CDR Tickets

Here are issues we've identified with the current QC report:

• The current QC report for the Misc docs does not have any options for displaying markup, references, images, etc.

• The QC report just pulls up a report without offering options, which we would need.

• We need to be able to view RLSO (both approved and proposed markup) and B/U (both approved and proposed markup).

• Not showing any proposed markup.

• Not showing citation numbers; the report is showing the title of the citation instead of a number.

• Not showing a reference list at the end of each main section.

• Not showing Table and Figure numbers.

• Not showing Referenced Table or Figure numbers.

• Not showing images.

• Comments are displayed as normal text (i.e., not within a colored Comment box).

~oseipokuw , which Misc. document where you using to test with?

I certainly do understand the desire of having all of the bells and whistles that our summary QC reports provide available for the Misc. documents as well, but I am thinking to myself what the effort for this request would be compared to the actual use or need of it.

It is my understanding, that we are trying to have two Misc. documents as Special Considerations available to be included in the summaries.  I am wondering how frequently these two documents will have to be modified - once a final version of these two documents have been created - and if it will make sense to reinvent the wheel to allow all of the functionality that we've implemented over the years for the summary QC reports.  We should also think about how important it is that we will do all these things independently for the Misc. document when we can see proposed markup and we can see table and figure numbering and we can see citation numbers and a reference section when we're viewing the QC report of the Summary that's using the linked document.

Some of the bullet point listed by ~oseipokuw will be simple changes and just happen to come out this way because the system is using default values:

• Not showing proposed markup
  The misc. documents aren't including the CSS to display proposed markup

• Not showing images
  The default for images is to display a placeholder

Other bullet points would need to be discussed in more detail:

• Not showing citation numbers
  The citations certainly need to be marked up in some way to be distinguishable from the regular text but if the citations should be numbered and linked it would mean a lot more effort.

• Not showing table and figure numbers
  Same as above.  If we want to display any number (or placeholder for a number) that wouldn't be much of an effort but I'm assuming there won't be a large amount of tables/figures present within that one special considerations document.  We will certainly not want to plan for figuring out what table/figure number this object would have within the full document and use that for the display of the Misc. doc QC report.

This is a long way of saying:  We should probably discuss how far we want to go with the requested changes to the Misc. Doc QC report.

I have now modified the Misc. Doc QC report to display the CitationLink elements with a placeholder simulating the display of a citation in the Summary QC report.  I'm displaying "[**]" in place of a citation.

Please let me know if you prefer a different alternative for the QC report, ~oseipokuw.

I noticed that the links for LOERef elements were not displayed in the QC report.  This has been fixed:

• CDR000154 - Miscellaneous Document Report Filter

I am still waiting to hear if the display of the CitationLink elements in the QC report is OK or if something different would be preferred.  The idea was to display the CitationLinks similarly in the QC report without having to create some type of artificial numbering.  The true numbering will be displayed as part of the summary QC reports. 

Hi Englisch, Volker (NIH/NCI) [C]  The display of the CitationLink in the Misc. Doc QC report is OK.

Approved Markup in the Misc. Document does not show up in the main summary QC report. 

Example: CDR0000812031 for Misc. Doc

                CDR0000799767   for Summary

Citations in the Misc. Document are displaying without titles and numbers in the main summary QC report. 

Example: CDR0000812031 for Misc. Doc

                CDR0000799767   for Summary

Also, no reference list at the end of the Section and no referenced table and figure numbers. I assume the changes have been wiped out from QA after Pauling landed on QA.

~oseipokuw , are you trying to review the changes to the Misc. filter for the special considerations on the QA server?  Those changes to the Misc filter aren't part of Pauling and are currently only available on DEV.

OK. Got it. We had done some testing on QA for OCECDR-5133 so, I must have thought that these changes were on QA. I will test on DEV and let you know.

I see.  You're correct, we did have some changes for the Special Consideration on QA but anything that was on QA before Pauling was deployed would have been erased with the deployment.

Right. All the changes are still on DEV. So, this is on hold until Pauling is out of the way. Thanks!

I've added the following filter to allow for citation links to be displayed:

• CDR0000811803.xml - Denormalization Filter: MiscellaneousDocument
  https://github.com/NCIOCPL/cdr-server/commit/099104a

Additionally, the QC filter has been modified:

• CDR0000000154.xml - Miscellaneous Document Report Filter
  https://github.com/NCIOCPL/cdr-server/commit/8b11e7b
  https://github.com/NCIOCPL/cdr-server/commit/ede0802

These changes have been copied to QA and are ready to be reviewed.

I think these comments belong here instead of OCECDR5133. 

Thanks Volker! All the changes are showing correctly in the QC report with the exception of

1. Referenced Table Numbers in the Miscellaneous Document

2. Approved Markup of list Items in the Miscellaneous Document

Please see CDR0000799767 (Summary) and CDR0000812031 (Misc. Doc.) on QA.

This ticket is for the misc. doc QC report, so there is a question if the table number (TableNumber and ReferencedTableNumber) should be marked in some fashion, like we do with the citations.  We also may want to adjust the CSS to display some placeholder for these within XMetaL.

Since the markup does display properly in the Misc. Doc QC report, the comment does belong in the other ticket, wouldn't you agree?

I've made filter and CSS changes to display a placeholder ([#]) for the table number in both, XMetaL and the Misc. QC report.  The following files have been updated:

• MiscellaneousDocument.css
  https://github.com/NCIOCPL/cdr-client/commit/94138a6 

• CDR000154.xml - Miscellaneous Document Report Filter
  https://github.com/NCIOCPL/cdr-server/commit/9168be5 

This is ready for review on DEV.

These filter and CSS changes have been copied to QA for review.

~oseipokuw , since you asked the filters for ticket OCECDR-5133 to be copied to the upper tiers I was wondering if this ticket is ready to be pushed as well.

Yes, this is also ready to go as well. Thanks!

Hi ~volker , It looks like I can close this ticket, right?

The filters and CSS have now been copied to STAGE and PROD.  

Please verify on PROD and close this ticket.

As a test, I have adjusted the Misc. Doc QC filter to display citations within insertion/deletion tags marked up in the QC report.  This will display the placeholder "[**]" marked up appropriately.

If you prefer this display for the Misc. Doc QC report, ~oseipokuw , let me know and I'll push this minor change to PROD as well.

Would you be able to present the placeholder in color? If not, then just having placeholder in the default font should be good.

I'm not sure what you're referring to.  We're usually using red as the color for insertion/deletion.  That's how the placeholder is now displayed.  

Are you looking for a different color?

Hi ~volker My comment about the marked up citations in misc doc has to do with the Summary QC report and not the Misc. Doc QC report. That is, if a citation in a Misc. Doc is marked up, we would prefer to see it in color in the References of the Summary QC report. However, I do understand that it will be a problem. If that cannot be done in any other way, like bolding the citation to indicate that it has been marked up (in the Misc Doc), then there is no need to make any changes to either the Misc Doc QC report or the Summary QC report.

I see.  You didn't mention anywhere in your comment that the comment was meant to relate to the Summary QC report and not to the Misc. QC report that this ticket is about.

You're also talking about the display of "Placeholders" which we don't use in the Summary QC report. We have introduced these [] placeholders in the Misc QC report because we can't give the citations the correct numbering without the knowledge of its position within a full summary section.  We're not using Placeholders in the Summary QC report because we're displaying the actual citation reference number and those are displayed marked up within the text.  The part that is not marked up is the citation itself within the References section and I think this is what you would like to have changed, right?

The missing markup for the marked-up citations within the Misc. Doc QC report is the same that was already discussed as part of OCECDR-5133.  We would have to re-arrange all of our summary filter sets to allow the denormalization of the misc. docs to be done before the revision markup filters are run.

The part that is not marked up is the citation itself within the References section and I think this is what you would like to have changed, right?

That is right, and my original comment was with regards to that. I think you're saying that it is the same issue we've already discussed in OCECDR-5133, right?

Understood. I think we can live with this 🙂.

Yes, that is correct.  It would be a huge effort to make such a change just to accommodate the 2 Special Consideration documents.

Now that we finished discussing the Summary QC report, what would you like to do with this ticket?  Have you had a chance to take a look at the changes on DEV, ~oseipokuw ?

Yes, I have but I would like Kirsten to also take a look and before moving the changes to the upper tiers.

Instead of showing the asterisks in the Misc. Doc QC report. Can you show the citation number within the Misc. Doc QC?

Instead of showing the asterisks in the Misc. Doc QC report. Can you show the citation number within the Misc. Doc QC?

I would need some additional information from you identifying the "correctness" of citation numbering you are after here:

• Are you just looking for replacing the [**] placeholder with a sequence number like [1], [2], [3], etc.

• Are you looking for replacing the placeholder and have the display like we have in the summaries, including to dedupe citations and combine, like [1-3], etc.

• Are you looking for replacing the placeholder and also create a "References" section?

Currently, we do not have use any citation processing as part of the Misc. QC report but we are using 3 or 4 different filters as part of the summary filter set just to achieve proper handling of the above. 

We can certainly display numbers instead of the placeholders for the Misc. QC report but how complicated do we want to make this?

• Are you just looking for replacing the [**] placeholder with a sequence number like [1], [2], [3], etc.

Yes, just a sequence of numbers should be fine. Thanks!

As discussed during our status meeting, I've added sequence numbers for the citations as listed in option (1).

This is ready for review on DEV.

Looks good. Please install on QA. Thanks!

The modified filter has been copied to QA for your review.

Verified on QA. Please install on PROD. Thanks!

The filter changes for the citation display have been copied to STAGE and PROD:

• CDR0000000154.xml  - Miscellaneous Document Report Filter
  https://github.com/NCIOCPL/cdr-server/commit/ee7bf757

Please verify and close this ticket.

Verified on PROD. Thanks!