Difference between revisions of "BibTex"

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m (New page: Nothing done yet but we're thinking about setup a BibTex capable server or a BibTex plugin for a wiki, so here is a raw links list for the moment. ==BibTex servers== * http://www.rennes.s...)
 
m (Reverted edits by Etegohy (Talk) to last revision by Ricardo)
 
(14 intermediate revisions by 2 users not shown)
Line 18: Line 18:
 
* http://www.plaschg.net/bibwiki/Main/Screenshots
  
* http://www.plaschg.net/bibwiki/Main/Screenshots
 
* http://twiki.org/cgi-bin/view/Plugins/BibtexPlugin
  
* http://twiki.org/cgi-bin/view/Plugins/BibtexPlugin
  +
==Let's try Connotea==
  +
===Installation===
  +
* http://www.connotea.org
  +
* http://www.connotea.org/code
  +
  +
It's much harder than I thought and there are probably still some tweaks I forgot to write down but here are already some hints:
  +
  +
Here is the list of Debian packages we installed (including dependencies):
  +
<pre>
  +
cat /var/log/dpkg.log.1 /var/log/dpkg.log|grep "status installed"|awk '{print $5}'
  +
  +
mysql-common
  +
libnet-daemon-perl
  +
libplrpc-perl
  +
libdbi-perl
  +
libmysqlclient15off
  +
libdbd-mysql-perl
  +
mysql-client-5.0
  +
psmisc
  +
mysql-server-5.0
  +
libevent1
  +
memcached
  +
libdevel-symdump-perl
  +
libperl5.8
  +
libapache2-mod-perl2
  +
libexpat1-dev
  +
ncbi-data
  +
libncbi6
  +
readseq
  +
libossp-uuid15
  +
libossp-uuid-perl
  +
libxml-parser-perl
  +
libmime-lite-perl
  +
libfcgi-perl
  +
libtimedate-perl
  +
libmailtools-perl
  +
libio-stringy-perl
  +
libconvert-binhex-perl
  +
libmime-perl
  +
libcompress-zlib-perl
  +
libsoap-lite-perl
  +
libgd2-xpm
  +
libgd-gd2-perl
  +
libio-string-perl
  +
bioperl
  +
libstring-crc32-perl
  +
libcache-memcached-perl
  +
libcgi-perl
  +
libclass-accessor-perl
  +
libclass-data-inheritable-perl
  +
libdbix-contextualfetch-perl
  +
libima-dbi-perl
  +
libclass-trigger-perl
  +
libuniversal-moniker-perl
  +
libversion-perl
  +
libclone-perl
  +
libclass-dbi-perl
  +
libclass-dbi-mysql-perl
  +
libclass-factory-util-perl
  +
libclass-singleton-perl
  +
libparams-validate-perl
  +
libdatetime-locale-perl
  +
libdatetime-timezone-perl
  +
libdatetime-perl
  +
libdatetime-format-strptime-perl
  +
libdatetime-format-builder-perl
  +
libdatetime-format-mysql-perl
  +
libfile-touch-perl
  +
libxml2-dev
  +
libjson-perl
  +
liblist-moreutils-perl
  +
libsql-abstract-perl
  +
libappconfig-perl
  +
libtemplate-perl
  +
libsub-uplevel-perl
  +
libtest-exception-perl
  +
libparse-recdescent-perl
  +
libdbix-fulltextsearch-perl
  +
libtext-wikiformat-perl
  +
libtime-piece-perl
  +
libwiki-toolkit-perl
  +
libalgorithm-diff-perl
  +
libvcs-lite-perl
  +
libwiki-toolkit-plugin-diff-perl
  +
libclass-errorhandler-perl
  +
libdatetime-format-mail-perl
  +
libdatetime-format-w3cdtf-perl
  +
libdigest-sha1-perl
  +
liburi-fetch-perl
  +
libfeed-find-perl
  +
liblwp-authen-wsse-perl
  +
libxml-libxml-common-perl
  +
libxml-namespacesupport-perl
  +
libxslt1.1
  +
libxml-xpath-perl
  +
libxml-rss-perl
  +
libyaml-perl
  +
libbtparse0
  +
libtext-bibtex-perl
  +
libxml-sax-perl
  +
libxml-libxml-perl
  +
libxml-libxslt-perl
  +
libxml-atom-perl
  +
libxml-feed-perl
  +
liblingua-en-nameparse-perl
  +
libtext-csv-perl
  +
libauthen-captcha-perl
  +
libio-pty-perl
  +
libipc-run-perl
  +
libnet-ip-perl
  +
libio-zlib-perl
  +
libarchive-tar-perl
  +
libset-infinite-perl
  +
libdatetime-set-perl
  +
liberror-perl
  +
libextutils-cbuilder-perl
  +
libextutils-parsexs-perl
  +
libmodule-build-perl
  +
libpod-escapes-perl
  +
libpod-simple-perl
  +
libtest-pod-perl
  +
libwant-perl
  +
libxml-twig-perl
  +
libxml-writer-perl
  +
</pre>
  +
That's 114 packages!
  +
  +
CPAN installed packages:
  +
<pre>
  +
find /usr/local/lib/perl/5.8.8/auto -name .packlist|sed 's#.*auto/\(.*\)/.packlist#\1#;s#/#::#g' | sort
  +
Apache::Emulator
  +
CGI::Wiki
  +
CGI::Wiki::Plugin::Diff
  +
Module::Optional
  +
Config::Scoped
  +
DateTime::Format::ISO8601
  +
DateTime::Incomplete (force)
  +
DateTime::Event::Recurrence
  +
HTML::Sanitizer (force)
  +
HTTP::OAI (force)
  +
Netscape::Bookmarks
  +
RDF::Core
  +
Set::Array
  +
Time::HR
  +
URI::OpenURL
  +
XML::Element
  +
</pre>
  +
  +
DONT USE /usr/bin/wiki-toolkit-setupdb but well /usr/local/bin/cgi-wiki-setupdb !!!
  +
  +
The install page grants only limited rights to the user on the DB but first thing it tried was a CREATE which failed so:
  +
GRANT ALL ON bibliotech.* TO connotea@localhost IDENTIFIED BY '...';
  +
  +
You've also to import the Clicks scheme into mysql, create a user and grant him rights on the DB and populate the config file /etc/bibliotech.conf:
  +
CLICKS {
  +
DBI_CONNECT = 'dbi:mysql:clicks'
  +
DBI_USERNAME = 'clicks'
  +
DBI_PASSWORD = '...'
  +
}
  +
  +
When you enroll on the website and follow the emailed link, you're redirected to a non-existing page: getting_started (it exists on the official site)
  +
  +
I had to backport bibutils which was only available in Sid, then changing the /etc/bibliotech.conf:
  +
BIBUTILS_PATH = /usr/bin/
  +
  +
If you modify the config file, you need to force caches to be cleaned:
  +
/etc/init.d/memcached restart
  +
/etc/init.d/apache2 reload
  +
then reload the page in the browser
  +
  +
===Still fuzzy parts===
  +
  +
TODO: search index & replicate...
  +
  +
/citation: needs access to /var/log/webcite.log
  +
tried:
  +
http://philsci-archive.pitt.edu/archive/00003626/
  +
=> Bookmarking Service[32103] ris 0 [Error from Bibliotech::CitationSource::ePrints::citations('http://philsci-archive.pitt.edu/archive/00003626/'): Can't locate object method "new" via package "HTTP::OAI::Identify" (perhaps you forgot to load "HTTP::OAI::Identify"?) at /home/install/connotea-code-1.8-beta/Bibliotech/CitationSource/ePrints.pm line 102.
  +
] calc http://philsci-archive.pitt.edu/archive/00003626/
  +
  +
proxy??
  +
  +
/admin
  +
  +
==Let's try [http://refbase.sourceforge.net/ refBASE]==
  +
===Installation===
  +
I assume you've already PHP & MySQL
  +
svn co https://refbase.svn.sourceforge.net/svnroot/refbase/trunk refbase
  +
  +
Edit initialize/db.inc.php => $hostName, $databaseName, $username, $password
  +
<br>Create a virtualhost for the new service and point your browser to it at /install.php
  +
<br>Follow instructions
  +
  +
Afterwards, you can manage users -> delete the initial user
  +
===Configuration===
  +
See http://wiki.refbase.net/index.php/Configuring_refbase
  +
  +
http://wiki.refbase.net/index.php/Documentation
  +
  +
Consider changing the upload_max_filesize in /etc/php5/apache2/php.ini to upload articles bigger than the default 2Mb.
  +
<br>Also for big exports (>40), consider changing the memory_limit to a higher value than 16M.
  +
  +
By default, given names are shortened on import. To avoid that, edit includes/import.inc.php and change all the occurrences of
  +
$shortenGivenNames = true;
  +
to
  +
$shortenGivenNames = false;
  +
  +
===Client===
  +
see http://wiki.refbase.net/index.php/Command_line_clients

Latest revision as of 21:35, 24 November 2010

Nothing done yet but we're thinking about setup a BibTex capable server or a BibTex plugin for a wiki, so here is a raw links list for the moment.

BibTex servers

Misc

Wiki plugins

Let's try Connotea

Installation

It's much harder than I thought and there are probably still some tweaks I forgot to write down but here are already some hints:

Here is the list of Debian packages we installed (including dependencies): 

cat /var/log/dpkg.log.1 /var/log/dpkg.log|grep "status installed"|awk '{print $5}'

mysql-common
libnet-daemon-perl
libplrpc-perl
libdbi-perl
libmysqlclient15off
libdbd-mysql-perl
mysql-client-5.0
psmisc
mysql-server-5.0
libevent1
memcached
libdevel-symdump-perl
libperl5.8
libapache2-mod-perl2
libexpat1-dev
ncbi-data
libncbi6
readseq
libossp-uuid15
libossp-uuid-perl
libxml-parser-perl
libmime-lite-perl
libfcgi-perl
libtimedate-perl
libmailtools-perl
libio-stringy-perl
libconvert-binhex-perl
libmime-perl
libcompress-zlib-perl
libsoap-lite-perl
libgd2-xpm
libgd-gd2-perl
libio-string-perl
bioperl
libstring-crc32-perl
libcache-memcached-perl
libcgi-perl
libclass-accessor-perl
libclass-data-inheritable-perl
libdbix-contextualfetch-perl
libima-dbi-perl
libclass-trigger-perl
libuniversal-moniker-perl
libversion-perl
libclone-perl
libclass-dbi-perl
libclass-dbi-mysql-perl
libclass-factory-util-perl
libclass-singleton-perl
libparams-validate-perl
libdatetime-locale-perl
libdatetime-timezone-perl
libdatetime-perl
libdatetime-format-strptime-perl
libdatetime-format-builder-perl
libdatetime-format-mysql-perl
libfile-touch-perl
libxml2-dev
libjson-perl
liblist-moreutils-perl
libsql-abstract-perl
libappconfig-perl
libtemplate-perl
libsub-uplevel-perl
libtest-exception-perl
libparse-recdescent-perl
libdbix-fulltextsearch-perl
libtext-wikiformat-perl
libtime-piece-perl
libwiki-toolkit-perl
libalgorithm-diff-perl
libvcs-lite-perl
libwiki-toolkit-plugin-diff-perl
libclass-errorhandler-perl
libdatetime-format-mail-perl
libdatetime-format-w3cdtf-perl
libdigest-sha1-perl
liburi-fetch-perl
libfeed-find-perl
liblwp-authen-wsse-perl
libxml-libxml-common-perl
libxml-namespacesupport-perl
libxslt1.1
libxml-xpath-perl
libxml-rss-perl
libyaml-perl
libbtparse0
libtext-bibtex-perl
libxml-sax-perl
libxml-libxml-perl
libxml-libxslt-perl
libxml-atom-perl
libxml-feed-perl
liblingua-en-nameparse-perl
libtext-csv-perl
libauthen-captcha-perl
libio-pty-perl
libipc-run-perl
libnet-ip-perl
libio-zlib-perl
libarchive-tar-perl
libset-infinite-perl
libdatetime-set-perl
liberror-perl
libextutils-cbuilder-perl
libextutils-parsexs-perl
libmodule-build-perl
libpod-escapes-perl
libpod-simple-perl
libtest-pod-perl
libwant-perl
libxml-twig-perl
libxml-writer-perl

That's 114 packages!

CPAN installed packages: 

find /usr/local/lib/perl/5.8.8/auto -name .packlist|sed 's#.*auto/\(.*\)/.packlist#\1#;s#/#::#g' | sort
Apache::Emulator
CGI::Wiki
CGI::Wiki::Plugin::Diff
  Module::Optional
Config::Scoped
DateTime::Format::ISO8601
DateTime::Incomplete                        (force)
  DateTime::Event::Recurrence
HTML::Sanitizer                             (force)
HTTP::OAI                                   (force)
Netscape::Bookmarks
RDF::Core
Set::Array
Time::HR
URI::OpenURL
XML::Element

DONT USE /usr/bin/wiki-toolkit-setupdb but well /usr/local/bin/cgi-wiki-setupdb !!!

The install page grants only limited rights to the user on the DB but first thing it tried was a CREATE which failed so: 

GRANT ALL ON bibliotech.* TO connotea@localhost IDENTIFIED BY '...';

You've also to import the Clicks scheme into mysql, create a user and grant him rights on the DB and populate the config file /etc/bibliotech.conf: 

CLICKS {
 DBI_CONNECT = 'dbi:mysql:clicks'
 DBI_USERNAME = 'clicks'
 DBI_PASSWORD = '...'
}

When you enroll on the website and follow the emailed link, you're redirected to a non-existing page: getting_started (it exists on the official site)

I had to backport bibutils which was only available in Sid, then changing the /etc/bibliotech.conf: 

 BIBUTILS_PATH = /usr/bin/

If you modify the config file, you need to force caches to be cleaned: 

/etc/init.d/memcached restart
/etc/init.d/apache2 reload

then reload the page in the browser

Still fuzzy parts

TODO: search index & replicate...

/citation: needs access to /var/log/webcite.log tried: http://philsci-archive.pitt.edu/archive/00003626/ => Bookmarking Service[32103] ris 0 [Error from Bibliotech::CitationSource::ePrints::citations('http://philsci-archive.pitt.edu/archive/00003626/'): Can't locate object method "new" via package "HTTP::OAI::Identify" (perhaps you forgot to load "HTTP::OAI::Identify"?) at /home/install/connotea-code-1.8-beta/Bibliotech/CitationSource/ePrints.pm line 102. ] calc http://philsci-archive.pitt.edu/archive/00003626/

proxy??

/admin

Let's try refBASE

Installation

I assume you've already PHP & MySQL 

svn co https://refbase.svn.sourceforge.net/svnroot/refbase/trunk refbase

Edit initialize/db.inc.php => $hostName, $databaseName, $username, $password
Create a virtualhost for the new service and point your browser to it at /install.php
Follow instructions

Afterwards, you can manage users -> delete the initial user

Configuration

See http://wiki.refbase.net/index.php/Configuring_refbase

http://wiki.refbase.net/index.php/Documentation

Consider changing the upload_max_filesize in /etc/php5/apache2/php.ini to upload articles bigger than the default 2Mb.
Also for big exports (>40), consider changing the memory_limit to a higher value than 16M.

By default, given names are shortened on import. To avoid that, edit includes/import.inc.php and change all the occurrences of 

$shortenGivenNames = true;

to 

$shortenGivenNames = false;

Client

see http://wiki.refbase.net/index.php/Command_line_clients

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