By rjerome on

I have recently released a module called biblio to manage lists of scholarly publications.

See liiscience.org for a live demo.

I this is of some use to the community

Ron.

⋅ Categories: Drupal 4.6.x

Comments

thart’s picture

thart commented

I've been waiting for something like this for such a long time! Thank you very much. The demo looks great. I'll try it myself really soon!

thart’s picture

thart commented

I can confirm that the module doesn't work in Drupal 4.7. :-(

When going to admin/modules it crashes with:

Fatal error: Only variables can be passed by reference in /home/eastasi/public_html/test2/modules/biblio/biblio.module on line 1193

And plans on a 4.7 compatible version soon?

rjerome’s picture

rjerome commented

Your right, I should have mentioned in my original post that it only supports 4.6 right now, but I will be porting to 4.7 within a few weeks.

Ron.

thart’s picture

thart commented

Thank you very much for your effort. I look forward using the 4.7 version. For now, I'll experiment with 4.6 and see how that goes.

notis’s picture

notis commented

This looks great on your site. Is there a documentaion somewhere on how to set up the database tables for us not so experienced users?
Best, Notis

rjerome’s picture

rjerome commented

You will find a brief descriiption of how to create the tables in the README.txt file (If that file doesn't exist, make sure you have the 4.6 version of the module and not the CVS version). The file biblio.mysql has the sql commands required to do the job.

Ron.

cirotix’s picture

cirotix commented

Great move. I have been waiting for such a module for quite some time (with some plan to eventually develop one if nothing was coming out).

My main question (appart from 4.7 support) is: is there any plan to support bibtex? I am willing to contribute on that if necessary but not before august.

Thank you for your nice module

stephenn-1’s picture

stephenn-1 commented

Another vote for bibtex support :)

rjerome’s picture

rjerome commented

When you say support bibtex, do you mean import, export or both?

It shouldn't be a big deal I don't think, and I was kind of expecting this would be the other major format request. I'll look into it.

Ron

wbhart’s picture

wbhart commented

Is there any way to have the biblio module only be available to users with a certain role?

rjerome’s picture

rjerome commented

Not at the present, but I can add that option.

Why don't you post a feature request here so I don't forget.

Ron.

pathscollide’s picture

pathscollide commented

This is great news! Very few CMSs have a good (or any kind of) biblio managment module. I'm interested in building subject-specific online academic research communities, based on the ideas driving services like RePEc (http://repec.org/) and ecommunics (http://www.ecommunics.org/). I think Drupal would be a great platform for this. This biblio module is a step in that direction.

It would be interesting to see a way to create a relational model within the site, where entries in the biblio module could be linked to author profiles and institution or research group profiles (and vice versa). And it would be nice if we could link a file to the biblio entry -- and be able to define who can add files (from everyone to only the admin), who can view files, who can delete files, etc.

EDIT: Presumably using upload.module or similar it should be possible to attach a file to this node type. But access control is another story...

Another thing that would be nice would be to have filtering by category integrated into the default interface (though this could be achieved to a certain extent by using standard taxonomy.module features).

rjerome’s picture

rjerome commented

Linking biblio entries with profiles is an interesting idea, I'll have to play with that one a bit.

I have used the upload module to attach files to publications, but as you say access control can be a bit of a problem.

Lately I have been toying with the idea of using the taxonomy module to provide the publication "types", I think this would provide some interesting side effects in terms of more closely integrating biblio entries within a site.

I originally built this to be more or less autonomous, but I believe I'm going to have to rethink that.

Ron.

misterbenj’s picture

misterbenj commented

when importing the .xml it shows a blank page and do not impot anything... and i am not able to create a .enw file from endnote...
here is a copy of the xml for an article :

<?xml version="1.0" encoding="UTF-8" ?>Untitled.enlEndNote117

Babu, C. S.

Lim, C.

Lim, C&#xD;Acad Sinica, Inst Biomed Sci, Taipei 11529, Taiwan&#xD;Acad Sinica, Inst Biomed Sci, Taipei 11529, Taiwan&#xA;Natl Tsing Hua Univ, Dept Chem, Hsinchu 300, Taiwan

Theory of ionic hydration: Insights from molecular dynamics simulations and experiment

Journal of Physical Chemistry B

J Phys Chem B&#xD;J Phys Chem B


Journal of Physical Chemistry B

J Phys Chem B

7958-7968

103

37

dilute aqueous-solutions

free-energy

born model

electron-transfer

liquid water

solvation

electrostatics

equation

solvent

radii

1999


Sep 16

1089-5647

ISI:000082706900028

blabla

238JJ&#xD;Times Cited:40&#xD;Cited References Count:54

<Go to ISI>://000082706900028

English

rjerome’s picture

rjerome commented

XML import currently only works with EndNote 4 - 7. I'm working on the 8+ version and it will probably be available in a week or so. You can try writing EndNote tagged fromat and importing that.

Ron.

misterbenj’s picture

misterbenj commented

Hi
I was still wondering if something new shows up for the Endnote X version or if it is too complicated to get it working fine? I was still expecting for my website :)

let me know

thanks

benjamin

abautu’s picture

abautu commented

Hi, I'm currently working on translating biblio to romanian.
I would advice you not to break messages into pieces like this:

$msg = t('Keywords will').' <b>'.t('NOT').'</b> '.t('be added to the vocabulary as specified in the Taxonomy section of the ').l(t('admin/settings/biblio'),'admin/settings/biblio').t(' page.');

This way, translation is really hard and for some languages the word order changes in negative phrases. You may use instead something like this:

$msg = t('Keywords will <b>NOT</b> be added to the vocabulary as specified in the Taxonomy section of the !link page.', array('!link' => l(t('admin/settings/biblio'),'admin/settings/biblio')));

Best wishes,
Andrei.

Anonymous’s picture

Anonymous (not verified) commented

Just to share an experience:

I updated a test Drupal from 5.0 to 5.3. It went smoothly.
There was a momentary glitch with Biblio but it went ok, as follows:

I had created a Publications View which uses content of type Biblio.
After the upgrade, the Publications View produced this error:

user warning: Unknown column 'biblio_coins' in 'field list' query: UPDATE biblio SET biblio_coins = etc. etc.

The Drupal Status page said the database was out of date & I should run update.php. The link it offered dumped me back at the upgrade page, where the directions said *do not update the database twice*.

This gave me pause as Drupal had already updated the database as part of the upgrade to 5.3.
I clicked 'update' anyway. A bunch of modules got updated, including biblio. I created some biblio items & the Publications View snarfed it up.

So, all's well. This is a great module. Thank you so much Ron.

Anonymous’s picture

Anonymous (not verified) commented

I don't want biblio content automatically promoted to front page.
Not a feature request (yet) as maybe it's there & I'm not seeing it in the admin interface.
?

abautu’s picture

abautu commented

Go to Administer > Content management > Content types. Click edit for biblio. Go to Workflow section and uncheck Promoted to front page.

Best wishes,
Andrei.

linur’s picture

linur commented

Hi, I need make you some question.

First, My English is bad.

I'm trying translate the biblio module in spanish but I can't find the following word:

Year of Publication

Authors

I hope you help me to fix that's.

Thanks in advance

Anonymous’s picture

Anonymous (not verified) commented

Año de publicación ?
Autores ?

You're the Spanish-speaker :)

Maybe the best idea is to look at academic Spanish publications.

Did I understand you?

good luck

Anonymous’s picture

Anonymous (not verified) commented

[Drupal 5.7]
Two things I don't understand, possibly connected:

1) how to style Biblio output
I have got some control over this - WebDeveloper/Firefox showed me the output is:
table tbody tr.even, table tbody tr.even td.menu-disabled
which I can affect in style.css.

Then I added my own 'research area' field to the biblio type (I want to pull up publications by research area), and I cannot figure out how to affect that field's appearance.
It shows up in WebDev as a field of three rows:
----------------------------------------------------------------------------------------------------
div #page-wrapper > div #main-wrapper > div #content-region-both > div #node-2 .node clear-block > div .content > div .field field-type-text field-field-research-area

div #page-wrapper > div #main-wrapper > div #content-region-both > div #node-2 .node clear-block > div .content > div .field field-type-text field-field-research-area > div .field-items

div #page-wrapper > div #main-wrapper > div #content-region-both > div #node-2 .node clear-block > div .content > table #attachements > thead > tr
----------------------------------------------------------------------------------------------------

Those div ids (div .field field-type-text field-field-research-area , div .field-items) are not in style.css (of course) and not in biblio.css (because, I guess, Biblio can't provide styles for fields that don't exist yet). But is there a default style for user-added fields? If so, where is it?
If there is no default style to override, then I guess I must create one from scratch.
In that case, should I copy biblio.css to my theme folder and do the overriding there?

2) When I Display fields in the Biblio module, the only one which shows up is the one I added. When I Manage fields, all the fields appear. The module is working properly. The field I added is a text-choice popup. WebDev or Firebug shows the field I added is being treated separately from the biblio style:

(carets removed because of display issue)

div class="content"
div id="biblio-node" /div
div class="field field-type-text field-field-research-area" /div [ the added field ]
table id="attachements"
/div

I don't see a biblio-node id in biblio.css -- ?

Thanks for reading all that - any suggestions?

Anonymous’s picture

Anonymous (not verified) commented

I'm wondering if there is a bug in this most excellent module.
I had created an additional field for the Biblio content type. (Previous post was about a difficulty with formatting the output)
I removed the field, and now when I try to list the fields, the message is “there are no fields configured for this content type.”
The mySQL client shows the biblio_fields table is still populated.

After removing this field, I created a new piece of content.
The removed field still showed up as a choice! And is shown as a keyword above the display of the content.
And I can sort on this keyword.
But none of the fields can be listed anymore.

Meanwhile I found the biblio_custom1, etc. fields.
I added biblio_custom1 and gave it the desired name, but it doesn't show up as a field to be filled out when I create content.

??

[Drupal 5.7. ]

Anonymous’s picture

Anonymous (not verified) commented

I upgraded to latest Biblio to see if I could solve the styling issue and figure out how adding fields works.
This produced what looks like a database issue, either that or the upgrade didn't work, or the html labels may not correspond to database fields.
It seems like contents aren't going into the expected fields in the database.

-- UPGRADED BIBLIO
I deactivated & uninstalled Biblio 5.x-1.8, moved it elsewhere, installed Biblio 5.x-1.15, activated it, ran update.php.]
The Modules page shows v1.8, after the update. And the Biblio Settings page shows a date of 9/07.
But the settings/biblio/defaults page had the original names for fields (I had changed biblio_custom_1 and it was back to its old self, so I assumed the upgrade went through).

-- CUSTOM TAG DIDN'T WORK - GAVE UP ON THAT
I tried setting the biblio_custom1 field name to a custom tag (“Research Area”) & created content.
The “Research Area” field did not show up as a choice.
[BTW I don't see how fields in table biblio_fields relate to the columns on that page - and the columns have no headings]

-- CREATED NEW FIELD INSTEAD
So insteated I created a field in settings/biblio/defaults:
Content Mgmt > Content Types > Biblio > Add Field > etc., and it shows up as a field.
Then I created content. [The Research Area popup appears before you choose a publication type.]
This works, pubs are created.

-- BIBLIOVIEW UNEXPECTED OUTPUT
“Biblioview” dutifully displays all pubs, but this is followed by a list of all items from an unrelated Menu called “Research Areas”, & the user name (or the site name, they are the same).

-- CUSTOMIZED VIEW: WHICH IS TITLE FIELD?
I created a customized view, to include only pubs within certain Research Areas.
In the Field popups, Biblio fields did not appear until I saved an as-yet uncustomized View.
Then they appeared, but which field to pick for Title?
There was no Biblio:Title field in the popup. It turned out to be the “Secondary” Title.

-- MISSING CONTENT? BEGAN TO QUERY DATABASE DIRECTLY
So I made a view {name, year, and secondary title} filtering on a certain Research Area.
It worked fine, displayed those pubs, but the secondary title column is missing a column label.
Further, the (secondary?) title of one of the pubs is not displayed. I did fill in that field for that pub.
The query:
select biblio_secondary_title from biblio;
shows that the title is missing in the database although I entered a title.

“select biblio_number from biblio;” --> three records, but they are empty.
”select biblio_authors from biblio;“ --> authors of all records appear

select * from biblio where nid={my record #}\G“ -->
Things get goofier; for the record which is properly displayed, in fact in the database the title appears in in biblio_coins, but biblio_secondary_title actually contains the proceedings name.
For the record which is missing a title, the title info is being stored in biblio_coins, but is not being put into biblio_secondary_title.
These are different biblio_types.

Either the upgrade didn't work (advice gratefully accepted on proper procedure) or something's wrong with the database, OR maybe the fields are labeled wrongly on the web page, that is, some glitches in relating the html field labels to the mysql database fields.

And I still don't know how to style the Research Area field I created (see older posts).

So, in sum: super module (I love the ability to stage pubs for download and the automatic filesize indication). But hard to figure out. I read the README. The Drupal site only says documentation “coming later”.

If I get this figured out I'll post it.

Anonymous’s picture

Anonymous (not verified) commented

The author showed me that upgrading this module requires moving the old version completely out of the Drupal tree.
It's not enough to move it to a directory, e.g., 'old' , within the modules directory.

That took care of the upgrade question.

ceuna’s picture

ceuna commented

Hello,

I'm new to Drupal. However, the installation of the core files went fine. Now I'm trying to get the module "biblio" right.

I want to get it at my clients site www.johannesvanderven.nl like at the example; www.liiscience.org. I did fill in just one test bibliographic entry at johannesvanderven.nl

So how can I connect a menu item, say "publications", with the module?

Thank you in advance!

rodrigo panchiniak fernandes’s picture

rodrigo panchiniak fernandes commented

Hi,

Biblio is great and very useful module. First of all, thanks for sharing it.

I'm trying to add ABNT NBR6023:2002 to styles list. This standard requires upper-case letters for some titles, specially for unknown authors. Is there a way to css-do that coding only in biblio_style_abnt.inc or I should add a style class to biblio.css? I suppose the first choice is the better but it do not work for me.

    case 100: //book - livro - monografia no todo
      if (!empty($authors))                                 // autor conhecido
      {
       ...
      }
      else{                                                 //autor deconhecido - unknown author 
        $url = biblio_get_title_url_info($node);
        $first_word = substr($node->title, 0, strpos($node->title,' '));
        $remaing_words .= $node->title;                       
        $output .= '<span style="text-transform:uppercase;">'; //to call a biblio.css style works fine  :-( 
        $output .= l($first_word, $url['link'], $url['options']);        
        $output .= '</span>';
        $posdelimitador = strpos($node->title,' '); 
        $output .=  substr($remaining, $posdelimitador);
      }

Best,

Rodrigo

zhenre’s picture

zhenre commented

I implemented a much cruder version of this using just CCK and views. Yours is much more robust and seems like it would be the way to go. I had a few features on mine which it would be nice if it were possible to implement within the more robust environment of your Biblio module.

The first was a convenient way of uploading images to act as an icon. I did this using file upload field and image-cache. I also had an abstract field. If this could be autopopulated from the DOI information that would be amazing (or otherwise manual cut and paste) works ok too.

I think this was mentioned in other comments, but it would also be great if you could associate publications with users and nodes. For example it would be great if a user's profile displayed their publications. If this were done automatically that would be amazing if it had to be added manually that would not be too onerous I think. Similarly linking to nodes would be great as that would allow one to display a list of publications associated with a given project. I've crudely (and I think probably wrongly) implemented a similar system on my website and it is a nice thing to have. For an academic website these two functions are really where you win with drupal. Put the publication in once and it gets displayed in all the appropriate places. Being able to load from doi or bibtex would make it even easier.

Another thing that would be nice would be a way to get citation information about the publications. It would be great if each publication knew how many citations it had, and if you could compute statistics about the whole bibliography. Not super important but fun.

Finally it would be amazing if it could query an online database for a specific author (or potentially more complicated queries), to automatically add publications as they are published, without having to do any manual data entry. It could present a list of unverified publications to be manually checked before being published.

I don't know too much about module development but would be willing to help implement any of these features if you'd provide guidance...just shoot me an email at zhenre@gmail.com