CDR Tickets

Added watchers.

Thanks for putting the issue in Robin! I just want to clarify that these are not really going to be modules, but rather individual summaries. Just in case it matters...

Patient or HP?

We will be creating individual summaries for both Patient and HP, but the patient summaries are more complicated since they will be more individualized, so for now we are just doing the HP's programmatically. We will need to do the same thing for both English and Spanish.

I think it would be helpful to have another conversation with Sharon to talk about the patient summaries separately. I think she has created a couple of pilot/examples we could look at.

I wasn't clear about the exact interpretation of "2nd-level headings" so I started with the idea that you were looking for the titles underneath the title for the whole summary.

• General Information About Unusual Cancers of Childhood

• Head and Neck Cancers

• Thoracic Cancers

• Abdominal Cancers

• Genital/Urinary Tumors

• Other Rare Childhood Cancers

• Changes to This Summary (04/04/2017)

In case that's not what you meant, I also pulled out the 3rd-level titles:

• Introduction

• Nasopharyngeal Carcinoma

• Esthesioneuroblastoma

• Thyroid Tumors

• Oral Cavity Cancer

• Salivary Gland Tumors

• Laryngeal Cancer and Papillomatosis

• Midline Tract Carcinoma Involving the

• Breast Cancer

• Lung Cancer

• Esophageal Tumors

• Thymoma and Thymic Carcinoma

• Cardiac Tumors

• Mesothelioma

• Adrenocortical carcinoma

• Gastric (Stomach) Cancer

• Cancer of the Pancreas

• Colorectal Carcinoma

• Neuroendocrine Tumors (Carcinoid Tumors)

• Gastrointestinal Stromal Tumors (GIST)

• Carcinoma of the Bladder

• Testicular Cancer (Non–Germ Cell)

• Ovarian Cancer (Non–Germ Cell)

• Carcinoma of the Cervix and Vagina

• Multiple Endocrine Neoplasia (MEN) Syndromes and Carney Complex

• Pheochromocytoma and Paraganglioma

• Skin Cancer (Melanoma, Basal Cell Carcinoma [BCC], and Squamous Cell Carcinoma [SCC])

• Intraocular (Uveal) Melanoma

• Chordoma

• Cancer of Unknown Primary Site

I just added Sharon as a watcher on this issue so that she can comment.

We count the first list above as first level headings, and the second list you made as second level headings. That is the list we expect to create individual summaries for.

Bob, first just a note about the list you generated. It looks like one of the names got cut off, presumably because the next word is a gene name ("Midline Tract Carcinoma Involving the _NUT _Gene (_NUT _Midline Carcinoma)"). We'll need to include the rest of the title (including the gene name) in the title of that summary, but I suspect the gene name tags won't be allowed. If we have to add the rest of that title manually, we can.

We reviewed the existing Unusual Cancers summary and discussed with Sharon and I think we're now ready to have you programmatically set up the first set of summary documents. We would like to do these in batches, beginning with the head & neck summaries, so Sharon doesn't have too many to keep in sync while she's getting them ready for publication. Here are the specific instructions.

1. Please ignore the Introduction section. Please also ignore the brief introductory text under each body system. This text will be deleted.

2. Please create summaries for the head and neck cancer types on DEV. This subset includes the following cancer types:

• Nasopharyngeal Carcinoma

• Esthesioneuroblastoma

• Thyroid Tumors

• Oral Cavity Cancer

• Salivary Gland Tumors

• Laryngeal Cancer and Papillomatosis

• Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma)

3. Please add the word "Childhood" to the beginning of the summary title for each summary listed above (e.g., "Childhood Nasopharyngeal Carcinoma").

4. Please copy and paste the full metadata section from the Unusual Cancers summary into each of the new "child" summaries. We will manually update the metadata (terminology, abstract, key words, summary description, summary URL, purpose text) in each of the new summary documents.

5. We plan to add a "Special Considerations for the Treatment of Childhood Cancer" section to each of the summaries, most likely using a module. This will be handled manually.

I think that's all for now. Let us know if you have any questions. Thanks!

I understand that this is not what you eventually want to see, for lots of reasons (don't get to see it XMetaL, no QC report, etc.), but before I actually create the CDR documents on DEV, please take a look at http://cdr-dev.cancer.gov/UnusualChildhoodCancers/index.html so we can have a reality check that we're on the same general page as far as the summary generation. If something jumps out at you as a "NO, DON'T DO IT THAT WAY" problem, or an "OOPS, WE FORGOT ABOUT ....," let me know and I'll do my best to make it the way you really want it. Otherwise, I'll go ahead and create the CDR documents.

This seems reasonable as you have it. Thanks, Bob.

The nasopharyngeal carcinoma HP summary was created quite a while ago when we were testing the module idea. Bob will not need to create a second document for this topic.

Documents created on DEV:

skipping Nasopharyngeal Carcinoma
created CDR0000780503 (Childhood Esthesioneuroblastoma)
created CDR0000780504 (Childhood Thyroid Tumors)
created CDR0000780505 (Childhood Oral Cavity Cancer)
created CDR0000780506 (Childhood Salivary Gland Tumors)
created CDR0000780507 (Childhood Laryngeal Cancer and Papillomatosis)
created CDR0000780508 (Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma))

I'm able to open the first two summaries but all others report a schema error.
Was this expected?

It looks like the title of the summary is in a Title element as opposed to a SummaryTitle element. This may be what is causing a validation error (and an issue with the DocTitle construction).

It wasn't expected. Sharon is putting together a list of any other anomalies.

Any chance I could get this list some time today, so that I'll be able to produce another set for review at our weekly meeting tomorrow?

Hi Bob, I'm attaching the list of unexpected findings from Sharon and Kirsten. I added comments throughout the document. The main issue continues to be the Summary Title – that has some trickle-down effects. However, a couple of other things she notes are broken SummaryFragmentRefs (including dynamic table/figure numbering) and some problems with LOERefs and GlossaryRefs in the QC reports.

Thanks, Robin. At this point I may only have time before tomorrow's meeting to do another run that renames the top-level Title element to SummaryTitle. From the comments, it looks like using the copy of the source summary on DEV would be preferable, right?

I think using the docs on DEV is a good idea for this test. Then we could at least rule out the citation problem. It will also give us a more reasonable expectation for how the other links (LOERefs, GlossaryRefs) will work. Thanks!

DEV has more than one summary with the doctitle "Unusual Cancers of Childhood Treatment;Treatment;Health professionals"; which one would you like me to use?

Please use CDR0000062872. The other one was just created by Volker a few days ago, presumably for testing the merged QC report.

created CDR0000780565 (Childhood Esthesioneuroblastoma)
created CDR0000780566 (Childhood Thyroid Tumors)
created CDR0000780567 (Childhood Oral Cavity Cancer)
created CDR0000780568 (Childhood Salivary Gland Tumors)
created CDR0000780569 (Childhood Laryngeal Cancer and Papillomatosis)
created CDR0000780570 (Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma))

This is looking much better. The few validation errors I am encountering have to do with the lack of an AltTitle (let's discuss whether it would be feasible to add that programmatically since it will match the SummaryTitle) and the fact that some of the summary content is not contained within a SummarySection (this is probably a data issue that we'll have to adjust manually--we could perhaps do this ahead of time). LOERefs, GlossaryRefs, and Citations all look good and the SummaryTitle issue has corrected the DocTitle problem.

The tables are also numbered appropriately in the Ch Thyroid Tumors summary and SummaryFragRefs pointing to sections of other summaries are working as expected.

Sharon, let us know if you see any other issues.

I'm going to try and squeeze in another run before this afternoon's meeting, putting in the AltTitle elements and trying to re-map the self-referential fragment links in the SummaryFragmentRef elements. In the meantime you might want to go ahead and add the missing SummarySection wrappers for the head and neck cancers in the DEV source document.

Hi Bob, Sharon added the SummarySection wrappers in the Unusual Cancers summary on DEV.

Haven't had a chance to look at these myself yet:

created CDR0000780575 (Childhood Esthesioneuroblastoma)
created CDR0000780576 (Childhood Thyroid Tumors)
created CDR0000780577 (Childhood Oral Cavity Cancer)
created CDR0000780578 (Childhood Salivary Gland Tumors)
created CDR0000780579 (Childhood Laryngeal Cancer and Papillomatosis)
created CDR0000780580 (Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma))

Here's a set with fewer problems :-)

created CDR0000780587 (Childhood Esthesioneuroblastoma)
created CDR0000780588 (Childhood Thyroid Tumors)
created CDR0000780589 (Childhood Oral Cavity Cancer)
created CDR0000780590 (Childhood Salivary Gland Tumors)
created CDR0000780591 (Childhood Laryngeal Cancer and Papillomatosis)
created CDR0000780592 (Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma))

I discussed the overall approach with Sharon this morning, and I wanted to clarify a few things that will influence our approach.

1. The plan is to work on the new small summaries by body system, beginning with head and neck. Sharon and Kirsten will complete and publish to Cancer.gov each batch of summaries before moving onto the next set. This means that the Unusual Cancers summary, which will also continue to get published during that time, will be decreasing in size over time and include links to the new smaller summaries helping our users learn where to find the new content.

2. This also means that some SummaryFragmentRefs may need to be checked/updated multiple times as the smaller summaries get created. We think it will be simplest to remove the support for correcting internal links since it will make updating the external (referring to other documents) links more complicated to fix.

3. A shell document (for generating a QC report) will need to be created at the outset with the first batch and added to as the summaries are completed. I'm not sure if it makes sense to do this programmatically. The shell document will contain the overall SummaryTitle and AltTitle as well as first- and second-level headings (second-level headings being the SummaryTitles of the new smaller summaries).

This (paring down the original summary as we go) is a change from the approach we were discussing yesterday afternoon, right? Do you need me to do a fresh run with the SummaryFragmentRef elements left as we found them? Should that run include generation of the shell document? Or do you want to do that as a manual process?

I don't think it's worth it to create the shell document programmatically. I will need to create this on DEV anyway for testing of the merged QC report.

I spoke with Kirsten today and she did have a couple of requests that we hope could be added to this task.

1. Sharon has already provided her with the summary URLs and I assume we will always know this information ahead of time. Could you add the summary URLs to the attribute inspector and also add the text that go into the SummaryURL element (usually the summary title)?
Here are the URLs for the current set:

Childhood Nasopharyngeal Cancer Treatment
/types/childhood-cancers/hp/child-nasopharyngeal-treatment-pdq Looks like this is the one being skipped.
Childhood Esthesioneuroblastoma Treatment
/types/childhood-cancers/hp/child-esthesioneuroblastoma-treatment-pdq
Childhood Thyroid Cancer Treatment
/types/childhood-cancers/hp/child-thyroid-treatment-pdq
Childhood Oral Cavity Cancer Treatment
/types/childhood-cancers/hp/child-oral-cavity-treatment-pdq
Childhood Salivary Gland Cancer Treatment
/types/childhood-cancers/hp/child-salivary-gland-treatment-pdq
Childhood Laryngeal Cancer Treatment
/types/childhood-cancers/hp/child-laryngeal-treatment-pdq
Childhood Midline Tract Carcinoma Treatment
/types/childhood-cancers/hp/child-midline-tract-treatment-pdq

2. Could you also add the Changes to This Summary section to each of the summaries? This section will have a Section Metadata and a Title with standard text in the first paragraph for all the summaries.

Since she would have to add this information for all the summaries manually, it would be helpful if they can be added programmitcally.

Rather than hard-code the URLs in the software, please provide a spreadsheet with one column showing the Summary Title and the other giving the value which should be put into the attribute for all of the summaries, not just the head and neck summaries.

Also, please tell me exactly what's supposed to go into the Changes to This Summary section, and where it's supposed to go.

I have added the spreadsheet. Do you want me include the domain info (http://www.cancer.gov) to all of the URLs?

Oh. You need the URLs for all the summaries and not just for the Head and Neck summaries.

I need to know what to put in the attribute value (which attribute?). If you tell me what the prefix should be for all the values you provide, that will work.

Right.

I don't think that is possible unless Sharon can provide that. I was hoping that we can provide them to you as and when the summaries are ready to be created.

The attribute is the cdr:xref. The prefix for all of them would be
"https://www.cancer.gov"

So in this case only the prefix will be present in the document and not the fully qualified URL.

OK, I'll add a command-line argument to specify which spreadsheet to use for each run.

So in this case only the prefix will be present in the document and not the fully qualified URL.

I don't know what that means.

Also, please tell me exactly what's supposed to go into the Changes to This Summary section, and where it's supposed to go.

<SummarySection>
<SectMetaData> <SectionType> Changes to summary </SectionType></SectionMetaData>
<Title> Changes to This Summary (Current Date )</Title>
<Para>The PDQ cancer information summaries are reviewed regularly and updated as

new information becomes available. This section describes the latest

changes made to this summary as of the date above. </Para>
</SummarySection>

I will add a screenshot shortly.

Great. Thank you! That makes my question above irrelevant.

There's a discrepancy between the comment (which has one Para element) and the screen shot (which has several, most of which are collapsed, so I can't tell what's in them).

It will be the last summary Section in each summary document.

Sorry about that. Please Ignore the paras in the screenshot. They have text in them and they are different for each summary. Just the one Para with the text I provided in the comment should be fine. Also, please ignore the links for "PDQ" and "Cancer" displayed in the screenshot.

Then perhaps it might be best to remove the attachment for the screen shot, lest someone coming behind us (or we ourselves) get confused later on.

Okay, just did. Thanks!

Decided in the weekly status meeting:

I will modify the software to

1. add the summary urls

2. add the Changes to this Summary section

3. back out the SummaryFragmentRef modifications

4. mark the new summaries as modules

... and then do another run on DEV, which William will review. Robin will create the template from which the composite QC report will be run, and test that report.

Exception: u'Childhood Esthesioneuroblastoma' not found in URL map

~oseipokuw: please provide a spreadsheet with titles in the first column which match exactly the summary title of the new documents. While you're at it, you might want to check the values in the second column; you have a bunch of non-breaking space characters at the end of the URL fragments: do you really want those in your attribute values?

I have uploaded a new file. Please try again. I have also tried to remove the extra spaces.

skipping Nasopharyngeal Carcinoma
created CDR0000780646 (u'Childhood Esthesioneuroblastoma')
created CDR0000780647 (u'Childhood Thyroid Tumors')
created CDR0000780648 (u'Childhood Oral Cavity Cancer')
created CDR0000780649 (u'Childhood Salivary Gland Tumors')
created CDR0000780650 (u'Childhood Laryngeal Cancer and Papillomatosis')
created CDR0000780651 (u'Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma)')

I see each of the titles you posted above start with a "u". Are you still getting errors with the updated spreadsheet?

Please append each of the titles in the Summary URL with " (PDQ®): Treatment". I can update the spreadsheet to reflect this but that won't match exactly with what is in the summary title.

I see each of the titles you posted above start with a "u". Are you still getting errors with the updated spreadsheet?

No, that's just the way Python represents the raw form of a Unicode string (notice that the u is outside the quote marks).

I'll modify the software for the new requirement and do another run later today.

skipping Nasopharyngeal Carcinoma
created CDR0000780658 (u'Childhood Esthesioneuroblastoma')
created CDR0000780659 (u'Childhood Thyroid Tumors')
created CDR0000780660 (u'Childhood Oral Cavity Cancer')
created CDR0000780661 (u'Childhood Salivary Gland Tumors')
created CDR0000780662 (u'Childhood Laryngeal Cancer and Papillomatosis')
created CDR0000780663 (u'Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma)')

These all look good. Can you please change the format of the date under the Changes to this Summary section to (MM/DAY/YEAR)? If that is not possible at this time, that is okay since the date will be updated anyway. Other than that everything looks good and ready to go.

This set uses the ambiguous date format (replacing the ISO format).

skipping Nasopharyngeal Carcinoma
created CDR0000780670 (u'Childhood Esthesioneuroblastoma')
created CDR0000780671 (u'Childhood Thyroid Tumors')
created CDR0000780672 (u'Childhood Oral Cavity Cancer')
created CDR0000780673 (u'Childhood Salivary Gland Tumors')
created CDR0000780674 (u'Childhood Laryngeal Cancer and Papillomatosis')
created CDR0000780675 (u'Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma)')

Thanks! They all look good.

I agree - this new batch looks good to me, too. Thanks, Bob!

I created a shell doc on DEV for the QC report (just head & neck summaries for now) - CDR0000780676. The B/U and RLSO QC reports for the shell doc look good to me, but I'd like to see what Sharon thinks, too. Sharon, maybe we can touch base about this on Monday.

Sharon and I reviewed the new summaries and the QC report of the shell doc and all looks good. We're ready to proceed.

Just confirming - "proceed" in this case means I should generate the H&N summaries on PROD?

Yes. Thanks!

skipping Nasopharyngeal Carcinoma
created CDR0000790381 (u'Childhood Esthesioneuroblastoma')
created CDR0000790382 (u'Childhood Thyroid Tumors')
created CDR0000790383 (u'Childhood Oral Cavity Cancer')
created CDR0000790384 (u'Childhood Salivary Gland Tumors')
created CDR0000790385 (u'Childhood Laryngeal Cancer and Papillomatosis')
created CDR0000790386 (u'Childhood Midline Tract Carcinoma Involving the NUT Gene (NUT Midline Carcinoma)')

Check these over carefully, please!

These look good on PROD. Thank you!

We’re ready to create the next batch of Unusual Cancers summaries. This batch will include the Thoracic Cancers section of the Unusual Cancers summary. I've tried to compile our many requests from the last batch into a single list below. We are awaiting feedback from Lindsay on a list of proposed URLs; I'll add that spreadsheet to the ticket when it's ready.

1. Please ignore the Introduction section. Please also ignore the brief introductory text at the top of the Thoracic Cancers section. This text will be deleted.

2. Please create summaries with an attribute of AvailableAsModule=Yes for the following thoracic cancer types on DEV. This subset includes the following cancer types:

• Breast Cancer

• Tracheobronchial Tumors*

• Pleuropulmonary Blastoma*

• Esophageal Tumors

• Thymoma and Thymic Carcinoma

• Cardiac Tumors

• Mesothelioma

*Note: these are subtypes of lung cancer, and are located one level deeper in the summary than the other types we have listed here. We plan to develop a separate summary for each of them for SEO reasons. If it would make more sense to create these two summaries manually, that’s fine.

1. Please add the word "Childhood" to the beginning of the summary title and “Treatment” to the end of the summary title for each summary listed above (e.g., "Childhood Breast Cancer Treatment").

2. Please copy and paste the full metadata section from the Unusual Cancers summary into each of the new "child" summaries. We will manually update the metadata (terminology, abstract, key words, summary description, and purpose text) in each of the new summary documents, with the exception of the summaryURL (see #5).

3. Please refer to the attached spreadsheet (SQK will provide once these are approved by Lindsay) for a list of approved URLs for each of the thoracic summaries.

4. Please add a Changes To This Summary section to each of the new “child” summaries. This section should be populated as follows:

<SummarySection>
<SectMetaData> <SectionType> Changes to summary </SectionType></SectionMetaData>
<Title> Changes to This Summary (MM/DD/YYYY )</Title>
<Para>The PDQ cancer information summaries are reviewed regularly and updated as new information becomes available. This section describes the latest changes made to this summary as of the date above. </Para>
</SummarySection>

7. We plan to manually add a "Special Considerations for the Treatment of Childhood Cancer" section to each of the summaries.

The list of URLs for the thoracic summaries is attached. Let me know if you need it in Excel. There's a comment about one of the URLs, but we'll just update that one manually if it needs to be changed after Lindsay's testing.

If this is OK as is, we're ready for the first run on DEV.

~bkline Would it be possible to run this for us today? Users have been waiting to start working on this on PROD.

I'll start working on this after today's meeting on the dictionary migration. Can I get the URLs as an Excel spreadsheet, please?

Thanks.

Thanks Bob! I have copied the URLs into a spreadsheet (attached) Thoracic Cancer Individual HP Summaries.xlsx

Before I create the documents in the DEV repository, please review the drafts here.

I had hoped that I would be able to use the spreadsheet to drive the script automatically, but it didn't work out that way, because the strings in the spreadsheet didn't match the section titles in the source document (for example, the Title element for the Breast Cancer section actually looks like this in the source document):

<Title>
  Breast
  <Insertion UserName="sershenca" Time="Monday, July 1, 2019 6:06:24 PM" RevisionLevel="proposed">Masses</Insertion>
  <Deletion UserName="sershenca" Time="Monday, July 1, 2019 6:06:21 PM" RevisionLevel="proposed">Cancer</Deletion>
</Title>

So I guess we'll just have to do one-off custom scripts for each batch. 😛

Before I create the documents in the DEV repository, please review the drafts here.

Please skip the "Childhood Tracheobronchial Tumors Treatment" and the "Childhood Pleuropulmonary Blastoma Treatment" summaries. They have been manually created on product already. Other than that they look good for live mode on DEV.

I think we need to back up a couple of steps. I got a little lost in the jumbled numbering of the collected steps above in the 22 August comment, and the fixing of the summary URL for the new summaries fell on the floor (missed in the review, presumably). Please take another careful look at the regenerated static summaries before I load them into the repository.

https://cdr-dev.cancer.gov/ThoracicChildhoodCancers/index.html

Thanks.

There seems to be an error in the URL for the Childhood Thymoma and Thymic Carcinoma Treatment summary. Other than that the rest seem okay.

https://www.cancer.gov/typeshttps://www.cancer/gov/types/thymoma/hp/child-thymoma-treatment-pdq"

See how it looks now. If everything looks good, I try generating the documents on DEV.

They look good. Thanks!

OK, the new summaries have been loaded on DEV. Please take a look.

They look good on DEV. Thanks!

Shall I create them on PROD?

Yes please.

CDR799416 - CDR799420.

Kirsten would want the summaries created only on PROD to avoid delays. Also, we agreed that the summaries could be created without the summary URLs (or we could create them with just the domain information which remains the same for each URL) and Kirsten will manually enter the URLs when they are ready. I will let you know when she is ready for the next batch.

Abdominal Cancer Individual HP Summaries.xlsx

I have attached the spreadsheet for the next batch - Abdominal. Please create the documents on PROD.
If you can do this quickly, it would be really appreciated. Thanks!

CDR799714 - CDR799719.

Thank you very much, Bob!

I have attached the next batch of summaries. This batch has all the URLs. Genital Urinary Individual HP Summaries.xlsx
~bkline It is okay to create the summaries before fixing the issue in OCECDR-4682

CDR799767-CDR799770.

Thank you ~bkline

Other Rare Cancer Individual HP Summaries.xlsx

This is the last batch of Unusual summaries. Please create the CDR records for these as soon as you get the chance. Thank you!

2019-12-13 09:37:01.499 [INFO] created 800107 (Childhood Multiple Endocrine Neoplasia (MEN) Syndromes and Carney Complex Treatment;Treatment;Health professionals)
2019-12-13 09:37:03.719 [INFO] created 800108 (Childhood Pheochromocytoma and Paraganglioma Treatment;Treatment;Health professionals)
2019-12-13 09:37:06.907 [INFO] created 800109 (Childhood Melanoma Treatment;Treatment;Health professionals)
2019-12-13 09:37:08.298 [INFO] created 800110 (Childhood Basal Cell Carcinoma and Squamous Cell Carcinoma of the Skin Treatment;Treatment;Health professionals)
2019-12-13 09:37:10.379 [INFO] created 800111 (Childhood Intraocular (Uveal) Melanoma Treatment;Treatment;Health professionals)
2019-12-13 09:37:12.468 [INFO] created 800112 (Childhood Chordoma Treatment;Treatment;Health professionals)
2019-12-13 09:37:14.314 [INFO] created 800113 (Childhood Carcinoma of Unknown Primary Treatment;Treatment;Health professionals)

Thank you!

Since that was the last batch, I am closing this ticket. Thank you!