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