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 testTestReadOnlyState()
{
// Test that LOVD is in the read-only state.
// First, log out of any session that might exist at this time.
$this->logout();
// There should be no link to register yourself.
// First, I had this findElements(), but Chrome doesn't like that at all, and times out.
// Firefox anyway took quite some time, because of the timeout that we have set if elements are not found immediately (normally needed if pages load slowly).
// $this->assertFalse((bool) count($this->driver->findElements(WebDriverBy::xpath('//a/b[text()="Register as submitter"]'))));
// New attempt to test for absence of register link.
$this->assertFalse(strpos($this->driver->findElement(WebDriverBy::xpath('//table[@class="logo"]//td[3]'))->getText(), 'Register as submitter'));
$this->driver->get(ROOT_URL . '/src/login');
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/login$/', $this->driver->getCurrentURL()));
// Verify warning exists. Finds any TD with this text.
$this->driver->findElement(WebDriverBy::xpath('//td[text()="This installation is currently configured to be read-only. Only Managers and higher level users can log in."]'));
// Attempt to log in, should fail in a specific way.
$this->enterValue(WebDriverBy::name('username'), 'submitter');
$this->enterValue(WebDriverBy::name('password'), 'test1234');
$element = $this->driver->findElement(WebDriverBy::xpath('//input[@value="Log in"]'));
$element->click();
// Should return a proper error message.
$this->assertEquals('This installation is currently configured to be read-only. Your user level is not sufficient to log in.', $this->driver->findElement(WebDriverBy::cssSelector('div[class=err]'))->getText());
// Also curators should fail.
$this->enterValue(WebDriverBy::name('username'), 'curator');
$this->enterValue(WebDriverBy::name('password'), 'test1234');
$element = $this->driver->findElement(WebDriverBy::xpath('//input[@value="Log in"]'));
$element->click();
// Should return a proper error message.
$this->assertEquals('This installation is currently configured to be read-only. Your user level is not sufficient to log in.', $this->driver->findElement(WebDriverBy::cssSelector('div[class=err]'))->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 testCheckCustomLinks()
{
// This test checks some basic functionality of the custom links. It
// doesn't require authorization, just checks some VLs if the links are
// rendered correctly.
// Load the common variant overview.
$this->driver->get(ROOT_URL . '/src/variants');
// Find a custom link, and move the mouse over it.
$oCustomLink = $this->driver->findElement(WebDriverBy::xpath('//table[@class="data"]/tbody/tr/td/span[text()="dbSNP"]'));
$this->driver->getMouse()->mouseMove($oCustomLink->getCoordinates());
// Now find the tooltip that should have shown.
$sToolTipLinkText = $this->driver->findElement(WebDriverBy::xpath('//div[@id="tooltip"]/a'))->getText();
$this->assertTrue(strpos($sToolTipLinkText, 'http') === 0 && strpos($sToolTipLinkText, 'SNP'));
// This test data does not have many links, try and find a PubMed link.
// Load the in_gene view.
$this->driver->get(ROOT_URL . '/src/variants/in_gene');
// Filter on Reference, so we can find this link on the first page.
$sSelector = WebDriverBy::name('search_VariantOnGenome/Reference');
$this->enterValue($sSelector, 'Fokkema');
$oElement = $this->driver->findElement($sSelector);
// Use json_decode to send enter key to browser.
$oElement->sendKeys(json_decode('"\\uE007"'));
// FIXME: It would be good if we can test for the VL to renew. Now just waiting a second.
sleep(1);
// Find a custom link, and move the mouse over it.
$oCustomLink = $this->driver->findElement(WebDriverBy::xpath('//table[@class="data"]/tbody/tr/td/span[text()="Fokkema et al (2011)"]'));
$this->driver->getMouse()->mouseMove($oCustomLink->getCoordinates());
// Now find the tooltip that should have shown.
$sToolTipLinkText = $this->driver->findElement(WebDriverBy::xpath('//div[@id="tooltip"]/a'))->getText();
$this->assertTrue(strpos($sToolTipLinkText, 'http') === 0 && strpos($sToolTipLinkText, 'pubmed'));
}
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 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());
}
/**
* 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 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 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 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 testUpdatetImport()
{
$this->driver->get(ROOT_URL . "/src/import");
$this->enterValue(WebDriverBy::name("import"), ROOT_PATH . "../tests/test_data_files/UpdateImport.txt");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="mode"]/option[text()="Update existing data (in beta)"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Import file']"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*The following sections are modified and updated in the database: Columns, Diseases, Individuals, Phenotypes, Screenings, Variants_On_Genome, Variants_On_Transcripts\\.$/', $this->driver->findElement(WebDriverBy::id("lovd_sql_progress_message_done"))->getText()));
}
public function testSecondInsertImport()
{
$this->driver->get(ROOT_URL . "/src/import");
$this->enterValue(WebDriverBy::name("import"), ROOT_PATH . "../tests/test_data_files/SecondInsertImport.txt");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="mode"]/option[text()="Add only, treat all data as new"]'));
$option->click();
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Import file']"));
$element->click();
$this->assertEquals("Done importing!", $this->driver->findElement(WebDriverBy::id("lovd_sql_progress_message_done"))->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 testMyTestCase()
{
$this->driver->get(ROOT_URL . "/src/phenotypes?create&target=00000001");
$this->enterValue(WebDriverBy::name("Phenotype/Additional"), "Phenotype Details");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="Phenotype/Inheritance"]/option[text()="Unknown"]'));
$option->click();
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="owned_by"]/option[text()="Test Owner (#00006)"]'));
$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 testCreateDiseaseIVA()
{
$this->driver->get(ROOT_URL . "/src/diseases?create");
$this->enterValue(WebDriverBy::name("symbol"), "IVA");
$this->enterValue(WebDriverBy::name("name"), "isovaleric acidemia");
$this->enterValue(WebDriverBy::name("id_omim"), "243500");
$option = $this->driver->findElement(WebDriverBy::xpath('//select[@name="genes[]"]/option[text()="IVD (isovaleryl-CoA dehydrogenase)"]'));
$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());
}
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 testUninstallLOVDTest()
{
$this->logout();
$this->login('admin', 'test1234');
$this->driver->get(ROOT_URL . "/src/uninstall");
$this->enterValue(WebDriverBy::name("password"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Next >>']"));
$element->click();
$this->enterValue(WebDriverBy::name("password"), "test1234");
$element = $this->driver->findElement(WebDriverBy::xpath("//input[@value='Uninstall LOVD']"));
$element->click();
$this->assertEquals("LOVD successfully uninstalled!\nThank you for having used LOVD!", $this->driver->findElement(WebDriverBy::cssSelector("div[id=lovd__progress_message]"))->getText());
}
public function testAddVCFFileToCMTIndividual()
{
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr[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();
$element = $this->driver->findElement(WebDriverBy::xpath("//tr[3]/td[2]/b"));
$element->click();
// $element = $this->driver->findElement(WebDriverBy::cssSelector("#0000000002 > td.ordered"));
$element = $this->driver->findElement(WebDriverBy::xpath("//td[text()='0000000002']"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants[\\s\\S]create&target=0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//tr[3]/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&target=0000000002$/', $this->driver->getCurrentURL()));
$element = $this->driver->findElement(WebDriverBy::xpath("//div/table/tbody/tr/td/table/tbody/tr/td[2]/b"));
$element->click();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/variants\\/upload[\\s\\S]create&type=VCF&target=0000000002$/', $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();
$this->assertTrue((bool) preg_match('/^[\\s\\S]*\\/src\\/submit\\/screening\\/0000000002$/', $this->driver->getCurrentURL()));
for ($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 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 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 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 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 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());
}
private function captcha()
{
$path = \Yii::getAlias('@runtime/tmp') . '/' . time() . '_' . rand() . '.png';
$this->driver->takeScreenshot($path);
$coordinates = $this->driver->findElement(WebDriverBy::cssSelector('.captchaImage'))->getCoordinates()->onPage();
if (Image::crop($path, $coordinates->getX(), $coordinates->getY(), 300, 60)) {
if (\Yii::$app->get('captcha')->run($path)) {
$this->driver->findElement(WebDriverBy::id('CaptchaInput'))->click();
$this->driver->findElement(WebDriverBy::id('CaptchaInput'))->sendKeys(\Yii::$app->get('captcha')->result());
$this->driver->findElement(WebDriverBy::name('submit_captcha'))->click();
sleep(2);
}
} else {
throw new Exception('Проблема при обрезании картинки');
}
}
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());
}
