CDR Tickets

This is another issue which got into the queue for level-of-effort estimation before the discussion of requirements and solutions the users have asked for.

Discussed in the CDR status meeting. We concluded that there are no further nuances which need clarifying discussion beyond what's been captured in the original description of the request. It looks like we need to:

1. Add an element to the glossary concept schema
2. Modify the publishing filter to pick up the new information
3. Modify the DTD (possibly) to allow for a new element
4. Put an entry in the link control tables to allow the new link type

I have taken care of #1 and #4 from the previous comment on DEV. Please check to make sure the new element does what it should. If so, please assign the issue to Volker so he can take care of #2 and #3.

Still need review of the schema, so Volker can proceed with the next steps.

What is the name of the new element you added to the concept schema?

RelatedGlossaryTermNameRef

Sorry to be weighing in so late on this, but I do have a question that I can't quite think through. I noticed that the element type is a "Glossary Concept Link" instead of a link to a term name, and I am trying to figure out how this would be rendered on Cancer.gov. If CIAT puts in a "GlossaryTermNameRef" link to the Concept document for the term name Cancell, when a user links on it, what would they see (since there are multiple term names for that concept)? Sorry if this is obvious, but I am a little confused (seems to be a more common state for me these days🙂)

I have changed the element type to a GlossaryNameLink, and modified the link control tables accordingly. Since this is a standalone link (not inline in a larger body of text), might it be less confusing to call the element RelatedGlossaryTermNameLink (since we typically use element names ending in "Ref" for the inline links)?

Yes, we can make this a link instead of a ref.

Element name changed.

I think that we need some CSS for this new element. Also, could the element be added when the RelatedInformation block is added (along with the related drug summary, related summary, and related external ref elements)?

I am wondering if it would be necessary to have the “UseWith” attribute on this new element to distinguish between English and Spanish applications of this new element.

That's a good question, William, and Margaret and I aren't too sure since this new element presents a slightly different case since we are linking to a single document for both English and Spanish terms. I will try to illustrate what we expect to happen with an example to help inform whether we need the UseWith attribute.

Example term: family history (Spanish: antecedentes familiares)

Related Information Glossary Term Link: pedigree;árbol genealógico (a single link at the bottom of the GTC document)

Beneath the English term definition for family history on Cancer.gov, we expect to see a link to "pedigree", which will bring up the English definition.

Beneath the Spanish term definition for antecendentes familiares on Cancer.gov, we expect to see a link to "árbol genealógico", which will bring up the Spanish definition.

Bob, is there enough information in the code already to inform which term to display in each case and which link to provide? Or do we need the UseWith attribute or some other solution to add this information? Thanks!

I think your analysis is correct (essentially, relationships between concepts are the same whichever language is in play), and I believe the software should be able to figure out which language is being linked from/to. Do you agree, Volker?

Yes, I agree. I don't see what added information a UseWith attribute would provide for these links. Cancer.gov should be able to match the proper language sections.

I consulted with Volker and Blair. Volker and I are agreed that we don't need the UseWith attribute on the new element in the CDR documents. All of us also agree that without modifications on the WCMS side (mostly, if not entirely, changes to GateKeeper), these new links won't show up on cancer.gov. We suspect, but aren't certain, that having the new elements show up in the published documents won't break GateKeeper, even if it doesn't know what to do with them. If we're wrong, the solution to that problem is to have Volker defer deployment of the filter and DTD changes until the WCMS side is ready. I'm going to re-assign this ticket to Volker, as looking over the comments it appears that tasks 2 and 3 (see the 2nd and 3rd comments above) haven't been addressed yet.

I'm going to re-assign this ticket to Volker, as looking over the comments it appears that tasks 2 and 3 (see the 2nd and 3rd comments above) haven't been addressed yet.

Did you already take care of
5. Update CSS
or should I throw that into my bucket?

Into the bucket.

5. Update CSS

The has been updated on DEV. The following files have been modified:

• GlossaryConcept.ctm

• GlossaryConcept.css

• GlossaryConcept_structure.css

2. Modify the publishing filter to pick up the new information
3. Modify the DTD (possibly) to allow for a new element

I've modified the publishing filters to handle the new RelatedGlossaryTermNameLink element:

• CDR616047.xml: Denormalization Filter: GlossaryTermName

• CDR616048.xml: Vendor Filter: GlossaryTermName

and I've modified the DTD to add a new element RelatedGlossaryTermRef:

• pdq.dtd

• pdqCG.dtd

This is ready for review on DEV.

Please note that the PublishPreview is not working at this point because the new DTD has not yet been installed on Gatekeeper.

Hi William, Could you possibly test this on Dev? I can enter the Related Information block in a Glossary Term Concept template, and I see the RelatedGlossaryTermName element,and hte CSS looks okay there. Since I am not authorized to actually edit a real glossary term concept document to try adding a link I can't test the functionality.

Hi Margaret,
I have been testing this today. I am not done yet but here a few that are done. I will let you know when I am completely done.

CDR0000621145
CDR0000621144
CDR0000736218
CDR0000619364
CDR0000621146

I am all done now. Here is the complete list of test documents:
CDR0000621145
CDR0000621144
CDR0000736218
CDR0000619364
CDR0000621146
CDR0000623799
CDR0000619364

How do we test this? Publish Preview isn't working. Also, shouldn't this show up in the QC reports along with the other Related Information links? We probably need another issue to modify the QC reports, right Volker?

Just a reminder that this won't achieve the desired end result until the WCMS team does some work on GateKeeper. See comment above posted 2013-10-22 12:01 (I miss Bugzilla, which numbered the comments).

How do we test this?

At the moment all we can do is to check the XML vendor output.

Publish Preview isn't working.

Publish preview isn't working currently because we're sending a new element that's not in the DTD that Gatekeeper has. I'm trying to update the DTD on Gatekeeper today (not sure if I have the permissions to do so). Once the DTD has been updated we will be able to test if Gatekeeper breaks by sending the new element.

We probably need another issue to modify the QC reports, right Volker?

Yes, I'm guessing that you would want to include this to the Concept QC report. I didn't even think about that.

We suspect, but aren't certain, that having the new elements show up in the published documents won't break GateKeeper, even if it doesn't know what to do with them.

I finished testing to run a publish preview report with the new element and Gatekeeper is complaining with an error

Could not find document in database for RelatedGlossaryTermRef document id from value: CDR0000446542

If we're wrong, the solution to that problem is to have Volker defer deployment of the filter and DTD changes until the WCMS side is ready.

Another option that Erika and I discussed is that we could remove that new element from the vendor output. When WCMS is ready for the new element all we would have to do is to update a single filter for the element to show up on Cancer.gov (which likely could be done outside of a release).

Volker: please confirm when you've settled on a final solution and it's checked into Subversion.

I have already made the changes to strip out the element from the vendor output but I was hoping that Margaret or Robin will weigh in. The users may rather not have that element in the CDR docs if it's not displaying on Cancer.gov.
I didn't want to version the changes until we decided that this is what we want.

I was also wondering which of the QC reports should be modified to include the new element (assuming that we will keep it in the documents) since none of the QC reports are currently listing the RelatedInformation.

Actually, both the Full QC report and the Glossary Concept QC report show the Related Information, so we would want to add this element to those reports. I am not entirely sure how to comment on the proposed fix except to say that I think CIAT probably wouldn't add the element to any documents until we are able to display them on Cancer.gov, so it is probably fine to strip out the element. Do you know if the Gatekeeper/Cancer.gov work that needs to be done is in a queue somewhere for them to work on it?

I've modified the Concept and Concept Full QC reports. The following filters and scripts have been updated:

• R12090: GlossaryConceptFull.py

• R12091: CDR315588.xml (Module: Vendor Cleanup Templates)

• R12091: CDR613261.xml (Glossary Term Concept QC Report Filter)

• R12091: CDR616047.xml (Denormalization Filter: GlossaryTermName)

• R12091: CDR616048.xml (Vendor Filter: GlossaryTermName)

Margaret and I also discussed to keep all of our changes in place and go ahead to strip the element from the vendor output in case it does get entered.
Erika is going to create a story for the next WCMS release that is linking to this issue.

I forgot to mention - there was a bug in the QC reports that prevented the RelatedDrugSummaryLink element from being displayed on the QC reports. This has been fixed as well.

Please review the changes to the QC reports on DEV.

This looks good to me. I checked the term Bevacizumab, which also just happens to have a GlossaryTermLink in addition to a DrugSummaryLink in the Related info, and both were present in both QC reports.

I checked a few GTC Full reports and they all checked out well. But when I click on the GT Concept QC report for each of them I get the attached window. After clicking OK, the report opens and displays correctly.

That has already been fixed but you will have to restart XMetaL in order for the alert message to go away.

The window went away after I restarted XMetal. Thanks!

Just a note regarding the DTD changes for this element: Since we're removing the RelatedGlossaryTermNameLink from the vendor output there is no need to update the two DTD files (one for the licensees and one for Cancer.gov) at this point. However, we'll have to remember that the DTD will need to be updated as an additional step once Gatekeeper is ready to accept this new element.

Saving the CSS changes in subversion:

• R12094: GlossaryTermConcept.ctm

• R12094: GlossaryTermConcept.css

• R12094: GlossaryTermConcept_structure.css

I updated the linking tables and tested it in Prod. We cannot fully test this issue until Cancer.gov is ready to accept the new element.

Erika:

I've added you as a watcher for this ticket so you can do your magic to get this into the WCMS release queue.

WCMS is nearly ready for us to deploy this to production. "Deploy" means at least backing out the filter code to strip the new information from the vendor output. Volker will check to see if there's anything else to be done. The WCMS release number with which we're coordinating is 6.6, estimate to hit production early in May.

On the CDR side, everything necessary to display the new element has already been completed and the changes are already in production.
The things that need to be done once Cancer.gov is able to accept the new element are:

• Provide WCMS with the new DTD

• Modify the Vendor Cleanup Filter (CDR315588) so that it doesn't strip out this new element

• Update the licensee DTD

• Update the licensee documentation

Volker, Margaret, and I discussed a couple of business process rules related to this issue today that I wanted to capture:

1. Links will only be made to terms within the same dictionary. In other words, we will not link a term in the genetics HP dictionary to a term in the NCI dictionary for patients and vice versa.

2. Links to other glossary terms can only be added AFTER the term has been translated and the Spanish has been published (if the term is one that will be translated).

Since this ticket is assigned to Margaret it wasn't really on my radar.
I have updated the vendor cleanup filter to allow the RelatedGlossaryTermLink to be included in the vendor output now:

• R12603: Module: Vendor Cleanup Templates (CDR315588)

The three GlossaryTerms that failed over the weekend are now validating.

Please review on PROD and close this bug.