{"id":28395139,"url":"https://github.com/databiosphere/bdcat-integration-tests","last_synced_at":"2025-06-27T01:31:37.206Z","repository":{"id":37669025,"uuid":"247141771","full_name":"DataBiosphere/bdcat-integration-tests","owner":"DataBiosphere","description":"This supports integration testing between components for the biodata catalyst grant.","archived":false,"fork":false,"pushed_at":"2023-03-20T21:56:35.000Z","size":3933,"stargazers_count":1,"open_issues_count":5,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-06-01T06:52:19.901Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/DataBiosphere.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-03-13T18:55:02.000Z","updated_at":"2022-09-06T22:39:20.000Z","dependencies_parsed_at":"2023-01-25T04:30:28.544Z","dependency_job_id":null,"html_url":"https://github.com/DataBiosphere/bdcat-integration-tests","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fbdcat-integration-tests","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fbdcat-integration-tests/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fbdcat-integration-tests/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fbdcat-integration-tests/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DataBiosphere","download_url":"https://codeload.github.com/DataBiosphere/bdcat-integration-tests/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fbdcat-integration-tests/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":258620054,"owners_count":22730508,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-05-31T19:39:16.841Z","updated_at":"2025-06-27T01:31:37.191Z","avatar_url":"https://github.com/DataBiosphere.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Biodata Catalyst Integration Testing\n\nDedicated to integration testing between components for the Biodata Catalyst grant.\n\n### How to Trigger Integration Tests Externally\n\nYou will need two tokens:\n\n1. A trigger token for the repository.\n\n1. A personal gitlab API key.\n\n**Note: It's recommended that you create a new github account to act as a test bot to own both tokens rather than using \npersonal accounts.\n\nTo create these two tokens, have your github testing account click the github sign-in button (do not register by \nemail) here: https://biodata-integration-tests.net \n\nIt will say that you are blocked.  Email either lblauvel at ucsc.edu or bhannafi at ucsc.edu to be unblocked \nand added to the integration testing repo.  Please include what team you're with and which external repos will be \nrunning the triggered tests.  Once the account is added, mint the two tokens needed:\n\n1. Make a personal access token (GITLAB_READ_TOKEN): https://docs.gitlab.com/ee/user/profile/personal_access_tokens.html#creating-a-personal-access-token\n\n1. Make a project trigger token (GITLAB_TRIGGER_TOKEN): https://docs.gitlab.com/ee/ci/triggers/#adding-a-new-trigger\n\nThe following is just an example of how to run the repo.  Please use best practice and don't declare env vars in plain \ntext as is done below (i.e. use base64 encoding and fetch from a secret or a secret file; don't allow tokens to be \ncaptured by stdout or your history (stdin)):\n\n```\n# download the repo and setup dependencies\ngit clone https://github.com/DataBiosphere/bdcat-integration-tests.git \u0026\u0026 cd bdcat-integration-tests\nvirtualenv -p python3.7 venv \u0026\u0026 . venv/bin/activate \u0026\u0026 pip install -r requirements.txt\n\n# declare the tokens\nexport GITLAB_READ_TOKEN=somethingsomething\nexport GITLAB_TRIGGER_TOKEN=somethingsomething\n\npython scripts/run_integration_tests.py\n```\n\n# Adding Tests\nSimply submit a PR and flag for review.\n\n# Feedback\nWe welcome feedback and suggestions from any Biodata Catalyst team on useful tests that would help to \nstrengthen the stability of interaction between components.  Please email lblauvel at ucsc.edu.\n\n# Current State of Testing\n\n| From / To     | Terra                    | Gen3                     | Dockstore                | Seven Bridges            | PIC-SURE                 | HeLx |\n| ------------- |:------------------------:|:------------------------:|:------------------------:|:------------------------:|:------------------------:| ----:|\n| Terra         | :heavy_multiplication_x: | :white_check_mark:       | :white_check_mark:       | :heavy_multiplication_x: | Future                   |      |\n| Gen3          | TBD                      | :heavy_multiplication_x: | TBD?                     | TBD?                     |                          |      |\n| Dockstore     |                          |                          | :heavy_multiplication_x: |                          |                          |      |\n| Seven Bridges | :heavy_multiplication_x: | :white_check_mark:       | TBD?                     | :heavy_multiplication_x: | Future                   |      |\n| PIC-SURE      |                          | TBD?                     |                          |                          | :heavy_multiplication_x: |      |\n| HeLx          | TBD?                     | TBD?                     |                          | TBD?                     |                          | :heavy_multiplication_x: |\n\n - :white_check_mark: : Implemented (probably not comprehensively; additional testing suggestions are very welcome)\n - :heavy_multiplication_x: : Not Applicable\n - TBD : To Be Done\n - Future : Tests will be needed, but the features have not been built yet\n\n\nCurrent tests (all are run in each component's Staging environment):\n\nAPI Test 1:\n - Create Terra workspace\n - Import static PFB from Gen3 into workspace\n - Check for success of PFB import into Terra workspace\n - Delete workspace\n\nAPI Test 2:\n - Import from Dockstore workflow to Terra workspace\n - Check presence of Dockstore workflow in Terra workspace\n - Delete Dockstore workflow from terra workspace\n\nAPI Test 3:\n - Run DRS URI in md5sum workflow in Terra\n - Check workflow run success\n \n Currently tested endpoints are:\n\n - https://firecloud-orchestration.dsde-alpha.broadinstitute.org/status\n - https://firecloud-orchestration.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/importPFB\n - https://firecloud-orchestration.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/importPFB/{job_id}\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/submissions\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/methodconfigs\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/methodconfigs?allRepos=true\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/methodconfigs/{billing_project}/{workflow}\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}/submissions/{submission_id}\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces\n - https://rawls.dsde-alpha.broadinstitute.org/api/workspaces/{billing_project}/{workspace}\n - https://staging.gen3.biodatacatalyst.nhlbi.nih.gov/user/data/download/{guid}\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabiosphere%2Fbdcat-integration-tests","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabiosphere%2Fbdcat-integration-tests","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabiosphere%2Fbdcat-integration-tests/lists"}