public function testAddScreeningToHealthyIndividual()
{
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b")));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/individual\\/00000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings[\\s\\S]create&target=00000001$/', $this->driver->getCurrentURL()));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Template[]"]/option[text()="RNA (cDNA)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Template[]"]/option[text()="Protein"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Technique[]"]/option[text()="array for Comparative Genomic Hybridisation"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Technique[]"]/option[text()="array for resequencing"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Technique[]"]/option[text()="array for SNP typing"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="genes[]"]/option[text()="IVD (isovaleryl-CoA dehydrogenase)"]'));
$option->click();
$this->check(WebDriverBy::name("variants_found"));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="LOVD3 Admin (#00001)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create screening information entry']"));
$element->click();
$this->assertEquals("Successfully created the screening entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testAddVariantLocatedWithinGeneToHealthyIndividual()
{
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b")));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&target=0000000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath('//b[contains(., "A variant that is located within a gene")]'));
// $element = $this->driver->findElement(WebDriverBy::xpath("//table[2]/tbody/tr/td[2]/b"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//tr[@id='IVD']/td[2]"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&reference=Transcript&geneid=IVD&target=0000000001$/', $this->driver->getCurrentURL()));
$this->uncheck(WebDriverBy::name("ignore_00000001"));
$this->enterValue(WebDriverBy::name("00000001_VariantOnTranscript/Exon"), "2");
$this->enterValue(WebDriverBy::name("00000001_VariantOnTranscript/DNA"), "c.456T>G");
$element = $this->driver->findElement(WebDriverBy::cssSelector("button.mapVariant"));
$element->click();
// Wait until RNA description field is filled after AJAX request.
$firstRNAInputSelector = '(//input[contains(@name, "VariantOnTranscript/RNA")])[1]';
$this->waitUntil(function ($driver) use($firstRNAInputSelector) {
$firstRNAInput = $driver->findElement(WebDriverBy::xpath($firstRNAInputSelector));
$firstRNAValue = $firstRNAInput->getAttribute('value');
return !empty($firstRNAValue);
});
// Check RNA description.
$firstRNAInput = $this->driver->findElement(WebDriverBy::xpath($firstRNAInputSelector));
$firstRNAValue = $firstRNAInput->getAttribute('value');
$this->assertTrue((bool) preg_match('/^r\\.\\([\\s\\S]\\)$/', $firstRNAValue));
// Check protein description.
$firstProteinInputSelector = '(//input[contains(@name, "VariantOnTranscript/Protein")])[1]';
$firstProteinInput = $this->driver->findElement(WebDriverBy::xpath($firstProteinInputSelector));
$firstProteinValue = $firstProteinInput->getAttribute('value');
$this->assertRegExp('/^p\\.\\(Tyr152[\\s\\S]*\\)$/', $firstProteinValue);
$GenomicDNAChange = $this->driver->findElement(WebDriverBy::name('VariantOnGenome/DNA'));
$this->assertEquals("g.40702987T>G", $GenomicDNAChange->getAttribute('value'));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="00000001_effect_reported"]/option[text()="Effect unknown"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="00000001_effect_concluded"]/option[text()="Effect unknown"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="allele"]/option[text()="Paternal (confirmed)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::linkText("PubMed"));
$element->click();
$this->enterValue(WebDriverBy::name("VariantOnGenome/Reference"), "{PMID:Fokkema et al (2011):21520333}");
$this->enterValue(WebDriverBy::name("VariantOnGenome/Frequency"), "0.05");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="effect_reported"]/option[text()="Effect unknown"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="effect_concluded"]/option[text()="Effect unknown"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="LOVD3 Admin (#00001)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="statusid"]/option[text()="Public"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create variant entry']"));
$element->click();
$this->assertEquals("Successfully created the variant entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testAccessSharingSubmitter()
{
$aUserRecords = CreateUsersSubmitterTest::userRecords();
if (count($aUserRecords) < 2) {
$this->fail('Cannot run test because CreateUsersSubmitterTest::userRecords() returned
too few records.');
}
// Example record: array('Test Submitter1', '*****@*****.**', 'testsubmitter1',
// 'testsubmitter1')
list($sSubName1, $sSubEmail1, $sSubUsername1, $sSubPass1) = $aUserRecords[0];
list($sSubName2, $sSubEmail2, $sSubUsername2, $sSubPass2) = $aUserRecords[1];
$this->logout();
$this->login($sSubUsername1, $sSubPass1);
// Create individual as first submitter.
$this->driver->get(ROOT_URL . "/src/individuals?create");
$this->enterValue(WebDriverBy::name("Individual/Lab_ID"), "dummy");
$createButton = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create individual information entry']"));
$createButton->click();
$this->waitUntil(WebDriverExpectedCondition::titleContains('Submission of'));
$header = $this->driver->findElement(WebDriverBy::xpath('//h2[@class="LOVD"]'));
$sIndividualID = substr($header->getText(), -8);
$this->logout();
$this->login($sSubUsername2, $sSubPass2);
// Try (unsuccessfully) to access individual.
$this->driver->get(ROOT_URL . '/src/individuals/' . $sIndividualID);
$infoBox = $this->driver->findElement(WebDriverBy::xpath('//table[@class="info"]/tbody/tr/td[@valign="middle"]'));
$this->assertEquals($infoBox->getText(), 'No such ID!');
$this->logout();
$this->login($sSubUsername1, $sSubPass1);
// Open access sharing page
$yourAccountLink = $this->driver->findElement(WebDriverBy::xpath('//a/b[text()="Your account"]'));
$yourAccountLink->click();
$sMenuSelector = '//img[@id="viewentryOptionsButton_Users"]';
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath($sMenuSelector)));
$optionsMenu = $this->driver->findElement(WebDriverBy::xpath($sMenuSelector));
$optionsMenu->click();
$sMenuItemSelector = '//a[text()="Share access to your entries with other users"]';
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath($sMenuItemSelector)));
$shareAccessItem = $this->driver->findElement(WebDriverBy::xpath($sMenuItemSelector));
$shareAccessItem->click();
// Share access with other submitter.
$sUserSelector = '//a[text()="' . $sSubName2 . '"]';
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath($sUserSelector)));
$userRow = $this->driver->findElement(WebDriverBy::xpath($sUserSelector));
$userRow->click();
$this->enterValue(WebDriverBy::xpath('//td/input[@type="password"]'), $sSubPass1);
$saveButton = $this->driver->findElement(WebDriverBy::xpath('//input[@value="Save access permissions"]'));
$saveButton->click();
$this->logout();
$this->login($sSubUsername2, $sSubPass2);
// Try (successfully) to access individual.
$this->driver->get(ROOT_URL . '/src/individuals/' . $sIndividualID);
$header = $this->driver->findElement(WebDriverBy::xpath('//h2[@class="LOVD"]'));
$this->assertEquals($header->getText(), 'View individual #' . $sIndividualID);
$nonpubFieldHead = $this->driver->findElement(WebDriverBy::xpath('//table[@class="data"]/tbody/tr[4]/th'));
$this->assertEquals($nonpubFieldHead->getText(), 'Remarks (non public)');
}
public function login()
{
$this->driver->get('https://web.skype.com');
$this->driver->wait()->until(function () {
return WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::id('username'));
});
$this->driver->findElement(WebDriverBy::id('username'))->sendKeys($this->username);
$this->driver->findElement(WebDriverBy::id('password'))->sendKeys($this->password);
$this->driver->findElement(WebDriverBy::cssSelector('form'))->submit();
$this->waitForSelector('[name=query]');
sleep(15);
return true;
}
public function testAddVCFFileToIVAIndividual()
{
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000003$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&target=0000000003$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//tr[3]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&target=0000000003$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&type=VCF&target=0000000003$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("variant_file"), ROOT_PATH . "../tests/test_data_files/ShortVCFfilev1.vcf");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="hg_build"]/option[text()="hg19"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="dbSNP_column"]/option[text()="VariantOnGenome/Reference"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="genotype_field"]/option[text()="Use Phred-scaled genotype likelihoods (PL)"]'));
$option->click();
$this->check(WebDriverBy::name("allow_mapping"));
$this->check(WebDriverBy::name("allow_create_genes"));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="LOVD3 Admin"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="statusid"]/option[text()="Public"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Upload VCF file']"));
$element->click();
$this->assertEquals("25 variants were imported, 1 variant could not be imported.", $this->driver->findElement(WebDriverBy::id("lovd__progress_message"))->getText());
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Continue »']"));
$element->click();
for ($second = 0;; $second++) {
if ($second >= 600) {
$this->fail("timeout");
}
$this->driver->get(ROOT_URL . "/src/ajax/map_variants.php");
if (strcmp("0 99 There are no variants to map in the database", $this->driver->findElement(WebDriverBy::tagName("body"))->getText())) {
break;
}
$this->assertNotContains("of 25 variants", $this->driver->findElement(WebDriverBy::tagName("body"))->getText());
sleep(1);
}
// Test whether a variant was parsed correctly via mutalyzer.
$this->driver->get(ROOT_URL . '/src/genes/ARSD');
$element = $this->driver->findElement(WebDriverBy::xpath('//tr[@class="data"]/td[text()="X"]'));
$element->click();
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath('//td[text()="p.(Gln318His)"]')));
}
public function testConfirmVariantToCMTIndividual()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Are you sure you are done with submitting the variants found with this screening[\\s\\S][\\s\\S]*$/', $this->getConfirmation()));
$this->chooseOkOnNextConfirmation();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/individual\\/00000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings[\\s\\S]create&target=00000001$/', $this->driver->getCurrentURL()));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Template[]"]/option[text()="RNA (cDNA)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Template[]"]/option[text()="Protein"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Technique[]"]/option[text()="Single Base Extension"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Technique[]"]/option[text()="Single-Strand DNA Conformation polymorphism Analysis (SSCP)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Screening/Technique[]"]/option[text()="SSCA, fluorescent (SSCP)"]'));
$option->click();
// $this->addSelection(WebDriverBy::name("genes[]"), "value=GJB1");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="genes[]"]/option[@value="GJB1"]'));
$option->click();
$this->check(WebDriverBy::name("variants_found"));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="LOVD3 Admin (#00001)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create screening information entry']"));
$element->click();
$this->assertEquals("Successfully created the screening entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&target=0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings\\/0000000002[\\s\\S]confirmVariants$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::id("check_0000000001"));
$element->click();
$this->enterValue(WebDriverBy::xpath("//td/input[@type='password']"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Save variant list']"));
$element->click();
$confirmElementSelector = WebDriverBy::xpath('//td[text()="Successfully confirmed the variant entry!"]');
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated($confirmElementSelector));
}
public function testAddPhenotypeInfoToHealthyIndividual()
{
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b")));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/individual\\/00000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/phenotypes[\\s\\S]create&target=00000001$/', $this->driver->getCurrentURL()));
// $this->selectWindow("null");
$this->enterValue(WebDriverBy::name("Phenotype/Age"), "35y");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="LOVD3 Admin (#00001)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="statusid"]/option[text()="Public"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create phenotype information entry']"));
$element->click();
$this->assertEquals("Successfully created the phenotype entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testCreateGeneIVD()
{
$this->driver->get(ROOT_URL . "/src/genes?create");
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::name("hgnc_id")));
$this->enterValue(WebDriverBy::name("hgnc_id"), "IVD");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Continue »']"));
$element->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="active_transcripts[]"]/option[text()="transcript variant 1 (NM_002225.3)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::name("show_hgmd"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::name("show_genecards"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::name("show_genetests"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create gene information entry']"));
$element->click();
$this->assertEquals("Successfully created the gene information entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
/**
* Waits up to $timeout seconds for an element to appear on the page.
* If the element doesn't appear, a timeout exception is thrown.
*
* ``` php
* <?php
* $I->waitForElement('#agree_button', 30); // secs
* $I->click('#agree_button');
* ?>
* ```
*
* @param $element
* @param int $timeout seconds
* @throws \Exception
*/
public function waitForElement($element, $timeout = 10)
{
$condition = WebDriverExpectedCondition::presenceOfElementLocated($this->getLocator($element));
$this->webDriver->wait($timeout)->until($condition);
}
public function testAddSummaryVariantLocatedWithinGene()
{
$element = $this->driver->findElement(WebDriverBy::id("tab_submit"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Please reconsider to submit individual data as well, as it makes the data you submit much more valuable![\\s\\S]*$/', $this->getConfirmation()));
$this->chooseOkOnNextConfirmation();
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::cssSelector("#ARSD > td.ordered"));
$element->click();
$this->assertContains("src/variants?create&reference=Transcript&geneid=ARSD", $this->driver->getCurrentURL());
for ($second = 0;; $second++) {
if ($second >= 60) {
$this->fail("timeout");
}
try {
if ($this->isElementPresent(WebDriverBy::name("ignore_00000002"))) {
break;
}
} catch (Exception $e) {
}
sleep(1);
}
$this->uncheck(WebDriverBy::name("ignore_00000003"));
$this->enterValue(WebDriverBy::name("00000002_VariantOnTranscript/Exon"), "3");
$this->enterValue(WebDriverBy::name("00000002_VariantOnTranscript/DNA"), "c.62T>A");
$element = $this->driver->findElement(WebDriverBy::cssSelector("button.mapVariant"));
$element->click();
// Wait until the first two RNA-change input fields contain data.
$firstRNAInputSelector = '(//input[contains(@name, "VariantOnTranscript/RNA")])[1]';
$secondRNAInputSelector = '(//input[contains(@name, "VariantOnTranscript/RNA")])[2]';
$this->waitUntil(function ($driver) use($firstRNAInputSelector, $secondRNAInputSelector) {
$firstRNAInput = $driver->findElement(WebDriverBy::xpath($firstRNAInputSelector));
$firstRNAValue = $firstRNAInput->getAttribute('value');
$secondRNAInput = $driver->findElement(WebDriverBy::xpath($secondRNAInputSelector));
$secondRNAValue = $secondRNAInput->getAttribute('value');
return !empty($firstRNAValue) && !empty($secondRNAValue);
});
// Check RNA description for first transcript.
$firstRNAInput = $this->driver->findElement(WebDriverBy::xpath($firstRNAInputSelector));
$firstRNAValue = $firstRNAInput->getAttribute('value');
$this->assertTrue((bool) preg_match('/^r\\.\\([\\s\\S]\\)$/', $firstRNAValue));
// Check protein description for first transcript.
$firstProteinInputSelector = '(//input[contains(@name, "VariantOnTranscript/Protein")])[1]';
$firstProteinInput = $this->driver->findElement(WebDriverBy::xpath($firstProteinInputSelector));
$firstProteinValue = $firstProteinInput->getAttribute('value');
$this->assertEquals("p.(Leu21Gln)", $firstProteinValue);
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="00000002_effect_reported"]/option[text()="Probably affects function"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="00000002_effect_concluded"]/option[text()="Probably does not affect function"]'));
$option->click();
$this->enterValue(WebDriverBy::name("00000003_VariantOnTranscript/Exon"), "3");
$this->enterValue(WebDriverBy::name("00000004_VariantOnTranscript/Exon"), "3");
$this->enterValue(WebDriverBy::name("00000005_VariantOnTranscript/Exon"), "3");
// Check DNA description for first transcript.
$firstDNAInputSelector = '(//input[contains(@name, "VariantOnTranscript/DNA")])[1]';
$firstDNAInput = $this->driver->findElement(WebDriverBy::xpath($firstDNAInputSelector));
$firstDNAValue = $firstDNAInput->getAttribute('value');
$this->assertEquals("c.62T>A", $firstDNAValue);
// Check RNA description for second transcript.
$secondRNAInput = $this->driver->findElement(WebDriverBy::xpath($secondRNAInputSelector));
$secondRNAValue = $secondRNAInput->getAttribute('value');
$this->assertTrue((bool) preg_match('/^r\\.\\([\\s\\S]\\)$/', $secondRNAValue));
// Check protein description for second transcript.
$secondProteinInputSelector = '(//input[contains(@name, "VariantOnTranscript/Protein")])[2]';
$secondProteinInput = $this->driver->findElement(WebDriverBy::xpath($secondProteinInputSelector));
$secondProteinValue = $secondProteinInput->getAttribute('value');
$this->assertEquals("p.(Leu21Gln)", $secondProteinValue);
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="00000003_effect_reported"]/option[text()="Probably affects function"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="00000003_effect_concluded"]/option[text()="Probably does not affect function"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="allele"]/option[text()="Maternal (confirmed)"]'));
$option->click();
$GenomicDNAChange = $this->driver->findElement(WebDriverBy::name('VariantOnGenome/DNA'));
$this->assertEquals("g.2843789A>T", $GenomicDNAChange->getAttribute('value'));
$element = $this->driver->findElement(WebDriverBy::linkText("PubMed"));
$element->click();
// Move mouse to let browser hide tooltip of pubmed link (needed for chrome)
$this->driver->getMouse()->mouseMove(null, 200, 200);
$this->enterValue(WebDriverBy::name("VariantOnGenome/Reference"), "{PMID:Fokkema et al (2011):21520333}");
$this->enterValue(WebDriverBy::name("VariantOnGenome/Frequency"), "55/18000");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="effect_reported"]/option[text()="Affects function"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="effect_concluded"]/option[text()="Affects function"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="LOVD3 Admin (#00001)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="statusid"]/option[text()="Public"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create variant entry']"));
$element->click();
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::cssSelector("table[class=info]")));
$this->assertContains("Successfully processed your submission and sent an email notification to the relevant curator", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testFindReplace()
{
// Upload variant data.
$this->driver->get(ROOT_URL . '/src/variants/upload?create&type=VCF');
$this->enterValue(WebDriverBy::name("variant_file"), ROOT_PATH . "../tests/test_data_files/ShortVCFfilev1.vcf");
$uploadButton = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Upload VCF file']"));
$uploadButton->click();
// Go to variant overview
$this->driver->get(ROOT_URL . '/src/variants');
// Open find and replace for Reference col.
$this->openFRMenuForCol(6);
// Click cancel button.
sleep(1);
$cancelButton = $this->driver->findElement(WebDriverBy::id('FRCancel_VOG'));
$cancelButton->click();
// Check if cancel button is hidden together with FR options menu by javascript.
$this->waitUntil(WebDriverExpectedCondition::invisibilityOfElementLocated(WebDriverBy::id('FRCancel_VOG')));
// Open find and replace for Reference col.
$this->openFRMenuForCol(6);
$columnReference = $this->driver->findElement(WebDriverBy::id('viewlistFRColDisplay_VOG'));
$this->assertEquals($columnReference->getText(), 'Reference');
$this->enterValue(WebDriverBy::name('FRReplace_VOG'), 'newvalue');
$previewButton = $this->driver->findElement(WebDriverBy::id('FRPreview_VOG'));
$previewButton->click();
// Click on header to close tooltip.
$previewTooltip = $this->driver->findElement(WebDriverBy::xpath('//div[@class="ui-tooltip-content" and contains(., "Preview changes")]'));
$mainHeader = $this->driver->findElement(WebDriverBy::xpath('//h2[contains(., "LOVD")]'));
$mainHeader->click();
// Check if tooltip is closed.
$this->waitUntil(WebDriverExpectedCondition::stalenessOf($previewTooltip));
$this->assertContains($this->driver->findElement(WebDriverBy::xpath('//th[@data-fieldname="VariantOnGenome/Reference_FR"]'))->getText(), 'Reference (PREVIEW)');
$aNewValueElements = $this->driver->findElements(WebDriverBy::xpath('//td[text()="newvalue"]'));
$this->assertEquals(count($aNewValueElements), 25);
$this->enterValue(WebDriverBy::xpath('//input[@type="password"]'), 'test1234');
$submitButton = $this->driver->findElement(WebDriverBy::id('FRSubmit_VOG'));
$submitButton->click();
$this->chooseOkOnNextConfirmation();
// Wait for refresh of viewlist with string "newvalue" in 6th column (Reference).
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath('//table[@id="viewlistTable_VOG"]/tbody/tr/td[position()=6 and text()="newvalue"]')));
// Open find & replace menu for field "DNA change (genomic) (hg19)"
$this->openFRMenuForCol(5);
// Set search field to 'C' and preview.
$this->enterValue(WebDriverBy::name('FRSearch_VOG'), 'C');
$previewButton = $this->driver->findElement(WebDriverBy::id('FRPreview_VOG'));
$previewButton->click();
// Click on tooltip to close it
$previewTooltip = $this->driver->findElement(WebDriverBy::xpath('//div[@class="ui-tooltip-content" and text()="Preview changes (14 rows affected)"]'));
$previewTooltip->click();
// Filter on 'Variant ID' > 10 during preview.
$sSearchIDSelector = WebDriverBy::name('search_id_');
$this->enterValue($sSearchIDSelector, '>10');
$searchIDElement = $this->driver->findElement($sSearchIDSelector);
// Use json_decode to send enter key to browser.
$searchIDElement->sendKeys(json_decode('"\\uE007"'));
// Check that viewlist is refreshed. (id='0000000004' should be filtered)
$this->waitUntil(function ($driver) {
$vlTable = $driver->findElement(WebDriverBy::id('viewlistTable_VOG'));
// Avoid checking text exactly during refresh.
try {
$sTableText = $vlTable->getText();
} catch (StaleElementReferenceException $e) {
// try again next poll
return false;
}
return strpos($sTableText, '0000000004') === false;
});
// Submit find & replace
$this->enterValue(WebDriverBy::xpath('//input[@type="password"]'), 'test1234');
$submitButton = $this->driver->findElement(WebDriverBy::id('FRSubmit_VOG'));
$submitButton->click();
// Check that filter has effect (otherwise 14 records are modified).
$alertText = $this->driver->switchTo()->alert()->getText();
$this->assertContains('You are about to modify 9 records', $alertText);
$this->chooseOkOnNextConfirmation();
// Wait until viewlist is refreshed.
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath('//td[@valign="middle" and contains(., "Find & Replace applied to column")]')));
// Open find and replace for Reference col.
$this->openFRMenuForCol(6);
$matchBeginningRadio = $this->driver->findElement(WebDriverBy::xpath('//input[@name="FRMatchType_VOG" and @value="2"]'));
$matchBeginningRadio->click();
$this->enterValue(WebDriverBy::name('FRReplace_VOG'), 'prefix');
// Find empty string at beginning of field and insert prefix string.
$previewButton = $this->driver->findElement(WebDriverBy::id('FRPreview_VOG'));
$previewButton->click();
// Click on tooltip to close it
$previewTooltip = $this->driver->findElement(WebDriverBy::xpath('//div[@class="ui-tooltip-content" and text()="Preview changes (15 rows affected)"]'));
$previewTooltip->click();
$this->enterValue(WebDriverBy::xpath('//input[@type="password"]'), 'test1234');
$submitButton = $this->driver->findElement(WebDriverBy::id('FRSubmit_VOG'));
$submitButton->click();
$this->chooseOkOnNextConfirmation();
$this->waitUntil(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::xpath('//td[text()="prefixnewvalue"]')));
}
/**
* Получить список организаций в категории
* @param string $cityHref Ссылка на страницу города
* @param string $rubricName Название рубрики
* @param string $rubricId Id рубрики
* @return array
*/
public function getOrganisationsByRubric($cityHref, $rubricName, $rubricId)
{
$rubricName = urlencode($rubricName);
$this->driver->get("{$cityHref}/search/{$rubricName}/rubricId/{$rubricId}");
$results = [];
//Особенность 2гис - элементы рендерят вначале несколько раз, ждем пока не зарендерятся
sleep(1);
$organisationList = $this->driver->findElements(WebDriverBy::className('mixedResults'));
if (isset($organisationList[0])) {
$organisations = $organisationList[0]->findElements(WebDriverBy::className('miniCard'));
foreach ($organisations as $organisation) {
$organisation->click();
//Ждем появления карточки организации
$this->driver->wait(5, 500)->until(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::className('firmCard')));
$firmCard = $this->driver->findElements(WebDriverBy::className('firmCard'));
if (isset($firmCard[0])) {
$results[] = $this->extractDataFromFirmCard($firmCard[0]);
}
}
} else {
//Если списка организаций нет - проверяем наличие карточки организации
$firmCard = $this->driver->findElements(WebDriverBy::className('firmCard'));
if (isset($firmCard[0])) {
$results[] = $this->extractDataFromFirmCard($firmCard[0]);
}
}
return $results;
}
echo $e->getTraceAsString() . PHP_EOL;
print "[view_car_details:2] Missing car anchor tag." . PHP_EOL;
$f++;
}
try {
if (!isset($element)) {
throw new Exception();
}
$element->click();
$s++;
} catch (Exception $e) {
print "[view_car_details:3] Cannot click element." . PHP_EOL;
$f++;
}
try {
$driver->wait(10, 500)->until(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::className("jumbotron")));
$s++;
} catch (Exception $e) {
print "[view_car_details:4] Never loaded page with jumbotron." . PHP_EOL;
$f++;
}
try {
$elements = $driver->findElements(WebDriverBy::cssSelector(".jumbotron label"));
$text = trim($elements[0]->getText());
if (strpos($text, "Number of Passengers:") == -1) {
throw new Exception();
}
$s++;
} catch (Exception $e) {
print "[view_car_details:5] Passenger text missing." . PHP_EOL;
$f++;
/**
* @param string $locator
* @param int|null $timeout
*/
public function waitForElement($locator, $timeout = null)
{
$this->_waitUntil(WebDriverExpectedCondition::presenceOfElementLocated($this->_getLocator($locator)), $timeout);
}
function login($driver)
{
print 'Logging in to WordPress... ';
try {
$driver->get(wordpress('/wp-login.php'));
usleep(250000);
$driver->findElement(WebDriverBy::id('user_login'))->sendKeys('admin');
$driver->findElement(WebDriverBy::id('user_pass'))->sendKeys('admin');
$driver->findElement(WebDriverBy::id('loginform'))->submit();
$driver->wait(2)->until(WebDriverExpectedCondition::presenceOfElementLocated(WebDriverBy::cssSelector('div.wrap h1, div.wrap h2')));
} catch (Exception $e) {
var_dump($driver->getPageSource());
print $e;
throw new UnexpectedValueException('Login failed.');
}
}
