mirror of
https://github.com/krislamo/puppet-pubcrawler
synced 2025-10-08 23:59:28 +00:00
move to github
This commit is contained in:
drew
42
manifests/config.pp
Normal file
42
manifests/config.pp
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@@ -0,0 +1,42 @@
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# generate one configuration file
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define pubcrawler::config (
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$bgcolor = $pubcrawler::bgcolor,
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$header_icon = $pubcrawler::header_icon,
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$searches = $pubcrawler::searches,
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$viewdays = $pubcrawler::viewdays,
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$relentrezdate = $pubcrawler::relentrezdate,
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$getmax = $pubcrawler::getmax,
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$fullmax = $pubcrawler::fullmax,
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$include_config = $pubcrawler::include_config,
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$search_URL = $pubcrawler::search_URL,
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$neighbour_URL = $pubcrawler::neighbour_URL,
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$retrieve_URL = $pubcrawler::retrieve_URL,
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$work_dir = $pubcrawler::work_dir,
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$extra_range = $pubcrawler::extra_range,
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$check = $pubcrawler::check,
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$prompt = $pubcrawler::prompt,
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$verbose = $pubcrawler::verbose,
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$mute = $pubcrawler::mute,
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$log_file = $pubcrawler::log_file,
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$base_URL = $pubcrawler::base_URL,
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$mail_features = $pubcrawler::mail_features,
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$lynx = $pubcrawler::lynx,
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$prefix = $pubcrawler::prefix,
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$system = $pubcrawler::system,
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$proxy_port = $pubcrawler::proxy_port,
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$proxy_auth = $pubcrawler::proxy_auth,
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$proxy_pass = $pubcrawler::proxy_pass,
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$time_out = $pubcrawler::time_out,
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$test_URL = $pubcrawler::test_URL,
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$no_test = $pubcrawler::no_test,
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$indent = $pubcrawler::indent,
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$no_decap = $pubcrawler::no_decap,
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$spacer = $pubcrawler::spacer,
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) {
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file {"/etc/pubcrawler/${name}.config":
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content => template('pubcrawler/product.config.erb'),
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require => Package['pubcrawler'],
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}
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}
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59
manifests/init.pp
Normal file
59
manifests/init.pp
Normal file
@@ -0,0 +1,59 @@
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# Install pubcrawler and configuration files.
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class pubcrawler (
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$site_specific_params = $pubcrawler::params::site_specific_params,
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$bgcolor = $pubcrawler::params::bgcolor,
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$header_icon = $pubcrawler::params::header_icon,
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$searches = $pubcrawler::params::searches,
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$viewdays = $pubcrawler::params::viewdays,
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$relentrezdate = $pubcrawler::params::relentrezdate,
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$getmax = $pubcrawler::params::getmax,
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$fullmax = $pubcrawler::params::fullmax,
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$include_config = $pubcrawler::params::include_config,
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$search_URL = $pubcrawler::params::search_URL,
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$neighbour_URL = $pubcrawler::params::neighbour_URL,
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$retrieve_URL = $pubcrawler::params::retrieve_URL,
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$work_dir = $pubcrawler::params::work_dir,
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$extra_range = $pubcrawler::params::extra_range,
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$check = $pubcrawler::params::check,
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$prompt = $pubcrawler::params::prompt,
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$verbose = $pubcrawler::params::verbose,
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$mute = $pubcrawler::params::mute,
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$log_file = $pubcrawler::params::log_file,
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$base_URL = $pubcrawler::params::base_URL,
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$mail_features = $pubcrawler::params::mail_features,
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$lynx = $pubcrawler::params::lynx,
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$prefix = $pubcrawler::params::prefix,
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$system = $pubcrawler::params::system,
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$proxy_port = $pubcrawler::params::proxy_port,
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$proxy_auth = $pubcrawler::params::proxy_auth,
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$proxy_pass = $pubcrawler::params::proxy_pass,
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$time_out = $pubcrawler::params::time_out,
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$test_URL = $pubcrawler::params::test_URL,
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$no_test = $pubcrawler::params::no_test,
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$indent = $pubcrawler::params::indent,
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$no_decap = $pubcrawler::params::no_decap,
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$spacer = $pubcrawler::params::spacer,
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) inherits pubcrawler::params {
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package { 'pubcrawler':
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ensure => installed,
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}
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file { '/etc/httpd/conf.d/pubcrawler.conf':
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owner => 'root',
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group => 'root',
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content => template('pubcrawler/http.pubcrawler.conf.erb'),
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}
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file { '/etc/cron.d/pubcrawler':
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owner => 'root',
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group => 'root',
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mode => '0644',
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content => template('pubcrawler/cron.erb'),
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}
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create_resources(pubcrawler::config, $site_specific_params)
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}
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413
manifests/params.pp
Normal file
413
manifests/params.pp
Normal file
@@ -0,0 +1,413 @@
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# Default parameters for Pubcrawler
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class pubcrawler::params {
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$bgcolor = '#fff'
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$header_icon = ''
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$viewdays = '14'
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$relentrezdate = '90'
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$getmax = '800'
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$fullmax = '500'
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$include_config = 'no'
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$search_URL = ''
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$neighbour_URL = ''
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$retrieve_URL = ''
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$extra_range = '1000'
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$check = '0'
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$prompt = '1'
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$verbose = '0'
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$mute = '0'
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$log_file = ''
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$base_URL = 'local_file'
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$mail_features = 'all'
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$lynx = ''
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$prefix = ''
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$system = ''
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$proxy_port = ''
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$proxy_auth = ''
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$proxy_pass = ''
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$time_out = '180'
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$test_URL = 'http://www.ncbi.nlm.nih.gov/'
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$no_test = '0'
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$indent = '125'
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$no_decap = ''
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$spacer = ''
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$searches = undef
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# override some of the above defaults in hash form to make
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# configurations specific for a site.
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$site_specific_params = {
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'AmoebaDB' => {
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bgcolor => '#C8C5A2',
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header_icon => '/a/images/AmoebaDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Acanthamoeba',
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term => 'Acanthamoeba [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences for Acanthamoeba',
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term => 'Acanthamoeba [ALL]',
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},
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],
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},
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'CryptoDB' => {
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bgcolor => '#ffcccc',
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header_icon => '/a/images/CryptoDB/title_s.png',
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searches => [
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{
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database => 'genbank',
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alias => 'New Genbank sequences, C. parvum',
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term => 'Cryptosporidium parvum [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences, C. hominis',
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term => 'Cryptosporidium hominis [ORGN]',
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},
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{
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database => 'genbank',
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alias => 'New Genbank sequences, C. muris',
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term => 'Cryptosporidium muris [ORGN]',
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},
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],
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},
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'EuPathDB' => {
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bgcolor => '#507494',
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header_icon => '/a/images/EuPathDB/title_s.png',
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searches => [
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Cryptosporidium',
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term => 'Cryptosporidium [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Encephalitozoon or Enterocytozoon',
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term => 'Enterocytozoon [ALL] or Encephalitozoon [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Entamoeba',
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term => 'Entamoeba [ALL]',
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},
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||||
{
|
||||
database => 'pubmed',
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alias => 'New PubMed articles on Giardia',
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term => 'Giardia [ALL]',
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},
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{
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database => 'pubmed',
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alias => 'New PubMed articles on Microsporidia',
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term => 'Edhazardia [ALL] OR Encephalitozoon [ALL] OR Enterocytozoon [ALL] OR Hamiltosporidium [ALL] OR Nematocida [ALL] OR Nosema [ALL] OR Vavraia [ALL]',
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},
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||||
{
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database => 'pubmed',
|
||||
alias => 'New PubMed articles on Piroplasma genera',
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term => 'Anthemosoma [ALL] OR Babesia [ALL] OR Cristalloidophora [ALL] OR Dactylosoma [ALL] OR Echinozoon [ALL] OR Haemohormidium [ALL] OR Sauroplasma [ALL] OR Theileria [ALL]',
|
||||
},
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||||
{
|
||||
database => 'pubmed',
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alias => 'New PubMed articles on Plasmodium',
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term => 'Plasmodium [ALL]',
|
||||
},
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||||
{
|
||||
database => 'pubmed',
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||||
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',
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||||
term => 'Trichomonas [ALL]',
|
||||
},
|
||||
{
|
||||
database => 'pubmed',
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||||
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]',
|
||||
},
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||||
{
|
||||
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]',
|
||||
},
|
||||
],
|
||||
},
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user