public function test_index_all_files()
{
$this->indexer->force_indexation();
$this->indexer->index_all_files();
$index_pathname = $this->indexer->get_main_index_pathname();
$contents_of_index = read_file_into_array($index_pathname);
$expected_contents_of_index = array("qugjuq/1n:153:oneRoot.csv\n", "aluk/1nn:312:oneSuffix.csv\n");
$this->assertEquals($expected_contents_of_index, $contents_of_index, "The main index is not correct.");
$this->assertEquals(2, $this->indexer->get_nb_indexed_entries(), "The total number of indexed morphemes should have been 2.");
$this->assertEquals(2, $this->indexer->get_nb_indexed_files(), "The total number of indexed files should have been 2.");
}
// Read the content of base ontology for encoding/decoding Medicine Safety Codes (MSC server).
$rule_owl = "\n\n";
$textual_rule = "\nClass: rule\n\tAnnotations:\n\t\trdfs:label \"CDS rule\",\n\t\trdfs:comment \"A rule is a logical description of a drug recommendation based on human genotype.\"\n\nClass: phenotype_rule\n\tAnnotations:\n\t\trdfs:label \"Phenotype rule\",\n\t\trdfs:comment \"A phenotype rule is a logical description of a patient phenotype based on its genotype.\"\n\n";
$report = "-- Report -- \n\n";
// Start with the content of the script report and error log.
$valid_polymorphism_variants = array();
// List of valid polymorphism variants from dbSNP (used to find errors and orientation mismatches).
$snps_covered_by_23andMe_v2 = read_file_into_array($snpCoveredBy23andMe_v2_file_location);
// Read the content of SNPs in 23andMe v2 format.
$snps_covered_by_23andMe_v3 = read_file_into_array($snpCoveredBy23andMe_v3_file_location);
// Read the content of SNPs in 23andMe v3 format.
$snps_covered_by_Affimetrix_DMET_chip = read_file_into_array($snpCoveredByAffimetrix_file_location);
// Read the content of SNPs in Affimetrix format.
$snps_covered_by_University_of_Florida_and_Standford_chip = read_file_into_array($snpCoveredByUniOfFloridaAndStandford_file_location);
// Read the content of the University of Florida and Standford format.
$snps_not_in_dbSNP = read_file_into_array($snps_not_in_dbSNP_file_location);
//Read the file that contains the SNPs to skip during the processing of dbSNP file.
/***************************
******* Functions *******
***************************/
//This function indicates if a SNP is part of the genotype of a patient in the ontology. This is needed because a patient's genotype is not only described using haplotypes, such as BRCA1*1, but also with SNPs, such as rs2297595.
function rankSNPInGenotype($rsid)
{
$rank_snps = array("rs9923231", "rs4149056", "rs9934438", "rs6025", "rs12979860", "rs67376798", "rs2297595");
foreach ($rank_snps as $element) {
if ($element == $rsid) {
return true;
}
}
return false;
}
**************************************************/
$owl = file_get_contents($pharmacogenomic_CDS_base_file_location) . "\n\n\n";
// Read the content of base ontology.
$msc_owl = file_get_contents($MSC_classes_base_file_location) . "\n\n\n";
// Read the content of base ontology for encoding/decoding Medicine Safety Codes (MSC server).
$report = "-- Report -- \n\n";
// Start with the content of the script report and error log.
$valid_polymorphism_variants = array();
// List of valid polymorphism variants from dbSNP (used to find errors and orientation mismatches).
$snps_covered_by_23andMe_v2 = read_file_into_array($snpCoveredBy23andMe_v2_file_location);
// Read the content of SNPs in 23andMe v2 format.
$snps_covered_by_23andMe_v3 = read_file_into_array($snpCoveredBy23andMe_v3_file_location);
// Read the content of SNPs in 23andMe v3 format.
$snps_covered_by_Affimetrix_DMET_chip = read_file_into_array($snpCoveredByAffimetrix_file_location);
// Read the content of SNPs in Affimetrix format.
$snps_covered_by_University_of_Florida_and_Standford_chip = read_file_into_array($snpCoveredByUniOfFloridaAndStandford_file_location);
// Read the content of the University of Florida and Standford format.
/***************************
******* Functions *******
***************************/
// Read file and transform it into an array of lines.
function read_file_into_array($file)
{
$search = array("\r\n", "\n");
$snp_array = [];
$handle = fopen($file, 'r');
if ($handle) {
while (!feof($handle)) {
$line = fgets($handle);
$line = str_replace($search, $replace = '', $line);
$snp_array[] = $line;
$pharmacogenomic_CDS_demo_file_location = "..\\ontology\\genomic-cds-demo.owl";
/*
* Initializing important variables
*/
$owl = file_get_contents($pharmacogenomic_CDS_base_file_location) . "\n\n\n";
// Content of main ontology (pharmacogenomic_CDS.owl) will be appended to this variable
$msc_owl = file_get_contents($MSC_classes_base_file_location) . "\n\n\n";
// Content of additional classes for encoding/decoding Medicine Safety Codes (MSC_classes.owl) will be appended to this variable
$report = "-- Report -- \n\n";
// Content of Report and error log (generate_genomic_CDS.report.txt) will be appended to this variable
$valid_polymorphism_variants = array();
// List of valid polymorphism variants from dbSNP (used to find errors and orientation mismatches)
$snps_covered_by_23andMe_v2 = read_file_into_array("..\\data\\assay-information\\SNPs covered by 23andMe v2.txt");
$snps_covered_by_23andMe_v3 = read_file_into_array("..\\data\\assay-information\\SNPs covered by 23andMe v3.txt");
$snps_covered_by_Affimetrix_DMET_chip = read_file_into_array("..\\data\\assay-information\\SNPs covered by Affymetrix DMET chip - PMID 20217574.txt");
$snps_covered_by_University_of_Florida_and_Standford_chip = read_file_into_array("..\\data\\assay-information\\SNPs covered by University of Florida and Stanford University chip - PMID 22910441.txt");
/*
* Functions
*/
function read_file_into_array($file)
{
$search = array("\r\n", "\n");
$snp_array = [];
$handle = fopen($file, 'r');
if ($handle) {
while (!feof($handle)) {
$line = fgets($handle);
$line = str_replace($search, $replace = '', $line);
$snp_array[] = $line;
}
fclose($handle);
