| Issue Number | 3426 |
|---|---|
| Summary | Missing Text from protocol ref report |
| Created | 2011-10-11 15:35:38 |
| Issue Type | Bug |
| Submitted By | Osei-Poku, William (NIH/NCI) [C] |
| Assigned To | Englisch, Volker (NIH/NCI) [C] |
| Status | Closed |
| Resolved | 2011-11-04 17:37:34 |
| Resolution | Fixed |
| Path | /home/bkline/backups/jira/ocecdr/issue.107754 |
BZISSUE::5120
BZDATETIME::2011-10-11 15:35:38
BZCREATOR::William Osei-Poku
BZASSIGNEE::Volker Englisch
BZQACONTACT::William Osei-Poku
The protocol ref report fails to display text under the ProtocolLink/Ref column for a particular ref when text in the section title element is marked up with another element [<Title> <GeneName>AMACR </GeneName> </Title>] - (GeneName in this case, and I didn't test other elements). When GeneName is removed and the text in the title is allowed to stay alone, [<Title> AMACR </Title>], the report would correctly display text under the ProtocolLink/Ref column for that protocol ref.
Please see run the protocol ref report for CDR0000299612 and look for the AMACR section.
Robin would like us to discuss this on Thursday.
BZDATETIME::2011-10-13 16:32:58
BZCOMMENTOR::Volker Englisch
BZCOMMENT::1
Is this the ProtocolLink/Ref report?
CIAT/OCCM Staff --> Reports
--> Summaries and Miscellaneous Documents
--> Summaries with Protocols Links/Refs Report
BZDATETIME::2011-10-14 16:11:42
BZCOMMENTOR::Volker Englisch
BZCOMMENT::2
The problem was that the text within the <GeneName /> was thrown out since the part of the program extracting the text and comment, etc. compared the text of the title found now with the text found earlier. Once the content of the element got thrown out but once it did not and therefore the string comparison failed.
I've fixed this problem in the program
SummariesWithProtocolLinks.py - R10217
This is ready for review on MAHLER.
BZDATETIME::2011-10-17 10:32:25
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::3
(In reply to comment #2)
> I've fixed this problem in the program
> SummariesWithProtocolLinks.py - R10217
>
> This is ready for review on MAHLER.
I attempted to run the report in Mahler but got a python script error (below). I assume it is because summaries in Mahler currently are failing schema validation because of the Summary Module schema changes.
<class 'cdr.Exception'> Python 2.7.1:
D:\Python\python.exe
Mon Oct 17 10:25:58 2011
A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.
D:\Inetpub\wwwroot\cgi-bin\cdr\SummariesWithProtocolLinks.py in
()
235 if cdrId:
236 try:
=> 237 docId = cdr.exNormalize(cdrId)[1]
238 except ValueError:
239 docId = None
docId undefined, cdr = <module 'cdr' from
'D:\cdr\Lib\Python\cdr.pyc'>, cdr.exNormalize = <function
exNormalize>, cdrId = '299612 '
D:\cdr\Lib\Python\cdr.py in exNormalize(id='299612 ')
185
186 if not result:
=> 187 raise Exception("Invalid CDR ID string: " + id)
188
189 idNum = int (result.group ('num'))
global Exception = <class 'cdr.Exception'>, id = '299612 '
<class 'cdr.Exception'>: Invalid CDR ID string: 299612
args = ('Invalid CDR ID string: 299612 ',)
message = 'Invalid CDR ID string: 299612 '
d:\cdr\Log\tmpfvbds3.html contains the description of this error.
BZDATETIME::2011-10-17 10:40:19
BZCOMMENTOR::Volker Englisch
BZCOMMENT::4
(In reply to comment #3)
> I attempted to run the report in Mahler but got a python script
error (below).
> ...
> <class 'cdr.Exception'>: Invalid CDR ID string: 299612
The problem is that you've entered a CDR-ID with a trailing blank
space.
This is a problem which should be fixed but has nothing to do with the
current issue and has been there all along.
BZDATETIME::2011-10-17 10:50:16
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::5
(In reply to comment #4)
> (In reply to comment #3)
> > I attempted to run the report in Mahler but got a python
script error (below).
> > ...
> > <class 'cdr.Exception'>: Invalid CDR ID string:
299612
>
> The problem is that you've entered a CDR-ID with a trailing blank
space.
> This is a problem which should be fixed but has nothing to do with
the current
> issue and has been there all along.
That is right. It worked without the trailing space. Please promote to Bach.
BZDATETIME::2011-10-17 14:26:16
BZCOMMENTOR::Volker Englisch
BZCOMMENT::6
The following program has been copied to FRANCK and BACH:
SummariesWithProtocolLinks.py - R10217
I've also fixed the code to handle trailing spaces (cdr.exNormalize()) but this is still on MAHLER for a little bit of testing.
Please verify on BACH and close this bug.
BZDATETIME::2011-10-20 12:01:55
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::7
(In reply to comment #6)
> The following program has been copied to FRANCK and BACH:
> SummariesWithProtocolLinks.py - R10217
>
> I've also fixed the code to handle trailing spaces
(cdr.exNormalize()) but this
> is still on MAHLER for a little bit of testing.
>
> Please verify on BACH and close this bug.
Verified on Bach. Issue closed. Thank you!
BZDATETIME::2011-11-03 15:00:37
BZCOMMENTOR::Bob Kline
BZCOMMENT::8
I don't think the fix to cdr.exNormalize() ever made it into version control, so it will be wiped out when I promote some other changes of the module to Bach in the near future.
BZDATETIME::2011-11-03 15:22:32
BZCOMMENTOR::Volker Englisch
BZCOMMENT::9
According to the SVN log it's in as R10220.
Are you not seeing it?
BZDATETIME::2011-11-03 16:07:10
BZCOMMENTOR::Bob Kline
BZCOMMENT::10
(In reply to comment #9)
> According to the SVN log it's in as R10220.
> Are you not seeing it?
Ah, I didn't look carefully at the regular expression; I just noticed that what was in subversion differed from what was on Bach. So the fix is in svn, but not on Bach.
BZDATETIME::2011-11-04 17:19:48
BZCOMMENTOR::Volker Englisch
BZCOMMENT::11
Is it OK to close this issue again and put it back to sleep?
BZDATETIME::2011-11-04 17:37:34
BZCOMMENTOR::Bob Kline
BZCOMMENT::12
Closing issue.
Elapsed: 0:00:00.000828