CDR Tickets

Issue Number 3231
Summary [Summary] QC Report Bugs
Created 2010-09-21 14:59:38
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To Englisch, Volker (NIH/NCI) [C]
Status Closed
Resolved 2010-10-18 12:17:11
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.107559
Description

BZISSUE::4919
BZDATETIME::2010-09-21 14:59:38
BZCREATOR::William Osei-Poku
BZASSIGNEE::Volker Englisch
BZQACONTACT::William Osei-Poku

In our last meeting, Margaret stated that CIAT has reported to her that there were bugs in some summaries QC reports that have not been fixed for a long time. Here are the bugs that have been reported by users:

In the Bold Underline report:

1) When bulleted lists are in deletion tags, the bullets (without text) continue to show up in the BU QC report.
2) Glossary terms that are in deleted text continue to show up in the table of glossary links at the end of the summary.

Example: You can see both of these bugs in 276462 Renal Cell Cancer, CDR version #62 (Final Markup AJCC cx 9/3/10 ef).

In both Redline and Bold report:

When there is a standalone Key Point (no paragraph following) the next Key Point displays up against it in the QC view.

Example: CDR0000062962 Childhood Brain Stem Glioma—second and third KeyPoints in the first summary section.

Comment entered 2010-09-21 15:26:21 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-21 15:26:21
BZCOMMENTOR::Volker Englisch
BZCOMMENT::1

These issues certainly needed to be reported and I am surprised the problems had never been mentioned before. However, I personally don't think that the issues are serious enough to make the QC reports unusable.

As for the deleted bulleted list items I vaguely remember that we had problems deleting the bullets at the time the QC reports were written. It may have been related to the poor support of CSS by older versions of browsers in use or my limited experience with CSS at the time. I'm confident we'll be able to handle this issue now.

Comment entered 2010-09-23 11:33:09 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-23 11:33:09
BZCOMMENTOR::Volker Englisch
BZCOMMENT::2

Status update:
[ ] Fix deleted bulleted lists to remove empty list items
[ ] Fix glossary term table to remove deleted glossary text
[X] Fix display of "standalone" KeyPoint entries

Comment entered 2010-09-24 16:26:02 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-24 16:26:02
BZCOMMENTOR::Volker Englisch
BZCOMMENT::3

Status update:
[X] Fix deleted bulleted lists to remove empty list items
[ ] Fix glossary term table to remove deleted glossary text
[X] Fix display of "standalone" KeyPoint entries

I've made changes to the QC filters to allow us to suppress deleted ListItems within lists.
The reason why these deletions didn't work in the first place was the fact that we are pushing Insertion/Deletion markup "down" to wrap text nodes instead of including elements inside the markup. When we do this we're loosing the information of which elements where included inside the markup. After the transformation we're unable to identify if a ListItem was marked up originally as this:
<ItemizedList>
<ListItem><Deletion>Text inside a list</Deletion></ListItem
</ItemizedList>

or this

<Deletion>
<ItemizedList>
<ListItem>Text inside a list</ListItem>
</ItemizedList>
</Deletion>
After the transformation both of these lists will look identical.
I've modified the filters to "remember" if the markup was outside or inside an element and can now use the information to suppress the display of deleted ListItems.

The following filters have been modified:
CDR315893 - Wrap nodes with Insertion or Deletion
CDR315892 - Clean up Insertion and Deletion
CDR434822 - Module: QC Filter Templates - Summary
CDR618263 - Denormalization Filter: Secondary Links
CDR380956 - Module: STYLE BU Insertion Deletion
CDR339576 - Module: InLine Markup Formatter

I'll finish this up next week after I talked to Diana regarding the display of the deleted Glossary Terms in the GT table and after lots of testing.

Comment entered 2010-09-27 12:23:00 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-27 12:23:00
BZCOMMENTOR::Volker Englisch
BZCOMMENT::4

(In reply to comment #3)
> I'll finish this up next week after I talked to Diana regarding the display of
> the deleted Glossary Terms in the GT table and after lots of testing.

My memory didn't fail me this time. The request to display the deleted GlossaryTerms in the Glossary table was done by design. This is not a bug.

I am CC-ing Diana to this issue since she would like to talk to the requester of this task to understand why this change is needed and possibly come up with a solution that fits both sides.
My suggestion would be to continue displaying the deleted GlossaryTerms in the table but display them not in regular font but maybe in italics, a different color, smaller font size, etc or - if we want to get fancy - we could provide a button that allows the users to turn the display on or off similar to the links in Bugzilla to Collapse or Expand all comments.

Comment entered 2010-09-27 13:45:30 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-27 13:45:30
BZCOMMENTOR::Volker Englisch
BZCOMMENT::5

Here is an option that might help everybody.
As a test I've added code to toggle the display of deleted GlossaryTerms.

Save the document to your computer, open it with FireFox or Chrome (I'm not sure yet why it's not working with IE) and click the link under the table header that says: "Toggle Display of deleted GlossaryTerms"

It'll turn on/off the display of deleted GlossaryTerms.

Comment entered 2010-09-27 13:45:30 by Englisch, Volker (NIH/NCI) [C]

Attachment GT_on_off.html has been added with description: Glossary Term toggle on/off

Comment entered 2010-09-28 11:54:44 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-09-28 11:54:44
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::6

Could we have the default text read: "Click to display deleted Glossary Terms” and when it is clicked and deleted Glossary Terms are displayed, it changes to read: "Click to suppress display of Glossary Terms”?

Comment entered 2010-09-28 14:20:46 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-28 14:20:46
BZCOMMENTOR::Volker Englisch
BZCOMMENT::7

Just to make sure:
I created this document as an option of what might be possible. I didn't create a solution to the request. Before I implement a solution I would first expect you, William, and Diana to have a discussion and let me know what you're decided to do for the report if anything.

Comment entered 2010-09-28 17:08:20 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-09-28 17:08:20
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::8

(In reply to comment #7)
> Just to make sure:
> I created this document as an option of what might be possible. I didn't
> create a solution to the request. Before I implement a solution I would first
> expect you, William, and Diana to have a discussion and let me know what you're
> decided to do for the report if anything.

Sent the ff email to Diana:

We (CIAT) put in a request to modify the Bold Underline QC report to not display deleted Glossary terms but Volker came up with an option that can turn on or off the deleted Glossary terms in the report, instead. I am wondering if this is Okay with you? If you do not object to the changes, I will ask Volker to proceed to implement the changes.
Please let me know if you have any questions.

Comment entered 2010-09-30 10:27:00 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-09-30 10:27:00
BZCOMMENTOR::Volker Englisch
BZCOMMENT::9

I've talked to Diana yesterday. She is OK to make the change allowing the display of the deleted glossary terms to be toggled on or off.

I will go ahead to implement this change.

Comment entered 2010-10-04 13:02:10 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-04 13:02:10
BZCOMMENTOR::Volker Englisch
BZCOMMENT::10

Status update:
[X] Fix deleted bulleted lists to remove empty list items
[X] Fix glossary term table to remove deleted glossary text
[X] Fix display of "standalone" KeyPoint entries

I have implemented the change that allows us to toggle the display of deleted GlossaryTerms in the table that's displayed at the end of the summary.

This is ready for review on MAHLER.

There is, however, one additional issue that has been brought up. GlossaryTermRefs are displayed in the QC reports as regular links (blue with underline) regardless of the insertion markup. If a single GlossaryTerm has been inserted in the text the RS QC report does not identify the link as an insertion. I'm hoping that I'll be able to fix this issue, too, but we first will need to identify what to change the current display to.

Comment entered 2010-10-05 13:28:08 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-10-05 13:28:08
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::11

(In reply to comment #2)

> [X] Fix display of "standalone" KeyPoint entries

I was able to verify the other two fixes on Mahler, but not the standalone KeyPoint issues. The bug still appears to be there.

Comment entered 2010-10-05 13:52:47 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-05 13:52:47
BZCOMMENTOR::Volker Englisch
BZCOMMENT::12

Ah, I see. I fixed the problem in the keypoints table but not in the text itself.

I'll have another look.

Comment entered 2010-10-06 14:18:28 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-06 14:18:28
BZCOMMENTOR::Volker Englisch
BZCOMMENT::13

Please check again on MAHLER. The KeyPoints should now display correctly.

Comment entered 2010-10-06 15:56:08 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-10-06 15:56:08
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::14

(In reply to comment #13)
> Please check again on MAHLER. The KeyPoints should now display correctly.

Verified on Mahler. Please promote to Bach.

Comment entered 2010-10-08 13:20:44 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-08 13:20:44
BZCOMMENTOR::Volker Englisch
BZCOMMENT::15

(In reply to comment #10)
> GlossaryTermRefs are displayed in the QC reports as regular links (blue with
> underline) regardless of the insertion markup. If a single GlossaryTerm has
> been inserted in the text the RS QC report does not identify the link as an
> insertion.

It had been decided at yesterday's status meeting - since this last issue wasn't part of the original bug report but is not ready yet for production - to create a new bug and go ahead to move the remaining changes to production.
I've created the OCECDR-3245.

Comment entered 2010-10-08 15:15:26 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-08 15:15:26
BZCOMMENTOR::Volker Englisch
BZCOMMENT::16

The fix for the reported issues required changes to the following filters:
CDR315892.xml - Clean up Insertion and Deletion
CDR335166.xml - Module: Checkbox Formatter
CDR339576.xml - Module: InLine Markup Formatter
CDR380956.xml - Module: STYLE BU Insertion Deletion
CDR409593.xml - Copy XML for Summary Report
CDR434822.xml - Module: QC Filter Templates - Summary
CDR441144.xml - Patient Summary QC Report - Bold/Underline
CDR686599.xml - Module: SCRIPT CdrJQuery

These filters are used within the following filter sets for which we will need to run diff reports on FRANCK:
Mailer Summary Set
Vendor QC Summary Set
Vendor Summary Set
QC DrugInfoSummary Set
QC GlossaryTerm Set (Redline/Strikeout)
QC MiscellaneousDocument Set (Redline/Strikeout)
QC Summary Patient Set
QC Summary Patient Set (Bold/Underline)
QC Summary Set
QC Summary Set (Bold/Underline)
QC GlossaryTerm Set
QC GlossaryTerm Set (Redline/Strikeout)
QC GlossaryTermName
QC GlossaryTermName with Concept Set
QC InScopeProtocol Admin Set
QC InScopeProtocol Citation Set
QC InScopeProtocol Full Set
QC InScopeProtocol HP Set
QC InScopeProtocol Patient Set
QC InScopeProtocol Set
QC MiscellaneousDocument Set
QC MiscellaneousDocument Set (Redline/Strikeout)
QC Term Set

Comment entered 2010-10-14 15:54:09 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-14 15:54:09
BZCOMMENTOR::Volker Englisch
BZCOMMENT::17

I discovered three minor problems while running the diff reports on FRANCK:
a) a bullet symbol had been misspelled (as part of some of my earlier testing)
b) the label for the glossary term button needed fixing and
c) the jQuery module had not been included for the Patient QC reports

These minor issues have been fixed.
CDR000158.xml: Patient Summary QC Report Filter - R9923
CDR339576.xml: Module: InLine Markup Formatter - R9923
CDR686599.xml: Module: SCRIPT CdrJQuery - R9923

Comment entered 2010-10-15 12:33:44 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-15 12:33:44
BZCOMMENTOR::Volker Englisch
BZCOMMENT::18

The filters have been copied to FRANCK and BACH:
CDR315892.xml: Clean up Insertion and Deletion - R9922
CDR335166.xml: Module: Checkbox Formatter - R9922
CDR380956.xml: Module: STYLE BU Insertion Deletion - R9922
CDR409593.xml: Copy XML for Summary Report - R9922
CDR434822.xml: Module: QC Filter Templates - Summary - R9922
CDR441144.xml: Patient Summary QC Report - Bold/Underline - R9922

CDR000158.xml: Patient Summary QC Report Filter - R9923
CDR339576.xml: Module: InLine Markup Formatter - R9923
CDR686599.xml: Module: SCRIPT CdrJQuery - R9923

Please verify on BACH and close this bug.

Please note that I did not run a diff report for every single filter set that uses one or more of these filters but I ran it for all protocol and summary filter sets. If there were any problems with one of the filters I'm certain we would have found out running the sets we've used.

Comment entered 2010-10-15 16:50:25 by Englisch, Volker (NIH/NCI) [C]

BZDATETIME::2010-10-15 16:50:25
BZCOMMENTOR::Volker Englisch
BZCOMMENT::19

The list of filter sets that I ran diff reports for:
Before After Filter Set
---— ---— --------------------------------------------
8063 8075 Vendor QC Summary Set
8062 8073 QC DrugInfoSummary Set
8061 8074 QC Summary Patient Set
8060 8072 QC Summary Patient Set (Bold/Underline)
8059 8071 QC Summary Set
8058 8070 QC Summary Set (Bold/Underline)
8054 8069 QC InScopeProtocol Admin Set
8053 8067 QC InScopeProtocol Full Set
8055 8066 QC InScopeProtocol HP Set
8056 8065 QC InScopeProtocol Patient Set
8057 8064 QC Term Set

Filter Sets that I did not run diff reports for:

  • Vendor Summary Set

  • QC GlossaryTerm Set (Redline/Strikeout)

  • QC MiscellaneousDocument Set (Redline/Strikeout)

  • QC GlossaryTerm Set

  • QC GlossaryTerm Set (Redline/Strikeout)

  • QC GlossaryTermName

  • QC GlossaryTermName with Concept Set

  • QC InScopeProtocol Citation Set

  • QC InScopeProtocol Set

  • QC MiscellaneousDocument Set

  • QC MiscellaneousDocument Set (Redline/Strikeout)

Comment entered 2010-10-18 12:17:11 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-10-18 12:17:11
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::20

(In reply to comment #18)
> The filters have been copied to FRANCK and BACH:
> CDR315892.xml: Clean up Insertion and Deletion - R9922
> CDR335166.xml: Module: Checkbox Formatter - R9922
> CDR380956.xml: Module: STYLE BU Insertion Deletion - R9922
> CDR409593.xml: Copy XML for Summary Report - R9922
> CDR434822.xml: Module: QC Filter Templates - Summary - R9922
> CDR441144.xml: Patient Summary QC Report - Bold/Underline - R9922
>
> CDR000158.xml: Patient Summary QC Report Filter - R9923
> CDR339576.xml: Module: InLine Markup Formatter - R9923
> CDR686599.xml: Module: SCRIPT CdrJQuery - R9923
>
> Please verify on BACH and close this bug.
>
Verified on Bach. Looks Great. Bug closed.

Thank you!

Attachments
File Name Posted User
GT_on_off.html 2010-09-27 13:45:30 Englisch, Volker (NIH/NCI) [C]

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