mirror of
https://github.com/krislamo/puppet-pubcrawler
synced 2024-09-19 17:20:36 +00:00
491 lines
16 KiB
Puppet
491 lines
16 KiB
Puppet
# 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]',
|
|
},
|
|
],
|
|
},
|
|
|
|
'VectorBase' => {
|
|
bgcolor => '#6ea05f',
|
|
header_icon => '/a/images/VEuPathDB/Logos-color-text-web/vectorbase.png',
|
|
searches => [
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Diptera',
|
|
term => 'Diptera [ALL]',
|
|
},
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Gastropoda',
|
|
term => 'Gastropoda [ALL]',
|
|
},
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Hemiptera',
|
|
term => 'Hemiptera [ALL]',
|
|
},
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Ixodida',
|
|
term => 'Ixodida [ALL]',
|
|
},
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Phthiraptera',
|
|
term => 'Phthiraptera [ALL]',
|
|
},
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Sarcoptiformes',
|
|
term => 'Sarcoptiformes [ALL]',
|
|
},
|
|
{
|
|
database => 'pubmed',
|
|
alias => 'New PubMed articles on Trombidiformes',
|
|
term => 'Trombidiformes [ALL]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Diptera',
|
|
term => 'Diptera [ORGN]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Gastropoda',
|
|
term => 'Gastropoda [ORGN]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Hemiptera',
|
|
term => 'Hemiptera [ORGN]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Ixodida',
|
|
term => 'Ixodida [ORGN]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Phthiraptera',
|
|
term => 'Phthiraptera [ORGN]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Sarcoptiformes',
|
|
term => 'Sarcoptiformes [ORGN]',
|
|
},
|
|
{
|
|
database => 'genbank',
|
|
alias => 'New Genbank sequences for Trombidiformes',
|
|
term => 'Trombidiformes [ORGN]',
|
|
}
|
|
],
|
|
},
|
|
|
|
}
|
|
|
|
}
|