CDR Tickets

Issue Number 3328
Summary [CTGov] force update of orphaned trials
Created 2011-03-21 12:08:30
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To Kline, Bob (NIH/NCI) [C]
Status Closed
Resolved 2011-05-04 09:49:46
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.107656
Description

BZISSUE::5021
BZDATETIME::2011-03-21 12:08:30
BZCREATOR::William Osei-Poku
BZASSIGNEE::Bob Kline
BZQACONTACT::William Osei-Poku

The following trials were included in the list of orphaned trials. We have researched and found out that the first 4 trials on the list below have new active NCT IDs making the NCT IDs currently in the trials inactive or alias. So, for the first 4 rows, replace the NCT ID in column 2 (INACTIVE) with the NCT ID in column 3 (ACTIVE). Also, make the original NCT ID that was in column 2 and alias. The last record is not receiving updates because of changes in the condition terms by NLM. Typically, we would force a download to update the trial but we have not been quite successful with that approach.

CDR ID INACTIVE ACTIVE
472034 NCT00389571 NCT00297895
595388 NCT00678223 NCT00678769
674892 NCT01143415 NCT01195415
583228 NCT00631930 NCT00600353
694188 NCT01278927

Comment entered 2011-03-21 12:25:44 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-03-21 12:25:44
BZCOMMENTOR::Bob Kline
BZCOMMENT::1

In keeping with the discussion in comments #16 and #17 of issue #4975, please create separate tasks for each set of cases which are identical. Thanks.

Comment entered 2011-03-21 12:46:29 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-03-21 12:46:29
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::2

(In reply to comment #1)
> In keeping with the discussion in comments #16 and #17 of issue #4975, please
> create separate tasks for each set of cases which are identical. Thanks.

Done! I created OCECDR-3329 for the last trial on the list. Thanks!

Comment entered 2011-03-29 07:46:04 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-03-29 07:46:04
BZCOMMENTOR::Bob Kline
BZCOMMENT::3

It's not clear to me that the remaining four cases all represent the same condition, nor is it clear what you want me to do with them. If by "... make the original NCT ID that was in column 2 and alias" you meant "... make the original NCT ID that is in column 2 an alias" isn't that just a question of placing that value in the document's NCT_Alias element? Why would we need to write a program to do that for 4 documents? Looking at the first case (CDR472034) it appears that the CT.gov import software is already importing NCT00297895 (and in fact the NCT_Alias has "NCT00389571" in it already). If you mean you want the Orphaned Trial report to stop reporting these all you have to do is supply a value for the reason_dropped column (didn't we build you an interface for doing that a couple of years ago?).

Comment entered 2011-03-29 11:12:51 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-03-29 11:12:51
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::4

(In reply to comment #3)
> It's not clear to me that the remaining four cases all represent the same
> condition, nor is it clear what you want me to do with them. If by "... make
> the original NCT ID that was in column 2 and alias" you meant "... make the
> original NCT ID that is in column 2 an alias" isn't that just a question of
> placing that value in the document's NCT_Alias element? Why would we need to
> write a program to do that for 4 documents?

Yes. Basically I am saying you should swap the NCT IDs since the documents weren't being updated because our records had the NCT IDs the opposite way.

Also, are you saying we should manually update the NCT IDs in the documents? We never do that for CTGovProtocol documents since they will be overwritten the next time the trials are updated. However, if that is not the case, then let me know and I will have the records updated manually.

>Looking at the first case
> (CDR472034) it appears that the CT.gov import software is already importing
> NCT00297895 (and in fact the NCT_Alias has "NCT00389571" in it already). If
> you mean you want the Orphaned Trial report to stop reporting these all you
> have to do is supply a value for the reason_dropped column (didn't we build you
> an interface for doing that a couple of years ago?).

This record has been updated since we first reviewed it so it should be Okay now and I believe the report will stop reporting it.

Comment entered 2011-03-29 17:20:06 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-03-29 17:20:06
BZCOMMENTOR::Bob Kline
BZCOMMENT::5

(In reply to comment #4)
> (In reply to comment #3)
> > Looking at the first case
> > (CDR472034) it appears that the CT.gov import software is already importing
> > NCT00297895 (and in fact the NCT_Alias has "NCT00389571" in it already). If
> > you mean you want the Orphaned Trial report to stop reporting these all you
> > have to do is supply a value for the reason_dropped column (didn't we build
> > you an interface for doing that a couple of years ago?).
>
> This record has been updated since we first reviewed it so it should be Okay
> now and I believe the report will stop reporting it.

OK, I skipped past the first trial and I'm looking at the next one (CDR595388):

<CTGovProtocol ....>
....
<IDInfo>
...
<NCTID>NCT00678769</NCTID>
<NCT_Alias>NCT00678223</NCT_Alias>
</IDInfo>
....
</CTGovProtocol>

What should I change for this trial?

Comment entered 2011-03-29 19:38:45 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-03-29 19:38:45
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::6

(In reply to comment #5)
> OK, I skipped past the first trial and I'm looking at the next one (CDR595388):
>
> <CTGovProtocol ....>
> ....
> <IDInfo>
> ...
> <NCTID>NCT00678769</NCTID>
> <NCT_Alias>NCT00678223</NCT_Alias>
> </IDInfo>
> ....
> </CTGovProtocol>
>
> What should I change for this trial?

It looks like the only thing you need to do with this one is to prevent it from showing up in the orphaned report since it appears to have the correct NCT IDs compared to what is on clinicaltrials.gov.

I also went ahead and checked the remaining two and for those, they currently have the INACTIVE NCT IDs in the records so they need to be changed to the ACTIVE NCT IDs.

Comment entered 2011-03-29 19:56:30 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-03-29 19:56:30
BZCOMMENTOR::Bob Kline
BZCOMMENT::7

(In reply to comment #6)

> It looks like the only thing you need to do with this one is to prevent it from
> showing up in the orphaned report since it appears to have the correct NCT IDs
> compared to what is on clinicaltrials.gov.

Again, why would we want to write a program to do that, when we built an interface so that CIAT could do it themselves? You might want to go back and review issue #4575.

Comment entered 2011-03-30 09:25:36 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-03-30 09:25:36
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::8

(In reply to comment #7)
> (In reply to comment #6)
>
> > It looks like the only thing you need to do with this one is to prevent it from
> > showing up in the orphaned report since it appears to have the correct NCT IDs
> > compared to what is on clinicaltrials.gov.
>
> Again, why would we want to write a program to do that, when we built an
> interface so that CIAT could do it themselves? You might want to go back and
> review issue #4575.

I didn't know the connection between the two reports. I've now used the interface to assign a reason for the drop which took it off the drop report/interface immediately but not the orphaned report. I am guessing there needs to be another download job for it to be dropped off the report, right?

Comment entered 2011-03-30 09:46:16 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-03-30 09:46:16
BZCOMMENTOR::Bob Kline
BZCOMMENT::9

(In reply to comment #8)

> I didn't know the connection between the two reports. I've now used the
> interface to assign a reason for the drop which took it off the drop
> report/interface immediately but not the orphaned report. I am guessing there
> needs to be another download job for it to be dropped off the report, right?

Actually, I just looked at the code and the issue for the newer report, and it doesn't appear that there was a requirement to skip trials that have a value in the reason_dropped column. Do you want to have that report modified to incorporate that step?

Comment entered 2011-03-30 16:05:59 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-03-30 16:05:59
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::10

(In reply to comment #9)
> (In reply to comment #8)
>
> > I didn't know the connection between the two reports. I've now used the
> > interface to assign a reason for the drop which took it off the drop
> > report/interface immediately but not the orphaned report. I am guessing there
> > needs to be another download job for it to be dropped off the report, right?
>
> Actually, I just looked at the code and the issue for the newer report, and it
> doesn't appear that there was a requirement to skip trials that have a value in
> the reason_dropped column. Do you want to have that report modified to
> incorporate that step?

I think it will be good to have that option but only if we can specifically mark certain trials to be skipped (like the trial in question). I believe it is not in all cases that we want a trial to be skipped.

Comment entered 2011-03-30 16:08:47 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-03-30 16:08:47
BZCOMMENTOR::Bob Kline
BZCOMMENT::11

You mean another method besides setting the "reason_dropped" column? In that case, you're probably better off using the two reports as they are, one of which reports the dropped trials regardless of whether that column has a value, and the other of which ignores the trials which have a value in the column.

Comment entered 2011-04-01 10:40:10 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-04-01 10:40:10
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::12

We decided in the meeting yesterday that Bob will modify the Orphaned report to include a comments column. The column will be populated by the comments or decisions entered in the Reason Dropped report for corresponding trials. When done this way, trials that should otherwise be skipped can continue to remain on the Orphaned report but because a reason or comment is displayed for the trial, users can skip them when reviewing the report in the future.

Bob:

We did not talk about creating a new issue for this modification so let me know if you want me to create a new one.

Comment entered 2011-04-01 10:53:06 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-04-01 10:53:06
BZCOMMENTOR::Bob Kline
BZCOMMENT::13

(In reply to comment #12)

> We decided in the meeting yesterday that Bob will modify the Orphaned report to
> include a comments column.

Enhancement installed on Mahler; ready for user testing.

Comment entered 2011-04-01 12:51:50 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-04-01 12:51:50
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::14

The orphaned trials report (1.CTGov trials not receiving updates) is missing from Mahler. We probably never put it there in the first place. It should go to

CIAT/OCCM Staff / CTGov Protocols /Management Reports /1.CTGov trials not receiving updates

Comment entered 2011-04-01 13:23:13 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-04-01 13:23:13
BZCOMMENTOR::Bob Kline
BZCOMMENT::15

Actually, that report only works on Bach, because that's the only server on which we run nightly CT.gov download jobs. I have installed the enhancement on Bach. Please test it there.

Comment entered 2011-04-04 10:23:12 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-04-04 10:23:12
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::16

(In reply to comment #15)
> Actually, that report only works on Bach, because that's the only server on
> which we run nightly CT.gov download jobs. I have installed the enhancement on
> Bach. Please test it there.

Verified on Bach. Thanks!

Comment entered 2011-04-18 10:09:33 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2011-04-18 10:09:33
BZCOMMENTOR::Bob Kline
BZCOMMENT::17

I have manually changed the mapping for the remaining two trials:

SWITCHING CDR674892 FROM NCT01143415 TO NCT01195415
SWITCHING CDR583228 FROM NCT00631930 TO NCT00600353

The import job has been run by hand. Please check the results to confirm that this is what you want.

Comment entered 2011-05-04 09:49:46 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-05-04 09:49:46
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::18

(In reply to comment #17)
> I have manually changed the mapping for the remaining two trials:
>
> SWITCHING CDR674892 FROM NCT01143415 TO NCT01195415
> SWITCHING CDR583228 FROM NCT00631930 TO NCT00600353
>
> The import job has been run by hand. Please check the results to confirm that
> this is what you want.

Verified. Closing Issue. Thanks!

Elapsed: 0:00:00.001327