Investigate the Ability to List Analysis and WF

[Buwujiu]

Detailed Description

End goal is to have a ui to show submitted analyses(seq exp) and what wf have been done on these analyses if any question is does our current gateway api let us query these info??

2 things we want the api to do:

1. list submitted analyses
   • we want to include a filter where we can select analysis states (or all states if no filter)
2. can list wf on these analyses if the api doesn't provide, need to implement these queries.

Exit Criteria

1. If the current API does not show submitted analyses and the wf that have been run on them, list the necessary steps in order to achieve that.
2. Make tickets for the next steps.

[UmmulkiramR]

@Buwujiu @joneubank

The query below can be used to fetch a submitted analysis and see if there were any workflows run on it. A code change is needed to add the code filter.

{
  analyses(filter: {analysisId: "<analysis_id>", code: "submission-song.collab", analysisState: PUBLISHED}) {
    content {
      analysisId
      analysisType
      studyId
      analysisState
      repositories {
        code
        country
        name
        organization
        type
        url
      }
      inputForRuns {
        state
        runId
        repository
        inputAnalyses {
          analysisId
          analysisType
          studyId
        }
      }
    }
  }
}

For any analyses 'inputForRuns' will be empty if there are no workflows run on it yet. Otherwise it will have information that looks like this

"inputForRuns": [
    {
      "state": "COMPLETE",
      "runId": "wes-59a5a5ff54e84fe9997ab276fb1d535d",
      "repository": "https://github.com/icgc-argo-workflows/dna-seq-processing-wfs",
      "inputAnalyses": [
        {
          "analysisId": "8e351daf-ca77-470d-b51d-afca77170dd9",
          "analysisType": "sequencing_experiment",
          "studyId": "SEQ-CA"
        }
      ]
    }
  ]

[UmmulkiramR]

Attaching the PR here song-search#80

[Buwujiu]

@lindaxiang @edsu7 to test in QA.

[lindaxiang]

@Buwujiu @UmmulkiramR test the queries in QA

1. The current APIs support to list and filter analysis based on the following fields:

   analysisId
   analysisState
   analysisType
   analysisVersion
   code
   donorId
   runId
   sampleId
   sampleType
   specimenId
   studyId

   Question to @UmmulkiramR : why does one analysis return two repositories like following, what's the meaning of local song?

   "repositories": [
           {
             "code": "song.collab",
             "country": "CA",
             "name": "Cancer Genome Collaboratory",
             "organization": "rdpc-collab",
             "type": "S3",
             "url": "https://song.rdpc-qa.cancercollaboratory.org"
           },
           {
             "code": "song.collab",
             "country": "CA",
             "name": "local song",
             "organization": "ICGC",
             "type": "S3",
             "url": "https://song.rdpc-qa.cancercollaboratory.org"
           }
         ]

2. For any analyses 'inputForRuns' will be empty if there are no workflows run on it yet. Otherwise it can return Run information including state, runId, repository and etc.

[Buwujiu]

Tested by Linda and Edmund, ready for prod deploy.

[UmmulkiramR]

Deployed on Prod.

[Buwujiu]

@lindaxiang @edsu7 Can you give it a test in prod? Thank you!