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 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 testWithoutMagium()
{
// This test is based off of my own test environment and so everything up until the Twitter authentication will
// not work. So ignore the first part.
$webDriver = RemoteWebDriver::create('http://*****:*****@data-strategy="twitter"]'));
$webDriver->wait()->until(ExpectedCondition::visibilityOf($element));
$element->click();
// Start from here
$configurationProvider = new StandardConfigurationProvider(new ConfigurationReader(), new ClassConfigurationReader(), new EnvironmentConfigurationReader());
$collector = new DefaultPropertyCollector();
$action = new AuthenticateTwitter($webDriver, new \Magium\Twitter\Themes\Twitter($configurationProvider, $collector), new Twitter($configurationProvider, $collector));
$action->execute();
$webDriver->quit();
}
public function testCreateIndividualDiagnosedWithCMT()
{
$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/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals[\\s\\S]create$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("Individual/Lab_ID"), "12345CMT");
$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("Individual/Reference"), "{PMID:Fokkema et al (2011):21520333}");
$this->enterValue(WebDriverBy::name("Individual/Remarks"), "No Remarks");
$this->enterValue(WebDriverBy::name("Individual/Remarks_Non_Public"), "Still no remarks");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="active_diseases[]"]/option[text()="CMT (Charcot Marie Tooth Disease)"]'));
$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 individual information entry']"));
$element->click();
$this->assertEquals("Successfully created the individual information entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
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 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());
}
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 testMakeUserCurator()
{
$this->driver->get(ROOT_URL . "/src/genes/IVD?authorize");
$element = $this->driver->findElement(WebDriverBy::linkText("Test Curator"));
$element->click();
$this->enterValue(WebDriverBy::xpath("//td/input[@type='password']"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Save curator list']"));
$element->click();
$this->assertEquals("Successfully updated the curator list!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testCreateGenderColumn()
{
$this->driver->get(ROOT_URL . "/src/columns/Individual/Gender");
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Columns"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Enable column"));
$element->click();
$this->enterValue(WebDriverBy::name("password"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Add/enable custom data column Individual/Gender']"));
$element->click();
}
public function testPostFinishAddVariantOnlyDescribedOnGenomicLevelToCMT()
{
$this->logout();
$this->login('collaborator', 'test1234');
$this->driver->get(ROOT_URL . "/src/");
// Move mouse to Screenings tab and click 'view all screenings' option.
$tabElement = $this->driver->findElement(WebDriverBy::id("tab_screenings"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$allVariantsLink = $this->driver->findElement(WebDriverBy::partialLinkText('View all screenings'));
$allVariantsLink->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings$/', $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()="Maternal (confirmed)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="chromosome"]/option[text()="X"]'));
$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();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create variant entry']"));
$element->click();
for ($second = 0;; $second++) {
if ($second >= 60) {
$this->fail("timeout");
}
try {
if ($this->isElementPresent(WebDriverBy::cssSelector("table[class=info]"))) {
break;
}
} catch (Exception $e) {
}
sleep(1);
}
$this->assertTrue((bool) preg_match('/^Successfully processed your submission and sent an email notification to the relevant curator[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText()));
}
public function find(RemoteWebDriver $webDriver)
{
switch ($this->type) {
case self::ID:
return $webDriver->findElement(WebDriverBy::id($this->value));
case self::CSS_SELECTOR:
return $webDriver->findElement(WebDriverBy::cssSelector($this->value));
case self::LINK_TEXT:
return $webDriver->findElement(WebDriverBy::linkText($this->value));
default:
throw new \LogicException('Invalid element search type: ' . $this->type);
}
}
public function testMakeUserCollaboratorGJB()
{
$this->driver->get(ROOT_URL . "/src/genes/GJB1?authorize");
// $this->selectWindow("null");
$element = $this->driver->findElement(WebDriverBy::linkText("Test Collaborator"));
$element->click();
// $this->uncheck("xpath=(//input[@name='allow_edit[]'])[2]");
$this->uncheck(WebDriverBy::xpath("(//input[@name='allow_edit[]'])[2]"));
$this->enterValue(WebDriverBy::xpath("//td/input[@type='password']"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Save curator list']"));
$element->click();
$this->assertEquals("Successfully updated the curator list!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testAddSummaryVariantVCFFile()
{
// Mouse hover over Submit tab, to make 'submit new data' link visible.
$tabElement = $this->driver->findElement(WebDriverBy::xpath("//img[@id='tab_submit']"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$element = $this->driver->findElement(WebDriverBy::linkText("Submit new data"));
$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("//tr[3]/td[2]/b"));
$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]/b"));
$element->click();
$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");
$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 testAddSummaryVariantSeattleseqFile()
{
// Mouse hover over Submit tab, to make 'submit new data' link visible.
$tabElement = $this->driver->findElement(WebDriverBy::xpath("//img[@id='tab_submit']"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$element = $this->driver->findElement(WebDriverBy::linkText("Submit new data"));
$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("//tr[3]/td[2]/b"));
$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 testAddVariantLocatedWithinGeneToIVAIndividual()
{
$this->driver->get(ROOT_URL . "/src/variants?create&reference=Transcript&geneid=IVD&target=0000000001");
$this->uncheck(WebDriverBy::name("ignore_00000001"));
$this->enterValue(WebDriverBy::name("00000001_VariantOnTranscript/Exon"), "2");
$this->enterValue(WebDriverBy::name("00000001_VariantOnTranscript/DNA"), "c.345G>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.(Met115Ile)", $firstProteinValue);
$GenomicDNAChange = $this->driver->findElement(WebDriverBy::name('VariantOnGenome/DNA'));
$this->assertEquals("g.40702876G>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()="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()="Test Owner (#00006)"]'));
$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 testCreateIndividualDiagnosedWithCMT()
{
$element = $this->driver->findElement(WebDriverBy::id("tab_submit"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals[\\s\\S]create$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("Individual/Lab_ID"), "12345CMT");
$element = $this->driver->findElement(WebDriverBy::linkText("PubMed"));
$element->click();
$this->enterValue(WebDriverBy::name("Individual/Reference"), "{PMID:Fokkema et al (2011):21520333}");
$this->enterValue(WebDriverBy::name("Individual/Remarks"), "No Remarks");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="active_diseases[]"]/option[text()="CMT (Charcot Marie Tooth Disease)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Create individual information entry']"));
$element->click();
$this->assertEquals("Successfully created the individual information entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
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 testCurateSubmittedData()
{
$element = $this->driver->findElement(WebDriverBy::id("tab_variants"));
$element->click();
// Move mouse to Variants tab and click 'view all genomic variants' option.
$tabElement = $this->driver->findElement(WebDriverBy::id("tab_variants"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$allVariantsLink = $this->driver->findElement(WebDriverBy::partialLinkText('View all genomic variants'));
$allVariantsLink->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::linkText("0000000001"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/0000000001$/', $this->driver->getCurrentURL()));
$this->assertEquals("Pending", $this->driver->findElement(WebDriverBy::xpath("//tr[13]/td/span"))->getText());
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Variants"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Publish (curate) variant entry"));
$element->click();
$this->assertEquals("Public", $this->driver->findElement(WebDriverBy::xpath("//tr[13]/td/span"))->getText());
$element = $this->driver->findElement(WebDriverBy::linkText("00000001"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals\\/00000001$/', $this->driver->getCurrentURL()));
$this->assertEquals("Pending", $this->driver->findElement(WebDriverBy::xpath("//tr[8]/td"))->getText());
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Individuals"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Publish (curate) individual entry"));
$element->click();
$this->assertEquals("Public", $this->driver->findElement(WebDriverBy::xpath("//tr[8]/td"))->getText());
// Move mouse to Variants tab and click 'view all genomic variants' option.
$tabElement = $this->driver->findElement(WebDriverBy::id("tab_variants"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$allVariantsLink = $this->driver->findElement(WebDriverBy::partialLinkText('View all genomic variants'));
$allVariantsLink->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::linkText("0000000002"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/0000000002$/', $this->driver->getCurrentURL()));
$this->assertEquals("Pending", $this->driver->findElement(WebDriverBy::xpath("//tr[13]/td/span"))->getText());
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Variants"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Publish (curate) variant entry"));
$element->click();
$this->assertEquals("Public", $this->driver->findElement(WebDriverBy::xpath("//tr[13]/td/span"))->getText());
}
public function testDeleteGeneIVD()
{
$this->driver->get(ROOT_URL . "/src/phenotypes/0000000003");
$element = $this->driver->findElement(WebDriverBy::id("tab_genes"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::id("viewentryOptionsButton_Genes"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Delete gene entry"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/genes\\/IVD[\\s\\S]delete$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("password"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Delete gene information entry']"));
$element->click();
$this->assertEquals("You are about to delete 1 transcript(s) and related information on 3 variant(s) on those transcripts. Please fill in your password one more time to confirm the removal of gene IVD.", $this->driver->findElement(WebDriverBy::xpath("//*/table[@class='info'][2]"))->getText());
$this->enterValue(WebDriverBy::name("password"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Delete gene information entry']"));
$element->click();
$this->assertEquals("Successfully deleted the gene information entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
// Wait for page redirect.
$this->waitUntil(WebDriverExpectedCondition::titleContains("View all genes"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/genes$/', $this->driver->getCurrentURL()));
}
public function testCreateIndividualDiagnosedWithIVA()
{
$this->driver->get(ROOT_URL . "/src/submit");
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/individuals[\\s\\S]create$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("Individual/Lab_ID"), "12345IVA");
$element = $this->driver->findElement(WebDriverBy::linkText("PubMed"));
$element->click();
$this->enterValue(WebDriverBy::name("Individual/Reference"), "{PMID:Fokkema et al (2011):21520333}");
$this->enterValue(WebDriverBy::name("Individual/Remarks"), "No Remarks");
$this->enterValue(WebDriverBy::name("Individual/Remarks_Non_Public"), "Still no remarks");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="active_diseases[]"]/option[text()="IVA (isovaleric acidemia)"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="Test Owner (#00006)"]'));
$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 individual information entry']"));
$element->click();
$this->assertEquals("Successfully created the individual information entry!", $this->driver->findElement(WebDriverBy::cssSelector("table[class=info]"))->getText());
}
public function testPostFinishAddScreeningToCMTIndividual()
{
// Wait for redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("View genomic variant"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/0000000006$/', $this->driver->getCurrentURL()));
// Move mouse to Screenings tab and click 'view all screenings' 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 screening to individual"));
$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"));
$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 testCreateGeneGJB()
{
// Mouse hover over genes tab, to make 'create a new gene entry' link visible.
$tabElement = $this->driver->findElement(WebDriverBy::id("tab_genes"));
$this->driver->getMouse()->mouseMove($tabElement->getCoordinates());
$element = $this->driver->findElement(WebDriverBy::linkText("Create a new gene entry"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/genes[\\s\\S]create$/', $this->driver->getCurrentURL()));
$this->enterValue(WebDriverBy::name("hgnc_id"), "GJB1");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Continue »']"));
$element->click();
// $this->addSelection(WebDriverBy::name("active_transcripts[]"), "value=NM_001097642.2");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="active_transcripts[]"]/option[@value="NM_001097642.2"]'));
$option->click();
$this->check(WebDriverBy::name("show_hgmd"));
$this->check(WebDriverBy::name("show_genecards"));
$this->check(WebDriverBy::name("show_genetests"));
$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());
$this->waitUntil(WebDriverExpectedCondition::titleContains("View GJB1 gene"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/genes\\/GJB1$/', $this->driver->getCurrentURL()));
}
public function testPostFinishAddScreeningToIVAIndividual()
{
$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 screening to individual"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/screenings[\\s\\S]create&target=00000002$/', $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());
// wait for page redirect
$this->waitUntil(WebDriverExpectedCondition::titleContains("Submission of"));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000004$/', $this->driver->getCurrentURL()));
}
/**
* @param array $by
* @return WebDriverBy
*/
protected function getStrictLocator(array $by)
{
$type = key($by);
$locator = $by[$type];
switch ($type) {
case 'id':
return WebDriverBy::id($locator);
case 'name':
return WebDriverBy::name($locator);
case 'css':
return WebDriverBy::cssSelector($locator);
case 'xpath':
return WebDriverBy::xpath($locator);
case 'link':
return WebDriverBy::linkText($locator);
case 'class':
return WebDriverBy::className($locator);
default:
throw new MalformedLocatorException("{$by} => {$locator}", "Strict locator can be either xpath, css, id, link, class, name: ");
}
}
/**
* Returns an element by the given link text.
* If nothing is found, an empty array will be returned.
*
* @param string $linkText Link text of expected element.
* @param int $attempts Attempts until the method will fail and return false.
*
* @return WebDriverElement[]|array
*/
public function getArrayByLinkText($linkText, $attempts = 2)
{
if ($this->isFailed()) {
return [];
}
$by = WebDriverBy::linkText($linkText);
return $this->getArrayBy($by, $attempts);
}
public function testWebDriverByLocators()
{
$this->module->amOnPage('/login');
$this->module->seeElement(WebDriverBy::id('submit-label'));
$this->module->seeElement(WebDriverBy::name('password'));
$this->module->seeElement(WebDriverBy::className('optional'));
$this->module->seeElement(WebDriverBy::cssSelector('form.global_form_box'));
$this->module->seeElement(WebDriverBy::xpath(\Codeception\Util\Locator::tabIndex(4)));
$this->module->fillField(WebDriverBy::name('password'), '123456');
$this->module->amOnPage('/form/select');
$this->module->selectOption(WebDriverBy::name('age'), 'child');
$this->module->amOnPage('/form/checkbox');
$this->module->checkOption(WebDriverBy::name('terms'));
$this->module->amOnPage('/');
$this->module->seeElement(WebDriverBy::linkText('Test'));
$this->module->click(WebDriverBy::linkText('Test'));
$this->module->seeCurrentUrlEquals('/form/hidden');
}
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());
}
/**
* Client expects that an element is selected by the given link text.
* Returns true when the element is selected and false otherwise.
* Retry the process two times or until the attempts argument count
* is reached when a stale element reference exception is thrown.
* Recommended usage in web driver waits.
*
* @param string $linkText Link text of expected element.
* @param int $attempts (Optional) Attempts until the method will fail and return false.
*
* @return bool
*/
public function expectsToBeSelectedByLinkText($linkText, $attempts = 2)
{
if ($this->isFailed()) {
return false;
}
$by = WebDriverBy::linkText($linkText);
return $this->expectsToBeSelected($by, $attempts);
}
public function testFalseUpdatetImport()
{
$this->driver->get(ROOT_URL . "/src/import");
$this->enterValue(WebDriverBy::name("import"), ROOT_PATH . "../tests/test_data_files/FalseUpdateImport.txt");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="mode"]/option[text()="Update existing data (in beta)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::name("simulate"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Import file']"));
$element->click();
$element = $this->driver->findElement(WebDriverBy::linkText("Show 33 warnings"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 8\\): Will not update column Individual\\/Age_of_death, too many fields are different from the database \\(col_order, width, standard, head_column, description_form, description_legend_short, description_legend_full, mysql_type, form_type, select_options, preg_pattern\\)\\. There is a maximum of 1 difference to prevent accidental updates\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 8\\): Can[\\s\\S]t update hgvs for column entry Individual\\/Age_of_death: Not allowed to change the HGVS standard status of any column\\. Value is currently "0" and value in the import file is "1"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 8\\): Incorrect value for field [\\s\\S]col_order[\\s\\S], which needs to be numeric, between 0 and 255\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 8\\): Incorrect value for field [\\s\\S]standard[\\s\\S], which should be 0 or 1\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 8\\): Select option #3 "yes\\(\\)[\\s\\S]* = Consanguineous parents" not understood\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 8\\): The [\\s\\S]Regular expression pattern[\\s\\S] field does not seem to contain valid PHP Perl compatible regexp syntax\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Columns, line 9\\): ID "Individual\\/Age_of_death" already defined at line 8\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Genes, line 14\\): Can[\\s\\S]t update chromosome for gene entry IVD: Not allowed to change the chromosome\\. Value is currently "15" and value in the import file is "151"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Genes, line 14\\): Can[\\s\\S]t update name for gene entry IVD: Not allowed to change the gene name\\. Value is currently "isovaleryl-CoA dehydrogenase" and value in the import file is "isovaleryl-CoA dehydrogenase1"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Genes, line 15\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Transcripts, line 20\\): Can[\\s\\S]t update id_ncbi for transcript entry 00001: Not allowed to change the NCBI ID\\. Value is currently "NM_002225\\.3" and value in the import file is "NM_999999\\.3"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Transcripts, line 20\\): Transcript "00001" does not match the same gene and\\/or the same NCBI ID as in the database\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Transcripts, line 21\\): ID "00001" already defined at line 20\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Diseases, line 27\\): Will not update disease 00000, too many fields are different from the database \\(symbol, name, id_omim\\)\\. There is a maximum of 1 difference to prevent accidental updates\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Diseases, line 27\\): Another disease already exists with this OMIM ID[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Diseases, line 27\\): Another disease already exists with the same name![\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Diseases, line 28\\): Will not update disease 00002, too many fields are different from the database \\(symbol, name, id_omim\\)\\. There is a maximum of 1 difference to prevent accidental updates\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Diseases, line 28\\): Another disease already exists with the same name![\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Genes_To_Diseases, line 34\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 39\\): Individual "00000022" does not exist in the database and is not defined \\(properly\\) in this import file\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 40\\): Will not update individual 00000002, too many fields are different from the database \\(panelid, panel_size\\)\\. There is a maximum of 1 difference to prevent accidental updates\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 40\\): The [\\s\\S]Panel ID[\\s\\S] can not link to itself; this field is used to indicate to which panel this individual belongs\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 40\\): Panel size of Individual "00000002" must be lower than the panel size of Individual "00000002"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 41\\): Will not update individual 00000003, too many fields are different from the database \\(fatherid, motherid, panelid\\)\\. There is a maximum of 1 difference to prevent accidental updates\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 41\\): Panel ID "00000001" refers to an individual, not a panel \\(group of individuals\\)\\. If you want to configure that individual as a panel, set its [\\s\\S]Panel size[\\s\\S] field to a value higher than 1\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 41\\): The [\\s\\S]fatherid[\\s\\S] can not link to itself; this field is used to indicate which individual in the database is the parent of the given individual\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 41\\): The fatherid "00000003" you entered does not refer to a male individual\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 41\\): Individual "00000022" does not exist in the database and is not defined \\(properly\\) in this import file\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 42\\): The motherid "00000002" refers to an panel \\(group of individuals\\), not an individual\\. If you want to configure that panel as an individual, set its [\\s\\S]Panel size[\\s\\S] field to value 1\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals, line 43\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Individuals_To_Diseases, line 49\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Phenotypes, line 54\\): Can[\\s\\S]t update diseaseid for phenotype entry 0000000001: Not allowed to change the disease\\. Value is currently "00001" and value in the import file is "00004"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Phenotypes, line 54\\): Can[\\s\\S]t update individualid for phenotype entry 0000000001: Not allowed to change the individual\\. Value is currently "00000001" and value in the import file is "00000022"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Phenotypes, line 54\\): Disease "00004" does not exist in the database and is not defined in this import file\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Phenotypes, line 54\\): Individual "00000022" does not exist in the database and is not defined in this import file\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Phenotypes, line 55\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Screenings, line 60\\): Can[\\s\\S]t update individualid for screening entry 0000000001: Not allowed to change the individual\\. Value is currently "00000001" and value in the import file is "00000022"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Screenings, line 60\\): Individual "00000022" does not exist in the database and is not defined in this import file\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Screenings, line 61\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Screenings_To_Genes, line 67\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Variants_On_Genome, line 72\\): Can[\\s\\S]t update position_g_start for variant entry 0000000001: Not allowed to change the genomic start position\\. Value is currently "40702876" and value in the import file is "abc"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Variants_On_Genome, line 72\\): The field \'position_g_start\' must contain a positive integer, "abc" does not match\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Variants_On_Genome, line 73\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Variants_On_Transcripts, line 78\\): Can[\\s\\S]t update position_c_start for variant entry 0000000001: Not allowed to change the start position\\. Value is currently "345" and value in the import file is "abc"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Variants_On_Transcripts, line 78\\): The field \'position_c_start\' must contain an integer, "abc" does not match\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Variants_On_Transcripts, line 80\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Error \\(Screenings_To_Variants, line 86\\): This line refers to a non-existing entry\\. When the import mode is set to update, no new inserts can be done\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Columns, line 8\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-02 15:42:07"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Columns, line 8\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00000"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Columns, line 8\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-02 15:42:07"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Columns, line 9\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-12 15:33:25"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Genes, line 14\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-02 15:42:21"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Genes, line 14\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Genes, line 14\\): Updated date field is set by LOVD\\. Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-02 15:42:48"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Transcripts, line 20\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-02 15:42:21"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Transcripts, line 20\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Transcripts, line 20\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-02 15:42:21"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Transcripts, line 21\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-12 15:33:40"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 26\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-02 15:42:23"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 26\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 26\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-02 15:42:23"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 27\\): Created by field is set by LOVD Value is currently "00000" and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 27\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-02 15:42:23"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 28\\): Created date field is set by LOVD Value is currently "[\\s\\S]*" and the value in the import file is "2015-06-03 10:29:37"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 28\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Diseases, line 28\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-02 15:42:23"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning: It is currently not possible to do an update on section Genes_To_Diseases via an import[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Individuals, line 39\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Individuals, line 39\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-03 11:30:26"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning: It is currently not possible to do an update on section Individuals_To_Diseases via an import[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Phenotypes, line 54\\): Created date field is set by LOVD Value is currently "2015-06-03 11:30:56" and the value in the import file is "2015-06-02 15:42:32"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Phenotypes, line 54\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Phenotypes, line 54\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-02 15:42:32"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Screenings, line 60\\): Created date field is set by LOVD Value is currently "2015-06-03 11:31:03" and the value in the import file is "2015-06-02 15:42:37"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Screenings, line 60\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Screenings, line 60\\): Edited date field is set by LOVD Value is currently empty and the value in the import file is "2015-06-02 15:42:37"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning: It is currently not possible to do an update on section Screenings_To_Genes via an import[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Variants_On_Genome, line 72\\): Created date field is set by LOVD Value is currently "2015-06-03 11:31:16" and the value in the import file is "2015-06-02 15:42:48"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning \\(Variants_On_Genome, line 72\\): Edited by field is set by LOVD Value is currently empty and the value in the import file is "00001"\\.[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
$this->assertTrue((bool) preg_match('/^[\\s\\S]*Warning: It is currently not possible to do an update on section Screenings_To_Variants via an import[\\s\\S]*$/', $this->driver->findElement(WebDriverBy::tagName("body"))->getText()));
}
