Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Galaxy API endpoints without a corresponding BioBlend method #352

Open
simonbray opened this issue Nov 5, 2020 · 3 comments
Open

Galaxy API endpoints without a corresponding BioBlend method #352

simonbray opened this issue Nov 5, 2020 · 3 comments
Labels
paper-cut

Comments

@simonbray
Copy link
Member

Let's try and document missing API endpoints (located https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/webapps/galaxy/api) in this issue.

(Not that we need to implement everything, but so the information is available.)

ping @beatrizserrano
@simonbray simonbray assigned simonbray and unassigned simonbray Nov 5, 2020
@nsoranzo
Copy link
Member

nsoranzo commented Nov 5, 2020

Is this for missing BioBlend endpoints that exist in Galaxy API, or missing Galaxy API endpoint?

@simonbray simonbray changed the title Missing endpoints Galaxy API endpoints without a corresponding bioblend function/method Nov 5, 2020
@nsoranzo nsoranzo changed the title Galaxy API endpoints without a corresponding bioblend function/method Galaxy API endpoints without a corresponding BioBlend method Nov 5, 2020
@mvdbeek
Copy link
Member

mvdbeek commented Nov 5, 2020 •
edited by simonbray
Loading

If you want to see a list of available endpoints I spent some time improving James' apispec PR last year:
galaxyproject/galaxy@dev...mvdbeek:openapi_spec

If you start Galaxy up on that branch and go to /api/docs you'll get this:

  • /api/histories/{history_id}/contents/{type}s
    • post
    • get
  • /api/histories/{history_id}/contents/{type}
    • put
    • delete
    • get
  • /api/histories/{history_id}/contents
    • post
    • get
    • put
  • /api/histories/{history_id}/contents/{id}
    • put
    • delete
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/display
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/permissions
    • put
  • /api/histories/{history_id}/contents/{history_content_id}/validate
    • put
  • /api/histories/{history_id}/contents/{history_content_id}/extra_files
    • get
  • /api/datasets/{dataset_id}/get_content_as_text
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/metadata_file
    • get
  • /api/groups/{group_id}/users
    • get
  • /api/groups/{group_id}/users/{id}
    • put
    • delete
    • get
  • /api/groups/{group_id}/roles
    • get
  • /api/groups/{group_id}/roles/{id}
    • put
    • delete
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/tags
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/tags/{tag_name}
    • delete
    • post
    • put
    • get
  • /api/histories/published
    • get
  • /api/histories/shared_with_me
  • /api/cloud/storage/
    • get
  • /api/cloud/storage/get
    • post
  • /api/cloud/storage/send
    • post
  • /api/histories/{history_id}/tags
    • get
  • /api/histories/{history_id}/tags/{tag_name}
    • delete
    • post
    • put
    • get
  • /api/workflows/{workflow_id}/tags
    • get
  • /api/workflows/{workflow_id}/tags/{tag_name}
    • delete
    • post
    • put
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/annotation
    • post
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/annotation/{id}
    • delete
  • /api/histories/{history_id}/annotation
    • post
    • get
  • /api/histories/{history_id}/annotation/{id}
    • delete
  • /api/workflows/{workflow_id}/annotation
    • post
    • get
  • /api/workflows/{workflow_id}/annotation/{id}
    • delete
  • /api/histories/{history_id}/contents/{history_content_id}/provenance
    • post
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/provenance/{id}
    • delete
    • get
  • /api/datasets
    • get
  • /api/datasets/{id}
    • get
  • /api/tool_data
    • get
  • /api/tool_data/{id}
    • delete
    • get
  • /api/tool_data/{id}/reload
  • /api/dataset_collections
    • post
    • get
  • /api/dataset_collections/{id}
    • get
  • /api/dataset_collections/{hdca_id}/contents/{parent_id}
  • /api/forms
    • post
    • get
  • /api/forms/{id}
    • get
  • /api/roles
    • post
    • get
  • /api/roles/{id}
    • get
  • /api/uploads
    • post
    • get
  • /api/remote_files
    • get
  • /api/remote_files/plugins
    • get
  • /api/groups
    • post
    • get
  • /api/groups/{id}
    • put
    • get
  • /api/quotas/deleted
    • get
  • /api/quotas/deleted/{id}
    • get
  • /api/quotas/deleted/{id}/undelete
    • post
  • /api/quotas
    • post
    • get
  • /api/quotas/{id}
    • put
    • delete
    • get
  • /api/cloud/authz/
    • get
    • post
  • /api/cloud/authz/{encoded_authz_id}
    • delete
    • put
  • /api/histories/{id}/custom_builds_metadata
    • get
  • /api/tools/fetch
    • post
  • /api/tools/all_requirements
  • /api/tools/error_stack
  • /api/tools/{id}/build
  • /api/tools/{id}/reload
  • /api/tools/tests_summary
  • /api/tools/{id}/test_data_path
  • /api/tools/{id}/test_data_download
  • /api/tools/{id}/test_data
  • /api/tools/{id}/diagnostics
  • /api/tools/{id}/citations
  • /api/tools/{id}/xrefs
  • /api/tools/{id}/download
  • /api/tools/{id}/requirements
  • /api/tools/{id}/install_dependencies
    • post
  • /api/tools/{id}/dependencies
    • post
    • delete
  • /api/tools/{id}/build_dependency_cache
    • post
  • /api/tools/{id}
    • get
  • /api/tools
    • post
    • get
  • /api/dynamic_tools
    • post
    • get
  • /api/dynamic_tools/{id}
    • delete
    • get
  • /api/entry_points
  • /api/entry_points/{id}/access
  • /api/dependency_resolvers/clean
    • post
  • /api/dependency_resolvers/dependency
    • get
    • post
  • /api/dependency_resolvers/requirements
  • /api/dependency_resolvers/unused_paths
    • get
    • put
  • /api/dependency_resolvers/toolbox
    • get
  • /api/dependency_resolvers/toolbox/install
    • post
  • /api/dependency_resolvers/toolbox/uninstall
    • post
  • /api/dependency_resolvers/{index}/clean
    • post
  • /api/dependency_resolvers/{index}/dependency
    • get
    • post
  • /api/dependency_resolvers/{index}/requirements
  • /api/dependency_resolvers
    • get
  • /api/dependency_resolvers/{id}
    • put
    • get
  • /api/container_resolvers
    • get
  • /api/container_resolvers/resolve
    • get
  • /api/container_resolvers/toolbox
    • get
  • /api/container_resolvers/resolve/install
    • post
  • /api/container_resolvers/toolbox/install
    • post
  • /api/container_resolvers/{index}
    • get
  • /api/container_resolvers/{index}/resolve
    • get
  • /api/container_resolvers/{index}/toolbox
    • get
  • /api/container_resolvers/{index}/resolve/install
    • post
  • /api/container_resolvers/{index}/toolbox/install
    • post
  • /api/workflows/get_tool_predictions
    • post
  • /api/users/deleted
    • get
  • /api/users/deleted/{id}
    • get
  • /api/users/deleted/{id}/undelete
    • post
  • /api/users
    • post
    • get
  • /api/users/{id}
    • put
    • delete
    • get
  • /api/genomes
    • get
  • /api/genomes/{id}
    • get
  • /api/genomes/{id}/indexes
  • /api/genomes/{id}/sequences
  • /api/visualizations
    • post
    • get
  • /api/visualizations/{id}
    • put
    • get
  • /api/visualizations/{id}/sharing
    • get
    • post
  • /api/plugins
    • get
  • /api/plugins/{id}
    • get
  • /api/workflows/build_module
  • /api/workflows/menu
    • get
    • put
  • /api/workflows
    • post
    • get
  • /api/workflows/{id}
    • put
    • delete
    • get
  • /api/histories/deleted
    • get
  • /api/histories/deleted/{id}
    • get
  • /api/histories/deleted/{id}/undelete
    • post
  • /api/histories
    • post
    • get
  • /api/histories/{id}
    • put
    • delete
    • get
  • /api/histories/{history_id}/citations
  • /api/histories/{id}/sharing
    • get
    • post
  • /api/configuration/dynamic_tool_confs
  • /api/configuration/tool_lineages
  • /api/configuration/toolbox
    • put
  • /api/configuration
    • get
  • /api/version
    • get
  • /api/whoami
    • get
  • /api/configuration/decode/{encoded_id}
    • get
  • /api/datatypes/sniffers
    • get
  • /api/datatypes/mapping
    • get
  • /api/datatypes/converters
    • get
  • /api/datatypes/edam_data
    • get
  • /api/datatypes/edam_formats
    • get
  • /api/datatypes/types_and_mapping
    • get
  • /api/datatypes
    • get
  • /api/search
    • post
  • /api/pages/{id}.pdf
    • get
  • /api/pages
    • post
    • get
  • /api/pages/{id}
    • delete
    • get
  • /api/pages/{id}/sharing
    • get
    • post
  • /api/pages/{page_id}/revisions
    • post
    • get
  • /api/histories/{id}/exports
    • put
  • /api/histories/{id}/exports/{jeha_id}
    • get
  • /api/histories/{history_id}/contents/archive
  • /api/histories/{history_id}/contents/archive/{filename}{.format}
  • /api/histories/{history_id}/contents/dataset_collections/{id}/download
    • get
  • /api/dataset_collections/{id}/download
    • get
  • /api/histories/{history_id}/jobs_summary
    • get
  • /api/histories/{history_id}/contents/{type}/jobs_summary
    • get
  • /api/workflows/upload
    • post
  • /api/workflows/{workflow_id}/download
    • get
  • /api/workflows/{workflow_id}/versions
    • get
  • /api/workflows/download/{workflow_id}
    • get
  • /api/workflows/import
    • post
  • /api/trs_search
    • get
  • /api/trs_consume/servers
    • get
  • /api/trs_consume/{trs_server}/tools/{tool_id}
    • get
  • /api/datasets/{dataset_id}/converted
  • /api/datasets/{dataset_id}/converted/{ext}
  • /api/datasets/{dataset_id}/permissions
    • put
  • /api/invocations
    • get
  • /api/workflows/{workflow_id}/invocations
    • get
    • post
  • /api/workflows/{workflow_id}/usage
    • get
    • post
  • /api/workflows/{workflow_id}/invocations/{invocation_id}
    • get
    • delete
  • /api/workflows/{workflow_id}/usage/{invocation_id}
    • get
    • delete
  • /api/invocations/{invocation_id}
    • get
    • delete
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/report
    • get
  • /api/workflows/{workflow_id}/usage/{invocation_id}/report
    • get
  • /api/invocations/{invocation_id}/report
    • get
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf
    • get
  • /api/workflows/{workflow_id}/usage/{invocation_id}/report.pdf
    • get
  • /api/invocations/{invocation_id}/report.pdf
    • get
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/biocompute/download
    • get
  • /api/workflows/{workflow_id}/usage/{invocation_id}/biocompute/download
    • get
  • /api/invocations/{invocation_id}/biocompute/download
    • get
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/biocompute
    • get
  • /api/workflows/{workflow_id}/usage/{invocation_id}/biocompute
    • get
  • /api/invocations/{invocation_id}/biocompute
    • get
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary
    • get
  • /api/workflows/{workflow_id}/usage/{invocation_id}/jobs_summary
    • get
  • /api/invocations/{invocation_id}/jobs_summary
    • get
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary
    • get
  • /api/workflows/{workflow_id}/usage/{invocation_id}/step_jobs_summary
    • get
  • /api/invocations/{invocation_id}/step_jobs_summary
    • get
  • /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id}
    • get
    • put
  • /api/workflows/{workflow_id}/usage/{invocation_id}/steps/{step_id}
    • get
    • put
  • /api/invocations/{invocation_id}/steps/{step_id}
    • get
    • put
  • /api/authenticate/baseauth/
    • get
  • /api/{path_info}
    • options
  • /api/display_applications
    • get
  • /api/display_applications/reload
    • post
  • /api/tours
    • get
  • /api/tours/{tour_id}
    • get
    • post
  • /api/users/{id}/api_key
    • post
  • /api/users/{id}/api_key/inputs
    • get
    • put
  • /api/users/{id}/information/inputs
    • get
    • put
  • /api/users/{id}/password/inputs
    • get
    • put
  • /api/users/{id}/permissions/inputs
    • get
    • put
  • /api/users/{id}/toolbox_filters/inputs
    • get
    • put
  • /api/users/{id}/custom_builds
    • get
  • /api/users/{id}/custom_builds/{key}
    • put
    • delete
  • /api/users/{id}/favorites/{object_type}
    • put
  • /api/users/{id}/favorites/{object_type}/{object_id}
    • delete
  • /api/webhooks
    • get
  • /api/webhooks/{webhook_id}/data
    • get
  • /api/tags
    • put
  • /api/libraries/{id}
    • patch
    • put
    • delete
    • get
  • /api/libraries/{encoded_library_id}/permissions
    • get
    • post
    • put
  • /api/libraries/datasets/{id}
    • get
  • /api/libraries/datasets/
    • post
  • /api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}
    • get
  • /api/libraries/datasets/{encoded_dataset_id}
    • patch
    • delete
  • /api/libraries/datasets/{encoded_dataset_id}/permissions
    • get
    • post
  • /api/libraries/datasets/download/{archive_format}
    • post
    • get
  • /api/libraries/deleted
    • get
  • /api/libraries/deleted/{id}
    • get
  • /api/libraries
    • post
    • get
  • /api/libraries/{library_id}/contents
    • post
    • get
  • /api/libraries/{library_id}/contents/{id}
    • put
    • delete
    • get
  • /api/libraries/{library_id}/contents/{library_content_id}/extended_metadata
    • post
    • get
  • /api/libraries/{library_id}/contents/{library_content_id}/extended_metadata/{id}
    • delete
  • /api/folders/{encoded_folder_id}/contents
    • post
  • /api/folders/{encoded_parent_folder_id}
    • post
  • /api/folders/{encoded_folder_id}
    • delete
    • patch
    • put
  • /api/folders
    • post
    • get
  • /api/folders/{id}
    • put
    • delete
    • get
  • /api/folders/{encoded_folder_id}/permissions
    • get
    • post
  • /api/folders/{folder_id}/contents
    • post
    • get
  • /api/folders/{folder_id}/contents/{id}
    • put
    • get
  • /api/jobs
    • post
    • get
  • /api/jobs/{id}
    • delete
    • get
  • /api/jobs/search
    • post
  • /api/jobs/{id}/inputs
    • get
  • /api/jobs/{id}/outputs
    • get
  • /api/jobs/{id}/build_for_rerun
    • get
  • /api/jobs/{id}/resume
    • put
  • /api/jobs/{id}/error
    • post
  • /api/jobs/{id}/common_problems
    • get
  • /api/jobs/{job_id}/metrics
    • get
  • /api/jobs/{job_id}/destination_params
    • get
  • /api/job_lock
    • get
    • put
  • /api/datasets/{dataset_id}/metrics
    • get
  • /api/jobs/{job_id}/parameters_display
    • get
  • /api/datasets/{dataset_id}/parameters_display
    • get
  • /api/jobs/{job_id}/files
    • post
    • get
  • /api/jobs/{job_id}/ports
    • post
  • /api/histories/{history_id}/contents/{history_content_id}/extended_metadata
    • post
    • get
  • /api/histories/{history_id}/contents/{history_content_id}/extended_metadata/{id}
    • delete
  • /api/tool_shed
    • get
  • /api/tool_shed/request
    • get
  • /api/tool_shed_repositories
    • post
    • delete
    • get
  • /api/tool_shed_repositories/check_for_updates
    • get
  • /api/tool_shed_repositories/{id}
    • delete
    • get
  • /api/tool_shed_repositories/reset_metadata_on_selected_installed_repositories
    • post
  • /api/tool_shed_repositories/reset_metadata_on_installed_repositories
    • post
  • /api/tool_shed_repositories/new/install_repository_revision
    • post
  • /api/metrics
    • post
  • /api/docs
    • get

Those should be all API routes known to Galaxy.

@simonbray
Copy link
Member Author

Oh, that's cool. Thanks @mvdbeek! @gallardoalba @beatrizserrano this should help you a lot.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
paper-cut
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@nsoranzo @mvdbeek @simonbray