Update PortalDataset.yaml

[anngvu]

Here's a mockup of what this might look like in the UI (maybe fancier than a link, should be an icon specific to the viewer). This would be useful for known viewers that can be linked to via a constant accession/url, such as cBioPortal, GEO, CELLxGENE.

Update: Suggestion for a better term other than "externalViewer" welcome.

[github-actions]

PR Preview Action v1.4.7
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2024-06-04 00:21 UTC

[github-actions]

Test Suite Report 24.5.1

Template Generation

template	result	link
ClinicalAssayTemplate	😄	template link
EpigeneticsAssayTemplate	😄	template link
FlowCytometryTemplate	😄	template link
GenomicsAssayTemplate	😄	template link
GenomicsAssayTemplateExtended	😄	template link
HumanCohortTemplate	😄	template link
ImagingAssayTemplate	😄	template link
LightScatteringAssayTemplate	😄	template link
MethylationArrayTemplate	😄	template link
MRIAssayTemplate	😄	template link
PharmacokineticsAssayTemplate	😄	template link
PlateBasedReporterAssayTemplate	😄	template link
ProcessedAlignedReadsTemplate	😄	template link
ProcessedExpressionTemplate	😄	template link
ProcessedVariantCallsTemplate	😄	template link
ProteomicsAssayTemplate	😄	template link
ProtocolTemplate	😄	template link
RNASeqTemplate	😄	template link
ScRNASeqTemplate	😄	template link
UpdateMilestoneReport	😄	template link
WESTemplate	😄	template link
WGSTemplate	😄	template link

Manifest Validation

manifest	result	expectation
GenomicsAssayTemplate_0.csv	😄	Lists can be blank if attr not required using ‘list like’ rule
GenomicsAssayTemplate_1.csv	😄	Mixing blanks and regular list values works
GenomicsAssayTemplate_2.csv	😄	Conditional validation for attributes is currently not supported
GenomicsAssayTemplate_control.csv	😄	There should be no issue with this template.
ScRNASeqTemplate_0.csv	😄	Single list val works by using ‘list like’ rule
ScRNASeqTemplate_1.csv	😄	Fail because of missing data in required field libraryStrand

Manifest Submission

manifest	pass
GenomicsAssayTemplate_0.csv	😄
GenomicsAssayTemplate_1.csv	😄
GenomicsAssayTemplate_2.csv	😄
GenomicsAssayTemplate_control.csv	😄
ScRNASeqTemplate_0.csv	😄

[allaway]

@anngvu , I have two thoughts:

• know we talked about this before and perhaps we decided against it, but one way to avoid a confusing catch-all term would be to add attributes for each of our external viewers, so instead of external viewer it could be something like view dataset on cbioportal and view dataset on cellxgene.

• A thought related to the above is that the portals already support linking to arbitrary identifiers (as long as you can come up with a regex for them) thanks to work @jay-hodgson and @cconrad8 did for the NFTC database. So, if we used the above approach, we could add it on our end as cbioportal:nst_nfosi_ntap and use the SRC feature to autolink that to https://identifiers.org/cbioportal:nst_nfosi_ntap (or any other value with a cbioportal: prefix)

[allaway]

(turns out this also works with https://n2t.net/cbioportal:nst_nfosi_ntap )

[anngvu]

@allaway Yeah, I know there's the attribute-per-viewer option, and I have reasons for not liking it. But anyway, there wasn't a pros and cons written down anywhere that I can find, so created issue #455 for more formal discussion/design documentation.

Good to know about the identifiers prefix!

[jaybee84]

Some alternate options for external viewer :

1. visualize data on -> does not work for link to GEO/SRA (that might be okay since this is specifically for viewers)
2. explore data
3. explore insights -> does not work for link to GEO/SRA (that might be okay since this is specifically for viewers)
4. additional portal
5. More Details
6. Additional resources
7. Extra Content
8. Further Details

4-8 are more generic and may work for links other than visualization portals.

[allaway]

@jaybee84 I likke Explore Insights and visualize data on! If we start linking to other raw data I think we should categorize that separately anyway, so probably not too much of a problem (does not work for link to GEO/SRA (that might be okay since this is specifically for viewers)