/demo_upsert/dca_config.json index a12c3f7..1cb6125 100644 --- a/dcc/demo_upsert/dca_config.json +++ b/dcc/demo_upsert/dca_config.json @@ -4,7 +4,7 @@ "synapse_asset_view": "syn51489635", "data_model_url": "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld", "data_model_info": "", - "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/dca-template-config.json", + "template_menu_config_file": "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/demo/dca-template-config.json", "logo_location": "", "logo_link": "", "dcc_help_link": "", diff --git a/schemas/dca_config.schema.json b/schemas/dca_config.schema.json index c4c20e2..6675031 100644 --- a/schemas/dca_config.schema.json +++ b/schemas/dca_config.schema.json @@ -1,14 +1,23 @@ { "title": "Configuration for individual DCCs in mtDCA", "description": "Configuration options for a specific DCC in mtDCA", - "type": "object", "required": [ "dcc", "dca", "schematic" ], "additionalProperties": false, "properties": { "dcc": { "description": "DCC parameters", "type": "object", - "required": [ "name", "synapse_asset_view", "data_model_url", "template_menu_config_file" ], + "required": [ + "name", + "synapse_asset_view", + "data_model_url", + "data_model_info", + "template_menu_config_file", + "logo_location", + "logo_link", + "dcc_help_link", + "portal_help_link" + ], "properties": { "name": { "description": "Name of the DCC", @@ -55,6 +64,12 @@ "dca": { "description": "DCA configuration options", "type": "object", + "required": [ + "use_compliance_dashboard", + "primary_col", + "secondary_col", + "sidebar_col" + ], "properties": { "use_compliance_dashboard": { "description": "Display the compliance dashboard. Unavaible at the moment", @@ -80,9 +95,26 @@ "schematic": { "description": "Schematic configuration options", "type": "object", - "required": [ "manifest_generate", "model_validate", "model_submit" ], + "required": [ + "global", + "manifest_generate", + "model_validate", + "model_submit" + ], "additionalProperties": false, "properties": { + "global": { + "description": "Parameters common to many schematic commands", + "type": "object", + "required": [ "data_model_labels" ], + "properties": { + "data_model_labels": { + "description": "Source for labels of the data model", + "type": "string", + "enum": [ "class_label", "display_label" ] + } + } + }, "manifest_generate": { "description": "Parameters to pass to Schematic manifest generate", "type": "object", @@ -103,25 +135,44 @@ "model_validate": { "description": "Parameteres to pass to Schematic model validate", "type": "object", - "required": [ "restrict_rules" ], + "required": [ + "restrict_rules", + "enable_cross_manifest_validation" + ], "additionalProperties": false, "properties": { "restrict_rules": { "description": "Schematic model validate option", "type": "boolean" + }, + "enable_cross_manifest_validation": { + "description": "Use cross manifest validation", + "type": "boolean" } } }, "model_submit": { "description": "Parameters to pass Schematic model submit", "type": "object", - "required": [ "use_schema_labels", "table_manipulation", - "manifest_record_type", "hide_blanks" ], + "required": [ + "table_manipulation", + "manifest_record_type", + "hide_blanks", + "annotation_keys", + "table_column_names", + "file_annotations_upload" + ], "additionalProperties": false, "properties": { - "use_schema_labels": { + "annotation_keys": { "description": "Schematic model submit option", - "type": "boolean" + "type": "string", + "enum": [ "class_label", "display_label" ] + }, + "table_column_names": { + "description": "Schematic model submit option", + "type": "string", + "enum": [ "class_label", "display_label", "display_name" ] }, "table_manipulation": { "description": "Schematic model submit option", @@ -136,11 +187,14 @@ "hide_blanks": { "description": "Schematic model submit option", "type": "boolean" + }, + "file_annotations_upload": { + "description": "Choose to add annotations to files during upload", + "type": "boolean" } - } + } } } } } } - diff --git a/test/smoke_test_dca_config.json b/test/smoke_test_dca_config.json index 28b6fe7..e2092cb 100644 --- a/test/smoke_test_dca_config.json +++ b/test/smoke_test_dca_config.json @@ -29,7 +29,7 @@ "table_manipulation": "replace", "manifest_record_type": "table_and_file", "hide_blanks": false, - "upload_file_annotations":true + "file_annotations_upload":true } } } diff --git a/test/test_cross_manifest_validation_type_dca_config.json b/test/test_cross_manifest_validation_type_dca_config.json index d54bf64..b8cd80b 100644 --- a/test/test_cross_manifest_validation_type_dca_config.json +++ b/test/test_cross_manifest_validation_type_dca_config.json @@ -22,7 +22,8 @@ "use_annotations": false }, "model_validate": { - "restrict_rules": false + "restrict_rules": false, + "enable_cross_manifest_validation": true }, "model_submit": { "use_schema_labels": true,