How to change default values for "Workflow Path" and "Test File Path" for the hosted workflow

masha · March 23, 2023, 6:29pm

Hello,
I created hosted workflow using Swagger UI and see default parameters values set for the workflow:
Workflow Path: /Dockstore.cwl
Test File Path :/test.json

I have two questions:

What is the purpose of the “Test File Path” parameter?
How can I create the hosted workflow without setting this “Test File Path” parameter? (remove the file once the workflow is created using PATCH request?)
Is there a way to set my own values for these parameters using Swagger UI POST request when I create the hosted workflow? I tried setting request parameter “workflow_path” or “defaultWorkflowPath” but neither one worked.

Thanks,
Masha

svonworl · March 23, 2023, 8:05pm

Hi Masha. Here’s some answers that might help:

The “test file path” points at a test input file that users can use to run your workflow. The contents of the test file will vary, but could look something like: https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2FGA4GH-DREAM%2Fdockstore-workflow-helloworld%2Fdockstore-workflow-helloworld/versions/1.0.0/PLAIN-CWL/descriptor/%2Ftest.cwl.json
In a hosted CWL workflow, the primary descriptor path is always set to /Dockstore.cwl, and the test file path to /test.json.
These paths are set to the above values at workflow creation time and can’t be changed.

For examples of how to create and add files to a hosted workflow, take a look at our integration tests:

github.com

dockstore/dockstore/blob/967a0b548a92928fe31c576c9a5cfbe2bfbcc4d9/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/SwaggerHostedWorkflowIT.java#L214-L241


      
          HostedApi hostedApi = new HostedApi(webClient);
          Workflow hostedWorkflow = hostedApi.createHostedWorkflow("name", null, DescriptorType.CWL.toString(), null, null);
          Assertions.assertNotNull(hostedWorkflow.getLastModifiedDate());
          Assertions.assertNotNull(hostedWorkflow.getLastUpdated());
          
          
// make a couple garbage edits
          SourceFile source = new SourceFile();
          source.setPath("/Dockstore.cwl");
          source.setAbsolutePath("/Dockstore.cwl");
          source.setContent("cwlVersion: v1.0\nclass: Workflow");
          source.setType(SourceFile.TypeEnum.DOCKSTORE_CWL);
          SourceFile source1 = new SourceFile();
          source1.setPath("sorttool.cwl");
          source1.setContent("foo");
          source1.setAbsolutePath("/sorttool.cwl");
          source1.setType(SourceFile.TypeEnum.DOCKSTORE_CWL);
          SourceFile source2 = new SourceFile();
          source2.setPath("revtool.cwl");
          source2.setContent("foo");
          source2.setAbsolutePath("/revtool.cwl");

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github.com

dockstore/dockstore/blob/develop/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/CRUDClientIT.java

/*
 *    Copyright 2018 OICR
 *
 *    Licensed under the Apache License, Version 2.0 (the "License");
 *    you may not use this file except in compliance with the License.
 *    You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0
 *
 *    Unless required by applicable law or agreed to in writing, software
 *    distributed under the License is distributed on an "AS IS" BASIS,
 *    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *    See the License for the specific language governing permissions and
 *    limitations under the License.
 */

package io.dockstore.client.cli;

import static io.dockstore.common.DescriptorLanguage.CWL;
import static io.dockstore.common.DescriptorLanguage.WDL;

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And please, let us know if you have any other questions!

Best regards,
Steve

masha · March 23, 2023, 8:20pm

Hi Steve,

Thank you so much for your prompt response and clarifications.

I see, too bad about the hardcoded names for the CWL files as Dockstore supports custom filenames for other types of the workflows (GitHub hosted ones, for example). May I ask why hosted workflows don’t allow custom filenames? Is there a plan to add such support?

Thank you for the pointer to example Java code on how to upload files to the hosted workflow. I got it working from Python already

Thank you,
Masha

svonworl · March 23, 2023, 11:06pm

Hi Masha. Glad to hear that your Python workflow creator is working!

Regarding the hardcoded file names in hosted workflows, I believe that we decided on that design to simplify the feature and make it easier to implement and use. At present, I’m not aware of plans to change it, but to formally push us in that direction, please do file an issue on our github repo.

Thanks,
Steve