| Issue Number | 4773 |
|---|---|
| Summary | [Glossary] Allow only publishable GTCs to publish to Cancer.gov |
| Created | 2020-02-03 20:02:02 |
| Issue Type | Improvement |
| Submitted By | Osei-Poku, William (NIH/NCI) [C] |
| Assigned To | Englisch, Volker (NIH/NCI) [C] |
| Status | Closed |
| Resolved | 2020-03-11 15:34:31 |
| Resolution | Fixed |
| Path | /home/bkline/backups/jira/ocecdr/issue.256115 |
Currently versions of a GTC document that have not been made publishable get picked up for publishing. That is, as long as they have been versioned and there is a linked publishable GTN. Please modify the vendor filters to allow only publishable versions of the GTC to publish to Cancer.gov.
Could you please include an example that I could look at or prepare a document on DEV?
Here are two sets of test documents you can use:
anticancer therapy (GTC: 639944; GTN: 639945)
biospecimen (GTC: 623872; GTN: 561324)
I want to make sure you understand what you are asking with this ticket, ~oseipokuw. If I make this change the users will not be able to view any changes in the concept document when running a QC report that uses this denormalization filter. The denormalization step will only include the publishable version of the concept. This is the same problem we just addressed with the summary modules.
If you're asking to implement a similar solution for the glossary documents that we've used for the summary modules - using a separate version of the document based on a parameter passed (QC report or not QC report) - then this ticket is not anymore a release independent filter change.
The second option is what we are expecting. I this can go in a release. Should I move it to Leibniz?
then this ticket is not anymore a release independent filter change.
Looking at the code it appears that Bob had already made the necessary modifications for all document types, not just for the Summaries. It's possible this requested change may not need a release after all.
I have another question, ~oseipokuw:
Currently, a QC report for the GTN requires a version of the linked GTC to be available. Since we used to pick up the same version for the PDQ Partner output and the GTN QC reports this made sense. If we're now splitting those two filter paths would you like to continue to pick up a version of the GTC for the QC reports or would you rather - as we do for summaries - use the CWD of the GTC?
I am not sure I understand your question. Do you mean, we do have the option to choose which version of the GTC to use for a GTN QC report?
Currently, the report is using the latest version of the GTC document. You're request is to use the latest publishable version for the PP report (and vendor output). For the QC report we can continue to use the latest version or we could instead use the CWD. You won't have the choice when you run the report but I can setup the filters now to use one or the other going forward.
I hope that makes sense.
Got it. Thanks! Please continue to use the latest version of the GTC document.
As I mentioned earlier, this will be different from our change to the summary modules. There we're using the CWD for the QC reports. Just making sure you're aware of the difference.
By the way, it turns out this change requires updates to the XMetaL macro file. Therefore I will have to move the ticket to Leibniz.
Understood. When you say the latest version, you mean whether the version is the CWD or publishable version, right?
No, the CWD will never be used when you're picking the latest version. It will be identical to the latest version but only until you start making changes.
You know that at any given time during the edit process your publishable version, latest (non-publishable) version, and CWD may be different with the CWD including the latest edits. As an example please look at CDR799624 on DEV. If you're running the PP report the pub-version of the GTC is displayed (indicated by the definition text "A gene that makes - pup-version- ...). If you're running the QC report, the CWD of the GTC is displayed (indicated by the definition text "A gene that makes - CWD - ...). The latest version (Version 4) of the GTC isn't displayed at the moment.
From what you're telling me you'd rather have the latest version (V-4) instead of the CWD included for the QC report.
Thanks! Let me give it some thought. I will post a comment I have had the chance to discuss with all users.
The following filter has been updated:
CDR616047 - Denormalization Filter: GlossaryTermName
commit [95d11bd3]
This version is using the publishable version for PP reports and the CWD for QC report. Waiting on William for the decision of which version of the document should be used for the QC report (last version or CWD).
This is ready for testing on DEV.
The following scripts have been updated on DEV:
CdrFilter.html (adding the isQC check-box)
QcReport.py
commit [b412d38] in Leibniz
The following files were using a version=-1 parameter and needed to be updated to version=0.
DrugInfoReports.py
GlossaryTermReports.py
MediaReports.py
QcReport.py
SummaryAndMiscReports.py
Commit: [leibniz 96149a7f]
Have you had a chance to talk to the users, ~oseipokuw?
Yes, we had the chance to discuss this and decided to leave the display of the GTC for the GTN reports as is. So, when we run PP, the publishable version should display and when we run the QC report, the CWD of the GTC should display. Essentially, it should continue to work the same way it is working now. Thanks!
Essentially, it should continue to work the same way it is working now.
You're referring to the way it is working on DEV right now when you say "the same way it is working now" and not the way it currently works on PROD, right?
That must be a trick question 🙂🙂. I have compared the current behavior on DEV vs. PROD and it looks to me that even on PROD, the CWD is displayed for at least the GTN w/ Concept QC report. Would you mind taking a look at CDR0000269460 on PROD? Please run the GTN w/GTC QC report for that term. It looks like the report is displaying the CWD.
It wasn't meant as a trick question. Please keep in mind that the request for this ticket is "allow only publishable GTCs to publish". The version of the filter on DEV already includes that change (while PROD does not). The second portion/path of the ticket is related to the QC report and there I had asked if you wanted to display the CWD or the GTC or the last version? On PROD we're displaying the last version, on DEV we're displaying the CWD.
Would you mind taking a look at CDR0000269460 on PROD? Please run the GTN w/GTC QC report for that term. It looks like the report is displaying the CWD.
How did you determine that the CWD was picked up? Both, the CWD and the last version have the same term definition. The definition resource has changed in the CWD and that information is not displayed in the QC report.
Anyway, it sounds we want to display the CWD of the concept document. I will change the filter to pick up the CWD instead of the last version for the QC reports.
The filter changes have been moved to the Leibniz branch:
CDR616047 - Denormalization Filter: GlossaryTermName
[leibniz 5e217d32]
This is ready for review on DEV.
We decided to modify the GTC full QC report to serve as pub preview for cases where users have not created a publishable version of the GTC but would like to view pub preview. I will create a ticket to address this in Maxwell.
Verified on DEV. Thanks!
Verified on QA. Thanks!
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