BibTex

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Revision as of 14:33, 9 June 2009 by <bdi>Ricardo</bdi> (talk | contribs) (Corrected 2 typos ("thought" was written "though" and "hints" was written "hits"))
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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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