Graphql: Submit Workflow Execution

[JeffreyThiessen]

What does this PR do and why?

Describe in detail what your merge request does and why.

• Added new graphql mutation SubmitWorkflowExecution which submits a workflow execution / pipeline.
• Added a new Validator for WorkflowExecution objects, which ensures samplesheet params attachments are formatted correctly.
  • This is not an issue when workflow executions are submitted via the Web UI, but graphql accepts any text so an invalid attachment could cause problems in the pipeline if not validated beforehand.

Screenshots or screen recordings

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How to set up and validate locally

Numbered steps to set up and validate the change are strongly suggested.

Get some data to use in a submission

query getProject{
  project(fullPath: "bacillus/bacillus-anthracis/outbreak-2022") {
    id
    name
    path
    samples(first:1){
      nodes{
        name
        id
        puid
        attachments{
          nodes{
            filename
            id
          }
        }
      }
    }
  }
}

Use the data returned from the previous step to populate the following submission mutation

mutation submitWE {
  submitWorkflowExecution (input:{
    name:"My Workflow from graphql 5"
    projectId: "gid://irida/Project/13d4c370-c707-4afa-8fe2-a26719508c02"
    updateSamples: false
    emailNotification: false
    workflowName: "phac-nml/iridanextexample"
    workflowVersion:"1.0.3"
    workflowParams: {
      assembler: "stub",
      random_seed: 1,
      project_name: "assembly"
    }
    workflowType: "NFL"
    workflowTypeVersion:"DSL2"
    workflowEngine:"nextflow"
    workflowEngineVersion: "23.10.0"
    workflowEngineParameters: [
      {
        key:"-r",
        value:"1.0.3"
      }
    ]
    workflowUrl: "https://github.com/phac-nml/iridanextexample"
    samplesWorkflowExecutionsAttributes:[
      {
        sample_id:"gid://irida/Sample/e978e898-f5f6-44a1-934a-418392d4c532"
        samplesheet_params:{
          sample: "INXT_SAM_AYMK34F2FG",
          fastq_1:"gid://irida/Attachment/dd4470cb-71b2-4d75-accf-f6954cc4c922",
          fastq_2:"gid://irida/Attachment/8299fc62-66fc-4915-959e-f4f97d51b061"
        }
      }
    ]
  }){
    workflowExecution{
      name
      id
    }
    errors{
      message
      path
    }
  }
}

PR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

• I have evaluated the PR acceptance checklist for this PR.

[ChrisHuynh333]

Looks good and works as described!

[ericenns]

I tried resetting the database on this branch but it failed due to the new validation of samplesheet_params can you please update the seed_workflow_executions method in db/seeds.rb so that this error no longer occurs.

Note: I only figured out that was the case after changing WorkflowExecution.create to WorkflowExecution.create! which causes an exception to be raised when the record is unable to be saved. Without that it was failing on line 197 in db/seeds.rb as it could not create the attachment without attachable_id

[JeffreyThiessen]

I tried resetting the database on this branch but it failed due to the new validation of samplesheet_params can you please update the seed_workflow_executions method in db/seeds.rb so that this error no longer occurs.

Note: I only figured out that was the case after changing WorkflowExecution.create to WorkflowExecution.create! which causes an exception to be raised when the record is unable to be saved. Without that it was failing on line 197 in db/seeds.rb as it could not create the attachment without attachable_id

Fixed in 02e498e

[ericenns]

This is looking good. Just a few comments and could you review the rubocop warnings present in the Files changed tab.

[github-actions]

Code Metrics Report

Coverage	Test Execution Time
92.9%	10m6s

Code coverage of files in pull request scope (96.9%)

Files	Coverage
app/controllers/workflow_executions_controller.rb	96.6%
app/graphql/mutations/submit_workflow_execution.rb	92.7%
app/graphql/types/mutation_type.rb	100.0%
app/models/workflow_execution.rb	100.0%
app/validators/workflow_execution_samplesheet_params_validator.rb	100.0%

---

Reported by octocov

[deepsidhu85]

While testing this PR out, I was able to use this for the samplesWorkflowExecutionAttributes JSON for the mutation which worked but it shouldn't have

{"samples_workflow_executions_attributes": {"sample_id": "gid://irida/Sample/c9427c0f-51e2-45b8-828c-6d32113eb679","samplesheet_params": {"sample": "INXT_SAM_AZBO256QCZ","fastq_1": "gid://irida/Attachment/141ea970-db29-4a97-9953-937986ff3ec5","fastq_2": "gid://irida/Attachment/f1179ccd-2308-4fb5-bb8b-25a900e387b5"}}}

Looks like we need to add validation to make sure that the sample_id and sample belong to the project that was set for the mutation, and validate that the attachments belong to this sample.

The reason the above shouldn't have worked is because the sample_id and sample don't belong to the project that was set in the mutation, and the attachments also do not belong to this sample

Steps to recreate:

Seed db if you already don't have it seeded
Login as [email protected]
Create a new project, sample, and upload a paired-end dataset
Run the submitWorkflowExecution mutation using http://localhost:3000/graphiql with the changes listed below the mutation:

 mutation($samples_workflow_executions_attributes: [JSON!]!){
      submitWorkflowExecution( input:{
        name: "testWE"
        projectId: "gid://irida/Project/b92623f7-6dc5-4ab6-a520-bf539b46a78a"
        updateSamples: false
        emailNotification: false
        workflowName: "phac-nml/iridanextexample"
        workflowVersion: "1.0.3"
        workflowParams: {
          assembler: "stub",
          random_seed: 1,
          project_name: "assembly"
        }
        workflowType: "NFL"
        workflowTypeVersion:"DSL2"
        workflowEngine:"nextflow"
        workflowEngineVersion: "23.10.0"
        workflowEngineParameters: [
          {
            key:"-r",
            value:"1.0.3"
          }
        ]
        workflowUrl: "https://github.com/phac-nml/iridanextexample"
        samplesWorkflowExecutionsAttributes: $samples_workflow_executions_attributes
        }) {
        workflowExecution{
          name
          id
        }
        errors{
          message
          path
        }
      }
    }

set the project_id to global id of created project above

In the hash for samplesWorkflowExecutionsAttributes, set the sample_id to a global id of a sample from another project, and set the sample with the puid of this sample. Set the fastq_1 and fastq_2 to the global ids of the attachments you uploaded above

Run the mutation and it should succeed in launching the workflow execution.