Refbase update_2021-01-28_15_58
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contrib/command_line/README
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contrib/command_line/README
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refbase command line clients
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============================
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Author
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------
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Matthias Steffens <refbase@extracts.de>
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About
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-----
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'refbase' is a command line client (written in perl) to search refbase.
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'refbase_import' is a client to import references into refbase.
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Use
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---
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Part I: Configuration
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- Both scripts may be edited in a text editor. It is suggested that you set:
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- %hosts
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- %loginParams
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Part II: Use
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- Both scripts will print help if run with an argument of '-h' or '--help'
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- They will print usage examples if run with '-X' or '--examples'
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See also:
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<http://cli.refbase.net>
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1183
contrib/command_line/refbase
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contrib/command_line/refbase
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contrib/command_line/refbase_import
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contrib/command_line/refbase_import
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#!/usr/bin/perl
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# Project: Web Reference Database (refbase) <http://www.refbase.net>
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# Copyright: Matthias Steffens <mailto:refbase@extracts.de> and the file's
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# original author(s).
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#
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# This code is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY. Please see the GNU General Public
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# License for more details.
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#
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# File: ./contrib/command_line/refbase_import
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# Repository: $HeadURL: file:///svn/p/refbase/code/branches/bleeding-edge/contrib/command_line/refbase_import $
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# Author(s): Matthias Steffens <mailto:refbase@extracts.de>
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#
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# Created: 06-Jun-06, 18:00
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# Modified: $Date: 2008-10-30 18:16:54 +0000 (Thu, 30 Oct 2008) $
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# $Author: msteffens $
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# $Revision: 1289 $
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# REFBASE_IMPORT -- a refbase command line interface
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# Purpose: Perl script that allows to upload data in various formats to a refbase online database from the command line
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# Usage: refbase_import [OPTIONS] [FILE]
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# Help: For help with the syntax type 'refbase_import -h'
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# To view some usage examples type 'refbase_import -X'
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# Further information is available at <http://cli.refbase.net/>
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# A list of supported import formats is given at <http://import.refbase.net/>
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# Version: 1.2
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# Requires: - a shell with Perl execution capabilities
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# - the Perl CPAN modules LWP::UserAgent, HTTP::Request::Common, HTTP::Response, HTTP::Cookies and URI::URL
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# - access with import permissions to a refbase database (refbase-0.9.0 or greater)
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# Limits: - The character encoding of your import data must match the encoding of your refbase database (i.e., 'latin1' or 'utf8')
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# - The authentication mechanism is currently limited in that a given password will be transferred as parameter in the POST request
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# --------------------------------------------------------------------------------------------------------------
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$version = "1.2";
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# Configure variables:
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# Specify the full URLs to any refbase servers that shall be queried:
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# Notes: - the given hash keys will work as shortcuts, e.g. '--host=local' would upload
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# data to your local refbase installation; one hash key must be named 'default',
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# all other keys can be freely chosen
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# - by default, data will be uploaded to the server labeled with key 'default'
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%hosts = (
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'default' => 'http://beta.refbase.net/',
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'local' => 'http://localhost/refs/',
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'beta' => 'http://beta.refbase.net/',
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'beta2' => 'http://refbase.textdriven.com/beta/',
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'demo' => 'http://demo.refbase.net/',
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'org' => 'http://www.refbase.org/'
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);
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# Specify the default values for all options that are not explicitly specified:
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%params = (
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# import options:
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'skipBadRecords' => '0', # -b|--skipbad -> must be '0' (don't skip records with unrecognized data format) or '1' (skip records with unrecognized data format)
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'importRecordsRadio' => 'all', # -i|--import -> must be 'all' (import all records) or 'only' (import only those records specified in 'importRecords')
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'sourceIDs' => '', # -p|--pmid -> this also applies for '--arxiv|--doi|--openurl' since they are essentially just aliases for '-p'
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'importRecords' => '1', # -r|--records -> must be a list of numbers and/or ranges (e.g., '1-5' will import the first five records; '1 3-5 7' will import records 1, 3, 4, 5 and 7)
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'formType' => 'data', # -t|--type -> must be 'data' (generic data import) or 'id' (import via ID)
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# fixed parameters:
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'client' => "cli-refbase_import-" . $version # the client ID of this command line utility
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);
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%outputParams = (
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# output options:
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'citeStyle' => '', # -C|--style => desired citation style, given name must match an entry within the database's MySQL table 'styles' (keep empty to use the database default)
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'format' => 'ascii', # -F|--format => output format must be 'html', 'rtf', 'pdf', 'latex', 'latex_bbl', 'markdown', 'ascii', 'ads', 'bibtex', 'endnote', 'isi', 'ris', 'atom', 'mods', 'oai_dc', 'odf', 'srw_dc', 'srw_mods', 'word' or '' (the empty string '' will produce the default 'ascii' output style)
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'showLinks' => '1', # -L|--showlinks => hide/display links column in HTML output; must be '0', '1', or '' (the empty string '' will produce the default output style, i.e. print any links)
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'citeOrder' => 'author', # -O|--order => cite order must be 'author', 'year', 'type', 'type-year', 'creation-date' or '' (the empty string '' will produce the default 'author' sort order)
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'viewType' => 'web' # -V|--view => view type of HTML output; must be 'Web', 'Print', 'Mobile' or '' (the empty string '' will produce the default 'Web' output style)
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);
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# Specify the default login credentials for a refbase user account:
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# Imported data will get associated with this user account
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%loginParams = (
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'loginEmail' => '', # -U|--user -> the login email address of an existing refbase user with import permissions
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'loginPassword' => '' # -P|--password -> the password for the given user account
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);
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# Specify the location of the cookie jar file:
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# This file will be used to store & retrieve cookies
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$cookieJarFile = "$ENV{HOME}/.lwpcookies.txt";
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# --------------------------------------------------------------------------------
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# NOTE: You shouldn't need to change anything below this line
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# CPAN modules:
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use LWP::UserAgent; # more info: <http://search.cpan.org/~gaas/libwww-perl-5.805/lib/LWP/UserAgent.pm>
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use HTTP::Request::Common; # more info: <http://search.cpan.org/~gaas/libwww-perl-5.805/lib/HTTP/Request/Common.pm>
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use HTTP::Response; # more info: <http://search.cpan.org/~gaas/libwww-perl-5.805/lib/HTTP/Response.pm>
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use HTTP::Cookies; # more info: <http://search.cpan.org/~gaas/libwww-perl-5.805/lib/HTTP/Cookies.pm>
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use URI::URL; # more info: <http://search.cpan.org/~gaas/URI-1.35/URI/URL.pm>
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# initialize variables:
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$host = $hosts{'default'};
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$format = '';
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# Extract options:
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# TODO: use Getopt::Long
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# general options:
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if (($ARGV[0] eq '--help') or ($ARGV[0] eq '-h') or ($ARGV[0] eq '')) { &usage (0); } # if the user asked for --help/-h or didn't provide any input, call the 'usage' subroutine
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elsif (($ARGV[0] eq '--version') or ($ARGV[0] eq '-v')) { &version (0); } # show version information
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elsif (($ARGV[0] eq '--examples') or ($ARGV[0] eq '-X')) { &examples (0); } # print some usage examples
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else {
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foreach (@ARGV) {
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# extract import options:
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if ($_ =~ /^(?:-b|--skipbad)=(.+)$/) { $params{'skipBadRecords'} = $1; }
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elsif ($_ =~ /^(?:-i|--import)=(.+)$/) { $params{'importRecordsRadio'} = $1; }
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elsif ($_ =~ /^(?:-p|--pmid|--arxiv|--doi|--openurl)=(.+)$/) { $params{'sourceIDs'} = $1; }
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elsif ($_ =~ /^(?:-r|--records)=(.+)$/) { $params{'importRecords'} = $1; }
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elsif ($_ =~ /^(?:-t|--type)=(.+)$/) { $params{'formType'} = $1; }
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# extract output options:
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elsif ($_ =~ /^(?:-C|--style)=(.+)$/) { $outputParams{'citeStyle'} = $1; }
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elsif ($_ =~ /^(?:-F|--format)=(.+)$/) { $outputParams{'format'} = $1; }
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elsif ($_ =~ /^(?:-L|--showlinks)=(.+)$/) { $outputParams{'showLinks'} = $1; }
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elsif ($_ =~ /^(?:-O|--order)=(.+)$/) { $outputParams{'citeOrder'} = $1; }
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elsif ($_ =~ /^(?:-V|--view)=(.+)$/) { $outputParams{'viewType'} = $1; }
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# extract server options:
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elsif ($_ =~ /^(?:-H|--host)=(.+)$/) { $host = $1; }
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elsif ($_ =~ /^(?:-P|--password)=(.+)$/) { $loginParams{'loginPassword'} = $1; }
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elsif ($_ =~ /^(?:-U|--user)=(.+)$/) { $loginParams{'loginEmail'} = $1; }
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# extract file:
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# (note that if multiple files were given, only the last given file will be honoured)
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elsif ($_ =~ /^(?!(-[biprtCFLOVHPU]|--(?:skipbad|import|pmid|arxiv|doi|openurl|records|type|style|format|showlinks|order|view|host|password|user))=)([^ ]+)/) { @sourceFile = $2; }
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}
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}
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# for '--type=data', check if a source file was specified:
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if (($params{'formType'} =~ /^data$/i) && (scalar @sourceFile == 0)) {
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print "There were validation errors regarding the data you submitted:\n\n";
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print "FILE: The file operand is missing! The generic data import feature ('--type=data')\n"
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. " requires a FILE to be specified. Type 'refbase_import -X' to see some usage\n"
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. " examples. For general help with the syntax type 'refbase_import -h'.\n\n";
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exit;
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}
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# for '--type=id' (or, previously: --type=pmid), check if at least one PubMed ID, arXiv ID, DOI or OpenURL was given:
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# TODO: improve identification/verification of the given IDs
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elsif (($params{'formType'} =~ /^(pm)?id$/i) && ($params{'sourceIDs'} !~ /\d+/)) {
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print "There were validation errors regarding the data you submitted:\n\n";
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print "sourceIDs: You must specify at least one PubMed ID, arXiv ID, DOI or OpenURL! The 'import via ID'\n"
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. " feature ('--type=id') requires the '-p, --pmid' option or one of '--arxiv|--doi|--openurl'\n"
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. " to be specified. Type 'refbase_import -X' to see some usage examples. For general help\n"
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. " with the syntax type 'refbase_import -h'.\n\n";
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exit;
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}
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# adjust form type value:
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if ($params{'formType'} =~ /^(pm)?id$/i) { # --type=id (or, previously: --type=pmid)
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$params{'formType'} = "importID";
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}
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else { # --type=data
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$params{'formType'} = "import";
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}
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# resolve any host shortcuts:
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if (exists($hosts{$host})) {
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$host = $hosts{$host};
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}
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elsif ($host !~ /^https?:\/\//i) {
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$host = $hosts{'default'}; # can't resolve given host, reset back to default
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}
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# assign correct URL params based on the '-F|--format' option:
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if (exists($outputParams{'format'})) {
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$format = $outputParams{'format'};
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if ($format =~ /^(html|rtf|pdf|latex|latex_bbl|markdown|ascii)$/i) {
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$outputParams{'submit'} = "Cite";
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}
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if ($format =~ /^(html|rtf|pdf|latex|latex_bbl|markdown|ascii)$/i) {
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$format =~ s/^latex_bbl$/LaTeX .bbl/i;
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$outputParams{'citeType'} = $format;
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}
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elsif ($format =~ /^(ads|bibtex|endnote|isi|ris|atom|mods|oai_dc|odf|srw(_dc|_mods)?|word)$/i) {
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$outputParams{'submit'} = "Export";
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$outputParams{'exportType'} = "file";
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if ($format =~ /^(ads|bibtex|endnote|isi|ris)$/i) {
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$outputParams{'exportFormat'} = $format;
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}
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elsif ($format =~ /^(atom|mods|oai_dc|odf|srw(_dc|_mods)?|word)$/i) {
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$outputParams{'exportFormat'} = $format . " xml";
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}
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}
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else {
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$outputParams{'citeType'} = "ascii";
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}
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delete($outputParams{'format'});
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}
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# construct URL:
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# (uses URI::URL)
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$importScript = "import_modify.php";
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$importURL = url($host . $importScript);
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# initialize new user agent:
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# (uses LWP::UserAgent)
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$userAgent = LWP::UserAgent->new;
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# set user agent string:
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$userAgent->agent("refbase_import/" . $version . " (http://cli.refbase.net/) ");
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# set cookie jar object:
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# LWP will collect cookies and respond to cookie requests via its cookie jar, thus
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# enabling the user agent to fetch a PHP session ID from the refbase login response
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# and automatically resend it upon next import request
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$userAgent->cookie_jar({ file => $cookieJarFile, autosave => 1 });
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# attempt to authenticate using the given login credentials:
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if (($loginParams{'loginEmail'} ne '') && ($loginParams{'loginPassword'} ne '')) {
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$loginSuccessful = &login(0); # call the 'login' subroutine
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}
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else {
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$loginSuccessful = 0;
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}
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if (!$loginSuccessful) {
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print "Login failed! You provided an incorrect email address or password.\n\n";
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exit;
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}
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# send POST request:
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# (uses HTTP::Request::Common & HTTP::Response)
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if ($params{'formType'} =~ /^importID$/i) { # --type=id (or, previously: --type=pmid)
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$request = POST $importURL, \%params;
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}
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else { # --type=data
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$params{'uploadFile'} = \@sourceFile;
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$request = POST $importURL, Content_Type => 'form-data', Content => \%params;
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}
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$response = $userAgent->request($request);
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if ($response->is_error()) {
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print STDERR $response->status_line, "\n";
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}
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else {
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$location = $response->header('Location');
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if ($location ne '') {
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if ($location =~ /show.php/) {
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# display imported records:
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foreach $key (keys %outputParams) {
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$location .= "&" . $key . "=" . $outputParams{$key};
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}
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if ($location =~ /&headerMsg=\D*(\d+)/i) {
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$location .= "&showRows=" . $1;
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}
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}
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# construct URL:
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# (uses URI::URL)
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$responseURL = url($host . $location);
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# send GET request:
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# (uses HTTP::Request::Common & HTTP::Response)
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$request = GET $responseURL;
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$response = $userAgent->request($request); # or use: $response = $userAgent->get($responseURL);
|
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}
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binmode STDOUT;
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print $response->content();
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}
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# --------------------------------------------------------------------------------
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# Login with login credentials given in '%loginParams':
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||||
sub login
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||||
{
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local ($status) = @_;
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||||
|
||||
# construct URL:
|
||||
# (uses URI::URL)
|
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$loginScript = "user_login.php";
|
||||
$loginURL = url($host . $loginScript);
|
||||
|
||||
# send POST request:
|
||||
# (uses HTTP::Request::Common & HTTP::Response)
|
||||
$request = POST $loginURL, \%loginParams;
|
||||
|
||||
$response = $userAgent->request($request);
|
||||
|
||||
if ($response->is_error()) {
|
||||
print STDERR $response->status_line, "\n";
|
||||
exit $status;
|
||||
}
|
||||
else {
|
||||
$location = $response->header('Location');
|
||||
|
||||
# upon successful login, refbase will redirect to 'index.php'
|
||||
if ($location =~ /index.php/) {
|
||||
return 1; # login successful
|
||||
}
|
||||
else {
|
||||
return 0; # login NOT successful
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
# --------------------------------------------------------------------------------
|
||||
|
||||
# Print usage and exit:
|
||||
sub usage
|
||||
{
|
||||
local ($status) = @_;
|
||||
|
||||
print "\nrefbase_import command line client, v" . $version . " by Matthias Steffens, http://cli.refbase.net/\n\n"
|
||||
|
||||
. "Usage: refbase_import [OPTIONS] [FILE]\n\n"
|
||||
|
||||
. "Notes: - Two import modes are supported:\n"
|
||||
. " 1) '--type=data' requires an import FILE to be specified;\n"
|
||||
. " for supported import formats, see: http://import.refbase.net/\n"
|
||||
. " 2) '--type=id' requires the '-p, --pmid' option or one of '--arxiv|--doi|--openurl' with\n"
|
||||
. " one or more whitespace-delimited PubMed IDs, arXiv IDs, DOIs or OpenURLs, respectively.\n"
|
||||
. " - Options syntax: [OPTION]=[VALUE], e.g. '-p=16351846' or '--pmid=\"16351846 16783713\"'.\n"
|
||||
. " - For each option, default values can be specified at the top of the script.\n"
|
||||
. " Current defaults are given in parentheses.\n\n"
|
||||
|
||||
. "General Options: -h, --help - display this help text\n"
|
||||
. " -v, --version - display version information\n"
|
||||
. " -X, --examples - display usage examples\n\n"
|
||||
|
||||
. "Import Options: -b, --skipbad - skip records with unrecognized data format ('" . $params{'skipBadRecords'} . "')\n"
|
||||
. " possible values: 0, 1\n"
|
||||
. " -i, --import - import all or only some records ('" . $params{'importRecordsRadio'} . "')\n"
|
||||
. " possible values: all, only\n"
|
||||
. " -p, --pmid, - IDs of records to import ('" . $params{'sourceIDs'} . "')\n"
|
||||
. " --arxiv, supported IDs: PubMed ID (PMID), arXiv ID, DOI, OpenURL\n"
|
||||
. " --doi, \n"
|
||||
. " --openurl \n"
|
||||
. " -r, --records - positional numbers and/or ranges of records to import ('" . $params{'importRecords'} . "')\n"
|
||||
. " requires the '--import=only' option\n"
|
||||
. " -t, --type - import type ('" . $params{'formType'} . "')\n"
|
||||
. " possible values: data, id\n\n"
|
||||
|
||||
. "Output Options: -C, --style - citation style ('" . $outputParams{'citeStyle'} . "')\n"
|
||||
. " -F, --format - output format ('" . $outputParams{'format'} . "')\n"
|
||||
. " possible values: html, rtf, pdf, latex, latex_bbl, markdown, ascii,\n"
|
||||
. " ads, bibtex, endnote, isi, ris, atom, mods, oai_dc,\n"
|
||||
. " odf, srw_dc, srw_mods, word\n"
|
||||
. " -L, --showlinks - hide/display links column in html output ('" . $outputParams{'showLinks'} . "')\n"
|
||||
. " possible values: 0, 1\n"
|
||||
. " -O, --order - sort order of returned records ('" . $outputParams{'citeOrder'} . "')\n"
|
||||
. " possible values: author, year, type, type-year, creation-date\n"
|
||||
. " -V, --view - view type of html output ('" . $outputParams{'viewType'} . "')\n"
|
||||
. " possible values: web, print, mobile\n\n"
|
||||
|
||||
. "Server Options: -H, --host - URL of the refbase database ('" . $host . "')\n"
|
||||
. " defined shortcuts: " . join(', ', sort keys(%hosts)) . "\n"
|
||||
. " -P, --password - password for given '-U, --user' account";
|
||||
|
||||
if ($loginParams{'loginPassword'} ne '') {
|
||||
print "\n (a default pwd has been defined)\n";
|
||||
}
|
||||
else {
|
||||
print " ('')\n";
|
||||
}
|
||||
|
||||
print " -U, --user - login email address of an existing refbase user with\n"
|
||||
. " import permissions ('" . $loginParams{'loginEmail'} . "')\n\n";
|
||||
|
||||
exit $status;
|
||||
}
|
||||
|
||||
# --------------------------------------------------------------------------------
|
||||
|
||||
# Print version number and exit:
|
||||
sub version
|
||||
{
|
||||
local ($status) = @_;
|
||||
print "\nrefbase_import command line client, version " . $version
|
||||
. "\ncheck for updates at http://cli.refbase.net/\n\n";
|
||||
exit $status;
|
||||
}
|
||||
|
||||
# --------------------------------------------------------------------------------
|
||||
|
||||
# Print examples and exit:
|
||||
sub examples
|
||||
{
|
||||
local ($status) = @_;
|
||||
print <<'END_EXAMPLES';
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
REFBASE_IMPORT USAGE EXAMPLES:
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
1) Import BibTeX records from file 'import.bib' using the defaults defined
|
||||
within the refbase_import script:
|
||||
|
||||
refbase_import import.bib
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
2) Import all Endnote records given in file 'import.enw' into your default
|
||||
refbase database:
|
||||
|
||||
refbase_import -t=data -i=all import.enw
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
3) Take RIS records from file 'import.ris' but import only the first three as
|
||||
well as the fifth and the tenth record into your local refbase database:
|
||||
|
||||
refbase_import -H=local -t=data -i=only -r=1-3,5,10 import.ris
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
4) Import MODS XML records from file 'mods.xml' into the refbase demo database
|
||||
using the defaults defined within the refbase_import script:
|
||||
|
||||
refbase_import -H=http://demo.refbase.net/ -U=user@refbase.net -P=user mods.xml
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
5) Fetch two records from PubMed.gov via their PMID (i.e. the unique PubMed
|
||||
identifier, in this example, records with PMIDs 16351846 and 16783713) and
|
||||
import them into your local refbase database:
|
||||
|
||||
refbase_import -H=local -t=id -p="16351846 16783713"
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
6) Fetch two records from CrossRef.org via their DOI (i.e. the unique Document
|
||||
Object Identifier, in this example, records with DOIs 10.3354/meps251037 and
|
||||
10.1103/PhysRev.47.777) and import them into your local refbase database:
|
||||
|
||||
refbase_import -H=local -t=id --doi="10.3354/meps251037 10.1103/PhysRev.47.777"
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
7) Fetch three records from arXiv.org via their arXiv ID (i.e. the unique arXiv
|
||||
identifier, in this example, records with arXiv IDs astro-ph/0609768, 0806.1829
|
||||
and 0802.0204v1) and import them into your local refbase database:
|
||||
|
||||
refbase_import -H=local -t=id --arxiv="astro-ph/0609768 0806.1829 0802.0204v1"
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
END_EXAMPLES
|
||||
exit $status;
|
||||
}
|
||||
|
||||
__END__
|
||||
42
contrib/endnote/README
Normal file
42
contrib/endnote/README
Normal file
@@ -0,0 +1,42 @@
|
||||
endnote2refbase
|
||||
===============
|
||||
|
||||
Author
|
||||
------
|
||||
Richard Karnesky <karnesky@gmail.com>
|
||||
|
||||
About
|
||||
-----
|
||||
This is an alternative to refbase's web-based import of Endnote data. It
|
||||
allows Endnote users to export a text file which can be imported into the
|
||||
refbase MySQL database.
|
||||
|
||||
Use
|
||||
---
|
||||
Part I: Endnote
|
||||
- Copy refbase.ens into your Endnote styles directory.
|
||||
On win32 systems, this is typically:
|
||||
C:\Program Files\Endnote\Styles
|
||||
On Mac systems, this is typically:
|
||||
Macintosh HD\Applications\EndNote #\Styles
|
||||
(where # corresponds to a version #)
|
||||
- Open the Endnote file you wish to import into refbase.
|
||||
- Choose the refbase Output Style
|
||||
- Export to 'endnote.txt'
|
||||
Part II: PHP [*]
|
||||
- Executing 'php endnote2mysql.php' will produce 'import.txt'
|
||||
('php' must be in your path or you should prefix it with the path to php)
|
||||
Part III: Check it!
|
||||
- As this is a preliminary script that has undergone little testing, it is
|
||||
suggested that you look at 'import.txt' in spreadsheet software.
|
||||
- New versions of Endnote dump UTF-8 data. You should be able to use this as
|
||||
is if you have a UTF-8 database. If you don't have a UTF-8 database, you
|
||||
should convert the file to the character encoding you do use (using iconv,
|
||||
recode, or <http://www.motobit.com/util/charset-codepage-conversion.asp>).
|
||||
Part IV: MySQL [*]
|
||||
- From within your MySQL command line interpreter (mysql -u root literature -p):
|
||||
LOAD DATA LOCAL INFILE "import.txt" INTO TABLE refs;
|
||||
|
||||
[*]If you are comfortable that the script works and are on a system with a POSIX
|
||||
shell (nearly all *nix, including OS X; Windows through Cygwin or similar),
|
||||
you may use Andreas Czerniak's en-importer.sh to automate Parts II-IV.
|
||||
51
contrib/endnote/en-importer.sh
Normal file
51
contrib/endnote/en-importer.sh
Normal file
@@ -0,0 +1,51 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
# EndNote - Importer to RefBase MySQL table
|
||||
#
|
||||
# Andreas Czerniak <ac@oceanlibrary.org>
|
||||
#
|
||||
# initial: 05-11-2005
|
||||
#
|
||||
# modified:
|
||||
# 2005-12-11 ; ac ; clean up static codes
|
||||
# 2005-12-15 ; rk ; remove "v.9", import into CVS
|
||||
# 2006-01-03 ; ac ; replace LOAD DATA INTO statement with mysqlimport - Thx. Matthias Steffens <refbase@extracts.de>
|
||||
#
|
||||
|
||||
if [ $# -lt 1 ]; then
|
||||
echo "Which endnote file ?"
|
||||
echo -e "\nusage: $0 endnote.file [database [mysql-options] ]\n"
|
||||
exit 127
|
||||
fi
|
||||
|
||||
ENFILE=$1
|
||||
|
||||
MYSQLDB=$2 || MYSQLDB="literature" # default: literature
|
||||
MYSQLOPTION=$3 || MYSQLOPTION="-p" # default: with password
|
||||
|
||||
if [ ! -d imported ] ; then
|
||||
mkdir imported
|
||||
fi
|
||||
|
||||
./endnote2mysql.php $1
|
||||
|
||||
if [ ! -f import.txt ] ; then
|
||||
echo "endnote2mysql convert failed !"
|
||||
exit 0
|
||||
fi
|
||||
|
||||
mv import.txt refs.txt
|
||||
mysqlimport --local $MYSQLOPTION $MYSQLDB "refs.txt" > sqloutput.txt
|
||||
|
||||
cat sqloutput.txt
|
||||
|
||||
rm refs.txt
|
||||
rm sqloutput.txt
|
||||
|
||||
cat $ENFILE | tail
|
||||
|
||||
echo "\n\nrows imported: "
|
||||
cat $ENFILE | wc -l
|
||||
|
||||
mv $ENFILE imported/.
|
||||
|
||||
63
contrib/endnote/endnote2mysql.php
Normal file
63
contrib/endnote/endnote2mysql.php
Normal file
@@ -0,0 +1,63 @@
|
||||
<?php
|
||||
// Project: Web Reference Database (refbase) <http://www.refbase.net>
|
||||
// Copyright: Matthias Steffens <mailto:refbase@extracts.de> and the file's
|
||||
// original author.
|
||||
//
|
||||
// This code is distributed in the hope that it will be useful,
|
||||
// but WITHOUT ANY WARRANTY. Please see the GNU General Public
|
||||
// License for more details.
|
||||
//
|
||||
// File: ./contrib/endnote/endnote2mysql.php
|
||||
// Author: Richard Karnesky <mailto:karnesky@northwestern.edu>
|
||||
//
|
||||
// Created: 18-Mar-05, 17:10
|
||||
// Modified: 19-Mar-05, 13:50
|
||||
|
||||
// WARNING
|
||||
// This hasn't been tested extensively & can cause weirdness. Give the data
|
||||
// a once over in a spreadsheet to confirm it looks OK before import!!!
|
||||
|
||||
// This processes the text file produced by using refbase.ens in Endnote:
|
||||
// - Fixes linefeeds, which Endnote can't handle well:
|
||||
// - trims carriage returns
|
||||
// - replaces newlines with '\n'
|
||||
// - trims '<REFBASE>' from the start of each citation
|
||||
// - replaces '</REFBASE>' with a newline character
|
||||
// - Replaces '<REFBASE J/>' with 'Journal' (a Field Name in Endnote)
|
||||
// - Inserts '\N' between multiple tabs (to explicitly NULL empty fields)
|
||||
// - Replaces '<Go to ISI>://*\t' with '\N' (bad URLs in Endnote)
|
||||
|
||||
// TODO:
|
||||
// - Tabs within fields aren't replaced! This can screw things up!
|
||||
// - Allow people to change import & export filenames
|
||||
// - More fields (particularly all dates, first author, number of authors)
|
||||
// - Better parsing of current fields (correct use of 'ed' vs 'eds)
|
||||
// - Automatically import via mysql (intentionally unimplemented for safety)
|
||||
// - Deprecate this whole darn mess by adding native import facilities ;-)
|
||||
|
||||
$fin = file_get_contents('endnote.txt');
|
||||
if (!$fin) {
|
||||
echo "Error! Couldn't open endnote.txt.";
|
||||
}
|
||||
else {
|
||||
$fin = str_replace("\r","",$fin);
|
||||
$fin = str_replace("\n","\\n",$fin);
|
||||
$fin = str_replace("<REFBASE>","",$fin);
|
||||
$fin = str_replace("</REFBASE>\\n","\n",$fin);
|
||||
$fin = str_replace("<REFBASE J/>","Journal",$fin);
|
||||
$fin = preg_replace("/(?<=\t)(?=\t)/","\\N",$fin);
|
||||
$fin = preg_replace("/<Go to ISI>:\/\/\S*/","\\N",$fin);
|
||||
}
|
||||
do {
|
||||
if (!($fout = fopen('import.txt', "w"))) {
|
||||
$rc = 1; break;
|
||||
}
|
||||
if (!fwrite($fout, $fin)) {
|
||||
$rc = 2; break;
|
||||
}
|
||||
$rc = true;
|
||||
} while (0);
|
||||
if ($fout) {
|
||||
fclose($fout);
|
||||
}
|
||||
?>
|
||||
BIN
contrib/endnote/refbase.ens
Normal file
BIN
contrib/endnote/refbase.ens
Normal file
Binary file not shown.
209
contrib/import_templates/import_template_base.php
Normal file
209
contrib/import_templates/import_template_base.php
Normal file
@@ -0,0 +1,209 @@
|
||||
<?php
|
||||
// Project: Web Reference Database (refbase) <http://www.refbase.net>
|
||||
// Copyright: Matthias Steffens <mailto:refbase@extracts.de> and the file's
|
||||
// original author(s).
|
||||
//
|
||||
// This code is distributed in the hope that it will be useful,
|
||||
// but WITHOUT ANY WARRANTY. Please see the GNU General Public
|
||||
// License for more details.
|
||||
//
|
||||
// File: ./import_template_base.php
|
||||
// Repository: $HeadURL: file:///svn/p/refbase/code/branches/bleeding-edge/contrib/import_templates/import_template_base.php $
|
||||
// Author(s): Matthias Steffens <mailto:refbase@extracts.de>
|
||||
//
|
||||
// Created: 11-Jan-06, 18:36
|
||||
// Modified: $Date: 2012-02-27 20:25:30 +0000 (Mon, 27 Feb 2012) $
|
||||
// $Author: msteffens $
|
||||
// $Revision: 1337 $
|
||||
|
||||
// Template for a batch import script.
|
||||
// Use this script to develop your own batch importer.
|
||||
// See the scripts 'import.php' and 'import_modify.php' for a working example.
|
||||
|
||||
|
||||
// Incorporate some include files:
|
||||
include 'initialize/db.inc.php'; // 'db.inc.php' is included to hide username and password
|
||||
include 'includes/include.inc.php'; // include common functions
|
||||
include 'initialize/ini.inc.php'; // include common variables
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// START A SESSION:
|
||||
// call the 'start_session()' function (from 'include.inc.php') which will also read out available session variables:
|
||||
start_session(true);
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Initialize preferred display language:
|
||||
// (note that 'locales.inc.php' has to be included *after* the call to the 'start_session()' function)
|
||||
include 'includes/locales.inc.php'; // include the locales
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Get the referring page (or set a default one if no referrer is available):
|
||||
if (!empty($_SERVER['HTTP_REFERER'])) // if the referrer variable isn't empty
|
||||
$referer = $_SERVER['HTTP_REFERER']; // on error, redirect to calling page
|
||||
else
|
||||
$referer = "import.php"; // on error, redirect to the web import form (if you've got your own import form, insert it's script name here)
|
||||
|
||||
// First of all, check if the user is logged in:
|
||||
if (!isset($_SESSION['loginEmail'])) // -> if the user isn't logged in
|
||||
{
|
||||
header("Location: user_login.php?referer=" . rawurlencode($referer)); // ask the user to login first, then he'll get directed back to the calling page
|
||||
|
||||
exit; // >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !EXIT! <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
|
||||
}
|
||||
|
||||
// now, check if the (logged in) user is allowed to import any record into the database:
|
||||
if (isset($_SESSION['user_permissions']) AND !preg_match("/allow_import|allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable does NOT contain either 'allow_import' or 'allow_batch_import'...
|
||||
{
|
||||
// return an appropriate error message:
|
||||
$HeaderString = returnMsg($loc["NoPermission"] . $loc["NoPermission_ForImport"] . "!", "warning", "strong", "HeaderString"); // function 'returnMsg()' is defined in 'include.inc.php'
|
||||
|
||||
header("Location: index.php"); // redirect back to main page ('index.php')
|
||||
|
||||
exit; // >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !EXIT! <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// PROCESS SOURCE DATA:
|
||||
|
||||
$parsedRecordsArray = array(); // initialize array variable which will hold parsed data of all records that shall be imported
|
||||
|
||||
// >>> insert your own code here that parses your source data into an array of arrays holding the extracted field data <<<
|
||||
|
||||
// ToDo:
|
||||
// (1) Obtain your source data via a web form, file upload, direct read-in of a local source file, etc
|
||||
// If your script allows input from the web, make sure to validate your data, see 'import.php' & 'import_modify.php' for an example
|
||||
// (2) Split your source data into individual bits representing individual records
|
||||
// (3) Loop over each record and extract the record's field data into an array;
|
||||
// For each record you should end up with an array structure similar to the one below ('$recordFieldParametersArray'):
|
||||
|
||||
// NOTES: - you can safely omit unneeded fields from your data array; for any fields that aren't present in the data array, the database will insert its default values
|
||||
// - the 'addRecords()' function will take care of the calculation fields ('first_author', 'author_count', 'first_page', 'volume_numeric' and 'series_volume_numeric')
|
||||
// - similarly, the *date/*time/*by fields ('created_date', 'created_time', 'created_by', 'modified_date', 'modified_time', 'modified_by') will be filled automatically
|
||||
// if no custom values (in correct date ['YYYY-MM-DD'] and time ['HH:MM:SS'] format) are given in your array
|
||||
// - you can pass any custom info for the 'location' field in your array; however, if you omit the 'location' field from the array
|
||||
// the 'addRecords()' function will insert name & email address of the currently logged-in user (e.g. 'Matthias Steffens (refbase@extracts.de)')
|
||||
// - the serial number(s) will be assigned automatically (and returned by the 'addRecords()' function in form of an array)
|
||||
// - this import example will only add to the main MySQL table ('refs'), but not to the 'user_data' table
|
||||
|
||||
// Example record data array. Commented fields will be filled automatically if not present (see notes above).
|
||||
// Comments behind field spec give the resulting calculation field values for this example:
|
||||
$recordFieldParametersArray = array(
|
||||
'author' => "FirstAuthor, Initials; SecondAuthor, Initials", // 'first_author' = "FirstAuthor, Initials"; 'author_count' = "2"
|
||||
'address' => "Address",
|
||||
'corporate_author' => "Corporate Author",
|
||||
'title' => "Title",
|
||||
'orig_title' => "Orig Title",
|
||||
'publication' => "Publication",
|
||||
'abbrev_journal' => "Abbrev Journal",
|
||||
'year' => "2005",
|
||||
'volume' => "2nd Volume", // 'volume_numeric' = "2"
|
||||
'issue' => "Issue",
|
||||
'pages' => "5 Pages", // 'first_page' = "5"
|
||||
'keywords' => "Keywords",
|
||||
'abstract' => "Abstract",
|
||||
'edition' => "2",
|
||||
'editor' => "Editor",
|
||||
'publisher' => "Publisher",
|
||||
'place' => "Place",
|
||||
'medium' => "Medium",
|
||||
'series_editor' => "Series Editor",
|
||||
'series_title' => "Series Title",
|
||||
'abbrev_series_title' => "Abbrev Series Title",
|
||||
'series_volume' => "3rd Series Volume", // 'series_volume_numeric' = "3"
|
||||
'series_issue' => "Series Issue",
|
||||
'issn' => "ISSN",
|
||||
'isbn' => "ISBN",
|
||||
'language' => "Language",
|
||||
'summary_language' => "Summary Language",
|
||||
'area' => "Area",
|
||||
'type' => "Type",
|
||||
'thesis' => "Diploma thesis",
|
||||
'expedition' => "Expedition",
|
||||
'doi' => "DOI",
|
||||
'conference' => "Conference",
|
||||
'url' => "URL",
|
||||
'call_number' => "Call Number",
|
||||
// 'location' => "Location",
|
||||
'contribution_id' => "Contribution Id",
|
||||
'online_publication' => "no",
|
||||
'online_citation' => "Online Citation",
|
||||
'file' => "File",
|
||||
'notes' => "Notes",
|
||||
'approved' => "no",
|
||||
// 'created_date' => "1999-11-30",
|
||||
// 'created_time' => "00:00:01",
|
||||
// 'created_by' => "Created By",
|
||||
// 'modified_date' => "1999-11-31",
|
||||
// 'modified_time' => "00:00:02",
|
||||
// 'modified_by' => "Modified By",
|
||||
'orig_record' => "-123"
|
||||
);
|
||||
|
||||
// (4) Append the array of extracted field data to the main data array which holds all records to import:
|
||||
$parsedRecordsArray[] = $recordFieldParametersArray; // in this example, we simply import a single record, adopt to your needs
|
||||
|
||||
$recordsCount = count($parsedRecordsArray); // count how many records are available
|
||||
|
||||
// check if the current user has batch import permission:
|
||||
if (($recordsCount > 1) AND isset($_SESSION['user_permissions']) AND !preg_match("/allow_batch_import/", $_SESSION['user_permissions'])) // if we're supposed to import several records BUT the 'user_permissions' session variable does NOT contain 'allow_batch_import'...
|
||||
{
|
||||
// return an appropriate error message:
|
||||
// (note that this error message will overwrite any '$headerMessage' that gets specified below)
|
||||
$HeaderString = returnMsg($loc["NoPermission"] . $loc["NoPermission_ForBatchImport"] . "!", "warning", "strong", "HeaderString", "", " " . $loc["Warning_OnlyFirstRecordImported"]) . ":"; // function 'returnMsg()' is defined in 'include.inc.php'
|
||||
|
||||
array_splice($parsedRecordsArray, 1); // remove all but the first record from the array of records that shall be imported
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// IMPORT RECORDS:
|
||||
|
||||
// Build an array structure suitable for passing to the 'addRecords()' function:
|
||||
$importDataArray = array(); // for an explanation of the structure of '$importDataArray', see the comments above the 'addRecords()' function (in 'include.inc.php')
|
||||
$importDataArray['type'] = "refbase"; // we use the "refbase" array format
|
||||
$importDataArray['version'] = "1.0"; // we use version "1.0" of the array structure
|
||||
$importDataArray['creator'] = "http://refbase.net"; // calling script/importer is "refbase" (insert the unique name of your importer here or give the web address of it's home page)
|
||||
$importDataArray['author'] = "Matthias Steffens"; // author/contact name of the person who's responsible for this script/importer (insert your own name here)
|
||||
$importDataArray['contact'] = "refbase@extracts.de"; // author's email/contact address (insert your email address here)
|
||||
$importDataArray['options'] = array('prefix_call_number' => "true"); // if "true", any 'call_number' string will be prefixed with the correct call number prefix of the currently logged-in user (e.g. 'IP<49> @ msteffens @ ')
|
||||
$importDataArray['records'] = $parsedRecordsArray; // this array will hold the record(s) (with each record being a sub-array of fields)
|
||||
|
||||
// Add all records to the database (i.e., for each record, add a row entry to MySQL table 'refs'):
|
||||
// ('$importedRecordsArray' will hold the serial numbers of all newly imported records)
|
||||
$importedRecordsArray = addRecords($importDataArray); // function 'addRecords()' is defined in 'include.inc.php'
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// DISPLAY RESULTS:
|
||||
|
||||
if (!empty($importedRecordsArray)) // if some records were successfully imported
|
||||
{
|
||||
$recordSerialsQueryString = "^(" . implode("|", $importedRecordsArray) . ")$";
|
||||
|
||||
$importedRecordsCount = count($importedRecordsArray);
|
||||
|
||||
if ($importedRecordsCount == 1)
|
||||
$headerMessage = $importedRecordsCount . " " . $loc["RecordSuccessfullyImported"] . ":";
|
||||
else // $importedRecordsCount > 1
|
||||
$headerMessage = $importedRecordsCount . " " . $loc["RecordsSuccessfullyImported"] . ":";
|
||||
|
||||
// display all newly added records:
|
||||
header("Location: show.php?serial=" . rawurlencode($recordSerialsQueryString) . "&headerMsg=" . rawurlencode($headerMessage));
|
||||
}
|
||||
else // nothing imported
|
||||
{
|
||||
// return an appropriate error message:
|
||||
$HeaderString = returnMsg($loc["NoRecordsImported"] . "!", "warning", "strong", "HeaderString"); // function 'returnMsg()' is defined in 'include.inc.php'
|
||||
|
||||
if (!empty($_SERVER['HTTP_REFERER'])) // if the referer variable isn't empty
|
||||
header("Location: " . $_SERVER['HTTP_REFERER']); // redirect to calling page
|
||||
else
|
||||
header("Location: index.php"); // redirect to main page ('index.php')
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
?>
|
||||
156
contrib/mediawiki/README
Normal file
156
contrib/mediawiki/README
Normal file
@@ -0,0 +1,156 @@
|
||||
refbase extension for MediaWiki
|
||||
===============================
|
||||
|
||||
Authors
|
||||
-------
|
||||
Richard Karnesky <karnesky@gmail.com>
|
||||
Thibault Marin <thibault.marin at gmx dot com>
|
||||
|
||||
About
|
||||
-----
|
||||
This is an extension to MediaWiki:
|
||||
<https://www.mediawiki.org/>
|
||||
It allows you to cite references by enclosing the serial or the citation key
|
||||
in tags such as:
|
||||
<refbase>17</refbase> or <refbase>Author2000</refbase>
|
||||
|
||||
To install the extension, download and extract the files in a directory called
|
||||
Refbase in your mediawiki extensions/ folder. Add the following code at the
|
||||
bottom of your LocalSettings.php:
|
||||
require_once( "$IP/extensions/Refbase/Refbase.php" );
|
||||
To verify that the extension is successfully installed, go to the
|
||||
"Special:Version" page on your wiki, you should see the Refbase extension in
|
||||
the list of parser hook extensions.
|
||||
|
||||
To configure the extension, add the following lines (modified to match your
|
||||
setup) after the 'require_once' line in your LocalSettings.php (omitted fields
|
||||
take the default value indicated here):
|
||||
$wgRefbaseDbHost = "localhost"; // refbase database host
|
||||
$wgRefbaseDbName = "literature"; // Database name
|
||||
$wgRefbaseDbUser = "litwww"; // User name for database
|
||||
$wgRefbaseDbPass = "%l1t3ratur3?"; // Database password
|
||||
$wgRefbaseDbCharset = "utf8"; // Database charset
|
||||
$wgRefbaseDbRefTable = "refs"; // Table with references
|
||||
$wgRefbaseDbUserDataTable = "user_data"; // Table with cite_key field
|
||||
$wgRefbaseDbAccessMethod = "mysql"; // Database access mode
|
||||
// 'mysql' or 'PDO'
|
||||
// Host for refbase instance (used for url links). This may differ from the
|
||||
// database host (requires a trailing slash)
|
||||
$wgRefbaseURL = "http://".$_SERVER['HTTP_HOST']."/refbase/";
|
||||
// HTTP (basic) authentication mode when accessing refbase instance (only
|
||||
// used with 'cite' and 'link' output types, when using a 'rb-*' citation
|
||||
// type), see below for details.
|
||||
$wgRefbaseURLAuth = ''; // '', 'default' or 'user:pass'
|
||||
A few options can also be set (see below for description):
|
||||
// Tag type
|
||||
$wgRefbaseDefaultTagType = 'serial'; // 'serial' or 'citekey'
|
||||
// Output type
|
||||
$wgRefbaseDefaultOutputType = 'cite_journal'; // 'cite_journal', 'cite'
|
||||
// or 'link'
|
||||
// Citation type
|
||||
$wgRefbaseDefaultCitationType = 'minimal'; // 'minimal' or 'rb-*'
|
||||
|
||||
Options
|
||||
-------
|
||||
0. Scope
|
||||
All options are set globally (by the $wgRefbaseDefault* variables) for the
|
||||
whole wiki. Most can also be modified for individual instances of the
|
||||
<refbase> tag by passing extra arguments to the tag, e.g. <refbase
|
||||
tagtype='citekey' output='cite'>XXX</refbase>.
|
||||
|
||||
1. Tag type
|
||||
Possible values: 'serial', 'citekey'
|
||||
Global setting
|
||||
$wgRefbaseDefaultTagType = 'serial';
|
||||
Individual setting
|
||||
<refbase tagtype='serial'>XXX</refbase>
|
||||
This option controls the interpretation of the tag input: when using the
|
||||
refbase tag in wikipages, e.g. <refbase>XXX</refbase>, the input key (XXX)
|
||||
can refer to the serial number ('serial' type) or the citation key
|
||||
('citekey' type). Note that if no entry is found using the selected tag
|
||||
type, a second search is performed with the other tag type.
|
||||
|
||||
2. Output type
|
||||
Possible values: 'cite_journal', 'cite', 'link'
|
||||
Global setting
|
||||
$wgRefbaseDefaultOutputType = 'cite_journal';
|
||||
Individual setting
|
||||
<refbase output='cite_journal'>XXX</refbase>
|
||||
This option determines the way citations are rendered in the wikipage. There
|
||||
are several modes:
|
||||
.'cite_journal': This is the default mode, used in version 0.9 of the
|
||||
extension. The output will use citation templates, as are used on
|
||||
Wikipedia:
|
||||
<https://en.wikipedia.org/wiki/Wikipedia:Citation_templates>
|
||||
Currently, only journal articles may be cited with this output type. In
|
||||
the future, this extension is likely to be modified. 'refbase' should
|
||||
be able to generate WP citation templates as an export format & this
|
||||
extension should make use of that functionality directly.
|
||||
.'cite': This mode uses the Cite extension
|
||||
<https://www.mediawiki.org/wiki/Extension:Cite>
|
||||
A footnote is generated for each citation using the <ref> tag. Multiple
|
||||
references to the same entry are automatically combined using the <ref
|
||||
name=YYY> option. To see the list of references a <references/> tag
|
||||
must be added to the wikipage where the bibliography should be
|
||||
displayed. See the Cite extension documentation for details. The
|
||||
footnote text is a citation following the 'citation type' option (see
|
||||
below).
|
||||
.'link': This is a simple renderer which does not require any installed
|
||||
template/extension. It simply writes the tag input (serial or citation
|
||||
key) to the wikipage, adding a tooltip and a hyperlink to the refbase
|
||||
entry. The tooltip contains the citation text (controlled by the
|
||||
citation type variable) and the hyperlink links to the refbase page (the
|
||||
base refbase installation location is given by the $wgRefbaseURL
|
||||
variable).
|
||||
|
||||
3. Citation type
|
||||
Possible values: 'minimal, 'rb-default', 'rb-MLA', 'rb-APA', etc.
|
||||
Global setting
|
||||
$wgRefbaseDefaultCitationType = 'minimal';
|
||||
Individual setting
|
||||
<refbase citationtype='minimal'>XXX</refbase>
|
||||
This option determines how citations are rendered in the 'cite' and 'link'
|
||||
output modes (it has no effect when using the 'cite_journal' output type).
|
||||
The two possible modes are:
|
||||
.'minimal': This generates a simple citation with the authors, title,
|
||||
publication and year.
|
||||
.'rb-*': This requests the citation text from the refbase web interface.
|
||||
The * in 'rb-*' can be 'default' (i.e. 'rb-default') or any acceptable
|
||||
citation style (defined in the 'styles' database).
|
||||
|
||||
4. Database connection mode
|
||||
Possible values: 'mysql', 'PDO'
|
||||
Global setting
|
||||
$wgRefbaseDbAccessMethod = 'mysql';
|
||||
Individual setting
|
||||
This option can only be set at the global level.
|
||||
This option selects the way the extension connects to the mysql database.
|
||||
The 'mysql' mode is getting deprecated in recent versions of php, but is
|
||||
still available for older installations.
|
||||
|
||||
5. HTTP authentication for requests to refbase instance
|
||||
Possible values: '', 'default' or 'user:pass'
|
||||
Global setting
|
||||
$wgRefbaseURLAuth = '';
|
||||
Individual setting
|
||||
This option can only be set at the global level.
|
||||
This option is used to pass an HTTP authentication token to the server
|
||||
hosting the refbase installation (basic authentication e.g. from apache
|
||||
server). If $wgRefbaseURLAuth is empty (''), no authentication is passed.
|
||||
If set to 'default', the current user/password token will be passed when
|
||||
requesting data from the refbase web interface (this is useful when both
|
||||
mediawiki and refbase are under the same basic server authentication). To
|
||||
specify an arbitrary user and password, set $wgRefbaseURLAuth to 'user:pass'
|
||||
where 'user' is the username and 'pass' the password for that user (note
|
||||
that the username cannot contain colon characters ':'). This option is
|
||||
relevant only when using the 'cite' or 'link' output types along with one of
|
||||
the 'rb-*' citation type.
|
||||
|
||||
Notes
|
||||
-----
|
||||
You may also be interested in the MonoBook skin, included in the
|
||||
'contrib/skins/mediawiki-monobook' directory from refbase.
|
||||
An installation of MediaWiki that uses this extension is the Northwestern
|
||||
University Center for Atom-Probe Tomography:
|
||||
<http://arc.nucapt.northwestern.edu/#Literature>
|
||||
|
||||
113
contrib/mediawiki/Refbase.Hooks.php
Normal file
113
contrib/mediawiki/Refbase.Hooks.php
Normal file
@@ -0,0 +1,113 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase hooks and parser
|
||||
*/
|
||||
class RefbaseHooks {
|
||||
|
||||
/**
|
||||
* Register <refbase> hook
|
||||
*/
|
||||
public static function efRefbaseParserInit( $parser ) {
|
||||
$parser->setHook( 'refbase',
|
||||
'RefbaseHooks::efRefbaseRender' );
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Define special formatting for this tag
|
||||
*/
|
||||
private static function makeOutputString ( $str ) {
|
||||
return $str;
|
||||
}
|
||||
|
||||
/**
|
||||
* Add <pre></pre> tags around error message and return
|
||||
*/
|
||||
private static function makeErrorOutputString ( $errMsg ) {
|
||||
$errMsg = "Refbase: <br/>" . $errMsg;
|
||||
$preMsg = Html::openElement( 'pre' ) . $errMsg .
|
||||
Html::closeElement( 'pre' );
|
||||
return self::makeOutputString( $preMsg );
|
||||
}
|
||||
|
||||
/**
|
||||
* Main function: parse input and create HTML table with events
|
||||
*/
|
||||
public static function efRefbaseRender( $input, array $args,
|
||||
Parser $parser,
|
||||
PPFrame $frame ) {
|
||||
// Global parameters
|
||||
global $wgRefbaseDefaultTagType;
|
||||
global $wgRefbaseDefaultOutputType;
|
||||
global $wgRefbaseDefaultCitationType;
|
||||
|
||||
// Read arguments
|
||||
if ( isset( $args['tagtype'] ) ) {
|
||||
$tagType = $args['tagtype'];
|
||||
} else {
|
||||
$tagType = $wgRefbaseDefaultTagType;
|
||||
}
|
||||
if ( ! ( strtolower( $tagType ) === 'serial' ) &&
|
||||
! ( strtolower( $tagType ) === 'citekey' ) ) {
|
||||
$errStr = wfMessage( 'refbase-error-tagtype' )->text();
|
||||
return self::makeErrorOutputString( $errStr );
|
||||
}
|
||||
if ( isset( $args['output'] ) ) {
|
||||
$outputType = $args['output'];
|
||||
} else {
|
||||
$outputType = $wgRefbaseDefaultOutputType;
|
||||
}
|
||||
if ( ! ( strtolower( $outputType ) === 'cite_journal' ) &&
|
||||
! ( strtolower( $outputType ) === 'link' ) &&
|
||||
! ( strtolower( $outputType ) === 'cite' ) ) {
|
||||
$errStr = wfMessage( 'refbase-error-outputtype' )->text();
|
||||
return self::makeErrorOutputString( $errStr );
|
||||
}
|
||||
if ( isset( $args['citationtype'] ) ) {
|
||||
$citationType = $args['citationtype'];
|
||||
} else {
|
||||
$citationType = $wgRefbaseDefaultCitationType;
|
||||
}
|
||||
if ( ! ( strtolower( $citationType ) === 'minimal' ) &&
|
||||
! ( strtolower( substr( $citationType, 0, 3 ) ) === 'rb-' ) ) {
|
||||
$errStr = wfMessage( 'refbase-error-citation-type' )->text();
|
||||
return self::makeErrorOutputString( $errStr );
|
||||
}
|
||||
|
||||
// Order tag types
|
||||
switch ( strtolower( $tagType ) ) {
|
||||
case 'serial':
|
||||
$tagTypeList = array( 'serial', 'citekey' );
|
||||
break;
|
||||
case 'citekey':
|
||||
$tagTypeList = array( 'citekey', 'serial' );
|
||||
break;
|
||||
}
|
||||
|
||||
// Instantiate renderer based on options
|
||||
$refbaseRenderer = RefbaseRenderer::create( $outputType,
|
||||
$citationType );
|
||||
// Request list of fields to extract
|
||||
$fieldList = $refbaseRenderer->getFieldList();
|
||||
|
||||
// Perform database query to get entry
|
||||
$refbaseDbConnector = new RefbaseConnector();
|
||||
$entry = "";
|
||||
if ( !$refbaseDbConnector->getEntry( $input, $tagTypeList, $entry,
|
||||
$fieldList ) ) {
|
||||
return self::makeErrorOutputString( $entry );
|
||||
}
|
||||
|
||||
// Generate output
|
||||
$citekey = $input;
|
||||
$renderOpts = array( 'citekey' => $citekey );
|
||||
$outputStr = "";
|
||||
if ( !$refbaseRenderer->render( $entry, $outputStr, $renderOpts ) ) {
|
||||
return self::makeErrorOutputString( $outputStr );
|
||||
}
|
||||
|
||||
$outputStr = $parser->recursiveTagParse( $outputStr );
|
||||
return self::makeOutputString( $outputStr );
|
||||
}
|
||||
}
|
||||
35
contrib/mediawiki/Refbase.i18n.php
Normal file
35
contrib/mediawiki/Refbase.i18n.php
Normal file
@@ -0,0 +1,35 @@
|
||||
<?php
|
||||
/**
|
||||
* This is a backwards-compatibility shim, generated by:
|
||||
* https://git.wikimedia.org/blob/mediawiki%2Fcore.git/HEAD/maintenance%2FgenerateJsonI18n.php
|
||||
*
|
||||
* Beginning with MediaWiki 1.23, translation strings are stored in json files,
|
||||
* and the EXTENSION.i18n.php file only exists to provide compatibility with
|
||||
* older releases of MediaWiki. For more information about this migration, see:
|
||||
* https://www.mediawiki.org/wiki/Requests_for_comment/Localisation_format
|
||||
*
|
||||
* This shim maintains compatibility back to MediaWiki 1.17.
|
||||
*/
|
||||
$messages = array();
|
||||
if ( !function_exists( 'wfJsonI18nShime97052c48294abb71' ) ) {
|
||||
function wfJsonI18nShime97052c48294abb71( $cache, $code, &$cachedData ) {
|
||||
$codeSequence = array_merge( array( $code ), $cachedData['fallbackSequence'] );
|
||||
foreach ( $codeSequence as $csCode ) {
|
||||
$fileName = dirname( __FILE__ ) . "/i18n/$csCode.json";
|
||||
if ( is_readable( $fileName ) ) {
|
||||
$data = FormatJson::decode( file_get_contents( $fileName ), true );
|
||||
foreach ( array_keys( $data ) as $key ) {
|
||||
if ( $key === '' || $key[0] === '@' ) {
|
||||
unset( $data[$key] );
|
||||
}
|
||||
}
|
||||
$cachedData['messages'] = array_merge( $data, $cachedData['messages'] );
|
||||
}
|
||||
|
||||
$cachedData['deps'][] = new FileDependency( $fileName );
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
$GLOBALS['wgHooks']['LocalisationCacheRecache'][] = 'wfJsonI18nShime97052c48294abb71';
|
||||
}
|
||||
105
contrib/mediawiki/Refbase.php
Normal file
105
contrib/mediawiki/Refbase.php
Normal file
@@ -0,0 +1,105 @@
|
||||
<?php
|
||||
// Copyright: Richard Karnesky <mailto:karnesky@gmail.com>
|
||||
// This code is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
|
||||
// Please see the GNU General Public License for more details.
|
||||
|
||||
|
||||
if( !defined( 'MEDIAWIKI' ) )
|
||||
{
|
||||
echo( "This is an extension to the MediaWiki package and cannot be run standalone.\n" );
|
||||
die( -1 );
|
||||
}
|
||||
|
||||
$wgExtensionCredits['parserhook'][] = array(
|
||||
'path' => __FILE__,
|
||||
'name' => 'Refbase',
|
||||
'author' => array( 'Richard Karnesky', 'Thibault Marin' ),
|
||||
'url' => 'https://www.mediawiki.org/wiki/Extension:Refbase',
|
||||
'descriptionmsg' => 'refbase-desc',
|
||||
'version' => '1.0',
|
||||
'license-name' => '' // Short name of the license, links LICENSE or COPYING file if existing - string, added in 1.23.0
|
||||
);
|
||||
|
||||
/**
|
||||
* Extension class
|
||||
*/
|
||||
$wgAutoloadClasses['RefbaseHooks'] =
|
||||
dirname( __FILE__ ) . '/Refbase.Hooks.php';
|
||||
$wgAutoloadClasses['RefbaseRenderer'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.Renderer.php';
|
||||
$wgAutoloadClasses['RefbaseRendererCitationTemplate'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.Renderer.CitationTemplate.php';
|
||||
$wgAutoloadClasses['RefbaseRendererLink'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.Renderer.Link.php';
|
||||
$wgAutoloadClasses['RefbaseRendererCite'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.Renderer.Cite.php';
|
||||
$wgAutoloadClasses['RefbaseConnector'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.Connector.php';
|
||||
$wgAutoloadClasses['RefbaseCitationCreator'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.CitationCreator.php';
|
||||
$wgAutoloadClasses['RefbaseCitationType'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.CitationCreator.php';
|
||||
$wgAutoloadClasses['RefbaseTools'] =
|
||||
dirname( __FILE__ ) . '/include/Refbase.Tools.php';
|
||||
|
||||
/**
|
||||
* Register hooks
|
||||
*/
|
||||
$wgHooks['ParserFirstCallInit'][] = 'RefbaseHooks::efRefbaseParserInit';
|
||||
|
||||
/**
|
||||
* Internationalization
|
||||
*/
|
||||
$wgMessagesDirs['Refbase'] = __DIR__ . '/i18n';
|
||||
$wgExtensionMessagesFiles['Refbase'] =
|
||||
dirname( __FILE__ ) . '/Refbase.i18n.php';
|
||||
|
||||
/**
|
||||
* Parameters (modify in LocalSettings.php)
|
||||
*/
|
||||
|
||||
// refbase database host
|
||||
$wgRefbaseDbHost = "localhost";
|
||||
|
||||
// Database name
|
||||
$wgRefbaseDbName = "literature";
|
||||
|
||||
// User name for database
|
||||
$wgRefbaseDbUser = "litwww";
|
||||
|
||||
// Database password
|
||||
$wgRefbaseDbPass = "%l1t3ratur3?";
|
||||
|
||||
// Database charset
|
||||
$wgRefbaseDbCharset = "utf8";
|
||||
|
||||
// Table with references
|
||||
$wgRefbaseDbRefTable = "refs";
|
||||
|
||||
// Table with user data (cite key)
|
||||
$wgRefbaseDbUserDataTable = "user_data";
|
||||
|
||||
// Extension to interface with database ('mysql' or 'PDO')
|
||||
$wgRefbaseDbAccessMethod = "mysql";
|
||||
|
||||
// Host for refbase instance (used for url links). This may differ from the
|
||||
// database host if using https for instance (requires a trailing slash)
|
||||
$wgRefbaseURL = "http://".$_SERVER['HTTP_HOST']."/refbase/";
|
||||
|
||||
// Default tag input: when using <refbase>XXX</refbase>, XXX can refer to the
|
||||
// serial number ('serial' type) or the citation key ('citekey' type)
|
||||
$wgRefbaseDefaultTagType = "serial";
|
||||
|
||||
// Default output type: may use cite_journal, cite or link
|
||||
$wgRefbaseDefaultOutputType = 'cite_journal';
|
||||
// Default citation type: 'minimal' or 'rb-default' (only for 'link' and 'cite' modes)
|
||||
//$wgRefbaseDefaultCitationType = 'minimal';
|
||||
$wgRefbaseDefaultCitationType = 'rb-default';
|
||||
|
||||
// Option to pass http authentication token when accessing the refbase web
|
||||
// interface (used for rb-* citation types). If empty, authentication is
|
||||
// disabled. If set to 'default', use the same token as the one used for the
|
||||
// mediawiki web site (if any). If this option is set to 'user:pass', then
|
||||
// 'user' and 'pass' will be used to form the token (the colon character ':' is
|
||||
// not allowed in the username).
|
||||
$wgRefbaseURLAuth = '';
|
||||
16
contrib/mediawiki/i18n/en.json
Normal file
16
contrib/mediawiki/i18n/en.json
Normal file
@@ -0,0 +1,16 @@
|
||||
{
|
||||
"@metadata": {
|
||||
"authors": [
|
||||
"thibault marin"
|
||||
]
|
||||
},
|
||||
"refbase-desc": "This extension allows inclusion of bibliographic references from a refbase installation.",
|
||||
"refbase-error-tagtype" : "Unsupported tag type (should be 'serial' or 'citekey').",
|
||||
"refbase-error-outputtype" : "Unsupported output type (should be 'cite_journal', 'cite' or 'link').",
|
||||
"refbase-error-dbquery" : "Error in database query: ",
|
||||
"refbase-error-mysqlconn" : "Could not connect to mysql database.",
|
||||
"refbase-error-mysqldb" : "Could not select mysql database: ",
|
||||
"refbase-error-notfound" : "Entry not found.",
|
||||
"refbase-error-cite_journal-type": "cite_journal mode can only display journal articles.",
|
||||
"refbase-error-citation-type" : "Citation type unsupported (should be 'minimal' or 'rb-???')."
|
||||
}
|
||||
16
contrib/mediawiki/i18n/qqq.json
Normal file
16
contrib/mediawiki/i18n/qqq.json
Normal file
@@ -0,0 +1,16 @@
|
||||
{
|
||||
"@metadata": {
|
||||
"authors": [
|
||||
"thibault marin"
|
||||
]
|
||||
},
|
||||
"refbase-desc": "{{desc}}",
|
||||
"refbase-error-tagtype" : "Error message displayed when the tag type used is not supported.",
|
||||
"refbase-error-outputttype" : "Error message displayed when the output type used is not supported.",
|
||||
"refbase-error-dbquery" : "Error message displayed when refbase database query failed (followed by error message).",
|
||||
"refbase-error-mysqlconn" : "Error message displayed when mysql connection failed (using the mysql extension).",
|
||||
"refbase-error-mysqldb" : "Error message displayed when mysql database selection failed (using the mysql extension), error message follows",
|
||||
"refbase-error-notfound" : "Error message displayed when key was not gound in database",
|
||||
"refbase-error-cite_journal-type": "Error message displayed when cite_journal is used with non-journal entry.",
|
||||
"refbase-error-citation-type" : "Error message displayed when trying to create a citation of an unsupported type."
|
||||
}
|
||||
144
contrib/mediawiki/include/Refbase.CitationCreator.php
Normal file
144
contrib/mediawiki/include/Refbase.CitationCreator.php
Normal file
@@ -0,0 +1,144 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Enum for citation types
|
||||
*/
|
||||
abstract class RefbaseCitationType {
|
||||
|
||||
// Minimal reference type (author, title, publication, year)
|
||||
const CT_MINIMAL = 0;
|
||||
|
||||
// Request citation from refbase installation (using show.php interface)
|
||||
const CT_RB = 1;
|
||||
|
||||
/**
|
||||
* Convert string to RefbaseCitationType
|
||||
*/
|
||||
static public function decodeCitationType ( $str, & $citeStyle ) {
|
||||
if ( strtolower( $str ) == 'minimal' ) {
|
||||
return self::CT_MINIMAL;
|
||||
} elseif ( preg_match( '/rb-(.*)/', strtolower( $str ),
|
||||
$citeStyle ) ) {
|
||||
return self::CT_RB;
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Helper class to generate citation text
|
||||
*/
|
||||
class RefbaseCitationCreator {
|
||||
|
||||
/// Citation type
|
||||
private $citationType;
|
||||
|
||||
/// Citation style (only with $citationType = CT_RB)
|
||||
private $citationStyle = "";
|
||||
|
||||
/// Location of refbase installation (may differ from $dbHost if using https
|
||||
/// for instance)
|
||||
protected $refbaseURL = "";
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
public function __construct( $citationTypeStr ) {
|
||||
global $wgRefbaseURL;
|
||||
$this->refbaseURL = $wgRefbaseURL;
|
||||
$this->citationType =
|
||||
RefbaseCitationType::decodeCitationType( $citationTypeStr,
|
||||
$citeStyle );
|
||||
if ( !empty( $citeStyle ) ) {
|
||||
$this->citationStyle = $citeStyle[1];
|
||||
}
|
||||
wfDebug('refbase-decode-in:' . $citationTypeStr . "\n");
|
||||
wfDebug('refbase-decode:' . $this->citationType . ", " . var_export($this->citationStyle,true)."\n");
|
||||
}
|
||||
|
||||
/**
|
||||
* Create citation text
|
||||
*/
|
||||
public function createCitation( $entry, & $cite ) {
|
||||
|
||||
switch( $this->citationType ) {
|
||||
|
||||
case RefbaseCitationType::CT_MINIMAL:
|
||||
$cite = $entry['author'] . ", " . $entry['title'] . ", " .
|
||||
$entry['publication'] . ", " . $entry['year'] . ".";
|
||||
break;
|
||||
|
||||
case RefbaseCitationType::CT_RB:
|
||||
$url = $this->refbaseURL . "show.php?" .
|
||||
"record=" . "27711"//$entry['serial'] .
|
||||
"&submit=Cite&exportType=text&citeType=ASCII";
|
||||
if ( !empty( $this->citationStyle ) ) {
|
||||
$url .= "&citeStyle=" . $this->citationStyle;
|
||||
}
|
||||
wfDebug('refbase-getcite:' . $url . "\n");
|
||||
|
||||
// Get citation from url (add http authentication if desired)
|
||||
global $wgRefbaseURLAuth;
|
||||
|
||||
if ( !empty( $wgRefbaseURLAuth ) ) {
|
||||
if ( strcmp( strtolower( $wgRefbaseURLAuth ),
|
||||
'default' ) == 0 ) {
|
||||
if ( isset( $_SERVER['PHP_AUTH_USER'] ) &&
|
||||
isset( $_SERVER['PHP_AUTH_PW'] ) ) {
|
||||
$username = $_SERVER['PHP_AUTH_USER'];
|
||||
$password = $_SERVER['PHP_AUTH_PW'];
|
||||
$authStr = "Authorization: Basic " .
|
||||
base64_encode( "$username:$password" );
|
||||
} else {
|
||||
$authStr = '';
|
||||
}
|
||||
} else {
|
||||
preg_match( "/([^:]*):(.*)$/", $wgRefbaseURLAuth, $out);
|
||||
$username = $out[1];
|
||||
$password = $out[2];
|
||||
$authStr = "Authorization: Basic " .
|
||||
base64_encode( "$username:$password" );
|
||||
}
|
||||
$param = array( 'http' => array( 'header' => $authStr ) );
|
||||
$context = stream_context_create( $param );
|
||||
$cite = trim( file_get_contents( $url, false, $context ) );
|
||||
} else {
|
||||
$cite = trim( file_get_contents( $url ) );
|
||||
}
|
||||
break;
|
||||
|
||||
default:
|
||||
$cite = wfMessage( 'refbase-error-citation-type' )->text();
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
/*
|
||||
* Get list of required fields to produce the citation in the desired format
|
||||
*/
|
||||
public function getFieldList() {
|
||||
|
||||
switch( $this->citationType ) {
|
||||
|
||||
case RefbaseCitationType::CT_MINIMAL:
|
||||
$fieldList = array( 'author',
|
||||
'title',
|
||||
'publication',
|
||||
'year' );
|
||||
break;
|
||||
|
||||
case RefbaseCitationType::CT_RB:
|
||||
$fieldList = array( 'serial' );
|
||||
break;
|
||||
|
||||
default:
|
||||
$fieldList = array();
|
||||
}
|
||||
|
||||
return $fieldList;
|
||||
}
|
||||
|
||||
}
|
||||
139
contrib/mediawiki/include/Refbase.Connector.php
Normal file
139
contrib/mediawiki/include/Refbase.Connector.php
Normal file
@@ -0,0 +1,139 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase database connector
|
||||
*/
|
||||
class RefbaseConnector {
|
||||
|
||||
/// Database location
|
||||
private $dbHost = "";
|
||||
|
||||
/// Database name
|
||||
private $dbName = "";
|
||||
|
||||
/// Database user
|
||||
private $dbUser = "";
|
||||
|
||||
/// Database password
|
||||
private $dbPass = "";
|
||||
|
||||
/// Character set
|
||||
private $dbCharset = "";
|
||||
|
||||
/// Reference table
|
||||
private $dbRefTable = "";
|
||||
|
||||
/// User data table (for cite key entry)
|
||||
private $dbUserDataTable = "";
|
||||
|
||||
/// Method to access database (mysql or PDO)
|
||||
private $dbAccessMethod = "";
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
public function __construct() {
|
||||
global $wgRefbaseDbHost;
|
||||
global $wgRefbaseDbName;
|
||||
global $wgRefbaseDbUser;
|
||||
global $wgRefbaseDbPass;
|
||||
global $wgRefbaseDbRefTable;
|
||||
global $wgRefbaseDbUserDataTable;
|
||||
global $wgRefbaseDbCharset;
|
||||
global $wgRefbaseDbAccessMethod;
|
||||
|
||||
// Read from global configuration
|
||||
$this->dbHost = $wgRefbaseDbHost;
|
||||
$this->dbName = $wgRefbaseDbName;
|
||||
$this->dbUser = $wgRefbaseDbUser;
|
||||
$this->dbPass = $wgRefbaseDbPass;
|
||||
$this->dbRefTable = $wgRefbaseDbRefTable;
|
||||
$this->dbUserDataTable = $wgRefbaseDbUserDataTable;
|
||||
$this->dbCharset = $wgRefbaseDbCharset;
|
||||
$this->dbAccessMethod = $wgRefbaseDbAccessMethod;
|
||||
}
|
||||
|
||||
/**
|
||||
* Query by serial number or cite key entry
|
||||
*/
|
||||
public function getEntry( $input, $tagTypeList, & $outputEntry,
|
||||
$fieldList ) {
|
||||
|
||||
// List of fields to extract (prefix 'r.' to each element)
|
||||
$fieldPref = $fieldList;
|
||||
array_walk( $fieldPref, function ( &$value, $key) {
|
||||
$value="r.$value";
|
||||
} );
|
||||
$fieldPref = join(",", $fieldPref);
|
||||
|
||||
$flagFound = false;
|
||||
for ( $i = 0; $i < count($tagTypeList) && ! $flagFound; $i++ ) {
|
||||
|
||||
$tagType = $tagTypeList[$i];
|
||||
|
||||
// Query string
|
||||
$queryStr = "";
|
||||
if ( $tagType === 'citekey' ) {
|
||||
$queryStr = "SELECT $fieldPref " .
|
||||
"FROM " . $this->dbRefTable . " r " .
|
||||
"INNER JOIN " . $this->dbUserDataTable . " u " .
|
||||
"ON r.serial = u.record_id " .
|
||||
"WHERE u.cite_key='$input'";
|
||||
} else {
|
||||
$queryStr = "SELECT $fieldPref " .
|
||||
"FROM " . $this->dbRefTable . " r " .
|
||||
"WHERE r.serial='$input'";
|
||||
}
|
||||
|
||||
if ( strtolower( $this->dbAccessMethod ) === 'pdo' ) {
|
||||
|
||||
// Connect and query
|
||||
$link = new PDO( 'mysql:host=' . $this->dbHost . ';dbname=' .
|
||||
$this->dbName . ';charset=' . $this->dbCharset,
|
||||
$this->dbUser, $this->dbPass );
|
||||
$dbexec = $link->prepare( $queryStr );
|
||||
|
||||
try {
|
||||
// Perform query
|
||||
$outputEntry = $dbexec->execute();
|
||||
} catch( PDOException $ex ) {
|
||||
$outputEntry = wfMessage( 'refbase-error-dbquery' )->text() .
|
||||
$ex->getMessage();
|
||||
return false;
|
||||
}
|
||||
|
||||
$outputEntry = $dbexec->fetch(PDO::FETCH_ASSOC);
|
||||
|
||||
} elseif ( strtolower( $this->dbAccessMethod ) === 'mysql' ) {
|
||||
|
||||
$link = mysqli_connect( $this->dbHost, $this->dbUser, $this->dbPass, $this->dbName ) or die("db error");
|
||||
if ( !$link ) {
|
||||
$outputEntry = wfMessage( 'refbase-error-mysqlconn' )->text();
|
||||
return false;
|
||||
}
|
||||
|
||||
$result = mysqli_query($link, $queryStr );
|
||||
if ( !$result ) {
|
||||
$outputEntry = wfMessage( 'refbase-error-dbquery' )->text() .
|
||||
mysqli_error($link);
|
||||
return false;
|
||||
}
|
||||
$outputEntry = mysqli_fetch_array($result);
|
||||
|
||||
}
|
||||
if ( !empty( $outputEntry ) ) {
|
||||
$flagFound = true;
|
||||
}
|
||||
}
|
||||
|
||||
if ( empty( $outputEntry ) ) {
|
||||
$outputEntry = wfMessage( 'refbase-error-notfound' )->text();
|
||||
return false;
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
113
contrib/mediawiki/include/Refbase.Renderer.CitationTemplate.php
Normal file
113
contrib/mediawiki/include/Refbase.Renderer.CitationTemplate.php
Normal file
@@ -0,0 +1,113 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase entry renderer using citation templates (cite_journal only for now)
|
||||
*/
|
||||
class RefbaseRendererCitationTemplate extends RefbaseRenderer {
|
||||
|
||||
/**
|
||||
* Constructor (simply inherit from parent)
|
||||
*/
|
||||
public function __construct() {
|
||||
parent::__construct();
|
||||
}
|
||||
|
||||
/**
|
||||
* List fields required to build template
|
||||
*/
|
||||
public function getFieldList() {
|
||||
return array( 'type',
|
||||
'serial',
|
||||
'author',
|
||||
'year',
|
||||
'title',
|
||||
'language',
|
||||
'publication',
|
||||
'volume',
|
||||
'issue',
|
||||
'pages',
|
||||
'place',
|
||||
'publisher',
|
||||
'issn',
|
||||
'doi' );
|
||||
}
|
||||
|
||||
/**
|
||||
* Prepare text for template (supports journal articles only)
|
||||
*/
|
||||
public function render( $entry, & $cite, $options ) {
|
||||
|
||||
$cite = "";
|
||||
$ret = true;
|
||||
if ( $entry["type"] == "Journal Article" ) {
|
||||
$cite .= "{{cite_journal|url=" . $this->refbaseURL . "show.php?";
|
||||
$cite .= "record=" . $entry['serial'];
|
||||
if( !empty( $entry["author"] ) ) {
|
||||
$author = $entry["author"];
|
||||
$aulast = RefbaseTools::extractAuthorsLastName
|
||||
( " *; *", " *, *", 1, $author );
|
||||
$aufirst = RefbaseTools::extractAuthorsGivenName
|
||||
( " *; *", " *, *", 1, $author );
|
||||
if( !empty( $aulast ) ) {
|
||||
$cite .= "|last=" . $aulast;
|
||||
}
|
||||
if( !empty( $aufirst ) ) {
|
||||
$cite .= "|first=" . $aufirst;
|
||||
if( !empty( $aulast ) ) {
|
||||
$cite .= "|authorlink=$aufirst $aulast";
|
||||
}
|
||||
}
|
||||
$authorcount = count( preg_split( "/ *; */", $author ) );
|
||||
$au = "";
|
||||
for ( $i=0; $i < $authorcount - 1; $i++ ) {
|
||||
$aul = RefbaseTools::extractAuthorsLastName
|
||||
( " *; *", " *, *", $i + 2, $author );
|
||||
$auf = RefbaseTools::extractAuthorsGivenName
|
||||
( " *; *", " *, *", $i + 2, $author );
|
||||
if ( !empty( $aul ) ) {
|
||||
if ( !empty( $auf ) ) {
|
||||
$au .= "[[$auf $aul|$aul, $auf]]; ";
|
||||
}
|
||||
}
|
||||
}
|
||||
if ( !empty( $au ) ) {
|
||||
$cite .= "|coauthors=" . trim( $au, '; ' );
|
||||
}
|
||||
}
|
||||
if( !empty( $entry["year"] ) ) {
|
||||
$cite .= "|year=" . $entry['year'];
|
||||
}
|
||||
if( !empty( $entry["title"] ) ) {
|
||||
$title = RefbaseTools::searchReplaceText( $entry['title'],
|
||||
true );
|
||||
$cite .= "|title=" . $title;
|
||||
}
|
||||
if( !empty( $entry["language"] ) )
|
||||
$cite .= "|language=" . $entry['language'];
|
||||
if( !empty( $entry["publication"] ) )
|
||||
$cite .= "|journal=" . $entry['publication'];
|
||||
if( !empty( $entry["volume"] ) )
|
||||
$cite .= "|volume=" . $entry['volume'];
|
||||
if( !empty( $entry["issue"] ) )
|
||||
$cite .= "|issue=" . $entry['issue'];
|
||||
if( !empty( $entry["pages"] ) )
|
||||
$cite .= "|pages=" . $entry['pages'];
|
||||
if( !empty( $entry["place"] ) )
|
||||
$cite .= "|location=" . $entry['place'];
|
||||
if( !empty( $entry["publiser"] ) )
|
||||
$cite .= "|publisher=" . $entry['publisher'];
|
||||
if( !empty( $entry["issn"] ) )
|
||||
$cite .= "|issn=" . $entry['issn'];
|
||||
if( !empty( $entry["doi"] ) )
|
||||
$cite .= "|doi=" . $entry['doi'];
|
||||
$cite .= "}}";
|
||||
$ret &= true;
|
||||
} else {
|
||||
$cite .= wfMessage( 'refbase-error-cite_journal-type' )->text();
|
||||
$ret &= false;
|
||||
}
|
||||
return $ret;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
48
contrib/mediawiki/include/Refbase.Renderer.Cite.php
Normal file
48
contrib/mediawiki/include/Refbase.Renderer.Cite.php
Normal file
@@ -0,0 +1,48 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase entry renderer using the Cite extension tag (<ref>)
|
||||
*/
|
||||
class RefbaseRendererCite extends RefbaseRenderer {
|
||||
|
||||
/// Object generating citations
|
||||
private $citationCreator;
|
||||
|
||||
/**
|
||||
* Constructor (simply inherit from parent)
|
||||
*/
|
||||
public function __construct( $citationType ) {
|
||||
parent::__construct();
|
||||
|
||||
$this->citationCreator = new RefbaseCitationCreator( $citationType );
|
||||
}
|
||||
|
||||
/**
|
||||
* List fields required to build template
|
||||
*/
|
||||
public function getFieldList() {
|
||||
$citeList = $this->citationCreator->getFieldList();
|
||||
return array_unique( array_merge( array(), $citeList ) );
|
||||
}
|
||||
|
||||
/**
|
||||
* Render output: add wiki link to refbase page, include citation in tooltip
|
||||
*/
|
||||
public function render( $entry, & $cite, $options ) {
|
||||
|
||||
$citekey = $options['citekey'];
|
||||
|
||||
$cite = "";
|
||||
// Simply link to refbase, and add tooltip
|
||||
// (form string [URL <span title="CITATION"> KEY </span>] )
|
||||
|
||||
$citation = "";
|
||||
$this->citationCreator->createCitation( $entry, $citation );
|
||||
|
||||
// Use #tag method to properly pass inputs to <ref>
|
||||
$cite .= "{{#tag:ref|$citation|name=$citekey}}";
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
}
|
||||
56
contrib/mediawiki/include/Refbase.Renderer.Link.php
Normal file
56
contrib/mediawiki/include/Refbase.Renderer.Link.php
Normal file
@@ -0,0 +1,56 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase entry renderer using simple hyperlink and tooltip
|
||||
*/
|
||||
class RefbaseRendererLink extends RefbaseRenderer {
|
||||
|
||||
/// Object generating citations
|
||||
private $citationCreator;
|
||||
|
||||
/**
|
||||
* Constructor (simply inherit from parent)
|
||||
*/
|
||||
public function __construct( $citationType ) {
|
||||
parent::__construct();
|
||||
|
||||
$this->citationCreator = new RefbaseCitationCreator( $citationType );
|
||||
}
|
||||
|
||||
/**
|
||||
* List fields required to build template
|
||||
*/
|
||||
public function getFieldList() {
|
||||
$citeList = $this->citationCreator->getFieldList();
|
||||
return array_unique( array_merge( array( 'serial' ), $citeList ) );
|
||||
}
|
||||
|
||||
/**
|
||||
* Render output: add wiki link to refbase page, include citation in tooltip
|
||||
*/
|
||||
public function render( $entry, & $cite, $options ) {
|
||||
|
||||
$citekey = $options['citekey'];
|
||||
$cite = "";
|
||||
// Simply link to refbase, and add tooltip
|
||||
// (form string [URL <span title="CITATION"> KEY </span>] )
|
||||
|
||||
// Display the key (cite_key or serial number as wiki text)
|
||||
$wikiText = $citekey;
|
||||
|
||||
// Add full citation as a tooltip
|
||||
$toolTip = "";
|
||||
$this->citationCreator->createCitation( $entry, $toolTip );
|
||||
|
||||
// Link to refbase page for current entry
|
||||
$link = $this->refbaseURL . "show.php?record=" . $entry['serial'];
|
||||
|
||||
// Build full string
|
||||
$cite .= "[" . $link . " ";
|
||||
$cite .= Html::openElement( 'span', array( 'title' => "\"" . $toolTip . "\"" ) );
|
||||
$cite .= $wikiText . Html::closeElement( 'span' ) . "]";
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
}
|
||||
46
contrib/mediawiki/include/Refbase.Renderer.php
Normal file
46
contrib/mediawiki/include/Refbase.Renderer.php
Normal file
@@ -0,0 +1,46 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase entry renderer
|
||||
*/
|
||||
abstract class RefbaseRenderer {
|
||||
|
||||
/// Location of refbase installation (may differ from $dbHost if using https
|
||||
/// for instance)
|
||||
protected $refbaseURL = "";
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
public function __construct() {
|
||||
global $wgRefbaseURL;
|
||||
$this->refbaseURL = $wgRefbaseURL;
|
||||
}
|
||||
|
||||
/**
|
||||
* Instantiation subclass instances
|
||||
*/
|
||||
public static function create( $outputType, $citationType = "" ) {
|
||||
if ( strtolower( $outputType ) == 'cite_journal' ) {
|
||||
return new RefbaseRendererCitationTemplate();
|
||||
} elseif ( strtolower( $outputType ) == 'link' ) {
|
||||
return new RefbaseRendererLink( $citationType );
|
||||
} elseif ( strtolower( $outputType ) == 'cite' ) {
|
||||
return new RefbaseRendererCite( $citationType );
|
||||
} else {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the list of fields to extract from the database
|
||||
*/
|
||||
abstract public function getFieldList();
|
||||
|
||||
/**
|
||||
* Render entries
|
||||
*/
|
||||
abstract public function render( $entry, & $cite, $options );
|
||||
|
||||
}
|
||||
|
||||
130
contrib/mediawiki/include/Refbase.Tools.php
Normal file
130
contrib/mediawiki/include/Refbase.Tools.php
Normal file
@@ -0,0 +1,130 @@
|
||||
<?php
|
||||
|
||||
/**
|
||||
* Refbase helper functions (cleanup strings, author extraction)
|
||||
*/
|
||||
class RefbaseTools {
|
||||
|
||||
|
||||
/// Character translation table
|
||||
private static $transtab_refbase_html = array(
|
||||
"/__(?!_)(.+?)__/" => "<u>\\1</u>", // the pattern for underline (__...__) must come before the one for italic (_..._)
|
||||
"/_(.+?)_/" => "<i>\\1</i>",
|
||||
"/\\*\\*(.+?)\\*\\*/" => "<b>\\1</b>",
|
||||
"/\\[super:(.+?)\\]/i" => "<sup>\\1</sup>",
|
||||
"/\\[sub:(.+?)\\]/i" => "<sub>\\1</sub>",
|
||||
"/\\[permil\\]/" => "‰",
|
||||
"/\\[infinity\\]/" => "∞",
|
||||
"/\\[alpha\\]/" => "α",
|
||||
"/\\[beta\\]/" => "β",
|
||||
"/\\[gamma\\]/" => "γ",
|
||||
"/\\[delta\\]/" => "δ",
|
||||
"/\\[epsilon\\]/" => "ε",
|
||||
"/\\[zeta\\]/" => "ζ",
|
||||
"/\\[eta\\]/" => "η",
|
||||
"/\\[theta\\]/" => "θ",
|
||||
"/\\[iota\\]/" => "ι",
|
||||
"/\\[kappa\\]/" => "κ",
|
||||
"/\\[lambda\\]/" => "λ",
|
||||
"/\\[mu\\]/" => "μ",
|
||||
"/\\[nu\\]/" => "ν",
|
||||
"/\\[xi\\]/" => "ξ",
|
||||
"/\\[omicron\\]/" => "ο",
|
||||
"/\\[pi\\]/" => "π",
|
||||
"/\\[rho\\]/" => "ρ",
|
||||
"/\\[sigmaf\\]/" => "ς",
|
||||
"/\\[sigma\\]/" => "σ",
|
||||
"/\\[tau\\]/" => "τ",
|
||||
"/\\[upsilon\\]/" => "υ",
|
||||
"/\\[phi\\]/" => "φ",
|
||||
"/\\[chi\\]/" => "χ",
|
||||
"/\\[psi\\]/" => "ψ",
|
||||
"/\\[omega\\]/" => "ω",
|
||||
"/\\[Alpha\\]/" => "Α",
|
||||
"/\\[Beta\\]/" => "Β",
|
||||
"/\\[Gamma\\]/" => "Γ",
|
||||
"/\\[Delta\\]/" => "Δ",
|
||||
"/\\[Epsilon\\]/" => "Ε",
|
||||
"/\\[Zeta\\]/" => "Ζ",
|
||||
"/\\[Eta\\]/" => "Η",
|
||||
"/\\[Theta\\]/" => "Θ",
|
||||
"/\\[Iota\\]/" => "Ι",
|
||||
"/\\[Kappa\\]/" => "Κ",
|
||||
"/\\[Lambda\\]/" => "Λ",
|
||||
"/\\[Mu\\]/" => "Μ",
|
||||
"/\\[Nu\\]/" => "Ν",
|
||||
"/\\[Xi\\]/" => "Ξ",
|
||||
"/\\[Omicron\\]/" => "Ο",
|
||||
"/\\[Pi\\]/" => "Π",
|
||||
"/\\[Rho\\]/" => "Ρ",
|
||||
"/\\[Sigma\\]/" => "Σ",
|
||||
"/\\[Tau\\]/" => "Τ",
|
||||
"/\\[Upsilon\\]/" => "Υ",
|
||||
"/\\[Phi\\]/" => "Φ",
|
||||
"/\\[Chi\\]/" => "Χ",
|
||||
"/\\[Psi\\]/" => "Ψ",
|
||||
"/\\[Omega\\]/" => "Ω",
|
||||
"/(?:\"|")(.+?)(?:\"|")/" => "“\\1”",
|
||||
"/ +- +/" => " – "
|
||||
);
|
||||
|
||||
// EXTRACT AUTHOR'S LAST NAME
|
||||
// this function takes the contents of the author field and will extract the last name of a particular author (specified by position)
|
||||
// (e.g., setting '$authorPosition' to "1" will return the 1st author's last name)
|
||||
// Note: this function assumes that:
|
||||
// 1. within one author object, there's only *one* delimiter separating author name & initials!
|
||||
// 2. author objects are stored in the db as "<author_name><author_initials_delimiter><author_initials>", i.e., initials follow *after* the author's name!
|
||||
// Required Parameters:
|
||||
// 1. pattern describing delimiter that separates different authors
|
||||
// 2. pattern describing delimiter that separates author name & initials (within one author)
|
||||
// 3. position of the author whose last name shall be extracted (e.g., "1" will return the 1st author's last name)
|
||||
// 4. contents of the author field
|
||||
public static function extractAuthorsLastName( $oldBetweenAuthorsDelim, $oldAuthorsInitialsDelim, $authorPosition, $authorContents ) {
|
||||
$authorsArray = preg_split( "/" . $oldBetweenAuthorsDelim . "/", $authorContents ); // get a list of all authors for this record
|
||||
$authorPosition = $authorPosition - 1; // php array elements start with "0", so we decrease the authors position by 1
|
||||
$singleAuthor = $authorsArray[$authorPosition]; // for the author in question, extract the full author name (last name & initials)
|
||||
$singleAuthorArray = preg_split( "/" . $oldAuthorsInitialsDelim . "/", $singleAuthor ); // then, extract author name & initials to separate list items
|
||||
$singleAuthorsLastName = $singleAuthorArray[0]; // extract this author's last name into a new variable
|
||||
return $singleAuthorsLastName;
|
||||
}
|
||||
|
||||
// EXTRACT AUTHOR'S GIVEN NAME
|
||||
// this function takes the contents of the author field and will extract the given name of a particular author (specified by position)
|
||||
// (e.g., setting '$authorPosition' to "1" will return the 1st author's given name)
|
||||
// Required Parameters:
|
||||
// 1. pattern describing delimiter that separates different authors
|
||||
// 2. pattern describing delimiter that separates author name & initials (within one author)
|
||||
// 3. position of the author whose last name shall be extracted (e.g., "1" will return the 1st author's last name)
|
||||
// 4. contents of the author field
|
||||
public static function extractAuthorsGivenName( $oldBetweenAuthorsDelim, $oldAuthorsInitialsDelim, $authorPosition, $authorContents ) {
|
||||
$authorsArray = preg_split( "/" . $oldBetweenAuthorsDelim . "/", $authorContents ); // get a list of all authors for this record
|
||||
$authorPosition = $authorPosition - 1; // php array elements start with "0", so we decrease the authors position by 1
|
||||
$singleAuthor = $authorsArray[$authorPosition]; // for the author in question, extract the full author name (last name & initials)
|
||||
$singleAuthorArray = preg_split( "/" . $oldAuthorsInitialsDelim . "/", $singleAuthor ); // then, extract author name & initials to separate list items
|
||||
if ( !empty($singleAuthorArray[1]) ) {
|
||||
$singleAuthorsGivenName = $singleAuthorArray[1]; // extract this author's last name into a new variable
|
||||
} else {
|
||||
$singleAuthorsGivenName = '';
|
||||
}
|
||||
return $singleAuthorsGivenName;
|
||||
}
|
||||
|
||||
// Perform search & replace actions on the given text input:
|
||||
// ('$includesSearchPatternDelimiters' must be a boolean value that specifies whether the leading and trailing slashes
|
||||
// are included within the search pattern ['true'] or not ['false'])
|
||||
public static function searchReplaceText( $sourceString, $includesSearchPatternDelimiters ) {
|
||||
// apply the search & replace actions defined in '$transtab_refbase_html' to the text passed in '$sourceString':
|
||||
foreach ( self::$transtab_refbase_html as $searchString => $replaceString ) {
|
||||
if ( !$includesSearchPatternDelimiters ) {
|
||||
$searchString = "/" . $searchString . "/"; // add search pattern delimiters
|
||||
}
|
||||
if ( preg_match($searchString, $sourceString ) ) {
|
||||
$sourceString = preg_replace( $searchString, $replaceString, $sourceString );
|
||||
}
|
||||
}
|
||||
return $sourceString;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
4
contrib/skins/README
Normal file
4
contrib/skins/README
Normal file
@@ -0,0 +1,4 @@
|
||||
The current method to change the appearance of refbase is to edit the style
|
||||
files in the 'css' subdirectory and/or to replace the 'header.inc.php' and
|
||||
'footer.inc.php' in the 'includes' subdirectory. This directory contains
|
||||
examples of customized versions of these files.
|
||||
20
contrib/skins/mediawiki-monobook/README
Normal file
20
contrib/skins/mediawiki-monobook/README
Normal file
@@ -0,0 +1,20 @@
|
||||
mediawiki-monobook skin for refbase
|
||||
===================================
|
||||
|
||||
Author
|
||||
------
|
||||
Richard Karnesky <karnesky@gmail.com>
|
||||
|
||||
About
|
||||
-----
|
||||
These files mimic the Monobook skin from MediaWiki:
|
||||
<http://www.mediawiki.org/>
|
||||
This is the default skin for the Wikipedia:
|
||||
<http://wikipedia.org/>
|
||||
|
||||
You may also be interested in the refbase extension for MediaWiki, included in the
|
||||
'contrib/mediawiki' directory from refbase.
|
||||
|
||||
An installation of refbase that uses this skin is the Northwestern University
|
||||
Center for Atom-Probe Tomography:
|
||||
<http://arc.nucapt.northwestern.edu/refbase/>
|
||||
235
contrib/skins/mediawiki-monobook/footer.inc.php
Normal file
235
contrib/skins/mediawiki-monobook/footer.inc.php
Normal file
@@ -0,0 +1,235 @@
|
||||
<?php
|
||||
// Copyright: Richard Karnesky <karnesky@gmail.com>
|
||||
// This code is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
|
||||
// Please see the GNU General Public License for more details.
|
||||
// File: ./includes/footer.inc.php
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Inserts the closing HTML </body> and </html> tags:
|
||||
function displayHTMLfoot()
|
||||
{
|
||||
?>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
<?php
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Displays the visible footer:
|
||||
function showPageFooter($HeaderString)
|
||||
{
|
||||
global $officialDatabaseName; // usage example: <a href="index.php">[? echo encodeHTML($officialDatabaseName); ?]</a>
|
||||
global $hostInstitutionAbbrevName; // usage example: <a href="[? echo $hostInstitutionURL; ?]">[? echo encodeHTML($hostInstitutionAbbrevName); ?] Home</a>
|
||||
global $hostInstitutionName; // (note: in the examples above, square brackets must be replaced by their respective angle brackets)
|
||||
global $hostInstitutionURL;
|
||||
global $helpResourcesURL;
|
||||
|
||||
global $loginWelcomeMsg; // these variables are globally defined in function 'showLogin()' in 'include.inc.php'
|
||||
global $loginStatus;
|
||||
global $loginLinks;
|
||||
|
||||
global $loc; // '$loc' is made globally available in 'core.php'
|
||||
?>
|
||||
</div></div></div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<div id="column-one">
|
||||
<div id="p-cactions" class="portlet">
|
||||
<h5>Views</h5>
|
||||
<ul>
|
||||
|
||||
<li id="ca-talk"
|
||||
class="selected" ><a href="index.php">References</a></li><li id="search"><a href="simple_search.php" title="search the main fields of the database">Simple Search</a></li>
|
||||
<li><a href="advanced_search.php" title="search all fields of the database">Advanced Search</a></li>
|
||||
<?php
|
||||
|
||||
// -------------------------------------------------------
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_add/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains 'allow_add'...
|
||||
{
|
||||
// ... include a link to 'record.php?recordAction=add...':
|
||||
?>
|
||||
|
||||
<LI id="ca-watch"><a href="record.php?recordAction=add" title="add a record to the database">Add Record</a>
|
||||
<?php
|
||||
}
|
||||
else {?>
|
||||
<LI id="ca-watch"><a href="/refbase-svn/record.php?recordAction=add" title="add a suggested record to the database">Add Record (suggest)</a>
|
||||
<?php }
|
||||
|
||||
// -------------------------------------------------------
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_import|allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains either 'allow_import' or 'allow_batch_import'...
|
||||
{
|
||||
// ... include a link to 'import.php':
|
||||
?>
|
||||
|
||||
<LI><a href="import.php" title="import records">Import</a>
|
||||
<?php
|
||||
} else {
|
||||
?>
|
||||
<LI><a href="/refbase-svn/import.php" title="import suggested records">Import (suggest)</a>
|
||||
<?php
|
||||
}?>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<div class="portlet" id="p-personal">
|
||||
<h5>Personal tools</h5>
|
||||
<div class="pBody">
|
||||
<ul>
|
||||
<li id="pt-userpage"><? echo preg_replace('/You\'re logged in as<br>/','',$loginStatus); ?></li><li id="pt-mytalk">
|
||||
<? echo $loginLinks; ?></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
<div class="portlet" id="p-logo">
|
||||
<a style="background-image:
|
||||
url(../skins/common/images/wiki.png);"
|
||||
href="../index.php/Seidman_Group"
|
||||
title="Seidman Group"></a>
|
||||
</div>
|
||||
<div class='portlet' id='p-Seidman_Group'>
|
||||
<h5>Seidman Group</h5>
|
||||
<div class='pBody'>
|
||||
|
||||
<ul>
|
||||
<li id="n-Seidman-Group"><a href="/Seidman_Group">Seidman Group</a></li>
|
||||
<li id="n-Research"><a href="/Category:Research">Research</a></li>
|
||||
<li id="n-People"><a href="/Category:People">People</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class='portlet' id='p-NUCAPT'>
|
||||
<h5>NUCAPT</h5>
|
||||
<div class='pBody'>
|
||||
<ul>
|
||||
<li id="n-Instruments"><a href="/Category:Tools">Instruments</a></li>
|
||||
<li id="n-Calendar"><a href="http://arc.nucapt.northwestern.edu/phpicalendar">Calendar</a></li>
|
||||
<li id="n-Visit"><a href="/Visit">Visit</a></li>
|
||||
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
<div class='portlet' id='p-Atom-Probe_Tomography'>
|
||||
<h5>Atom-Probe Tomography</h5>
|
||||
<div class='pBody'>
|
||||
<ul>
|
||||
<li id="n-References"><a href="http://arc.nucapt.northwestern.edu/refbase">References</a></li>
|
||||
|
||||
<li id="n-AtomProbe-mailing-list"><a href="http://arc.nucapt.northwestern.edu/mailman/listinfo/atomprobe">AtomProbe mailing list</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
<div class="portlet" id="p-tb">
|
||||
<h5>Search</h5>
|
||||
<div class="pBody">
|
||||
<?php echo buildQuickSearchElements($query, $queryURL, $showQuery, $showLinks, $showRows, $citeStyle, $citeOrder, $displayType); ?>
|
||||
<ul>
|
||||
<li><a href="simple_search.php" title="search the main fields of the database">Simple Search</a>
|
||||
<li><a href="advanced_search.php" title="search all fields of the database">Advanced Search</a>
|
||||
<?php
|
||||
|
||||
// -------------------------------------------------------
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_sql_search/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains 'allow_sql_search'...
|
||||
{
|
||||
// ... include a link to 'sql_search.php':
|
||||
?>
|
||||
|
||||
<li><a href="sql_search.php" title="search the database by use of a SQL query">SQL Search</a>
|
||||
<?php
|
||||
}
|
||||
|
||||
// -------------------------------------------------------
|
||||
?>
|
||||
<li><a href="library_search.php" title="search the library of the <? echo encodeHTML($hostInstitutionAbbrevName); ?>">Library Search</a>
|
||||
</ul>
|
||||
|
||||
</div></div>
|
||||
<div class="portlet" id="p-tc">
|
||||
<h5>Toolbox</h5>
|
||||
<div class="pBody">
|
||||
<ul>
|
||||
<?php
|
||||
|
||||
// -------------------------------------------------------
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_add/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains 'allow_add'...
|
||||
{
|
||||
// ... include a link to 'record.php?recordAction=add...':
|
||||
?>
|
||||
|
||||
<LI><a href="record.php?recordAction=add" title="add a record to the database">Add Record</a>
|
||||
<?php
|
||||
}
|
||||
|
||||
// -------------------------------------------------------
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_import|allow_batch_import/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains either 'allow_import' or 'allow_batch_import'...
|
||||
{
|
||||
// ... include a link to 'import.php':
|
||||
?>
|
||||
|
||||
<LI><a href="import.php" title="import records">Import</a>
|
||||
<?php
|
||||
}
|
||||
|
||||
// -------------------------------------------------------
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_details_view/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains 'allow_details_view'...
|
||||
{
|
||||
// ... include a link to 'show.php':
|
||||
?>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<LI><a href="show.php" title="display details for a particular record by entering its database serial number">Show Record</a>
|
||||
<?php
|
||||
}
|
||||
if (isset($_SESSION['user_permissions']) AND preg_match("/allow_cite/", $_SESSION['user_permissions'])) // if the 'user_permissions' session variable contains 'allow_cite'...
|
||||
{
|
||||
// ... include a link to 'extract.php':
|
||||
?>
|
||||
|
||||
<LI><a href="extract.php" title="extract citations from a text and build an appropriate reference list">Extract Citations</a><?php
|
||||
}
|
||||
|
||||
// -------------------------------------------------------
|
||||
?>
|
||||
</ul>
|
||||
</div></div></div>
|
||||
|
||||
|
||||
|
||||
<div class="visualClear"></div>
|
||||
<div id="footer">
|
||||
<div id="f-poweredbyico"><a href="http://www.refbase.net/"><img src="img/refbase_credit.gif" alt="refbase"></a></div><ul id="f-list">
|
||||
<li><? echo date('j M Y'); ?></li>
|
||||
<li id="f-about"><a
|
||||
href="/index.php/Seidman_Group" title="Seidman Group">NUCAPT: Northwestern University Center for Atom-Probe Tomography</a></li> </ul>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
<?php
|
||||
}
|
||||
?>
|
||||
164
contrib/skins/mediawiki-monobook/header.inc.php
Normal file
164
contrib/skins/mediawiki-monobook/header.inc.php
Normal file
@@ -0,0 +1,164 @@
|
||||
<?php
|
||||
// Project: Web Reference Database (refbase) <http://www.refbase.net>
|
||||
// Copyright: Matthias Steffens <mailto:refbase@extracts.de> and the file's
|
||||
// original author(s).
|
||||
//
|
||||
// This code is distributed in the hope that it will be useful,
|
||||
// but WITHOUT ANY WARRANTY. Please see the GNU General Public
|
||||
// License for more details.
|
||||
//
|
||||
// File: ./contrib/skins/mediawiki-monobook/header.inc.php
|
||||
// Repository: $HeadURL: file:///svn/p/refbase/code/branches/bleeding-edge/contrib/skins/mediawiki-monobook/header.inc.php $
|
||||
// Author(s): Richard Karnesky <mailto:karnesky@gmail.com>
|
||||
//
|
||||
// Created: 31-Oct-06, 00:28
|
||||
// Modified: $Date: 2012-02-27 20:25:30 +0000 (Mon, 27 Feb 2012) $
|
||||
// $Author: msteffens $
|
||||
// $Revision: 1337 $
|
||||
|
||||
// This is the header include file.
|
||||
// It contains functions that provide the HTML header
|
||||
// as well as the visible header that gets displayed on every page.
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Inserts the HTML <head>...</head> block as well as the initial <body> tag:
|
||||
//
|
||||
// TODO: include OpenSearch elements in HTML header
|
||||
// (see examples at <http://www.opensearch.org/Specifications/OpenSearch/1.1#Response_metadata_in_HTML.2FXHTML>)
|
||||
function displayHTMLhead($pageTitle, $metaRobots, $metaDescription, $additionalMeta, $includeJavaScript, $includeJavaScriptFile, $viewType, $rssURLArray)
|
||||
{
|
||||
global $officialDatabaseName; // these variables are defined in 'ini.inc.php'
|
||||
global $contentTypeCharset;
|
||||
global $defaultStyleSheet;
|
||||
global $printStyleSheet;
|
||||
global $mobileStyleSheet;
|
||||
global $useVisualEffects;
|
||||
global $databaseBaseURL;
|
||||
global $databaseKeywords;
|
||||
global $defaultFeedFormat;
|
||||
?>
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
|
||||
"http://www.w3.org/TR/html4/loose.dtd">
|
||||
<html>
|
||||
<head profile="http://a9.com/-/spec/opensearch/1.1/">
|
||||
<title><?php echo $pageTitle; ?></title>
|
||||
<meta name="date" content="<?php echo date('d-M-y'); ?>">
|
||||
<meta name="robots" content="<?php echo $metaRobots; ?>">
|
||||
<meta name="description" lang="en" content="<?php echo $metaDescription; ?>">
|
||||
<meta name="keywords" lang="en" content="<?php echo $databaseKeywords; ?>"><?php
|
||||
|
||||
if (!empty($additionalMeta))
|
||||
echo $additionalMeta;
|
||||
?>
|
||||
|
||||
<meta http-equiv="content-language" content="<?php echo getUserLanguage(); ?>">
|
||||
<meta http-equiv="content-type" content="text/html; charset=<?php echo $contentTypeCharset; ?>">
|
||||
<meta http-equiv="Content-Style-Type" content="text/css"><?php
|
||||
|
||||
if (preg_match("/^Print$/i", $viewType))
|
||||
{
|
||||
?>
|
||||
|
||||
<link rel="stylesheet" href="<?php echo $printStyleSheet; ?>" type="text/css" title="CSS Definition"><?php
|
||||
}
|
||||
elseif (preg_match("/^Mobile$/i", $viewType))
|
||||
{
|
||||
?>
|
||||
|
||||
<link rel="stylesheet" href="<?php echo $mobileStyleSheet; ?>" type="text/css" title="CSS Definition"><?php
|
||||
}
|
||||
else
|
||||
{
|
||||
?>
|
||||
|
||||
<link rel="stylesheet" href="<?php echo $defaultStyleSheet; ?>" type="text/css" title="CSS Definition"><?php
|
||||
}
|
||||
|
||||
if (!empty($rssURLArray) AND isset($_SESSION['user_permissions']) AND preg_match("/allow_rss_feeds/", $_SESSION['user_permissions'])) // if some RSS URLs were specified AND the 'user_permissions' session variable contains 'allow_rss_feeds'...
|
||||
{
|
||||
foreach ($rssURLArray as $rssURL)
|
||||
{
|
||||
if ($defaultFeedFormat == "Atom XML")
|
||||
$feedContentType = "application/atom+xml";
|
||||
else // RSS XML
|
||||
$feedContentType = "application/rss+xml";
|
||||
|
||||
// ...include a link tag pointing to a dynamic RSS feed for the current query:
|
||||
?>
|
||||
|
||||
<link rel="alternate" type="<?php echo $feedContentType; ?>" href="<?php echo $databaseBaseURL . $rssURL['href']; ?>" title="<?php echo $rssURL['title']; ?>"><?php
|
||||
}
|
||||
}
|
||||
?>
|
||||
|
||||
<link rel="unapi-server" type="application/xml" title="unAPI" href="<?php echo $databaseBaseURL; ?>unapi.php">
|
||||
<link rel="search" type="application/opensearchdescription+xml" title="<?php echo encodeHTML($officialDatabaseName); ?>" href="<?php echo $databaseBaseURL; ?>opensearch.php?operation=explain"><?php
|
||||
|
||||
if ($includeJavaScript OR (isset($_SESSION['userAutoCompletions']) AND ($_SESSION['userAutoCompletions'] == "yes")) OR ($useVisualEffects == "yes"))
|
||||
{
|
||||
// ...include common refbase JavaScript functions:
|
||||
?>
|
||||
|
||||
<script language="JavaScript" type="text/javascript" src="javascript/common.js"></script><?php
|
||||
}
|
||||
|
||||
if ((isset($_SESSION['userAutoCompletions']) AND ($_SESSION['userAutoCompletions'] == "yes")) OR ($useVisualEffects == "yes"))
|
||||
{
|
||||
// ...include the Prototype & script.aculo.us JavaScript frameworks:
|
||||
?>
|
||||
|
||||
<script language="JavaScript" type="text/javascript" src="javascript/prototype.js"></script>
|
||||
<script language="JavaScript" type="text/javascript" src="javascript/scriptaculous.js?load=effects,controls"></script><?php
|
||||
}
|
||||
|
||||
if (!empty($includeJavaScriptFile))
|
||||
{
|
||||
// ...include additional JavaScript functions:
|
||||
?>
|
||||
|
||||
<script language="JavaScript" type="text/javascript" src="<?php echo $includeJavaScriptFile; ?>"></script><?php
|
||||
}
|
||||
?>
|
||||
|
||||
</head>
|
||||
<body><?php
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// Displays the visible header:
|
||||
function showPageHeader($HeaderString)
|
||||
{
|
||||
global $officialDatabaseName; // these variables are defined in 'ini.inc.php'
|
||||
global $hostInstitutionAbbrevName;
|
||||
global $hostInstitutionName;
|
||||
global $hostInstitutionURL;
|
||||
global $helpResourcesURL;
|
||||
|
||||
global $loginWelcomeMsg; // these variables are globally defined in function 'showLogin()' in 'include.inc.php'
|
||||
global $loginStatus;
|
||||
global $loginLinks;
|
||||
|
||||
global $loc; // '$loc' is made globally available in 'core.php'
|
||||
?>
|
||||
|
||||
<div id="globalWrapper">
|
||||
|
||||
<div id="column-content">
|
||||
<div id="content">
|
||||
<a name="top" id="contentTop"></a>
|
||||
<h1 class="firstHeading"><? echo encodeHTML($officialDatabaseName); ?></h1>
|
||||
<div id="bodyContent">
|
||||
<h3 id="siteSub">From NUCAPT</h3>
|
||||
|
||||
<div id="contentSub"></div>
|
||||
<!-- start content -->
|
||||
<h2><? echo $HeaderString; ?></h2>
|
||||
|
||||
|
||||
<?php
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
?>
|
||||
1777
contrib/skins/mediawiki-monobook/main.css
Normal file
1777
contrib/skins/mediawiki-monobook/main.css
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user