CDR Tickets

Issue Number 3021
Summary [CTGov] Schema and imports software changes to include Citations in CTGovProtocol document
Created 2009-11-09 16:42:02
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To Kline, Bob (NIH/NCI) [C]
Status Closed
Resolved 2010-01-05 10:15:25
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.107349
Description

BZISSUE::4697
BZDATETIME::2009-11-09 16:42:02
BZCREATOR::William Osei-Poku
BZASSIGNEE::Bob Kline
BZQACONTACT::William Osei-Poku

In the CIAT/OCCM Review meeting today, we discussed the possibility of including and updating Citations for NCI trials in the converted documents, in the future. Since we are already copying elements and blocks from the InScopeProtocol document, Lakshmi gave the approval to include the RelatedPublications and PublishedResults blocks in the CTGovProtocol document.

Please, modify the CTGovProtocol Schema to include the RelatedPublications and PublishedResults blocks from the InScopeProtocol document. These ‘new’ blocks should be included in the PDQAdminInfo block.

Also, for newly transferred trials, the blocks should be copied to the converted documents if they exist.

I believe in OCECDR-2769 we had already included citations as part of the new data elements we will be bringing into the CTGovProtocol. As a result of this, I am guessing we may not need to preserve these blocks when the CTGovProtocol is updated with new or updated data from NLM. We may need to discuss this in detail.
I will add a comment in OCECDR-3014 so that Alan can include this in the global (for transferred trials).

Comment entered 2009-11-09 17:13:05 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-11-09 17:13:05
BZCOMMENTOR::Bob Kline
BZCOMMENT::1

Should I

(a) hold off on implementing this until testing and promotion of changes
for #4685, #4688, #4689, #4684, #4667, and #4664 is complete,
implementing (and testing) this change separately from (before) #4444?
(b) hold off on implementing this until testing and promotion of changes
for #4685, #4688, #4689, #4684, #4667, and #4664 is complete,
implementing (and testing) this change together with #4444?
(c) implement it now and start the testing for #4685, #4688, #4689, #4684,
#4667, and #4664 over again?
(d) implement it now, folding in the changes for #4444, and test everything
together?

It would be preferable if CIAT could come up with a complete set of changes in a given area, with fully developed specs, have it implemented, test it, and deploy it before introducing the next set of enhancements in the same part of the system. I realize that's not always possible, but it seems right now as if we've gone out of our way to swing to the opposite end of the spectrum from the ideal. I'm working on these overlapping tasks as fast as I can, trying to get them safely off the road before the next 18-wheeler comes barreling down the highway, but I feel like I'm losing the battle. With so many balls in the air at once, the risk that we're going to drop some is too high for comfort.

Comment entered 2009-11-10 07:20:29 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-11-10 07:20:29
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::2

(In reply to comment #1)
> Should I
>
> (a) hold off on implementing this until testing and promotion of changes
> for #4685, #4688, #4689, #4684, #4667, and #4664 is complete,
> implementing (and testing) this change separately from (before) #4444?
> (b) hold off on implementing this until testing and promotion of changes
> for #4685, #4688, #4689, #4684, #4667, and #4664 is complete,
> implementing (and testing) this change together with #4444?
> (c) implement it now and start the testing for #4685, #4688, #4689, #4684,
> #4667, and #4664 over again?
> (d) implement it now, folding in the changes for #4444, and test everything
> together?
>
We have not started publishing citations for CTGovProtocol documents on Cancer.gov yet. Unlike the other elements we are copying from the InScopeProtocol document, which are either needed for the transfer process or to fix problems on Cancer.gov, this one can wait for bug# 4444.

The idea to make this change now appeared to be a good one because we will also have been able to include this change in the global in OCECDR-3014. However, since this issue is not as critical as the other issues, I have lowered the priority to 8 (like OCECDR-2769).

Comment entered 2009-11-10 09:31:52 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-11-10 09:31:52
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::3

(In reply to comment #2)
> (In reply to comment #1)

> since this issue is not as critical as the other issues, I have lowered the
> priority to 8 (like OCECDR-2769).

Lowering priority now (to P6 instead of P8 as I mentioned above).

Comment entered 2009-11-27 15:15:08 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-11-27 15:15:08
BZCOMMENTOR::Bob Kline
BZCOMMENT::4

Do you want this implemented and tested with #4444, or before #4444?

Comment entered 2009-11-30 07:25:54 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-11-30 07:25:54
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::5

(In reply to comment #4)
> Do you want this implemented and tested with #4444, or before #4444?

Before #4444.

Comment entered 2009-11-30 15:39:56 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-11-30 15:39:56
BZCOMMENTOR::Bob Kline
BZCOMMENT::6

Schema changes installed on Mahler; ready for user testing. For the other changes, you indicated in the original request that you wanted a detailed discussion to take place first. If those other changes really are intended to be covered by this issue, you may want to modify the issue title to reflect the full scope of the request.

Comment entered 2009-12-02 10:26:32 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-02 10:26:32
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::7

(In reply to comment #6)
> Schema changes installed on Mahler; ready for user testing. For the other
> changes, you indicated in the original request that you wanted a detailed
> discussion to take place first. If those other changes really are intended to
> be covered by this issue, you may want to modify the issue title to reflect the
> full scope of the request.

It appears to me that Lakshmi wants us to restrict this change to only NCI trials, as in trials from the Center for Cancer Research only. Let's discuss this at the meeting tomorrow to get more information before proceeding further. I will therefore wait after the meeting to make changes to this issue.

Meanwhile I have added transfer blocks to the following trials (to be imported after tomorrow's meeting).
NCT00509587 - CDR0000557347
NCT00516503 - CDR0000560732
NCT00516607 - CDR0000560823
NCT00685828 - CDR0000596490
NCT00702949 - CDR0000598191
NCT00275041 - CDR0000456255
NCT00265733 - CDR0000456449

Comment entered 2009-12-03 15:53:21 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-03 15:53:21
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::8

I have modified the title of this issue to indicate that there should be both schema and import software changes.

Also, at this afternoon's CDR status meeting, Lakshmi said it is OK to preserve the elements when the trials are updated.

Comment entered 2009-12-04 12:32:12 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-12-04 12:32:12
BZCOMMENTOR::Bob Kline
BZCOMMENT::9

(In reply to comment #8)
> I have modified the title of this issue to indicate that there should be both
> schema and import software changes.
>
> Also, at this afternoon's CDR status meeting, Lakshmi said it is OK to preserve
> the elements when the trials are updated.

I thought you were also going to capture the requirements for the remainder of the work on this issue. For example, I remember that Lakshmi said she didn't want the copying of the blocks to be restricted only to certain trials (despite the language in comment #7), right?

Comment entered 2009-12-04 12:53:35 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-04 12:53:35
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::10

(In reply to comment #9)
> (In reply to comment #8)
> > I have modified the title of this issue to indicate that there should be both
> > schema and import software changes.
> >
> > Also, at this afternoon's CDR status meeting, Lakshmi said it is OK to preserve
> > the elements when the trials are updated.
>
> I thought you were also going to capture the requirements for the remainder of
> the work on this issue. For example, I remember that Lakshmi said she didn't
> want the copying of the blocks to be restricted only to certain trials (despite
> the language in comment #7), right?

That is correct. Sorry, for not including this information.

Comment entered 2009-12-07 16:43:08 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-12-07 16:43:08
BZCOMMENTOR::Bob Kline
BZCOMMENT::11

I have implemented this on Mahler. Do you have some test documents for trying it out?

Comment entered 2009-12-07 16:48:12 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-07 16:48:12
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::12

(In reply to comment #11)
> I have implemented this on Mahler. Do you have some test documents for trying
> it out?

Yes. The following trials should be good to use as test documents.

NCT00509587 - CDR0000557347
NCT00516503 - CDR0000560732
NCT00516607 - CDR0000560823
NCT00685828 - CDR0000596490
NCT00702949 - CDR0000598191
NCT00275041 - CDR0000456255
NCT00265733 - CDR0000456449

Comment entered 2009-12-08 14:45:04 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-12-08 14:45:04
BZCOMMENTOR::Bob Kline
BZCOMMENT::13

(In reply to comment #12)
> (In reply to comment #11)
> > I have implemented this on Mahler. Do you have some test documents for trying
> > it out?
>
> Yes. The following trials should be good to use as test documents.
>
> NCT00509587 - CDR0000557347
> NCT00516503 - CDR0000560732
> NCT00516607 - CDR0000560823
> NCT00685828 - CDR0000596490
> NCT00702949 - CDR0000598191
> NCT00275041 - CDR0000456255
> NCT00265733 - CDR0000456449

I kicked off fresh download and import jobs on Mahler. The import job hasn't completed yet, but those seven test documents you identified above have been processed. Please take a look.

Comment entered 2009-12-09 09:58:43 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-09 09:58:43
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::14

(In reply to comment #13)
> (In reply to comment #12)
> > (In reply to comment #11)
> > > I have implemented this on Mahler. Do you have some test documents for trying
> > > it out?
> >
> > Yes. The following trials should be good to use as test documents.
> >
> > NCT00509587 - CDR0000557347
> > NCT00516503 - CDR0000560732
> > NCT00516607 - CDR0000560823
> > NCT00685828 - CDR0000596490
> > NCT00702949 - CDR0000598191
> > NCT00275041 - CDR0000456255
> > NCT00265733 - CDR0000456449
>
> I kicked off fresh download and import jobs on Mahler. The import job hasn't
> completed yet, but those seven test documents you identified above have been
> processed. Please take a look.

Verified on Mahler. Please promote to Bach and Franck. They all look good. I will create another issue or add a comment in OCECDR-3007 to change the background to match that of the other blocks in the PDQ Admin Info block.

Comment entered 2009-12-09 10:27:34 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-12-09 10:27:34
BZCOMMENTOR::Bob Kline
BZCOMMENT::15

Promoted to Bach and Franck.

Comment entered 2009-12-09 12:22:32 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-09 12:22:32
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::16

(In reply to comment #14)
> (In reply to comment #13)
> > (In reply to comment #12)
> > > (In reply to comment #11)
> will create another issue or add a comment in OCECDR-3007 to change the
> background to match that of the other blocks in the PDQ Admin Info block.

Added this request to OCECDR-3007.

Comment entered 2009-12-15 17:51:31 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-15 17:51:31
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::17

(In reply to comment #15)
> Promoted to Bach and Franck.

We have come across one document with published results which produced a validation error. We have fixed all the errors manually and excluded the published results blocks as the errors appear to have something to do with the published results. Also comparing the CTGOV Schema on Mahler and Bach, the Published results blocks do not appear to be on Bach yet.

Here is the protocol - CDR 67685.

Comment entered 2009-12-15 19:15:31 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-12-15 19:15:31
BZCOMMENTOR::Bob Kline
BZCOMMENT::18

Schemas on Bach and Franck should be ok now.

Comment entered 2009-12-16 10:28:11 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-16 10:28:11
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::19

(In reply to comment #18)
> Schemas on Bach and Franck should be ok now.

I am getting a "No link type is defined for field Citation in document type CTGovProtocol (error)" when I copy the published results from the InScopeProtocol document. When I attempt to relink the citation, I get a "No links permitted from this element" error.

This is for protocol 67685 on Bach.

Comment entered 2009-12-16 10:30:09 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2009-12-16 10:30:09
BZCOMMENTOR::Bob Kline
BZCOMMENT::20

You need to go into "Manage Linking Tables" and allow for the links.

Comment entered 2009-12-16 11:08:01 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2009-12-16 11:08:01
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::21

(In reply to comment #20)
> You need to go into "Manage Linking Tables" and allow for the links.

Done. Thank you!

Comment entered 2010-01-05 10:15:25 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-01-05 10:15:25
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::22

Verified on Bach. Issue Closed. Thank you!

Elapsed: 0:00:00.000631