mirror of
https://github.com/krislamo/puppet-pubcrawler
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256 lines
12 KiB
Plaintext
256 lines
12 KiB
Plaintext
############ PubCrawler configuration file ############
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####### (for PubCrawler Version higher than 0.53) ######
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############################################################
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# #
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# lines beginning with hash marks (#) are ignored. #
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# #
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# PubCrawler home page: #
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# http://www.pubcrawler.ie #
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# #
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# Specify your file locations and search options here. #
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# Each line is in the format FIELD space VALUE. #
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# Any leading or trailing quotes will be chopped off. #
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# Hash marks separate comments from data. #
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# You must specify a value for all 6 mandatory fields. #
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# #
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############################################################
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############################################################
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################# MANDATORY SETTINGS #######################
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############################################################
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project <%= @name %>
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# Identifier for a project. This value is displayed in the header
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# of the results page.
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background_color <%= @bgcolor %>
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# background color for sectional headers of the result page.
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header_icon <%= @header_icon %>
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# relative or absolute URL for icon to display in results page
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# header.
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<%- if @html_file -%>
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html_file <%= @html_file %>
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<%- else -%>
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html_file /usr/share/pubcrawler/html/<%= @name %>/index.html
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<%- end -%>
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# html_file is the name of the output HTML file for results
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# it will be written to the specified working directory
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# unless an absolute pathname is given
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viewdays <%= @viewdays %>
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# viewdays is the number of days each document will be shown.
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relentrezdate <%= @relentrezdate %>
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# relentrezdate (relative date of insertion into Entrez)
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# is the maximum age (in days) of database entries to be reported.
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# NOTE: sometimes records first appear in the databases several
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# days or even weeks later than indicated by their database
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# date-stamp, i.e. with non-zero values of relentrezdate.
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# Therefore relentrezdate needs to be high enough to find these
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# records. A relentrezdate of 90 days is suggested (if you make
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# relentrezdate too huge the searches will be very slow.)
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# other valid entries are:
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# '1 year', '2 years', '5 years', '10 years', and 'no limit'
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getmax <%= @getmax %>
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# getmax is the maximum number of documents to be retrieved
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# for each search carried out.
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fullmax <%= @fullmax %>
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# fullmax is the maximum number of documents for which a full
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# report is being presented
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# if more documents were retrieved, these can be accessed
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# through a hyperlink (in groups of up to fullmax articles)
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include_config <%= @include_config %>
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# include_config (yes/no) specifies whether or not to append
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# this config-file to the end of the output file
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#-------------------------------------------------------------------#
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############################################################
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################## OPTIONAL SETTINGS #######################
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############################################################
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search_URL <%= @search_URL %>
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# URL where searches are being sent to
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# defaults to
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# https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
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neighbour_URL <%= @neighbour_URL %>
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# URL where neighbourhood searches are being sent to
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# defaults to
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# https://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi
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retrieve_URL <%= @retrieve_URL %>
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# URL where documents are retrieved from
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# defaults to
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# https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
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<%- if @work_dir -%>
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work_dir <%= @work_dir %>
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<%- else -%>
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work_dir /var/lib/pubcrawler/<%= @name %>
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<%- end -%>
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# specify a directory in which databases, output and log file
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# will be located
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# if no value given, the current working directory will be used
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extra_range <%= @extra_range %>
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# specifies the number of documents combined in a link
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# minimum value is 1, defaults to 'fullmax'
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check <%= @check %>
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# if set to '1' program will just check all settings
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# without performing the actual search
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# RECOMMENDED FOR THE FIRST RUN!
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prompt <%= @prompt %>
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# for Mac-users only:
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# if this option is set to '1' the program will ask you
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# explicitly for command line options
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# NOTE: THIS IS NOT SUITABLE FOR AUTOMATED USE!
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verbose <%= @verbose %>
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# verbose 0 runs silently and makes log file
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# verbose 1 writes log output on screen
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mute <%= @mute %>
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# mute 0 writes some messages to STDERR
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# mute 1 stops ALL messages going to STDERR
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# unless an error was encountered
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log_file <%= @log_file %>
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# name of file for log-output
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# (verbose has to be set to '0')
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#base_URL 'http://www.gen.tcd.ie/pubcrawler/pubcrawler_output.html'
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base_URL <%= @base_URL %>
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# specify a URL, that will be used for
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# the 'Back to Top' link in the output page
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# 'local_file' makes links relative to results file
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# mail joe@hotmail.earth.com
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# if the hash mark ('#') at the beginning of the above line
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# is removed, PubCrawler will send the results file to
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# the given address at the end of each run. You can specify
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# multiple addresses using commas (no spaces!).
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# notify jfk@hotmail.earth.com#joe
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# if the hash mark ('#') at the beginning of the above line
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# is removed, PubCrawler will send a notification to
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# the given address (minus '#joe') at the end of each run
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# The recipient will be addressed with joe (optional).
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# You can specify multiple addresses using commas (no spaces!).
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mail_features <%= @mail_features %>
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# comma-separated list of extra features for the mail
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# to be sent (without them it will be plain text). These are:
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# css,javascript,entrez_links,pubcrawler_links,images,html,description
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# or simply 'all' for everything
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lynx <%= @lynx %>
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# for Unix-users only:
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# if you don't want to use the libwww-Perl module and
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# have an alternative browser installed, that works from the
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# command line, like 'Lynx', you can use it by entering the
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# command that evokes it (e.g. lynx '/usr/bin/lynx')
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# NOTE: THIS OVERRIDES ANY PROXY SETTINGS!
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#header 'head.html'
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# specify a location of a header (in HTML-style) that will be used
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# for the output file (disabled unless hash mark is removed)
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prefix <%= @prefix %>
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# if you would like a different prefix to be used
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# for standard files (configuration, database, log)
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# insert it here (default is program name up to first dot):
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system <%= @system %>
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# name of operating system
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# might need the explicit assignment of an adequate value
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# ('MacOS','Win','Unix', or 'Linux')
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# if Perl is not configured properly
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#### PROXY SETTING (if desired and/or necessary) ####
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#proxy www.tcd.ie/proxy.cgi
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# insert either a proxy server (eg. 'proxy.domain.com')
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# or the address of a proxy configuration file
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# if known (eg. 'www.domain.com/proxy.cgi')
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# and uncomment
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proxy_port <%= @proxy_port %>
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# port of the proxy server,defaults to '80'
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proxy_auth <%= @proxy_auth %>
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proxy_pass <%= @proxy_pass %>
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# in case you need to submit a username and a password
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# for accessing your proxy, you can fill it in here:
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# CAUTION! Having passwords stored in a file means a
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# possible security risk! Please delete after usage
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# or use the according command line option!
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# !!! Please make sure that the module MIME::Base64 is
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# installed for the proxy authorization to work!!!
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time_out <%= @time_out %>
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# specify how many SECONDS to give remote servers
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# in creating responses before the library disconnects
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# (defaults to 180 seconds if no value is given)
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test_URL <%= @test_URL %>
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# test-URL for proxy-test
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no_test <%= @no_test %>
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# if a proxy is given, the internet connection is tested
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# at the start of the program by default; this can be
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# suppressed if a value of '1' is given here
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indent <%= @indent %>
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# amount of pixels that output is being shifted to the right
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no_decap <%= @no_decap %>
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# put 1 inbetween single quotes if you want to disable
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# processing of the entrez documents (chopping of head and tail
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# and collecting UIs)
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spacer <%= @spacer %>
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# specify a gif that will be inserted in the output to shift
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# text past the left, blue column
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# (defaults to: http://www.gen.tcd.ie/pubcrawler/pics/spacer.gif)
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#-----------------------------------------------------------------------------#
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############################################################
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################# SEARCH SPECIFICATION #####################
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############################################################
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###########################################################################
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###### Entrez abbreviations for fields #
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###### (see http://www4.ncbi.nlm.nih.gov/PubMed/linking.html). #
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###### combine fields with AND, OR, BUTNOT and parentheses. #
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# #
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# for PubMed : one of AFFL, ALL, AUTH, ECNO, JOUR, MESH, MAJR, PAGE, #
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# PDAT, PTYP, KYWD, WORD, TITLE, or VOL. #
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# for Nucleotide : one of ACCN, AUTH, PDAT, ECNO, FKEY, GENE, JOUR, KYWD, #
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# MDAT, ORGN, PROP, PROT, SQID, SLEN, SUBS, or #
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# WORD. #
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# #
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# where ACCN = Accession Number, AFFL = Afilliation, ALL = all fields, #
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# AUTH = Author Name, ECNO = E. C. Number, FKEY = Feature Key, #
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# GENE = gene name, JOUR =journal name, KYWD = Keywords, #
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# MAJR = MeSH major topic, MDAT = modification date, #
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# MESH = mesh term,ORGN = organism, PACC = Primary Accesion Number, #
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# PAGE = first page, PDAT = publication/creation date, #
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# PROP = Properties, PROT = protein name, PTYP = Publication Type, #
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# SUBS = Substance, TITL = title word, WORD = text word, #
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# VOL = volume. #
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###########################################################################
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##### Each search-specification has to be written on one line.
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##### The first word must specify the database:
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##### pubmed, pm_neighbour, genbank, or gb_neighbour
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##### Any following words enclosed in single quotes (') will be used
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##### as an alias for this query, otherwise they will be considered
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##### Entrez-search-terms, as will the rest of the line.
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##### You can have as many different searches as you wish. The results of all
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##### searches will be combined according to their aliases.
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##### You CAN NOT use the same alias for searches at different databases!
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##### Write your search descriptions below this line.
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##### (Upper/lower case does not matter.)
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<%- if @searches and @searches.kind_of?(Array) -%>
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<%- @searches.each do |search| -%>
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<%= search['database'] %> '<%= search['alias'] %>' <%= search['term'] %>
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<%- end -%>
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<%- end -%>
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