CDR Tickets

Issue Number 3090
Summary [CiteMs] PMID Link Format
Created 2010-02-17 11:53:19
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To alan
Status Closed
Resolved 2010-08-05 12:42:04
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.107418
Description

BZISSUE::4766
BZDATETIME::2010-02-17 11:53:19
BZCREATOR::William Osei-Poku
BZASSIGNEE::Alan Meyer
BZQACONTACT::William Osei-Poku

Here is another issue from CMS users. Like the previous issues, this does not stop them from working.

Email from Cynthia---

From the web interface of the CMS the PMID links currently take the users to the medline format of the citation in text only which means there are no links available for our users to link to get the full text. This has been happening since PubMed switched to their newest version and users have had to copy and paste the pmid from the cms into pubmed to see the links.
Below is an example:
When you click the pmid link from the cms for the following example citation you are taken to the following page.
http://www.ncbi.nlm.nih.gov/pubmed/19438459?dopt=medline

We need for the CMS pmid link to take us to the following page instead.
http://www.ncbi.nlm.nih.gov/pubmed/19438459?dopt=abstract
Note the change from “dopt=medline” to “dopt=abstract”.

Comment entered 2010-02-23 11:23:36 by alan

BZDATETIME::2010-02-23 11:23:36
BZCOMMENTOR::Alan Meyer
BZCOMMENT::1

I've been putting these off for now, but at some point I'll
try to dig into all of these issues.

Comment entered 2010-06-29 17:43:49 by alan

BZDATETIME::2010-06-29 17:43:49
BZCOMMENTOR::Alan Meyer
BZCOMMENT::2

I think this is likely to be very easy, but I'll need some guidance on which specific screens need changing. There currently appear to be about 50 web pages in the application that link to "...dopt=medline". I presume that only one or a few of these should be changed.

If that's right, then one way to identify them would be to cut the URL from the location bar at the top of the screen for each screen that contains a link that has to change from "medline" to "abstract", and paste the link into an email to send to me.

If there is more than one place on the page that has a link, please identify the one that needs to change. In some cases there may be lists of links, for example in a list of 10 citations, all 10 may have a link that needs to change. However for our purposes, that's just one place that gets generated in a loop. I'll find it easily enough.

If all of the dopt=medline links need to change, I'll change all of them. If almost all need to change but just one or a few need to stay the same, then just identify the ones that need to stay the same and I'll change all the rest.

--
I've removed Brent Carter from the CC list for this issue and added Cynthia.

Comment entered 2010-06-29 18:21:00 by Boggess, Cynthia (NIH/NCI) [C]

BZDATETIME::2010-06-29 18:21:00
BZCOMMENTOR::Cynthia Boggess
BZCOMMENT::3

Links to PubMed are available for all citation record views in the CMS so 50 sounds about right. Although there are a few pages(i.e updating premedline records) where we will need to kept dopt=medline, but let me get back to you on that after I confirm this with Minaxi.

Comment entered 2010-06-30 10:42:11 by Boggess, Cynthia (NIH/NCI) [C]

BZDATETIME::2010-06-30 10:42:11
BZCOMMENTOR::Cynthia Boggess
BZCOMMENT::4

I discussed this with Minaxi and we have both aggreed that all links to pubmed should be in the abstract format. We use the medline format in the import utility but the web interface we need the abstract view only.

Comment entered 2010-07-02 01:19:58 by alan

BZDATETIME::2010-07-02 01:19:58
BZCOMMENTOR::Alan Meyer
BZCOMMENT::5

I wrote a program that read every program in the web application, searched for "&dopt=medline", and changed it to "&dopt=abstract". 60 program were modified, some more than once. Not all of the programs are actually used. Some are backups that the previous programmers made. But rather than try to figure out what is not used, I just processed all of them.

The results are in the development system. I have done some testing, but haven't tried to test each of the 60 programs.

The attached file was output by my transformation program. Each line gives the name of a web program followed by a colon and the number of lines inside that program that were modified. For example:

cipssearch.asp: 0 - no changes
cipssearchresults.asp: 2 - two lines changed
cipsviewlist.asp: 1 - one line changed

Please have a look and see if it looks right.

Comment entered 2010-07-02 01:19:58 by alan

Attachment results has been added with description: List of modified files

Comment entered 2010-07-06 21:23:07 by alan

BZDATETIME::2010-07-06 21:23:07
BZCOMMENTOR::Alan Meyer
BZCOMMENT::6

Marking this resolved-fixed, ready for user test.

Comment entered 2010-07-07 09:53:04 by Boggess, Cynthia (NIH/NCI) [C]

BZDATETIME::2010-07-07 09:53:04
BZCOMMENTOR::Cynthia Boggess
BZCOMMENT::7

The pmid links are displaying correctly in abstract format. I have tested in both staff and client interfaces.

Comment entered 2010-07-13 10:21:15 by alan

BZDATETIME::2010-07-13 10:21:15
BZCOMMENTOR::Alan Meyer
BZCOMMENT::8

Not having heard anything to the contrary, I propose to put this into production tonight along with the change to the picklists.

Someone stop me if that is incorrect.

Comment entered 2010-07-13 10:22:02 by alan

BZDATETIME::2010-07-13 10:22:02
BZCOMMENTOR::Alan Meyer
BZCOMMENT::9

(In reply to comment #8)

> ... along with the change to the picklists.

I should have said "coversheets".

Comment entered 2010-07-13 10:34:35 by Boggess, Cynthia (NIH/NCI) [C]

BZDATETIME::2010-07-13 10:34:35
BZCOMMENTOR::Cynthia Boggess
BZCOMMENT::10

I have no objection to moving this to production. I have tested it extensively and everything looks fine.

Comment entered 2010-07-14 00:58:18 by alan

BZDATETIME::2010-07-14 00:58:18
BZCOMMENTOR::Alan Meyer
BZCOMMENT::11

I placed all of the modified code for this and the coversheet changes into version control but ran into a snag in updating the production server. All of my attempts to copy files into the live directory resulted in "Permission denied" errors. I tried using the IIS administrative interface to stop the application and then the whole web server but it still wouldn't allow me to copy things into the live directory.

I suspect that this is a trivial problem reflecting my lack of experience administering the Microsoft IIS and that one of our systems administrators can fix it for me in five minutes. But it's late now and none of them are around.

I'll have to wait until I can talk to one. It should happen in the next couple of days.

Sorry about the delay.

Comment entered 2010-07-20 20:42:20 by alan

BZDATETIME::2010-07-20 20:42:20
BZCOMMENTOR::Alan Meyer
BZCOMMENT::12

I've put the changes into production.

Please let me know if there is any problem.

Comment entered 2010-08-05 12:42:04 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-08-05 12:42:04
BZCOMMENTOR::Bob Kline
BZCOMMENT::13

Closed at status meeting.

Attachments
File Name Posted User
results 2010-07-02 01:19:58

Elapsed: 0:00:00.001832