CDR Tickets

Issue Number 5138
Summary [Summary] Modify Summaries Citations Report to include citations in top-level sections that have been marked up
Created 2022-09-14 19:21:04
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To Englisch, Volker (NIH/NCI) [C]
Status Closed
Resolved 2022-10-19 15:10:47
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.327450
Description

It looks like the Summaries Citations report does not display citations that are within a section that has a markup around the top-level section block. The report however, displays citations with insertion or deletion markup around the individual elements.  It would be good to have the report display all citations within the summary document even if the markup is placed around the top-level block.

I have marked up this test summary doc CDR0000668479 on QA for troubleshooting and testing.

  1. I have placed a deletion markup around the first citation in the summary document - “Enhancing well-being during breast cancer recurrence: preliminary findings from a phase III study”  - Gotay CC.

This citation always displays in the report even with the deletion markup around the element.

2. I also placed a deletion markup around the top-level section

“Cellular Classification of Pancreatic Cancer”.

When you run the Summaries Citation report, this citation “The papillary-cystic neoplasm of the pancreas. An increasingly recognized clinicopathologic entity.” – Sanchez, J A which previously displayed in the report when the top-level section was not marked up, no longer displays.

To run the report, go to the reports menu for Summaries and Misc Docs

It is #5 under Management QC reports

On the next page, enter the CDR ID of the summary to generate the QC report.

Comment entered 2022-09-15 10:19:19 by Englisch, Volker (NIH/NCI) [C]

What is the difference between the images "citation - sanchez.png" and "image-2022-09-14-19-20-23-955.png"? If they are identical can we delete one of them?

Comment entered 2022-09-15 12:02:31 by Osei-Poku, William (NIH/NCI) [C]

I deleted the duplicate attachment. Thanks!

Comment entered 2022-09-15 12:52:04 by Englisch, Volker (NIH/NCI) [C]

OK, I see the issue.  That's a Pauling ticket.

 

For my information:

The denormalization portion doesn't create a "ReferenceList" element for deleted SummarySections.  Need to modify 

  • SummaryCitations.py - line 215. Need to include Deletion, Insertion in the iteration set.

Comment entered 2022-10-19 15:10:32 by Englisch, Volker (NIH/NCI) [C]

The following script has been modified to include the missing citations:

This is ready for review on DEV.

Comment entered 2023-05-09 11:53:44 by Osei-Poku, William (NIH/NCI) [C]

Verified on QA.

Comment entered 2023-07-05 08:26:54 by Osei-Poku, William (NIH/NCI) [C]

Verified on PROD. Thanks!

Attachments
File Name Posted User
citation - gotay.png 2022-09-14 19:15:44 Osei-Poku, William (NIH/NCI) [C]
citation - sanchez.png 2022-09-14 19:21:50 Osei-Poku, William (NIH/NCI) [C]

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