Errors using Import by Pubmed ID and Import by search terms

Posted by TJ43 on September 15, 2009 at 2:24am

3 followers

Issue Summary

When using 'Import by Pubmed ID' the following error is encountered:
Fatal error: Call to a member function asXML() on a non-object in /homepages/21/d240079828/htdocs/drupal-6.13/sites/all/modules/entrez/entrez.module on line 468

PMID searched for is 18223323

When using 'Import by search terms' the following message is consistently returned:

An error occurred when requesting data from PubMed. Try again later.

Search terms are: d842v GIST
Date window used for search is Jan1, 2008 to Dec 30, 2008

Comments

#1

Posted by Stefan Freudenberg on September 15, 2009 at 10:12am

Thanks for the bug report. Could you post the related watchdog log messages (if there are any) to help me fix the problem?

#2

Posted by Stefan Freudenberg on September 15, 2009 at 10:46am

Thanks for the bug report. Could you post the related watchdog log messages (if there are any) to help me fix the problem? Filter the recent log entries by type "entrez" to find them.

#3

Posted by TJ43 on September 15, 2009 at 3:42pm

SQL result

Attachment	Size
Entrez.jpg	190.09 KB

#4

Posted by Stefan Freudenberg on September 15, 2009 at 4:26pm

Thanks a lot. Your server probably does not allow certain php functions to treat url's as files. I am going to fix that problem in code. As an intermediate measure you could ask your system administrator to set "allow_url_fopen = On" in the php.ini.

#5

Posted by TJ43 on September 15, 2009 at 11:28pm

Stefan,

Our shared host provider is 1and1.com. For now we have a very basic account without php.ini access. However, I created the php.ini file in my Drupal directory and it works. We are now importing citations with both a PMID and with a search term.

Is there any documentation on the "Moderate Biblios" tab? I see the new Biblio nodes under "Awaiting Moderation" and "Approved" tabs but am not seeing anything in the Bulk Operations frame. There is also a drop down menu '[Edit]|[Export]|[Clone]' which takes me to a Views edit page.

Thanks for your work on Entrez. We are excited about using this for our research site.

Jim
www.lrgscience.org

#6

Posted by Stefan Freudenberg on September 17, 2009 at 10:22am

Assigned to:

Anonymous

» mlncn

#7

Posted by mlncn on September 18, 2009 at 6:40am

Hello Jim,

What do you mean by the "Bulk Operations frame"? The column? There should be checkmarks next to each Biblio node in the view to which mass actions can be applied using the bulk operations dropdown.

Perhaps attaching a screenshot could help us see the issue? Thanks!

The semi-hidden "[Edit]|[Export]|[Clone]" links are a convenience provided by the Views module on every view, and only have to do with changing or duplicating the view configuration rather than using it.

^{ben, agaric}

#8

Posted by TJ43 on September 21, 2009 at 7:06am

Ben,

The bulk operations area of the screen does not appear to have any menu items or dropdowns.

Thanks for the info on the Views links. I thought perhaps an option was needed in the view for this page.

Screen shot is attached.

Thanks again,

Jim
www.lrgscience.org

Attachment	Size
Entrez Screen Shot.JPG	219.04 KB

#9

Posted by mlncn on October 8, 2009 at 9:31am

Sorry for the delay in responding. It is indeed a bug and am posting the workaround and an issue for myself to follow up on here:

http://drupal.org/node/598912

Project:	Entrez Database Import
Version:	6.x-1.0-beta1
Component:	Code
Category:	support request
Priority:	normal
Assigned:	mlncn
Status:	active
Issue tags:	Science Collaboration

Errors using Import by Pubmed ID and Import by search terms

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