public function testAddSummaryVariantOnlyDescribedOnGenomicLevel()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View genomic variant"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/0000000003$/', $this->driver->getCurrentURL()));
$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();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&reference=Genome$/', $this->driver->getCurrentURL()));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="allele"]/option[text()="Paternal (confirmed)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="chromosome"]/option[text()="15"]'));
$option->click();
$this->enterValue(WebDriverBy::name("VariantOnGenome/DNA"), "g.40702976G>T");
$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"), "11/10000");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="effect_reported"]/option[text()="Effect unknown"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create variant entry']"));
$element->click();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
}
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 testPostFinishAddPhenotypeInfoToIVAIndividual()
{
$element = $this->driver->findElement(WebDriverBy::id("tab_individuals"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals\\/IVD$/', $this->driver->getCurrentURL()));
// $element = $this->driver->findElement(WebDriverBy::cssSelector("#00000002 > td.ordered"));
$element = $this->driver->findElement(WebDriverBy::xpath("//td[text()='00000002']"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals\\/00000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Individuals"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Add phenotype information to individual"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/phenotypes[\\s\\S]create&target=00000002$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("Phenotype/Additional"), "Additional phenotype information");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Phenotype/Inheritance"]/option[text()="Familial"]'));
$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 phenotype information entry']"));
$element->click();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
// Wait for page redirect.
$this->waitUntil(WebDriverExpectedCondition::titleContains("View phenotype"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/phenotypes\\/0000000003$/', $this->driver->getCurrentURL()));
}
public function testAddVariantLocatedWithinGeneToCMTIndividual()
{
// 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/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->click();
$element = $this->driver->findElement(WebDriverBy::linkText("GJB1"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&reference=Transcript&geneid=GJB1&target=0000000001$/', $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.34G>T");
$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 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.(Gly12Cys)", $firstProteinValue);
$GenomicDNAChange = $this->driver->findElement(WebDriverBy::name('VariantOnGenome/DNA'));
$this->assertEquals("g.70443591G>T", $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()="Maternal (confirmed)"]'));
$option->click();
$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"), "0.003");
$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 testCreateAnnouncementReadOnly()
{
// Create an announcement, that switches LOVD into the read-only state.
// This test assumes you're logged in as manager or admin.
$sAnnouncement = 'This is a test announcement. LOVD will be closed for registrations, and lower level users can not log in.';
$this->driver->get(ROOT_URL . '/src/announcements?create');
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/announcements[\\s\\S]create$/', $this->driver->getCurrentURL()));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="type"]/option[text()="Warning"]'));
$option->click();
$this->enterValue(WebDriverBy::name('announcement'), $sAnnouncement);
$this->enterValue(WebDriverBy::name('start_date'), '');
// No value, means active from now().
$this->enterValue(WebDriverBy::name('end_date'), '');
// No value, means active until '9999-12-31 23:59:59'.
$this->check(WebDriverBy::name('lovd_read_only'));
$this->enterValue(WebDriverBy::name('password'), 'test1234');
$element = $this->driver->findElement(WebDriverBy::xpath('//input[@value="Create announcement"]'));
$element->click();
$this->driver->findElement(WebDriverBy::xpath('//td[text()="Successfully created the announcement!"]'));
// Finds any TD with this text.
// Also check if announcement is actually visible.
$this->assertEquals($sAnnouncement, $this->driver->findElement(WebDriverBy::cssSelector('table[class=info]'))->getText());
// Wait for redirect...
$this->waitUntil(WebDriverExpectedCondition::titleContains('View announcement'));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/announcements\\/\\d{5}$/', $this->driver->getCurrentURL()));
}
public function testAddScreeningToCMTIndividual()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/individual\\/00000001$/', $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();
// $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"));
$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 testAddVariantOnlyDescribedOnGenomicLevelToIVAIndividual()
{
// wait for page 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("//table[2]/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&reference=Genome&target=0000000002$/', $this->driver->getCurrentURL()));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="allele"]/option[text()="Paternal (confirmed)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="chromosome"]/option[text()="15"]'));
$option->click();
$this->enterValue(WebDriverBy::name("VariantOnGenome/DNA"), "g.40702876G>T");
$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"), "11/10000");
$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());
}
/**
* Получить токен для полного доступа
* @param $url string
* @param $recursion bool
*/
public function getToken($url, $recursion = true)
{
$this->driver->get($url);
$this->driver->findElement(WebDriverBy::name('email'))->sendKeys($this->login);
$this->driver->findElement(WebDriverBy::name('pass'))->sendKeys($this->password);
$this->driver->findElement(WebDriverBy::id('install_allow'))->click();
sleep(3);
while ($this->driver->findElements(WebDriverBy::xpath('//input[@name=\'captcha_key\']'))) {
$this->captcha();
$this->driver->findElement(WebDriverBy::name('pass'))->sendKeys($this->password);
$this->driver->findElement(WebDriverBy::id('install_allow'))->click();
sleep(3);
}
$this->driver->wait(60, 1000)->until(WebDriverExpectedCondition::titleContains('VK | Request Access'));
$this->driver->findElement(WebDriverBy::id('install_allow'))->click();
$this->driver->wait(60, 1000)->until(WebDriverExpectedCondition::titleContains('OAuth Blank'));
$urlCurrent = $this->driver->getCurrentURL();
$parseUrl = parse_url($urlCurrent);
if (!isset($parseUrl['fragment']) && $recursion == true) {
return $this->getToken($url, false);
}
$query = $parseUrl['fragment'];
parse_str($query, $data);
return $data;
}
public function testPostFinishAddPhenotypeInfoToCMTIndividual()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000003$/', $this->driver->getCurrentURL()));
// Move mouse to Individuals tab and click 'view all individuals' option.
$tabElement = $this->driver->findElement(WebDriverBy::id("tab_individuals"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$allIndividualsLink = $this->driver->findElement(WebDriverBy::partialLinkText('View all individuals'));
$allIndividualsLink->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::cssSelector("td.ordered"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals\\/00000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Individuals"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Add phenotype information to individual"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/phenotypes[\\s\\S]create&target=00000001$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("Phenotype/Additional"), "Additional phenotype information");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Phenotype/Inheritance"]/option[text()="Familial"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create phenotype information entry']"));
$element->click();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View phenotype"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/phenotypes\\/0000000002$/', $this->driver->getCurrentURL()));
}
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 nextAction()
{
$this->webdriver->wait()->until(ExpectedCondition::elementExists($this->theme->getShippingMethodContinueButtonXpath(), WebDriver::BY_XPATH));
$this->webdriver->wait()->until(ExpectedCondition::visibilityOf($this->webdriver->byXpath($this->theme->getShippingMethodContinueButtonXpath())));
$this->webdriver->byXpath($this->theme->getShippingMethodContinueButtonXpath())->click();
$this->webdriver->wait()->until(WebDriverExpectedCondition::not(WebDriverExpectedCondition::visibilityOf($this->webdriver->byXpath($this->theme->getShippingMethodContinueCompletedXpath()))));
return true;
}
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 nextAction()
{
if ($this->bypassNextStep) {
return true;
}
$this->testCase->byXpath($this->theme->getShippingContinueButtonXpath())->click();
$this->webdriver->wait()->until(WebDriverExpectedCondition::not(WebDriverExpectedCondition::visibilityOf($this->webdriver->byXpath($this->theme->getShippingContinueCompletedXpath()))));
return true;
}
public function testFinishIndividualDiagnosedHealthy()
{
// wait for page 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("//tr[3]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
}
public function nextAction()
{
$this->webdriver->byXpath($this->theme->getPaymentMethodContinueButtonXpath())->click();
try {
$this->webdriver->wait()->until(WebDriverExpectedCondition::not(WebDriverExpectedCondition::visibilityOf($this->webdriver->byXpath($this->theme->getPaymentMethodContinueCompleteXpath()))));
} catch (StaleElementReferenceException $e) {
// it is possible that the page rendered with unexpected timing which may lead to a harmless StaleElementReferenceException
}
return true;
}
public function testMyTestCase()
{
$this->driver->get(ROOT_URL . "/src/submit/screening/0000000002");
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//tr[3]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
$this->waitUntil(WebDriverExpectedCondition::titleContains("View individual"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals\\/00000001$/', $this->driver->getCurrentURL()));
}
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 testProfileScreen()
{
$this->loginAndWait()->click('a.view-profile');
$this->see('#profileWrapper')->typeIn('#profileWrapper input[name="name"]', 'Mr Bar')->typeIn('#profileWrapper input[name="email"]', '*****@*****.**')->enter()->see('.sweet-alert')->press(WebDriverKeys::ESCAPE)->notSee('.sweet-alert');
$avatar = $this->el('a.view-profile img');
// Expect the Gravatar to be updated
static::assertEquals('https://www.gravatar.com/avatar/36df72b4484fed183fad058f30b55d21?s=256', $avatar->getAttribute('src'));
// Check "Confirm Closing" and validate its functionality
$this->click('#profileWrapper input[name="confirmClosing"]');
$this->refresh()->waitUntil(WebDriverExpectedCondition::alertIsPresent());
$this->driver->switchTo()->alert()->dismiss();
// Reverse all changes for other tests to not be affected
$this->typeIn('#profileWrapper input[name="name"]', 'Koel Admin')->typeIn('#profileWrapper input[name="email"]', '*****@*****.**')->enter()->see('.sweet-alert')->press(WebDriverKeys::ESCAPE)->notSee('.sweet-alert')->click('#profileWrapper input[name="confirmClosing"]');
}
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 testAddPhenotypeInfoToCMTIndividual()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/individual\\/00000001$/', $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->enterValue(WebDriverBy::name("Phenotype/Additional"), "Additional phenotype information");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Phenotype/Inheritance"]/option[text()="Familial"]'));
$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 testAddSummaryVariantSeatlleseqFile()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View genomic variant"));
$this->assertContains("/src/variants/0000000167", $this->driver->getCurrentURL());
$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("//tr[3]/td[2]"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&type=SeattleSeq$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("variant_file"), ROOT_PATH . "../tests/test_data_files/ShortSeattleSeqAnnotation138v1.txt");
$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="autocreate"]/option[text()="Create genes and transcripts"]'));
$option->click();
$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 SeattleSeq file']"));
$this->clickNoTimeout($element);
for ($second = 0;; $second++) {
if ($second >= 300) {
$this->fail("timeout");
}
try {
if ($this->isElementPresent(WebDriverBy::xpath("//input[@value='Continue »']"))) {
break;
}
} catch (Exception $e) {
}
sleep(1);
}
$this->assertContains("138 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();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
}
public function testAddSummaryVariantVCFFile()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View genomic variant"));
$element = $this->driver->findElement(WebDriverBy::id("tab_submit"));
$element->click();
$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("//tr[3]/td[2]"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&type=VCF$/', $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();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
for ($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);
}
}
public function testCreateDiseaseCMT()
{
$this->driver->get(ROOT_URL . "/src/diseases?create");
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/diseases[\\s\\S]create$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("symbol"), "CMT");
$this->enterValue(WebDriverBy::name("name"), "Charcot Marie Tooth Disease");
$this->enterValue(WebDriverBy::name("id_omim"), "302800");
// $this->addSelection(WebDriverBy::name("genes[]"), "value=GJB1");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="genes[]"]/option[@value="GJB1"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create disease information entry']"));
$element->click();
$this->assertEquals("Successfully created the disease information entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View disease"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/diseases\\/00001$/', $this->driver->getCurrentURL()));
}
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 login()
{
$this->open->open('http://www.gmail.com/');
$this->testCase->assertElementExists('Email');
$this->testCase->assertElementExists('next');
$element = $this->webdriver->byId('Email');
$element->sendKeys($this->accountInformation->getEmailAddress());
$element = $this->webdriver->byId('next');
$element->click();
$this->webdriver->wait()->until(WebDriverExpectedCondition::elementToBeClickable(WebDriverBy::id('Passwd')));
$this->testCase->assertElementExists('Passwd');
$this->testCase->assertElementExists('signIn');
$element = $this->webdriver->byId('Passwd');
$element->sendKeys($this->accountInformation->getPassword());
$element = $this->webdriver->byId('signIn');
$element->click();
$this->webdriver->wait()->until(WebDriverExpectedCondition::titleContains('Inbox'));
}
public function testPostFinishAddVariantOnlyDescribedOnGenomicLevelToIVAIndividual()
{
$this->driver->get(ROOT_URL . "/src/screenings/IVD");
$element = $this->driver->findElement(WebDriverBy::id("tab_screenings"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings\\/IVD$/', $this->driver->getCurrentURL()));
// $element = $this->driver->findElement(WebDriverBy::cssSelector("#0000000002 > td.ordered"));
$element = $this->driver->findElement(WebDriverBy::xpath("//td[text()='0000000002']"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings\\/0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Screenings"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Add variant to screening"));
$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("//table[2]/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&reference=Genome&target=0000000002$/', $this->driver->getCurrentURL()));
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="allele"]/option[text()="Paternal (confirmed)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="chromosome"]/option[text()="15"]'));
$option->click();
$this->enterValue(WebDriverBy::name("VariantOnGenome/DNA"), "g.40702876G>T");
$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"), "11/10000");
$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();
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View genomic variant"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/0000000333$/', $this->driver->getCurrentURL()));
}
public function testAddSeattleseqFileToHealthyIndividual()
{
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of screening"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]"));
$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("//tr[3]/td[2]"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&target=0000000001$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[2]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&type=SeattleSeq&target=0000000001$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("variant_file"), ROOT_PATH . "../tests/test_data_files/ShortSeattleSeqAnnotation138v1.txt");
$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="autocreate"]/option[text()="Create genes and transcripts"]'));
$option->click();
$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 SeattleSeq file']"));
$this->clickNoTimeout($element);
for ($second = 0;; $second++) {
if ($second >= 300) {
$this->fail("timeout");
}
try {
if ($this->isElementPresent(WebDriverBy::xpath("//input[@value='Continue »']"))) {
break;
}
} catch (Exception $e) {
}
sleep(1);
}
$this->assertEquals("138 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();
}
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());
}
/**
* Включаем доступ сторонним программам
* @throws Exception
* @throws \Facebook\WebDriver\Exception\NoSuchElementException
* @throws \Facebook\WebDriver\Exception\TimeOutException
* @throws null
*/
public function accessThirdPartyPrograms()
{
$this->driver->get('https://mail.rambler.ru/');
if (strpos($this->driver->getTitle(), 'Входящие') === false) {
$this->driver->findElement(WebDriverBy::name('login'))->sendKeys($this->email);
$this->driver->findElement(WebDriverBy::id('form_password'))->sendKeys($this->password);
$this->driver->findElement(WebDriverBy::cssSelector('button.form-button.form-button_submit'))->click();
$this->driver->wait(60, 1000)->until(WebDriverExpectedCondition::titleContains('Входящие'));
}
$this->driver->get('https://mail.rambler.ru/#/settings/clients/');
sleep(1);
if (!$this->driver->findElement(WebDriverBy::cssSelector('fieldset.settingsFieldset.settingsFieldsetExternal > label > input.uiCheckbox'))->isSelected()) {
do {
$this->driver->findElement(WebDriverBy::cssSelector('fieldset.settingsFieldset.settingsFieldsetExternal > label > input.uiCheckbox'))->click();
sleep(1);
$this->captcha();
$this->driver->navigate()->refresh();
sleep(1);
} while (!$this->driver->findElement(WebDriverBy::cssSelector('fieldset.settingsFieldset.settingsFieldsetExternal > label > input.uiCheckbox'))->isSelected());
}
}
