Build public release catalog

nih-cfde / cfde-deriva

Collaboration point for miscellaneous CFDE-deriva scripts

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Build public release catalog #179

Closed karlcz closed 3 years ago

karlcz commented 3 years ago

We need to rebuild the public catalog with DCC submitted content.

[x] Identify release constituent submissions (see detailed sub-tasks below)
[x] Build new release candidate catalog
[x] Switch it into place as catalog "1"

Get DCC and CFDE-CC approved submissions

[x] HMP
[x] HuBMAP
[x] LINCS
[x] GTEx
[x] Kids First
[ ] ~SPARC~
[ ] ~IDG~
[x] Metabolomics
[x] ExRNA

Make sure they supply the newly required dcc_primary_contact.dcc_abbreviation

[x] HMP
[x] HuBMAP
[x] LINCS
[x] GTEx
[x] Kids First
[ ] ~SPARC~
[ ] ~IDG~
[x] Metabolomics
[x] ExRNA

ACharbonneau commented 3 years ago

DCCs and whether we expect them to submit data:

4DN: No
MoTrPAC: No
HMP: Yes. Submitted and Approved
HuBMAP: Yes, Submitted and Approved
LINCS: Yes. Submitted and Approved
GTEx: Yes. Submitted and Approved
Kids First: Yes. Submitted and Approved
SPARC: ~Yes~
IDG: ~Yes~
Metabolomics: Yes. Submitted and Approved
ExRNA: Yes. Submitted and Approved

karlcz commented 3 years ago

@ACharbonneau please see new checklists in issue summary. Given the late change to the dcc_primary_contact table, I think we should make this an explicit check rather than assume the approval decisions were checking this detail...

ACharbonneau commented 3 years ago

Thats fine. I don't know how to check it without downloading all the bags tho. Is there a way to view that table in the portal?

karlcz commented 3 years ago

If the submissions prepared successfully to allow review, you can view the table contents via chaise, but I guess we don't provide navigation to the DCC Primary Contact table right now. :-/

Here's the clumsy workaround:

Follow "browse data" link for a submission in registry
Notice you are on the "file" table in the browser location URL
Edit the browser location from "file" to "primary_dcc_contact"

E.g. this is the initial browsing URL for a recent submission, followed by the edited URL to see the dcc contact table instead:

@.***(RID)

ACharbonneau commented 3 years ago

I checked them all for abbreviations. They're set.

karlcz commented 3 years ago

I have tested the release tool on app-dev so I think we're set to cook staging or prod releases when ready.

ACharbonneau commented 3 years ago

I should have them all in staging by lunch today (monday)

karlcz commented 3 years ago

The release candidate is built at a temporary location https://app.nih-cfde.org/chaise/recordset/#118/CFDE:file