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README.md Normal file
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Installs Pubcrawler from EuPathDB-specific RPM and manages
`/etc/pubcrawler/` configuration files.
The RPM includes a `/etc/cron.d` job that runs all *.config in `/etc/pubcrawler`.
`pubcrawler::params` defines the common set of configuration parameters.
See `templates/product.config.erb` in this module for documentation on
each parameter.
A configuration file will be generated in `/etc/pubcrawler` for each
key in the `$site_specific_params` hash. All site-specific configuration
files will use values in `$default_params` unless overridden in the
`$site_specific_params`. For example, AmoebaDB will use '14' for
`viewdays` whereas CryptoDB will use '120' because it is has been
overriden in the `$site_specific_params` hash for the `CryptoDB` key.
...
$viewdays = '14'
...
$site_specific_params = {
'AmoebaDB' => {
'bgcolor' => '#C8C5A2',
'header_icon' => '/a/images/AmoebaDB/title_s.png',
'searches' => [
...
],
},
'CryptoDB' => {
'bgcolor' => '#ffcccc',
'header_icon' => '/a/images/CryptoDB/title_s.png',
'viewdays' => '120',
'searches' => [
...
],
},
...
}
### Hiera
The values in `::pubcrawler::params` can be overridden in heira.
pubcrawler::site_specific_params:
AmoebaDB:
bgcolor: '#C8C5A2'
header_icon: '/a/images/AmoebaDB/title_s.png'
searches:
- database: pubmed
alias: Entamoeba
term: Entamoeba [ALL]
- database: pubmed
alias: Acanthamoeba
term: Acanthamoeba [ALL]
In this example, the `$site_specific_params` in `::pubcrawler::params`
will be replaced with a hash containing only AmoebaDB - so only
AmoebaDB will be configured.
Other individual params can be set in heira.
pubcrawler::fullmax: 666
### Configuration Testing
To run a single configuration manually, use
PRODUCT=TrichDB
sudo -u nobody /usr/share/pubcrawler/bin/pubcrawler.pl -c /etc/pubcrawler/${PRODUCT}.config
Results are written to `/usr/share/pubcrawler/html/ToxoDB/`

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# generate one configuration file
define pubcrawler::config (
$bgcolor = $pubcrawler::bgcolor,
$header_icon = $pubcrawler::header_icon,
$searches = $pubcrawler::searches,
$viewdays = $pubcrawler::viewdays,
$relentrezdate = $pubcrawler::relentrezdate,
$getmax = $pubcrawler::getmax,
$fullmax = $pubcrawler::fullmax,
$include_config = $pubcrawler::include_config,
$search_URL = $pubcrawler::search_URL,
$neighbour_URL = $pubcrawler::neighbour_URL,
$retrieve_URL = $pubcrawler::retrieve_URL,
$work_dir = $pubcrawler::work_dir,
$extra_range = $pubcrawler::extra_range,
$check = $pubcrawler::check,
$prompt = $pubcrawler::prompt,
$verbose = $pubcrawler::verbose,
$mute = $pubcrawler::mute,
$log_file = $pubcrawler::log_file,
$base_URL = $pubcrawler::base_URL,
$mail_features = $pubcrawler::mail_features,
$lynx = $pubcrawler::lynx,
$prefix = $pubcrawler::prefix,
$system = $pubcrawler::system,
$proxy_port = $pubcrawler::proxy_port,
$proxy_auth = $pubcrawler::proxy_auth,
$proxy_pass = $pubcrawler::proxy_pass,
$time_out = $pubcrawler::time_out,
$test_URL = $pubcrawler::test_URL,
$no_test = $pubcrawler::no_test,
$indent = $pubcrawler::indent,
$no_decap = $pubcrawler::no_decap,
$spacer = $pubcrawler::spacer,
) {
file {"/etc/pubcrawler/${name}.config":
content => template('pubcrawler/product.config.erb'),
require => Package['pubcrawler'],
}
}

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manifests/init.pp Normal file
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# Install pubcrawler and configuration files.
class pubcrawler (
$site_specific_params = $pubcrawler::params::site_specific_params,
$bgcolor = $pubcrawler::params::bgcolor,
$header_icon = $pubcrawler::params::header_icon,
$searches = $pubcrawler::params::searches,
$viewdays = $pubcrawler::params::viewdays,
$relentrezdate = $pubcrawler::params::relentrezdate,
$getmax = $pubcrawler::params::getmax,
$fullmax = $pubcrawler::params::fullmax,
$include_config = $pubcrawler::params::include_config,
$search_URL = $pubcrawler::params::search_URL,
$neighbour_URL = $pubcrawler::params::neighbour_URL,
$retrieve_URL = $pubcrawler::params::retrieve_URL,
$work_dir = $pubcrawler::params::work_dir,
$extra_range = $pubcrawler::params::extra_range,
$check = $pubcrawler::params::check,
$prompt = $pubcrawler::params::prompt,
$verbose = $pubcrawler::params::verbose,
$mute = $pubcrawler::params::mute,
$log_file = $pubcrawler::params::log_file,
$base_URL = $pubcrawler::params::base_URL,
$mail_features = $pubcrawler::params::mail_features,
$lynx = $pubcrawler::params::lynx,
$prefix = $pubcrawler::params::prefix,
$system = $pubcrawler::params::system,
$proxy_port = $pubcrawler::params::proxy_port,
$proxy_auth = $pubcrawler::params::proxy_auth,
$proxy_pass = $pubcrawler::params::proxy_pass,
$time_out = $pubcrawler::params::time_out,
$test_URL = $pubcrawler::params::test_URL,
$no_test = $pubcrawler::params::no_test,
$indent = $pubcrawler::params::indent,
$no_decap = $pubcrawler::params::no_decap,
$spacer = $pubcrawler::params::spacer,
) inherits pubcrawler::params {
package { 'pubcrawler':
ensure => installed,
}
file { '/etc/httpd/conf.d/pubcrawler.conf':
owner => 'root',
group => 'root',
content => template('pubcrawler/http.pubcrawler.conf.erb'),
}
file { '/etc/cron.d/pubcrawler':
owner => 'root',
group => 'root',
mode => '0644',
content => template('pubcrawler/cron.erb'),
}
create_resources(pubcrawler::config, $site_specific_params)
}

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# Default parameters for Pubcrawler
class pubcrawler::params {
$bgcolor = '#fff'
$header_icon = ''
$viewdays = '14'
$relentrezdate = '90'
$getmax = '800'
$fullmax = '500'
$include_config = 'no'
$search_URL = ''
$neighbour_URL = ''
$retrieve_URL = ''
$extra_range = '1000'
$check = '0'
$prompt = '1'
$verbose = '0'
$mute = '0'
$log_file = ''
$base_URL = 'local_file'
$mail_features = 'all'
$lynx = ''
$prefix = ''
$system = ''
$proxy_port = ''
$proxy_auth = ''
$proxy_pass = ''
$time_out = '180'
$test_URL = 'http://www.ncbi.nlm.nih.gov/'
$no_test = '0'
$indent = '125'
$no_decap = ''
$spacer = ''
$searches = undef
# override some of the above defaults in hash form to make
# configurations specific for a site.
$site_specific_params = {
'AmoebaDB' => {
bgcolor => '#C8C5A2',
header_icon => '/a/images/AmoebaDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Entamoeba',
term => 'Entamoeba [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Acanthamoeba',
term => 'Acanthamoeba [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Entamoeba',
term => 'Entamoeba [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Acanthamoeba',
term => 'Acanthamoeba [ALL]',
},
],
},
'CryptoDB' => {
bgcolor => '#ffcccc',
header_icon => '/a/images/CryptoDB/title_s.png',
searches => [
{
database => 'genbank',
alias => 'New Genbank sequences, C. parvum',
term => 'Cryptosporidium parvum [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences, C. hominis',
term => 'Cryptosporidium hominis [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences, C. muris',
term => 'Cryptosporidium muris [ORGN]',
},
],
},
'EuPathDB' => {
bgcolor => '#507494',
header_icon => '/a/images/EuPathDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Cryptosporidium',
term => 'Cryptosporidium [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Encephalitozoon or Enterocytozoon',
term => 'Enterocytozoon [ALL] or Encephalitozoon [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Entamoeba',
term => 'Entamoeba [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Giardia',
term => 'Giardia [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Microsporidia',
term => 'Edhazardia [ALL] OR Encephalitozoon [ALL] OR Enterocytozoon [ALL] OR Hamiltosporidium [ALL] OR Nematocida [ALL] OR Nosema [ALL] OR Vavraia [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Piroplasma genera',
term => 'Anthemosoma [ALL] OR Babesia [ALL] OR Cristalloidophora [ALL] OR Dactylosoma [ALL] OR Echinozoon [ALL] OR Haemohormidium [ALL] OR Sauroplasma [ALL] OR Theileria [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Plasmodium',
term => 'Plasmodium [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Toxoplasma or Eimeria or Neospora',
term => 'Toxoplasma [ALL] or Eimeria [ALL] or Neospora [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Trichomonas',
term => 'Trichomonas [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on other Apicomplexan organisms',
term => 'Apicomplexa OR Apicomplexan OR Eimeria OR Gregarina OR Neospora OR Sarcocystis OR Theileria NOT Cryptosporidium NOT Plasmodium NOT Toxoplasma [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Leishmania or Trypanosoma or Crithidia',
term => 'Trypanosoma [ALL] or Leishmania [ALL] or Crithidia [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Cryptosporidium',
term => 'Cryptosporidium [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Entamoeba',
term => 'Entamoeba [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Giardia',
term => 'Giardia [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Microsporidia',
term => 'Edhazardia [ORGN] OR Encephalitozoon [ORGN] OR Enterocytozoon [ORGN] OR Hamiltosporidium [ORGN] OR Nematocida [ORGN] OR Nosema [ORGN] OR Vavraia [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Piroplasma genera',
term => 'Anthemosoma OR Babesia OR Cristalloidophora OR Dactylosoma OR Echinozoon OR Haemohormidium OR Sauroplasma OR Theileria [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Plasmodium',
term => 'Plasmodium [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Toxoplasma',
term => 'Toxoplasma [ORGN] or Eimeria [ORGN] or Neospora [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Trichomonas',
term => 'Trichomonas [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for other Apicomplexan organisms',
term => 'Apicomplexa NOT Toxoplasma NOT Plasmodium NOT Cryptosporidium [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Leishmania or Trypanosoma or Crithidia',
term => 'Leishmania [ORGN] or Trypanosoma [ORGN] or Crithidia [ORGN]',
},
],
},
'FungiDB' => {
bgcolor => '#cd919e',
header_icon => '/a/images/FungiDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Aspergillus or Candida or Coccidioides or Cryptococcus or Fusarium or Gibberella or Magnaporthe or Neurospora or Puccinia or Rhizopus or Saccharomyces',
term => 'Aspergillus [ALL] or Candida [ALL] or Coccidioides [ALL] or Cryptococcus [ALL] or Fusarium [ALL] or Gibberella [ALL] or Magnaporthe [ALL] or Neurospora [ALL] or Puccinia [ALL] or Rhizopus [ALL] or Saccharomyces [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Aspergillus or Candida or Coccidioides or Cryptococcus or Fusarium or Gibberella or Magnaporthe or Neurospora or Puccinia or Rhizopus or Saccharomyces',
term => 'Aspergillus [ORGN] or Candida [ORGN] or Coccidioides [ORGN] or Cryptococcus [ORGN] or Fusarium [ORGN] or Gibberella [ORGN] or Magnaporthe [ORGN] or Neurospora [ORGN] or Puccinia [ORGN] or Rhizopus [ORGN] or Saccharomyces [ORGN]',
},
],
},
'GiardiaDB' => {
bgcolor => '#993333',
header_icon => '/a/images/GiardiaDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Giardia',
term => 'Giardia [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Giardia',
term => 'Giardia [ORGN]',
},
],
},
'HostDB' => {
bgcolor => '#e08265',
header_icon => '/a/images/HostDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on host parasite interaction',
term => 'host parasite interaction [ALL]',
},
],
},
'MicrosporidiaDB' => {
bgcolor => '#C4BAD3',
header_icon => '/a/images/MicrosporidiaDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Microsporidia',
term => 'Edhazardia [ALL] OR Encephalitozoon [ALL] OR Enterocytozoon [ALL] OR Hamiltosporidium [ALL] OR Nematocida [ALL] OR Nosema [ALL] OR Vavraia [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Microsporidia',
term => 'Edhazardia [ORGN] OR Encephalitozoon [ORGN] OR Enterocytozoon [ORGN] OR Hamiltosporidium [ORGN] OR Nematocida [ORGN] OR Nosema [ORGN] OR Vavraia [ORGN] or Anncaliia [ORGN] or Vittaforma [ORGN]',
},
],
},
'PiroplasmaDB' => {
bgcolor => '#e08265',
header_icon => '/a/images/PiroplasmaDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Piroplasma genera',
term => 'Anthemosoma [ALL] OR Babesia [ALL] OR Cristalloidophora [ALL] OR Dactylosoma [ALL] OR Echinozoon [ALL] OR Haemohormidium [ALL] OR Sauroplasma [ALL] OR Theileria [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Piroplasma genera',
term => 'Anthemosoma [ORGN] OR [ORGN] Babesia [ORGN] OR Cristalloidophora [ORGN] OR Dactylosoma [ORGN] OR Echinozoon [ORGN] OR Haemohormidium [ORGN] OR Sauroplasma [ORGN] OR Theileria [ORGN]',
},
],
},
'PlasmoDB' => {
bgcolor => '#bbaacc',
header_icon => '/a/images/PlasmoDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Plasmodium',
term => 'Plasmodium [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Plasmodium',
term => 'Plasmodium [ORGN]',
},
],
},
'SchistoDB' => {
bgcolor => '#cd919e',
header_icon => '/a/images/SchistoDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles related to Schistosoma',
term => 'Schistosoma [ALL] or schistosoma [ALL] or blood-fluke [ALL] or Schistosomatidae [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Schistosoma',
term => 'Schistosoma [ORGN]',
},
],
},
'ToxoDB' => {
bgcolor => '#cd919e',
header_icon => '/a/images/ToxoDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Toxoplasma',
term => 'Toxoplasma [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Eimeria',
term => 'Eimeria [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Eimeria',
term => 'Gregarina [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Neospora',
term => 'Neospora [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Toxoplasma, Eimeria, or Neospora',
term => 'Toxoplasma [ORGN] or Eimeria [ORGN] or Neospora [ORGN] or Gregarina [ORGN]',
},
],
},
'TrichDB' => {
bgcolor => '#993333',
header_icon => '/a/images/TrichDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Trichomonas',
term => 'Trichomonas [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Trichomonas',
term => 'Trichomonas [ORGN]',
},
],
},
'TriTrypDB' => {
bgcolor => '#dfbba6',
header_icon => '/a/images/TriTrypDB/title_s.png',
searches => [
{
database => 'pubmed',
alias => 'New PubMed articles on Trypanosoma',
term => 'Trypanosoma [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Leishmania',
term => 'Leishmania [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Crithidia',
term => 'Crithidia [ALL]',
},
{
database => 'pubmed',
alias => 'New PubMed articles on Endotrypanum',
term => 'Endotrypanum [ALL]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Trypanosoma',
term => 'Trypanosoma [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Crithidia',
term => 'Crithidia [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Endotrypanum',
term => 'Endotrypanum [ORGN]',
},
{
database => 'genbank',
alias => 'New Genbank sequences for Leishmania',
term => 'Leishmania [ORGN]',
},
],
},
}
}

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20 4 * * * nobody /usr/share/pubcrawler/bin/pubcrawler-runall

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Alias /pubcrawler /usr/share/pubcrawler/html
<Directory /usr/share/pubcrawler/html>
Options FollowSymLinks Includes
AllowOverride None
Order allow,deny
Allow from all
</Directory>

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############ 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 -%>