Dockstore '/workflows/published/{workflowId}' returns inconsistent workflow_path for workflows imported via GitHub App

[yihming]

Hello,

I’ve been using Dockstore API “/workflows/published/{workflowId}” to get the path of a published WDL workflow.

However, I found that if a workflow is imported using GitHub App with “.dockstore.yml” associated, its top-level “workflow_path” will be pointed to this yml file, instead of the correct WDL file.

For example, I have a WDL workflow “Cellranger”: one with ID 14403 imported manually (Dockstore), while the other with ID 17687 imported using GitHub App (Dockstore).

The manually imported workflow has the top-level “workflow_path” be "/workflows/cellranger/cellranger_workflow.wdl". However, the GitHub App imported workflow has the top-level “workflow_path” be "/.dockstore.yml".

Can anyone help me understand why this inconsistency happens? If there is something I didn’t set up correctly for the GitHub App imported workflow, could you please guide me on fixing it?

Thanks!

Sincerely,
Yiming

[yihming]

Below is the request returned JSON content of workflow ID 17687. You can see that “workflow_path” near the bottom of the file is incorrectly pointed to “/.dockstore.yml”, while all its versions in “workflowVersions” has “workflow_path” set correctly to the WDL file.

{
    "type": "BioWorkflow",
    "descriptorType": "WDL",
    "aliases": {},
    "author": "Cumulus Team",
    "checker_id": null,
    "conceptDoi": null,
    "dbCreateDate": 1647045825923,
    "dbUpdateDate": 1647321162414,
    "defaultTestParameterFilePath": "/test/dummy.json",
    "defaultVersion": "2.0.0",
    "description": null,
    "descriptorTypeSubclass": "NOT_APPLICABLE",
    "email": "cumulus-support@googlegroups.com",
    "forumUrl": null,
    "full_workflow_path": "github.com/lilab-bcb/cumulus/Cellranger",
    "gitUrl": "git@github.com:lilab-bcb/cumulus.git",
    "has_checker": false,
    "id": 17687,
    "input_file_formats": [],
    "isChecker": false,
    "is_published": true,
    "labels": [],
    "lastUpdated": 1647045825826,
    "last_modified": -1946344664,
    "last_modified_date": 1647321097000,
    "licenseInformation": {
        "licenseName": "BSD 3-Clause \"New\" or \"Revised\" License"
    },
    "mode": "DOCKSTORE_YML",
    "orcidPutCode": null,
    "organization": "lilab-bcb",
    "output_file_formats": [],
    "parent_id": null,
    "path": "github.com/lilab-bcb/cumulus",
    "repository": "cumulus",
    "sourceControl": "github.com",
    "source_control_provider": "GITHUB",
    "starredUsers": [],
    "topicId": 5139,
    "users": null,
    "workflowName": "Cellranger",
    "workflowVersions": [
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "8c4c30df8cced2b66ff0aa953004d2b3964fafac",
            "dbUpdateDate": 1647321162415,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120824,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1647321097000,
            "legacyVersion": false,
            "name": "master",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "master",
            "referenceType": "BRANCH",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120824,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": "Cumulus Team",
            "authors": [
                {
                    "affiliation": "Genentech",
                    "email": "cumulus-support@googlegroups.com",
                    "name": "Cumulus Team",
                    "role": null
                }
            ],
            "commitID": "2a38884053711a8ff7faa6921895156ffbbddfda",
            "dbUpdateDate": 1647314337046,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": "cumulus-support@googlegroups.com",
            "frozen": false,
            "hidden": false,
            "id": 121513,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1647314211000,
            "legacyVersion": false,
            "name": "2.0.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "2.0.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 121513,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "91336094646217564a4f8e7b31c03c3c6bf2e84b",
            "dbUpdateDate": 1647308472439,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120838,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1626757855000,
            "legacyVersion": true,
            "name": "1.5.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "1.5.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120838,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "592c8688c7e3caffc8556f1991c8d744a084c9c6",
            "dbUpdateDate": 1647045928833,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120839,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1621281942000,
            "legacyVersion": true,
            "name": "1.4.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "1.4.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120839,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "65b8a1dccccd9bfa2d68c73a936a6cb53ca1dd49",
            "dbUpdateDate": 1647045928833,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120840,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1612326715000,
            "legacyVersion": true,
            "name": "1.3.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "1.3.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120840,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "99b9eb567a3046245db340341841ac8832108c04",
            "dbUpdateDate": 1647045928834,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120842,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1611102063000,
            "legacyVersion": true,
            "name": "1.2.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "1.2.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120842,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "925d4cde41b052ec8ab21643447f608dae1896f0",
            "dbUpdateDate": 1647045928835,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120843,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1609211475000,
            "legacyVersion": true,
            "name": "1.1.0",
            "orcidAuthors": null,
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            "referenceType": "TAG",
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            "synced": true,
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            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120843,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "38c81c4b6a13a288c6663c1cb17f8945367af467",
            "dbUpdateDate": 1647045928836,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120846,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1600893571000,
            "legacyVersion": true,
            "name": "1.0.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "1.0.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120846,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "a7158ea5034bf02ffe43081d0eb1aa0807505b05",
            "dbUpdateDate": 1647045928837,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120848,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1594698889000,
            "legacyVersion": true,
            "name": "0.15.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "0.15.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120848,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "5baa05ac7376ab1d9258800b6cf9040c4dfe9e09",
            "dbUpdateDate": 1647045928838,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120849,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1583286353000,
            "legacyVersion": true,
            "name": "0.14.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "0.14.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120849,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "c937a832718aacbe75a0fdbca9cde682c48e2407",
            "dbUpdateDate": 1647045928838,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120850,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1581095332000,
            "legacyVersion": true,
            "name": "0.13.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "0.13.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120850,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "eb4bfa45cecfc8b17316718fc5dd52cb07bdfbe8",
            "dbUpdateDate": 1647045928839,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120851,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1576899114000,
            "legacyVersion": true,
            "name": "0.12.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "0.12.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120851,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "b9871af8682eed810b083ac22ee2079f8cc09c21",
            "dbUpdateDate": 1647045928839,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120852,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1575447979000,
            "legacyVersion": true,
            "name": "0.11.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "0.11.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120852,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "7eb291667d7025ff33952524d0b90a1bbcb569e7",
            "dbUpdateDate": 1647045928840,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 120853,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1574746317000,
            "legacyVersion": true,
            "name": "0.10.0",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "0.10.0",
            "referenceType": "TAG",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 120853,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        }
    ],
    "workflow_path": "/.dockstore.yml"
}

[yihming]

In contrast, below is the request returned JSON content (have to delete part of it due to word limit) of workflow ID 14403, which was imported manually. You can see that “workflow_path” at the bottom is pointed to the correct WDL file.

{
    "type": "BioWorkflow",
    "descriptorType": "WDL",
    "aliases": {},
    "author": null,
    "checker_id": null,
    "conceptDoi": null,
    "dbCreateDate": 1590953871675,
    "dbUpdateDate": 1645230651184,
    "defaultTestParameterFilePath": "/test.json",
    "defaultVersion": "master",
    "description": null,
    "descriptorTypeSubclass": "NOT_APPLICABLE",
    "email": null,
    "forumUrl": null,
    "full_workflow_path": "github.com/klarman-cell-observatory/cumulus/Cellranger",
    "gitUrl": "git@github.com:klarman-cell-observatory/cumulus.git",
    "has_checker": false,
    "id": 14403,
    "input_file_formats": [],
    "isChecker": false,
    "is_published": true,
    "labels": [],
    "lastUpdated": 1590953871674,
    "last_modified": 7498632,
    "last_modified_date": 1644979973000,
    "licenseInformation": {
        "licenseName": "BSD 3-Clause \"New\" or \"Revised\" License"
    },
    "mode": "FULL",
    "orcidPutCode": null,
    "organization": "klarman-cell-observatory",
    "output_file_formats": [],
    "parent_id": null,
    "path": "github.com/klarman-cell-observatory/cumulus",
    "repository": "cumulus",
    "sourceControl": "github.com",
    "source_control_provider": "GITHUB",
    "starredUsers": [],
    "topicId": null,
    "users": null,
    "workflowName": "Cellranger",
    "workflowVersions": [
       ... ...
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "cd3d7dad302db3193d3a34b93a32e5859792dd96",
            "dbUpdateDate": 1643667148600,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 112425,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1643468832000,
            "legacyVersion": true,
            "name": "shareseq_master",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "shareseq_master",
            "referenceType": "BRANCH",
            "subClass": null,
            "synced": true,
            "valid": true,
            "validations": null,
            "verified": false,
            "verifiedSource": null,
            "verifiedSources": [],
            "versionEditor": null,
            "versionMetadata": {
                "id": 112425,
                "orcidPutCode": null,
                "parsedInformationSet": null
            },
            "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl",
            "workingDirectory": "workflows/cellranger"
        },
        {
            "aliases": null,
            "author": null,
            "authors": [],
            "commitID": "e547384bf84a1d62ba8d1c17f525984d8fd66d38",
            "dbUpdateDate": 1643667148601,
            "description": null,
            "descriptionSource": null,
            "dirtyBit": false,
            "doiStatus": "NOT_REQUESTED",
            "doiURL": null,
            "email": null,
            "frozen": false,
            "hidden": false,
            "id": 112427,
            "images": null,
            "input_file_formats": [],
            "last_modified": 1642626035000,
            "legacyVersion": true,
            "name": "shareseq_mkfastq_bug",
            "orcidAuthors": null,
            "output_file_formats": [],
            "reference": "shareseq_mkfastq_bug",
            "referenceType": "BRANCH",
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            "workingDirectory": "workflows/cellranger"
        }
    ],
    "workflow_path": "/workflows/cellranger/cellranger_workflow.wdl"
}

[Richard-Hansen]

Hi Yiming,

Thanks for reaching out! The behavior you’re describing is expected. The value associated with the workflow_path key in the JSON returned from the Dockstore /workflows/published/{workflowId} API endpoint references the file used by Dockstore to sync the workflow. This means that depending on synchronization method (manual or GitHub Apps) or even language (WDL vs NFL) you can see different values under workflow_path.

Furthermore, the Dockstore proprietary API (although perfectly acceptable to use) is not guaranteed to maintain form or structure between versions. If you are intending to program against an API supported by Dockstore for workflow information, I would suggest the GA4GH TRS API, which Dockstore guarantees stability for.

For example, this API endpoint will list the files associated with an entry: Swagger UI.
To get the file information for one of your workflows listed above you would hit the following endpoint: https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Flilab-bcb%2Fcumulus%2FCellranger/versions/master/WDL/files.
This can also be run from the Swagger UI:

Let me know if that answers your questions. If not, feel free to reach out with details regarding your specific use case, and I’ll be able to provide more detailed guidance!

Thanks,
Richard