# BibTex

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.

## 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 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;