return deaccessioned version of dataset in more cases

[jp-tosca]

What this PR does / why we need it:
API only returns Deaccessioned Dataset Version if user has edit privileges

Which issue(s) this PR closes:
Closes #10164

Special notes for your reviewer:

We agreed to change the parameter name from includeFiles with excludeFiles, this is the default and the lack of the parameter will default to false so files are expected to be included by default if this parameter is not provided.

getVersionFiles, getVersionFileCounts and getDownloadSize act exactly as before, this check would execute every time includeDeaccessioned was set to true, getDatasetVersionCitation will skip this test when includeDeaccessioned is true and getVersion will check for when includeDeaccessioned is true and excludeFiles is false. This change also replaced includeFiles with excludeFiles which is the default behaviour.

This change required to update Datasets.getDatasetVersionOrDie which impacted the following methods:

• getVersion {id}/versions/{versionId: Will check file permissions when files when excludeFiles and includeDeaccessioned are true.
• getVersionFiles {id}/versions/{versionId}/files: Will check file permissions when includeDeaccessioned is true.
• getVersionFileCounts {id}/versions/{versionId}/files/counts: Will check file permissions when includeDeaccessioned is true.
• getDownloadSize {identifier}/versions/{versionId}/downloadsize: Will check file permissions when includeDeaccessioned is true.
• getDatasetVersionCitation {id}/versions/{versionId}/citation: Won't check file permissions.
• listVersions {id}/versions: replaced includeFiles with excludeFiles which is the default.

Suggestions on how to test this:
Have a Dataset with one deaccessioned version, here is the test matrix that I used and a flow chart that i made:

Deaccesioned dataset	Include Deacessioned	Exclude files	User can edit	Result
N	Y	Y	Y	OK
N	Y	Y	N	OK
N	Y	N	Y	OK
N	Y	N	N	OK
N	N	Y	Y	OK
N	N	Y	N	OK
N	N	N	Y	OK
N	N	N	N	OK
Y	Y	N	Y	OK
Y	Y	N	N	ERR
Y	Y	Y	Y	OK
Y	Y	Y	N	OK
Y	N	N	Y	ERR
Y	N	N	N	ERR
Y	N	Y	Y	ERR
Y	N	Y	N	ERR

[coveralls]

coverage: 20.165%. remained the same
when pulling 43855c3 on 10164-bug-api-datasets-versions-fix
into 5cbb895 on develop.

[sekmiller]

@landreev can you hear me now?

[pdurbin]

I haven't wrapped my head around the substantive change in this PR but I'm leaving comments about docs and tests, at least.

[jp-tosca]

I would still like to check with @ekraffmiller about the citation API, on dev branch I was able to access to the citation of a deaccessioned dataset when the parameter is provided, but I found a bug(?) that this parameter will also give the citation of a draft.

[qqmyers]

A couple minor suggestions for changes. Overall - looks good. Very clear testing instructions.

[pdurbin]

@jp-tosca can you please resolve merge conflicts?

[qqmyers]

Looks good - just the merge issues to fix.

[jp-tosca]

Merge conflicts have been solved. 🥳

[github-actions]

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