Implement Workflow Retrieval Phase Ruleset

[EttoreM]

This PR addresses #48.

Rules implemented (so far)

#	Rule	sh:severity
1	There SHOULD be a DownloadAction entity representing the action of downloading the referenced workflow.	sh:Warning
2	RootDataEntity --> mentions SHOULD reference the DownloadAction entity, if this exists.	sh:Warning
3	DownloadAction --> name MUST be a human-readable summary of the download action.	sh:Violation
4	DownloadAction MAY have startTime property if action begun	sh:Info
5	DownloadAction --> startTime MUST follow the RFC 3339 standard	sh:Violation
6	DownloadAction SHOULD have endTime property if action ended	sh:Warning
7	DownloadAction --> endTime MUST follow the RFC 3339 standard	sh:Violation
8	DownloadAction SHOULD have actionStatus property	sh:Warning
9	DownloadAction --> actionStatus MUST one of the allowed values	sh:Violation
10	The RO-Crate of the downloaded Workflow MAY be represented by an entity of type Dataset (i) (ii)	sh:Info
11	The RO-Crate of the downloaded Workflow SHOULD be referenced by DownloadAction --> result (i) (ii)	sh:Warning
12	The property sameAs of the entity representing the downloaded workflow MUST point to the same entity as RootDataEntity --> mainEntity (ii)	sh:Violation
13	DownloadedWorkflow --> distribution MUST reference the same entity as DownloadAction --> object (ii)	sh:Violation

(i) The validator will fire up this rule as not met with a MAY whether the user has downloaded the workflow RO-Crate or nor, or whether the Workflow RO-Crate was downloaded in the current RO-Crate or outside of it.

---

Rules not yet implemented

The following rule was not implemented as a SHACL shape, as it is not clear how this would be done. Also, the rules that are logically subsequent to this one have been implemented assuming the Workflow RO-Crate has indeed been downloaded (this may need to be reconsidered @elichad , @douglowe , @alexhambley)

#	Rule	sh:severity
1	The Workflow RO-Crate MAY be downloaded and unpacked into this crate.	sh:Warning

[douglowe]

I've updated the Workflow Retrieval phase in the spreadsheet.

We need to look at the downloaded Workflow RO-Crate, as well as the workflow retrieval object.

        {
            "@id": "workflow/289/",
            "sameAs": {
                "@id": "https://workflowhub.eu/workflows/289?version=1"
            },
            "@type": "Dataset",
            "name": "CWL Protein MD Setup tutorial with mutations",
            "conformsTo": {
                "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
            },
            "distribution": {
                "@id": "https://workflowhub.eu/workflows/289/ro_crate?version=1"
            }
        },

The existence of this object is only a MAY - but we have a few SHOULD requirements to fulfil if it does exist. I can't see anything within this object which marks it specifically as the downloaded workflow ro-crate - so I think we will have to infer this from the 'sameAs' field.

[douglowe]

Partial review, sorry. I'll try to complete it later today.

[douglowe]

I don't think we should specific a minimum length for these strings.

[EttoreM]

The requirement is that the name MUST be a descriptive, human-readable summary of the download action. I totally agree that 10 characters (or any other number) for minimum length is arbitrary. On the other end this is a baseline rule encouraging users to insert meaningful names rather than, say "XY".
I think we should reach an agreement on this point (@elichad, @douglowe , @alexhambley @stain). Just as a reminder, a minimal length of 10 was already enforced for at least another phase that has been merge into dev.

[douglowe]

I'm happy with this now - other than the minimum length of a string ;-) but we can cover that in the meeting now

[douglowe]

I can rebase this though - so we don't have the merge conflicts

[douglowe]

I wonder if this is causing the errors for the CI/CD tests - which are complaining about not getting a string literal.

I would replace this code with:

expected_triggered_issues=[
     "The entity represented the downloaded workflow is not properly defined in the "
     + "RO-Crate and/or it is not referenced by `DownloadAction` --> `result`."
]