workflowhub-eu / about Goto Github PK

When you view the webpage https://workflowhub.eu/ in a window with small enough to make the little menu button appear on the top right, the menu does not display. Clicking on the menu shows the search box only. Tested on Linux, Chrome and Firefox and Opera.

BioSchemas/specifications#581 raises this point

What's the ideal way for this to work, we'll probably be submitting workflows to workflowhub ourselves.

    Do we annotate our WFs with ld+json, knowing WFHub will do it too, resulting in "two copies" for anyone scanning for workflows?
    Do we not annotate ours, knowing the "canonical" version can be kept in WF Hub?
    Do we just annotate ours, and somehow WF Hub will discover these and pick them up, saving us from doing anything?

I keep looking into working with wf hub but still haven't found good options for syncing all of our workflows programmatically, and I'm very interested in anything that helps us automate that!

The current spec says:

The Crate MUST contain a data entity of type ["File", "SoftwareSourceCode", "ComputationalWorkflow"] as the Main Workflow.

This could be interpreted as saying that the types must be exactly ["File", "SoftwareSourceCode", "ComputationalWorkflow"], while WorkflowHub actually allows for more types to appear on the list. This is required by the Provenance Run Crate profile (which adds HowTo), so I propose we change the spec as follows:

The Crate MUST contain a Main Workflow data entity whose types MUST include File, SoftwareSourceCode and ComputationalWorkflow.

From Nine Best Practices for Research Software Registries and Repositories: A Concise Guide:

• Provide a public scope statement
  https://workflowhub.eu/ says:

  WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. The registry supports any workflow in its native repository. WorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. This is achieved through extensive use of open standards and tools, including Common Workflow Language (CWL), RO-Crate, BioSchemas and TRS, in accordance with the FAIR principle

• Provide guidance for users
  https://about.workflowhub.eu/ incl. new User Guide (#32)
• Provide guidance to software contributors
  https://docs.seek4science.org/tech/contributing-to-seek.html
• Establish an authorship policy
  Not explicit
• Share your metadata schema
  https://workflowhub.eu/api https://about.workflowhub.eu/Workflow-RO-Crate/
• Stipulate conditions of use
  https://workflowhub.eu/home/terms
• State a privacy policy
  https://workflowhub.eu/home/privacy
• Provide a retention policy
  https://about.workflowhub.eu/About-WorkflowHub/ says:

  WorkflowHub has a sustainability plan that ensures the availability of its contributions and metadata up to and beyond 2026. If and when it reaches its end of service then the published contributions and metadata will be archived as RO-Crates and made available through a public repository, such as Zenodo, Figshare or another appropriate resource at that time. DOI registrations will in this case be updated to link to the archived deposits.

• Disclose your end-of-life policy
  (See above)

For examples, see https://scicodes.net/best-practices-for-software-registries-and-repositories/

I think we have most of these already, but may just need to link to our policies/schemas/docs, and perhaps make them more explicit here on these About pages and from the main hub.

Add a comment to this issue to join the https://github.com/workflowhub-eu team.

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The example crate does not contain an entity of @type ["File", "SoftwareSourceCode", "ComputationalWorkflow"]

Thought the profile here https://about.workflowhub.eu/Workflow-RO-Crate/ says it should

the Main entity does not have @type computational workflow:

    {
      "@id": "example_workflow.cwl",
      "@type": [
        "File",
        "SoftwareSourceCode",
        "HowTo"
      ],
      "programmingLanguage": {
        "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl"
      },
      "name": "Example Workflow",
      "image": {
        "@id": "diagram.svg"
      }
    },

https://about.workflowhub.eu/Updating-a-registered-workflow/

Can now update all parts of the workflow.

Please note this will change again when git support is added.

On https://about.workflowhub.eu/Registering-a-workflow-with-a-diagram-and-abstract-CWL/ in : !Projects*: Every workflow registration is linked to one or more projects. If you can not select the correct project, please go to Joining a project. - Link is 404 error link

How do we remove a duplicate organisation?

We would like to remove this one
https://workflowhub.eu/institutions/40#people

And move people from the above profile to this one
https://workflowhub.eu/institutions/81#people

Thanks

...due to the bold style changing the width and causing the line to wrap.

See: https://about.workflowhub.eu/About-WorkflowHub/ and hover over "workflow-centric Research Objects"

https://workflowhub.eu/home/terms says

The Data Controller for the WorkflowHub is EOSC-Life WorkflowHub work package, contact at [email protected]. If the WorkflowHub is accessed at a different URL, the data controller is likely someone else

but the GDPR regulations says

‘controller’ means the natural or legal person, public authority, agency or other body which, alone or jointly with others, determines the purposes and means of the processing of personal data; where the purposes and means of such processing are determined by Union or Member State law, the controller or the specific criteria for its nomination may be provided for by Union or Member State law;

EOSC-Life WorkflowHub work package is not the correct work package name, and in addition a work package is not a natural or legal person. Do we want to claim it as an “other body”? Another problem is that the contact list given does not go to the work package or work package leaders.

I suggest to list The University of Manchester, UK as the legal entity that is the Data Controller, as employers of the individuals of that list, and as the formal consortium agreement member of EOSC-Life and the hosting provider of the virtual machine that runs the workflowhub.eu instance. So effectively UoM is already the data controller.

The controller has legal responsibilities, so to avoid individuals working on this potentially be legally responsible, it should be the employer, as the legal entity, that is the Data Controller

The following points are based on going through the wiki:

• there is no homepage for the user guide (or none I could find), you either access a project page (https://github.com/workflowhub-eu/about/wiki) or a guide on uploading workflows (https://github.com/workflowhub-eu/about/wiki)

• a bit of introduction on the homepage would be interesting, and another one in the "workflow upload"

• the difference between uploading and referencing workflows should be explained

• the workflow type should be explained

• for "uploading galaxy workflows", I would guess that specifying how to retrieve the ".ga" file would be useful information to some users.

I would like to report an issue on the Adding files page at /docs/adding-files/. Description of the issue:

Under https://about.workflowhub.eu/docs/adding-files/#upload--import-a-local-file & https://about.workflowhub.eu/docs/adding-files/#git
"Abstract CWL" link does not seem to work: https://about.workflowhub.eu/docs/adding-files/#bookmark=id.9p7blcbntfn5

I would like to report an issue on the Complete workflow metadata page at /docs/complete-workflow-metadata/. Description of the issue: appears that links are broken

They are

For some reason, many markdown links like [Title](#bookmark=kix.gqofhtf06fx) are surrounded in <code> tags resulting in the raw markdown in the final webpage. Though the links wouldn't work. (Similar to #34 ?)

In https://about.workflowhub.eu/How-to-register-your-workflow(s)-in-WorkflowHub/ the HTML generated is

<summary>
<p>Common Workflow Language (.cwl)&lt;/summary&gt;</p>_

So the close of the summary is escaped and appears as

Common Workflow Language (.cwl)</summary>

More information will soon be available.

Links at https://about.workflowhub.eu/docs/before-you-start either return error 404 or they point at the current page.

Buttons and choices appear only if there is "permission" to see them - like edit an Organisation. Instead all should appear always, and if they are disabled then there should be an explanation WHY and HOW to get the button enabled

A requirement for reporting to funders and for future funding bids are usage analytics and contribution/download/access dashboards

• accesses
• downloads and views
• access launches

it is not sufficient to just report how many workflows etc- the funders and the project management needs data for evidence of use.

A place to collect requirements for the Workflow RO-Crate requirements.

The current specification is described at https://github.com/workflowhub-eu/about/blob/master/Workflow-RO-Crate.md

Pick one and use it throughout the docs/site.

WorkflowHub is more popular currently, so probably use that.

Building on from #12 then instead of just a free-text field for "Related Links" (former "Discussion Channel") it would be nice to have a suggested list of link relations for the user to select from.

Part of this idea is that given a list of suggested links like documentation the user is more likely to fill it in than if it's all free-form.

These kind of links would be part of the value added by Workflow Hub - in theory people can put them in their GitHub README but frequently they don't.

Zenodo calls this "Related Identifiers" - see right margin on https://zenodo.org/record/4012124 for example.

Our drop-down list could also be based on (or be compatible with) DataCite schema's relationType although some of these may not make sense on workflows. (They may make sense on other SEEK types)

Mockup (based on Zenodo's form):

New in latest DataCite is also typing the resource at the other end - this is often just as useful:

However we may need "Other" as well with a text-field to fill in.

Here is the list Zenodo use:

For us this upload is this workflow. See https://schema.datacite.org/meta/kernel-4.3/doc/DataCite-MetadataKernel_v4.3.pdf#page=46 (page 46) for full DataCite list.

As commented in #12 if we have the types of links we can not just present them in nicer ways but also provide them programmatically in the RO-Crate, BioSchemas markup and in DataCite export.

Other more generic link relations registries are IANA link relations which is used in <link rel="cite-as" href="https://doi.org/10.1234/abcd"> and <a rel="preview" href="thumbnail.png"> in HTML and equivalent Link: HTTP header although they are probably more important for internal site navigation.

I think that the latest RO-Crate way is to put the profile conformance on the RootDataset.

Looking at the current CoC again, this is fine for me. The only thing for me is the email for reporting. [email protected] is probably not the right one (I have no idea who this goes to), and we likely need/want more than one person looking at it ?

Dear all,
thanks so much for making workflowhub a real platform where scientists and others can share their workflows in a citable fashion. In the LEAPS community, we would love to share some more knowledge of automated workflow engines with interested scientists. For this, we are setting up a co-working sprint early in 2023.
It would be great if someone from the core wfhub team could volunteer to present wfhub on Jan 27, 2023, to us (20-25 min talk, sometime between 10-12am CET).
Please reach out to me, in case you are interested. We would love to have you!
Best,
Peter

In https://about.workflowhub.eu/How-to-register-your-workflow(s)-in-WorkflowHub/

many of the workflow types have

More information will soon be available.

The BioExcel workflows have multiple websites, documentation, tutorials, source code and live Jupyter Notebook deployments.

While it is possible to list these within the rich-text of the Description, this is cumbersome to get consistent. It is also not easy to access such links programmatically (e.g. for inclusion in RO-Crate or DataCite metadata)

The existing "Discussion Channels" almost does the job, e.g. from example https://dev.workflowhub.eu/workflows/116

Links can be added with a label, as shown above. This issue simply asks to rename "Discussion Channels" to "Related Links" of which a discussion channel would be one of possible links.

I'll make a separate issue about having drop-down selection for type of link.

Talk about how it marks up the page and embeds it in RO-Crate

I am trying to use the api documentation but the links are not working. It sees we have to use fairdomhub.org as entry point for calls but it returns a message of redirecting. I would like to send the ro-crate file parsed and mined from readme descriptions in order to automatize migration to workflowhub.

https://gist.github.com/alaninmcr/f37c271d6ae04a074269da0090cc233e

Currently there is no help at all for asset management and its opaque. This impacts on the permissions of what can be done when by whom.

For example,

what is a housekeeper? what is a gatekeeper? does it matter? must I assign these? just some simple words here would help, instean of making me read a complicated document.