CDR Tickets

Issue Number 4463
Summary [Citations] Problem Importing Citation on PROD
Created 2018-04-19 17:10:10
Issue Type Bug
Submitted By Juthe, Robin (NIH/NCI) [E]
Assigned To Kline, Bob (NIH/NCI) [C]
Status Closed
Resolved 2018-05-02 16:15:12
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.224530
Description

I'm running into problems importing the following citation on PROD: PMID: 29277811

The CDR error message reads:

An error has occurred

Unable to find article title

Comment entered 2018-04-19 17:38:51 by Kline, Bob (NIH/NCI) [C]

Can you give me a rough idea of the time when the attempted import failed?

Comment entered 2018-04-19 17:40:56 by Juthe, Robin (NIH/NCI) [E]

I tried it a few times - twice right before I entered this ticket (5:05 or so) and once just now (5:40). Thanks!

Comment entered 2018-04-19 17:41:51 by Juthe, Robin (NIH/NCI) [E]

The title starts with a gene name - not sure if that could be a problem? I've imported several other citations successfully in the past half hour.

Comment entered 2018-04-19 17:53:11 by Kline, Bob (NIH/NCI) [C]

Yep, that's the problem. Here's the patch for the workaround:

--- a/Inetpub/wwwroot/cgi-bin/cdr/CiteSearch.py
+++ b/Inetpub/wwwroot/cgi-bin/cdr/CiteSearch.py
@@ -110,7 +110,7 @@ def getPubmedArticle(doc):
 #----------------------------------------------------------------------
 def getArticleTitle(article):
     for node in article.findall("MedlineCitation/Article/ArticleTitle"):
-        return node.text
+        return cdr.get_text(node)

 #----------------------------------------------------------------------
 # Retrieve an XML document for a Pubmed article from NLM.
Comment entered 2018-04-23 08:36:17 by Kline, Bob (NIH/NCI) [C]

I propose that we merge this fix into the patch for OCECDR-4434, which we are planning to apply next month.

Comment entered 2018-05-02 16:15:12 by Kline, Bob (NIH/NCI) [C]

Patch applied on DEV. We will apply this along with the patch for OCECDR-4434. Ready for user testing.

https://github.com/NCIOCPL/cdr-admin/commit/96383433

Comment entered 2018-05-03 12:12:24 by Juthe, Robin (NIH/NCI) [E]

Verified on DEV. Thanks!

Comment entered 2018-05-03 17:21:34 by Juthe, Robin (NIH/NCI) [E]

I also confirmed that an abstract beginning with a gene name (e.g., PMID: 28620008) also displayed correctly in the citation record.

Comment entered 2018-05-15 16:09:25 by Kline, Bob (NIH/NCI) [C]

CBIIT has applied the patch to STAGE. Please test importing a citation whose title begins with markup on that tier.

Comment entered 2018-05-16 10:59:32 by Juthe, Robin (NIH/NCI) [E]

I was able to import PMID 29277811 successfully on STAGE. thanks!

Comment entered 2018-05-16 12:41:19 by Kline, Bob (NIH/NCI) [C]

The patch is on PROD. Please import PMID 29277811 on that tier.

Comment entered 2018-05-16 12:45:54 by Juthe, Robin (NIH/NCI) [E]

Done. Verified on PROD. Thank you!

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