Can't get import in Endnote tag format to work
p0732658 - September 10, 2006 - 14:23
| Project: | Bibliography Module |
| Version: | 4.7.x-1.x-dev |
| Component: | User interface |
| Category: | support request |
| Priority: | normal |
| Assigned: | Unassigned |
| Status: | closed |
Description
Hi !
I've ben trying to use the import featurre but without any success. Everytime I try, there is a few second delay where I see the little mouse working, but nothing happen when it's done. I even check in my database but nothing is imported in it. I'm quite certain m'y import file is well formated in Endnote tag. In desparation, I've tried to import the data directly in my database using phpMyAdmin, but I can't access the information in Drupal. Am I doing something wrong, or is there something wrong with my Drupal installation.
Thank you,
Denis Boudreau
#1
I tried exporting a biblio from the demo site both in the Endnote tag format and the XML format. After downloading both records, I tried importing then into my Website with the Biblio import function. Either case didn't work. Therefore, the problem isn't with the formating of the file to import. I tried uninstalling the Biblio module, but without any success. Should I tried re-installing Drupal, then Biblio ?
#2
Have you checked your logs to see what's happening -- they could give you a clue as to where the problem is. You should see a record in the content logs when each of the biblio nodes is created. If you're not getting that far, try your php or html error logs.
good luck.
jt
#3
I can't see any trace of the importation process into Drupal logs. Is this normal ? About the php log, I guest I have to check into the control panel of my Web site provider ?
#4
If possible, you might want to turn on PHP error reporting in the php.ini file (error_reporting = E_ALL and display_errors = On) and see if you get any errors reported.
#5
I dont have access to the php.ini. I would have to ask my web hosting provider to check that for me.
Would my problem have anything to do with any of the EndNote .inc files. I've notice those files in the CVS repos and realize that none of those are in my biblio module directory.
#6
You don't need the .inc files unless you are actually running the CVS version. If you downloaded a tar.gz package, all of the required files will be in it.
I still think it's a PHP error, so why don't you try adding the following line to your settings.php file in the appropriate sites directory (probably sites/default) ...
ini_set('display_errors', 1);
Ron.
#7
I tried adding the line ini_set('display_errors', 1);, but I don't even get a display of the errors.
#8
I wasn't sure if that would work, I guess I know the answer now.
I still think it's probably a PHP error, the only way to know for sure is to get your isp to check the logs.
#9
My ISP doesn't want to give me access to the PHP logs, so I guest I'm sreed. Anymores thoughs about my problem ?
#10
Could you attach a copy of your tagged file to this thread so I can verify that it works.
#11
There is one the files I tried importing...
#12
I was able to import that file, but it did take some time. You might want to try cutting it down to one entry and see what happens.
#13
I have tried importing only one biblio into Biblio. I evend tried exporting biblios from the demo site, then importing them into mine. The result is always the same : Niet ! Nada ! No ! Non !
The only solution I have find is importing true phpAdmin. After exporting biblos from EndNote into XML, I converted the file to CVS with the help of MS-Excel - ie oppening an XML file with Excel automatly convert the file into tables. Next, I organised my data to match the biblo framework (number and order of colums. After populating the missing data (id number, dates, etc.), I imported the CVS file into my biblio table with the help of phpMyAdmin.
At first, I could not see anything into Drupal. After populating some Drupal node tables, this problem was solve. Now, I able to access somes biblio. However, whenever I try to created another page, book, etc, I always get an MySQL duplicate entrie error. My though is that I probably forgot to populate some Drupal tables, but I can't figure wich ones.
I aware my approche is probably not the best one. But, I wanted to import more than 300 entries ! If I figure out what I've done wrong so far, I want to import another 200 entries ! Any toughts what others tables I shoulds populates ?
Denis
#14
Hi Denis,
Every biblio entry has a corresponding entry in the node table and they are linked by the nid field.
What if you install apache, php, mysql and drupal on your local computer and then you can setup your site locally and then just do a database dump and restore onto your public web server when you are satisfied that everything is working. The advantage of this is you will have control over the php installation and can turn on error checking if required.
I run this way on both my desktop and laptop for development purposes and it works quite well. Once it's all setup, you just fire up your browser and point it to http://localhost/.
Ron.
#15
Something else just occurred to me... Have you tried importing the EndNote XML format file?
#16
Hi Ron !
I followed your suggestion and installed Drupal on my computer. I had a lots of problems getting it to run because I couldn't access the modules pages. After playing arround with the php.ini and my .htacess files I got it to work, but I'm getting somes MySQL errors somethings and I can't figure out why. I'm running PHP 5 and MySQL 5. Regarding Biblio, I tried importing an EndNote file I downloded from you site but whit no sucess. Could the problem be with Firefox ? Are you using Linux or Windows and wich versions of PHP and MySQL have you installed on your computer. Maybe you could send me a copy of your php.ini and httpd files ? This problem is getting anoying and I'm starting to thing my karma doesn't aggry with Biblio !
Denis
#17
... and No ! I tried importing xml files, but it doesn't work either.
#18
Hi Denis,
Attached you will find a copy of my php.ini, httpd.conf and my.ini. I am running Apache 2, php5 and mysql 4.3, they are installed in c:\web\apache2, c:\web\php5 and c:\web\mysql.
It is a bit of a pain to get all this stuff working on a PC but once it's working it really does work quite well for development.
What mysql errors are you getting?
#19
Hi Ron !
I couldn't get Apache working in my Windows XP partition. I opted for XAMPP wich work almost ''out of the box''. I closely look at the php.ini file and I set it to match yours. Everything want fine for installing Drupal and it works like a chamed. However, I still can't get importation to work in Biblio. I'have check the php logs and I couldn't see anything. What should I look for ? Plus, could the problem be in the httpd.conf file ? I ask my ISP to activite domphp and it will be tomorow, but I doult it have anything to do whit my problem since it is active in my local installation. I will try again to get everything working in my Linux partition and examine closely the php logs...
#20
Turn on error reporting in the php.ini file (error_reporting = E_ALL and display_errors = On) and see if you get any errors reported.
#21
Hi Ron,
Fortunately, I have full access to my server. I turned on error reporting in my php.ini file and set display_errors to "On" as well.
But nothing happens when importing my bibliography files of whatever format (BibTeX or Endnote), and no error is reported.
If you're interested in having access to my server to run some tests, or if you think I might be of some help, just let me know.
Robert
#22
Hi again, Ron,
I just got the import form working!
The issue seemingly comes when Drupal localization is not set to "English"; in my Drupal site, I added the French localization as the default one. And as I said in my previous post, the import form silently fails, whatever bib format I choose.
BUT... if I switch back to "English" in my profile, the import form perfectly works!
Isn't that a good place to start?
Want me to add this post in the "bug report" category?
Robert
#23
Hmm, that's a good one! I suspect this is outside the realm of the biblio module, but at least I can try to reproduce the issue now and I'll see if I can track it down.
Ron.
#24
I've just installed the biblio module 3 days ago and it's working fine as far as manual entry of bibliographic data is concerned (see http://cms.softtester.org/drupal/biblio/). But I can't seem to make import or export work properly using any of the format options. I would get a message that "File was successfully uploaded" as well as a link to the node where the file is loaded. When I click on this link however, the file is empty. Here are the error messages I'm getting:
With EndNote Tagged:
I would get a message that "File was successfully uploaded" as well as a link to the node where the file is loaded. When I click on this link however, the file is empty. Scroll down in the linked page above and here's what you see:
With EndNote 7 XML:
With BibTex:
I looked at the referenced lines in the biblio.module file and here they are:
I love this module. Thanks rjerome! Your help on this one would be much appreciated.
Glenda
#25
Hi Glenda,
Could you try modifying the lines which are giving the errors, and removing the './' part such that a line which looks like this...
require_once('./'.base_path() . drupal_get_path('module', 'biblio') . '/bibtex.php');would be changed to this...
require_once(base_path() . drupal_get_path('module', 'biblio') . '/bibtex.php');I think that will probably fix your problem. As it is, and extra / is being added to the path, which shouldn't make any difference but apparently your installation isn't happy with it. Let me know if that fixes you problem and I will make the changes to the released code.
Ron.
#26
Thanks for the prompt reply Ron but I'm still getting the same error messages. I'm just starting to learn PHP but I'll try tinkering a bit more with the code and see what it does.
Glenda
#27
Oh, it's not exactly the same error message, the extra / was taken out but an error message nonetheless:
#28
Hmmm, this is very strange. I think it must have something to do with your installation, since I don't see this on any of the machines I am running on (and no one else has reported this).
Can you give me any details about your installation? OS? WebServer? PHP version? DocumentRoot?
#29
Thanks for your time on this Ron - I tried tinkering but it's making things worse. My site is hosted on a shared web server with a hosting company. Here are some installation and setting details:
Question: Was I supposed to have endnote8_parser.inc included in the download file? (It's not there.)
Muchas gracias!
Glenda
#30
I suspect that this is a simple include path issue. My guess is that the webserver document root is set to something like "/home/softtest/public_html/" and thus the include path "/drupal/modules/biblio" is not being found.
Try adding the following to your sites/.../settings.php
ini_set('include_path', '.:/usr/lib/php:/usr/local/lib/php:/home/softtest/public_html/cms');As for the endnote8_parser.inc file, that's only in the CVS version right now.
Ron.
#31
It's really strange Ron. I included that line to the other ini_set lines in the settings.php file but I still get the ff error message:
I don't understand it because the line referring to the path in 1718 is right and the base path to endnote7_parser.inc is right too. I can't understand why there my installation is having trouble opening '/drupal/modules/biblio/endnote7_parser.inc'. I have changed the version from 8 to 7 in my EndNote XML file but this did not help. When I go back to the import page the message looks like this:
Does this mean that it is looking for endnote7_parser.inc in /home/softtest/public_html/cms/drupal/modules/biblio/biblio.module itself rather than in /home/softtest/public_html/cms/drupal/modules/biblio/?
Well, I think you've spent so much time helping me so I think I'll make the best of the manual entry for now. Thanks!
Glenda
#32
Do you know the full UNIX path to the biblio module directory?
You might try adding a "/." to the end of the line I gave you before like this...
ini_set('include_path', '.:/usr/lib/php:/usr/local/lib/php:/home/softtest/public_html/cms/.');or maybe just...
ini_set('include_path', '.:/usr/lib/php:/usr/local/lib/php:/cms/.');Basically you have to make sure that "/drupal/modules/biblio/endnote7_parser.inc" is in the include_path. Now if the webserver document root was pointing to "/usr/local/lib/php:/home/softtest/public_html/cms" then the first entry in the include path (".") would make everything work, but I suspect that the document root is set one level higher.
#33
Hi Ron, the import and export functions for EndNote Tagged and BibTex are working well but I still could not get import and export to work with the EndNote XML option. I've commented out the lines pertaining to outputting EndNote XML on the interface so users will not choose that and get an error message. Still hope to figure out the correct path to the parsers. Thanks for all of your help.
Glenda
#34
Hi Glenda,
This is even stranger than I thought since the bibtex import function includes bibtex.php from the exact same directory as the endnote7_parser.inc file, so if bibtex works, endnote should also work.
You might want to find the line which includes the bibtex.php file and make sure that the line that includes the endnote7_parser.inc file is the same.
Ron.
#35