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* Move DCC config folders in dcc folder * Add dcc tenant config file * Move test fileview configs to test directory * Add github link to each dcc config file * Update links in dca demo config * Remove dcc_config.csv in favour of tenants.json * Update paths to template config files and logos for each DCC * Fix name of EL dca config file * Remove brackets from demo upsert config * Remove out array from json config menu * Update links to template drop down for tests * Use relative filepaths instead of githubusercontent link to config files in demo config * Use relative filepath to dca demo config in tenants.json * Use relative filepath instead of url to reference config files. * Update configs to use relative filepath instead of githubusercontent url * Add schemas for tenants.json and dca_config.json * Change tenants array to an oject * change tenants from array to object and add tenant object * Update dca config schema * correct manifest submit type for GF * Add uri-refernce format to the URL properties of dca config schema * Change tenant schema to an array of objects. Define object specifications in defs * Update tenants.json to an object of arrays * Add github workflow to validate tenants.json * Fix whitespace * remove - from workflow name * remove path trigger for testing * use docker form of json validate * switch json inputs to env vars * fix variable name * add repo to json filepath * tenants.schema not tenant.schema * maybe we don't need the repo dir * remove filler ID field and try using http for schema * test removing the schema * commit an invalid tenants.json to test validation * Fix tenants.json * Add tenant json paths to trigger workflow * Update workflow description * test validate dcc config workflow * fix indentation * Modify smoke test config for test * try filtering modified files * fix smoke test config * test smoke test change * Change file to trigger dca config validation workflow * remove extra echo * test edit to config * remove extra parenthesis from echo * test edit to smoke test json * print config var * change smoke test * remove single quotes in grep * test formatting output with xargs * remove schema from dca config schema for compatibility * set output to json * try splitting file changed list with tr * use space-delimited string for changed file output * quote echo * echo the changed files variable * create filter_file step id to reference varible * fix smoke test config * remove printing config variable for debugging * Update template path for mrt test config * change files changed string to csv instead of space-delimited to handle filenames with spaces * pipe changed files output to tr again to remove new liens * make json files list comma-separated * print env variables to debug * print env variables to debug 2 * print env variables to debug 3 * use sed to remove last comma * Remove printing of env var for debugging * test adding template config workflow in R * remove template config generation workflow. This is in the example data model repo. * Add json schema for template dropdown config * Add workflow to validate template config files * filter files that trigger validation workflows on PR * only run validation if template json files have changed
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# ------------------------------------------------------------------------------ | ||
# Validate a dcc config file against the dca_config schema | ||
# ------------------------------------------------------------------------------ | ||
name: validate dcc config | ||
on: | ||
push: | ||
paths: | ||
- 'dcc/*dca_config.json' | ||
- 'test/*dca_config.json' | ||
- 'schemas/dca_config.schema.json' | ||
pull_request: | ||
branches: | ||
- 'main' | ||
- 'staging' | ||
- 'dev' | ||
paths: | ||
- 'dcc/*dca_config.json' | ||
- 'test/*dca_config.json' | ||
- 'schemas/dca_config.schema.json' | ||
|
||
jobs: | ||
validate-dcc-config: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- id: files | ||
uses: masesgroup/retrieve-changed-files@v3 | ||
with: | ||
format: 'csv' | ||
- id: filter_files | ||
name: Filter files to dca_config.json files | ||
run: | | ||
echo "configs=$(echo ${{ steps.files.outputs.added_modified }} | tr ',' '\n' | grep dca_config\\.json | tr '\n' ',' | sed 's/\(.*\),/\1 /')" >> "$GITHUB_OUTPUT" | ||
- uses: actions/checkout@v4 | ||
- name: Validate JSON | ||
uses: docker://orrosenblatt/validate-json-action:latest | ||
env: | ||
INPUT_SCHEMA: schemas/dca_config.schema.json | ||
INPUT_JSONS: ${{ steps.filter_files.outputs.configs }} | ||
|
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# ------------------------------------------------------------------------------ | ||
# Validate a dca template config file against the dca template config schema | ||
# ------------------------------------------------------------------------------ | ||
name: Validate Template Config | ||
on: | ||
push: | ||
paths: | ||
- 'dcc/*dca-template-config.json' | ||
- 'test/*dca-template-config.json' | ||
- 'schemas/dca_template_config.schema.json' | ||
pull_request: | ||
branches: | ||
- 'main' | ||
- 'staging' | ||
- 'dev' | ||
paths: | ||
- 'dcc/*dca-template-config.json' | ||
- 'test/*dca-template-config.json' | ||
- 'schemas/dca_template_config.schema.json' | ||
|
||
jobs: | ||
validate-template-config: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- id: files | ||
uses: masesgroup/retrieve-changed-files@v3 | ||
with: | ||
format: 'csv' | ||
- id: filter_files | ||
name: Filter files to dca-template-config.json files | ||
run: | | ||
echo "configs=$(echo ${{ steps.files.outputs.added_modified }} | tr ',' '\n' | grep dca-template-config\\.json | tr '\n' ',' | sed 's/\(.*\),/\1 /')" >> "$GITHUB_OUTPUT" | ||
- uses: actions/checkout@v4 | ||
- name: Validate JSON | ||
if: ${{ steps.filter_files.outputs.configs != '' }} | ||
uses: docker://orrosenblatt/validate-json-action:latest | ||
env: | ||
INPUT_SCHEMA: schemas/dca_template_config.schema.json | ||
INPUT_JSONS: ${{ steps.filter_files.outputs.configs }} |
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# ------------------------------------------------------------------------------ | ||
# Validate the tenants.json file against the tenants.schema.json schema | ||
# ------------------------------------------------------------------------------ | ||
name: validate tenants config | ||
on: | ||
push: | ||
paths: | ||
- 'tenants.json' | ||
- 'schemas/tenants.schema.json' | ||
pull_request: | ||
branches: | ||
- 'main' | ||
- 'staging' | ||
- 'dev' | ||
paths: | ||
- 'tenants.json' | ||
- 'schemas/tenants.schema.json' | ||
|
||
jobs: | ||
validate-tenants-config: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- name: Validate JSON | ||
uses: docker://orrosenblatt/validate-json-action:latest | ||
env: | ||
INPUT_SCHEMA: schemas/tenants.schema.json | ||
INPUT_JSONS: tenants.json |
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{ | ||
"project_name":"AD Knowledge Portal", | ||
"synapse_asset_view":"syn51324810", | ||
"data_model_url":"https://raw.githubusercontent.com/adknowledgeportal/data-models/main/divco.data.model.v1.jsonld", | ||
"template_menu_config_file":"dcc/ADKP/dca-template-config.json", | ||
"logo_location":"dcc/ADKP/ADKnowledgePortal.png", | ||
"logo_link":"https://adknowledgeportal.synapse.org", | ||
"manifest_output_format":"excel", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"file_only", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e71", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"BTC DCC", | ||
"synapse_asset_view":"syn51407795", | ||
"data_model_url":"https://raw.githubusercontent.com/Sage-Bionetworks/btc-data-models/main/btc.model.jsonld", | ||
"template_menu_config_file":"dcc/BTC/dca-template-config.json", | ||
"manifest_output_format":"excel", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e72", | ||
"sidebar_col":"#191920" | ||
} |
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{ | ||
"project_name":"EL", | ||
"synapse_asset_view":"syn51753858", | ||
"data_model_url":"https://raw.githubusercontent.com/Sage-Bionetworks/ELITE-data-models/main/example.model.jsonld", | ||
"template_menu_config_file":"dcc/EL/dca-template-config.json", | ||
"manifest_output_format":"excel", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e71", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"Gray Foundation", | ||
"synapse_asset_view":"syn28142805", | ||
"data_model_url":"https://raw.githubusercontent.com/gf-dcc/data-model/v1.1.0-rc/GF.jsonld", | ||
"template_menu_config_file":"dcc/GF/dca-template-config.json", | ||
"manifest_output_format":"google_sheet", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":true, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e71", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"HTAN All Projects", | ||
"synapse_asset_view":"syn20446927", | ||
"data_model_url":"https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", | ||
"template_menu_config_file":"dcc/HTAN/dca-template-config.json", | ||
"logo_location":"dcc/HTAN/HTAN_text_logo.png", | ||
"logo_link":"https://humantumoratlas.org", | ||
"manifest_output_format":"google_sheet", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"file_only", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#605ca8", | ||
"secondary_col":"#5F008C", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"Cancer Complexity Knowledge Portal - Database", | ||
"synapse_asset_view":"syn27210848", | ||
"data_model_url":"https://raw.githubusercontent.com/mc2-center/data-models/main/mc2.model.jsonld", | ||
"template_menu_config_file":"dcc/MC2/dca-template-config.json", | ||
"logo_location":"dcc/MC2/cckp_logo.png", | ||
"logo_link":"https://cancercomplexity.synapse.org", | ||
"manifest_output_format":"excel", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":false, | ||
"submit_table_manipulation":"upsert", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#407BA0", | ||
"secondary_col":"#5BB0B5", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"NF-OSI", | ||
"synapse_asset_view":"syn16858331", | ||
"data_model_url":"https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v8.0.1/NF.jsonld", | ||
"template_menu_config_file":"dcc/NF-OSI/dca-template-config.json", | ||
"manifest_output_format":"google_sheet", | ||
"manifest_use_annotations":true, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":true, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e71", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"VEOIBD", | ||
"synapse_asset_view":"syn51397378", | ||
"data_model_url":"https://raw.githubusercontent.com/VEOIBD/data_models/main/veoibd.data.model.jsonld", | ||
"template_menu_config_file":"dcc/VEOIBD/dca-template-config.json", | ||
"logo_location":"dcc/VEOIBD/VEOIBD Logo.png", | ||
"logo_link":"https://veoibd.org", | ||
"manifest_output_format":"excel", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":true, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"upsert", | ||
"submit_manifest_record_type":"file_only", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e72", | ||
"sidebar_col":"#191920" | ||
} |
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{ | ||
"project_name":"DCA Demo", | ||
"synapse_asset_view":"syn33715412", | ||
"data_model_url":"https://raw.githubusercontent.com/Sage-Bionetworks/data-models/main/example.model.jsonld", | ||
"data_model_info": "", | ||
"template_menu_config_file":"dcc/demo/dca-template-config.json", | ||
"logo_location":"dcc/demo/Logo_Sage_Logomark.png", | ||
"logo_link":"https://synapse.org", | ||
"dcc_help_link": "", | ||
"manifest_output_format":"google_sheet", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":true, | ||
"submit_table_manipulation":"replace", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e71", | ||
"sidebar_col":"#191919" | ||
} |
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{ | ||
"project_name":"DCA Demo Upsert", | ||
"synapse_asset_view":"syn51489635", | ||
"data_model_url":"https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld", | ||
"template_menu_config_file":"dcc/demo_upsert/dca-template-config.json", | ||
"manifest_output_format":"excel", | ||
"manifest_use_annotations":false, | ||
"validate_restrict_rules":false, | ||
"submit_use_schema_labels":false, | ||
"submit_table_manipulation":"upsert", | ||
"submit_manifest_record_type":"table_and_file", | ||
"submit_hide_blanks":false, | ||
"use_compliance_dashboard":false, | ||
"primary_col":"#2a668d", | ||
"secondary_col":"#184e71", | ||
"sidebar_col":"#191919" | ||
} |
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