Redirecting from organism analysis page to workflow landing page in Galaxy

[nekrut]

Now that we have a set of BRC-specific workflows that can be used on VEuPathDb genomes we can enable link outs from an organism page.

What needs to happen

1. Suppose a user is on this page: https://brc-analytics.org/data/organisms/GCA_000002765_3
2. The user clicks on the "Regulation" workflow "Analyze" button (corresponding to https://galaxyproject.github.io/iwc/workflow/a2f66906-e9e3-42f9-8629-390017ed2db0)
3. This gets the user to https://test.galaxyproject.org/ workflow landing page
4. The reference genome drop-down of this workflow is pre-filled with
   

How to construct the redirect

@mvdbeek - please, fiil in here

Steps to implement are...

@hunterckx

1. create a mapping from workflow type to workflow ID.
2. On any workflow button on the analysis page e.g., https://brc-analytics.dev.clevercanary.com/data/organisms/GCA_001189475_1.
   1. enable the button if its name is in the mapping.
   2. When the button is clicked, use the command curl 'https://test.galaxyproject.org/api/workflow_landings'
      -H 'Content-Type: application/json'
      --data-raw '{"workflow_id":"https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12","workflow_target_type":"trs_url","request_state": {"reference_genome":"mm10"}}' to request a workflow landing id. Replace the reference_genome with the assembly_version_id for the page.
   3. The API call will return with a response that includes the workflow_landing tagged as "UUID."
   4. Use the UUID to construct a URL like https://test.galaxyproject.org/workflow_landings/5d6eceda-4593-4cc0-ba16-da6b810deb10 and open this URL in a new tab.
   5. if the workflow_landing id request fails in step 3, then show the error page (let's discuss the error flow)

[mvdbeek]

❯ curl 'https://test.galaxyproject.org/api/workflow_landings' \
  -H 'Content-Type: application/json' \
  --data-raw '{"workflow_id":"https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12","workflow_target_type":"trs_url","request_state": {"reference_genome":"mm10"}}'
{"uuid":"5d6eceda-4593-4cc0-ba16-da6b810deb10","workflow_id":"https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12","workflow_target_type":"trs_url","request_state":{"reference_genome":"mm10"},"state":"unclaimed"}

is an example request response pair. Then redirect the user to https://test.galaxyproject.org/workflow_landings/5d6eceda-4593-4cc0-ba16-da6b810deb10.

Note that the API will likely change to include a mandatory public argument in the request body, for brc purposes that should be true.

For this particular workflow "reference_genome": "mm10" is the key value pair that specifies the genome. The value can be any of the GCA_* accessions. The key that specifies the reference genome is going to be workflow specific and, as is the workflow id, so we'll need to have a list of workflows.

You can find the openapi schema here: https://test.galaxyproject.org/api/docs#/workflows/create_landing_api_workflow_landings_post

[NoopDog]

Super, thanks.

Do we have any other workflow name to workflow_target_type pairs? e.g.

Regulation, https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12

Cheers,
D

[nekrut]

Super, thanks.

Do we have any other workflow name to workflow_target_type pairs? e.g.

Regulation, https://dockstore.org/api/ga4gh/trs/v2/tools/#workflow/github.com/iwc-workflows/chipseq-pe/main/versions/v0.12

Cheers, D

You mean do we have more workflows? Yes. I'm checking them one by one. Will probably take me whole weekend.

[NoopDog]

No worries and thanks...

D

[mvdbeek]

workflow_target_type is always trs_url, the categories should probably be listed by hand or be taken from https://dockstore.org/organizations/iwc

[NoopDog]

@nekrut, would you like to provide a short paragraph of 1-2 sentences explaining how these workflows are a "preview" and run on test and what will happen once the previews are live on prod?

General instructions on the flow to run a workflow would also be helpful. e.g.

1. Select your Analysis type.
2. You will be directed to a test instance to preview the workflow.
3. Login with your Gmail or Google Workplace backed email address.
4. Login and...

We can put a simple guide on the site as well with markdown/images in a "Help and Docs" section. We can create a second ticket for that.

A 3rd sentence would be helpful to explain what the non-clickable workflows are, e.g., "The following workflows are under development and will be available soon." or similar.

[NoopDog]

@hunterckx lets also

1. Divide up the workflows into two sections: Preview and Coming Soon. So the "Regulation" would be in the preview section and everything else in the coming soon section.
2. For the coming soon use the original text box on the top as the first element.
3. I will work with Anton to get text for the top of the preview section...

[NoopDog]

Complete! Thx!