function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("pharmgkb");
// set and print application parameters
$this->AddParameter('files', true, 'all|drugs|genes|diseases|relationships|pathways|rsid|variant_annotations|offsides|twosides', 'all', 'all or comma-separated list of files to process');
$this->AddParameter('indir', false, null, '/data/download/pharmgkb/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/pharmgkb/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.pharmgkb.org/commonFileDownload.action?filename=');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv, $path)
{
parent::__construct();
$this->SetDefaultNamespace("wormbase");
// set and print application parameters
$this->AddParameter('files', true, null, '|all|geneIDs|functional_description|gene_association|gene_interactions|phenotype_association', '', 'files to process');
#The files subject to RDF from wormbase
$this->AddParameter('indir', false, null, $path, 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, $path, 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("uniprot");
// set and print application parameters
$this->AddParameter('files', true, 'all|citations|keywords|locations|taxonomy|tissues|uniprot|uniparc|uniref', 'all', 'all or comma-separated list of files to process');
$this->AddParameter('indir', false, null, '/data/download/uniprot/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/uniprot/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.uniprot.org/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
//
parent::__construct();
$this->SetDefaultNamespace("irefindex");
// set and print application parameters
$this->AddParameter('files', true, 'all|10090|10116|4932|559292|562|6239|7227|9606|other', 'all', 'all or comma-separated list of files to process');
$this->AddParameter('indir', false, null, '/data/download/irefindex/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/irefindex/', 'directory to place rdfized files');
$this->AddParameter('version', false, null, '03022013', 'dated version of files to download');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.no.embnet.org/irefindex/data/current/psi_mitab/MITAB2.6/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("taxon");
// set and print application parameters
$this->AddParameter('files', true, null, 'all|taxdmp|gi2taxid_nucleotide|gi2taxid_protein', '', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/taxonomy/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/taxonomy/', 'directory to place rdfized files');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("chembl");
// set and print application parameters
$this->AddParameter('files', true, 'all|compounds|targets|assays|references|properties', '', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/gene/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/gene/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('user', false, false, 'dba', 'set the user to access the mysql chembl database');
$this->AddParameter('pass', false, false, 'dba', 'set the password of the user to access the mysql chembl database');
$this->AddParameter('db_name', false, null, 'chembl_14', 'set the database table to configure/access the mysql database');
$this->AddParameter('download_url', false, null, 'ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("sider");
// set and print application parameters
$this->AddParameter('files', true, 'all|label_mapping|adverse_effects_raw|indications_raw|meddra_freq_parsed', 'all', 'all or comma-separated list of ontology short names to process');
$this->AddParameter('indir', false, null, '/data/download/sider/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/sider/', 'directory to place rdfized files');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('graph_uri', false, null, null, 'specify a graph uri to generate nquads');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://sideeffects.embl.de/media/download/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("goa");
// set and print application parameters
$this->AddParameter('files', true, 'all|arabidopsis|chicken|cow|dicty|dog|fly|human|mouse|pdb|pig|rat|uniprot|worm|yeast|zebrafish', 'all', 'all or comma-separated list of files to process');
$this->AddParameter('indir', false, null, '/data/download/goa/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/goa/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("iproclass");
// set and print application parameters
$this->AddParameter('indir', false, null, '/data/download/iproclass/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/iproclass/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.pir.georgetown.edu/databases/iproclass/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("affymetrix");
// set and print application parameters
$this->AddParameter('files', true, null, 'all', '');
$this->AddParameter('indir', false, null, '/data/download/' . $this->GetNamespace() . '/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/' . $this->GetNamespace() . '/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.affymetrix.com/support/technical/annotationfilesmain.affx', '');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("drugbank");
// set and print application parameters
$this->AddParameter('files', true, 'all|drugbank.xml.zip', 'all', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/' . $this->GetNamespace() . '/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/' . $this->GetNamespace() . '/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.drugbank.ca/system/downloads/current/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("sabiork");
// set and print application parameters
$this->AddParameter('files', true, null, 'all', 'entries to process: comma-separated list or hyphen-separated range');
$this->AddParameter('indir', false, null, '/data/download/' . $this->GetNamespace() . '/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/' . $this->GetNamespace() . '/', 'directory to place rdfized files');
$this->AddParameter('download', false, 'true|false', 'false', 'Force data download');
$this->AddParameter('download_url', false, null, 'http://sabiork.h-its.org/sabioRestWebServices/', 'Download API');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
//
parent::__construct();
$this->SetDefaultNamespace("ctd");
// set and print application parameters
$this->AddParameter('files', true, 'all|chem_gene_ixns|chem_gene_ixn_types|chemicals_diseases|chem_go_enriched|chem_pathways_enriched|genes_diseases|genes_pathways|diseases_pathways|chemicals|diseases|genes|pathways', 'all', 'all or comma-separated list of files to process');
$this->AddParameter('indir', false, null, '/data/download/ctd/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/ctd/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://ctdbase.org/reports/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("unists");
// set and print application parameters
$this->AddParameter('files', true, null, 'all|markers|map_reports|pcr_reports', '', 'files to process');
$this->AddParameter('indir', false, null, '/home/jose/tmp/unists/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/home/jose/tmp/n3/unists/', 'directory to place rdfized files');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/repository/UniSTS/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("ndc");
// set and print application parameters
$this->AddParameter('files', true, 'all|product|package', 'all', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/ndc/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/ndc/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/UCM070838.zip');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("sgd");
// set and print application parameters
$this->AddParameter('files', true, 'all|dbxref|features|domains|protein|goa|goslim|complex|interaction|phenotype|pathways|mapping', 'all', 'all or comma-separated list of files to process');
$this->AddParameter('indir', false, null, '/data/download/sgd/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/sgd/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://downloads.yeastgenome.org/');
$this->AddParameter('ncbo_api_key', false, null, '24e19c82-54e0-11e0-9d7b-005056aa3316');
$this->AddParameter('ncbo_download_dir', false, null, '/data/download/ncbo', 'directory of ncbo ontologies');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->AddParameter('sync', false, 'true|false', 'false', 'update all files or just download ones not present');
$this->AddParameter('files', true, 'all|compounds|substances|bioactivity', 'all', 'files to process');
$this->AddParameter('indir', false, null, '../../download/pubchem/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '../../data/pubchem', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide a graph uri to generate n-quads');
$this->AddParameter('workspace', false, null, '../../workspace/pubchem/', 'directory to mount pubchem FTP server');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download_url', false, null, 'ftp.ncbi.nlm.nih.gov/pubchem/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("clinicaltrials");
$this->AddParameter('process', true, 'crawl|download|local', 'local', 'select how to process files from the clinical open trials website');
$this->AddParameter('files', false, 'all|study|results', 'all', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/clinicaltrials/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/clinicaltrials/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'specify a graph uri to generate nquads');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('remote_server', false, null, 'http://clinicaltrials.gov/ct2/crawl');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("sider");
// set and print application parameters
$this->AddParameter('files', true, 'all|MGI_Strain|MGI_PhenotypicAllele|HMD_HGNC_Accession', 'all', 'all or comma-separated list to process');
$this->AddParameter('indir', false, null, '/data/download/mgi/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/mgi/', 'directory to place rdfized files');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('graph_uri', false, null, null, 'specify a graph uri to generate nquads');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.informatics.jax.org/pub/reports/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("biomodels");
// set and print application parameters
$this->AddParameter('files', true, null, 'all|curated|biomodel#|start#-end#', 'entries to process: comma-separated list or hyphen-separated range');
$this->AddParameter('indir', false, null, '/data/download/' . $this->GetNamespace() . '/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/' . $this->GetNamespace() . '/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.ebi.ac.uk/biomodels/models-main/publ/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("omim");
// set and print application parameters
$this->AddParameter('files', true, null, 'all|omim#', 'entries to process: comma-separated list or hyphen-separated range');
$this->AddParameter('indir', false, null, '/data/download/' . $this->GetNamespace() . '/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/' . $this->GetNamespace() . '/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://grcf.jhmi.edu/OMIM/');
$this->AddParameter('omim_api_url', false, null, 'http://api.omim.org/api/entry?include=all&format=json');
$this->AddParameter('omim_api_key', false, null, '06402537D15CFD3880C99805B2AACA9858FAEE37', 'the OMIM key to download entries');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("hgnc");
// set and print application parameters
$this->AddParameter('indir', false, null, '/data/download/hgnc/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/hgnc/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download file');
$this->AddParameter('download_url', false, null, 'http://www.genenames.org/cgi-bin/hgnc_downloads?title=HGNC+output+data&hgnc_dbtag=on&preset=all&status=Approved&status=Entry+Withdrawn&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("pathwaycommons");
// set and print application parameters
$this->AddParameter('files', true, 'all|biogrid|cell-map|hprd|humancyc|imid|intact|mint|nci-nature|reactome', 'all', 'biopax OWL files to process');
$this->AddParameter('indir', false, null, '/data/download/' . $this->GetNamespace() . '/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/' . $this->GetNamespace() . '/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.pathwaycommons.org/pc-snapshot/current-release/biopax/by_source/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("mesh");
// set and print application parameters
$this->AddParameter('files', true, null, 'all|descriptor_records|qualifier_records|supplementary_records', '', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/mesh/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/mesh/', 'directory to place rdfized files');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'http://www.nlm.nih.gov/cgi/request.meshdata');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("geneid");
// set and print application parameters
$this->AddParameter('files', true, 'all|geneinfo|gene2accession|gene2ensembl|gene2go|gene2pubmed|gene2refseq|gene2sts|gene2unigene|gene2vega', '', 'files to process');
$this->AddParameter('indir', false, null, '/data/download/gene/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/gene/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/gene/DATA/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
$this->SetDefaultNamespace("homologene");
//set and print the application options
$this->AddParameter('download', false, 'true|false', 'false', 'set true to download files');
$this->AddParameter('indir', false, null, '/data/download/homologene', 'directory to download files');
$this->AddParameter('outdir', false, null, '/data/rdf/homologene/', 'directory to place rdfized files');
$this->AddParameter('graph_uri', false, null, null, 'provide the graph uri to generate n-quads instead of n-triples');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
$this->AddParameter('force', false, 'true|false', 'true', 'remove old files and copy over');
$this->AddParameter('download_url', false, null, 'ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
//create necessary directories if they don't exist
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
if ($this->GetParameterValue('graph_uri')) {
$this->SetGraphURI($this->GetParameterValue('graph_uri'));
}
return TRUE;
}
function __construct($argv)
{
parent::__construct();
// set and print application parameters
$this->AddParameter('files', true, null, 'all', 'entries to process: comma-separated list or hyphen-separated range');
$this->AddParameter('indir', false, null, '/data/download/biopax/', 'directory to download into and parse from');
$this->AddParameter('outdir', false, null, '/data/rdf/biopax/', 'directory to place rdfized files');
$this->AddParameter('gzip', false, 'true|false', 'true', 'gzip the output');
if ($this->SetParameters($argv) == FALSE) {
$this->PrintParameters($argv);
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('indir')) === FALSE) {
exit;
}
if ($this->CreateDirectory($this->GetParameterValue('outdir')) === FALSE) {
exit;
}
return TRUE;
}
