def test_hmdc_build(self):
"""
@Status this test has been updated for the new hmdc pages
checks the human and mouse build numbers on the HMDC query page
"""
#displays the HMDC qf
self.driver.get(PUBLIC_URL + "/diseasePortal")
#find the pulldown and select Genome Location
selectorbox = self.driver.find_element_by_class_name("queryBuilder")
pulldown = selectorbox.find_element_by_tag_name("select").find_elements_by_tag_name("option")
#print [x.text for x in pulldown]
searchTextItems = iterate.getTextAsList(pulldown)
#verifies all the items listed in the pulldown are correct and in order
self.assertEqual(searchTextItems, ['Please select a field', 'Gene Symbol(s) or ID(s)','Gene Name','Phenotype or Disease Name', 'Phenotype or Disease ID(s)', 'Genome Location', 'Gene File Upload'])
#click the Genome Location option
pulldown[5].click()
#self.assertIn("Genome Location", pulldown[3].Text)
#finds the human and mouse genome build numbers
buildnumber = self.driver.find_element_by_class_name('radio-group')
# get the parent element
mainbuild = buildnumber.find_elements_by_tag_name('label')
wait.forAjax(self.driver)
#confirms that GRCh38 is displayed
#print [x.text for x in mainbuild]
searchTextItems = iterate.getTextAsList(mainbuild)
self.assertEqual(searchTextItems, ['Human (GRCh38)', 'Mouse (GRCm38)'])
"""
def test_assaytype_column_sort(self):
"""
@status: Tests that the assay type column sort works correctly
Assay Type column:
* Not applicable is not shown
* sort order should be type (with not specified last), followed by assay type and gene
* reverse order should still leave not specified last
* blot assays are last by default
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/gxd")
genebox = driver.find_element_by_name('nomenclature')
# put your marker symbol
genebox.send_keys("pax6")
genebox.send_keys(Keys.RETURN)
#find the Image tab
imagetab = driver.find_element_by_id("imagestab")
#click the image tab
imagetab.click()
wait.forAjax(driver)
time.sleep(.5)
assaylist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-assayType')
items = assaylist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["Immunohistochemistry", "Immunohistochemistry"])
assayheader = driver.find_element_by_id("imagesdata").find_element_by_css_selector('th.yui-dt-col-assayType')
#click the gene header column to sort
assayheader.click()
wait.forAjax(driver)
time.sleep(.5)
assaylist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-assayType')
items = assaylist[2].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["RT-PCR"])
def test_specimen_note(self):
"""
@status: Tests that the specimen notes are correctly displayed
specimen notes should be fully displayed
"""
driver = self.driver
driver.get(PWI_URL)
# opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id("accids")
# put your J number in the box
accidbox.send_keys("J:36691")
accidbox.submit()
# finds the specimens link and clicks it
driver.find_element_by_link_text("Specimens").click()
wait.forAjax(driver)
# finds the specimen notes column and then the first 7 items
summarytable = driver.find_element_by_id("specimenSummaryTable")
specnotes = summarytable.find_elements_by_css_selector("td:nth-child(13)")
specnote1 = specnotes[0]
specnote2 = specnotes[1]
specnote3 = specnotes[2]
specnote4 = specnotes[3]
specnote5 = specnotes[4]
specnote6 = specnotes[5]
specnote7 = specnotes[6]
# asserts the first 7 specimen notes are correct and in correct order
self.assertEqual(specnote1.text, "2.5% paraformaldehyde ")
self.assertEqual(specnote2.text, "2.5% paraformaldehyde ")
self.assertEqual(specnote3.text, "Fixed in 2.5% paraformaldehyde. With N-glycannase pretreatment. ")
self.assertEqual(specnote4.text, "2.5% paraformaldehyde ")
self.assertEqual(specnote5.text, "2.5% paraformaldehyde ")
self.assertEqual(specnote6.text, "2.5% paraformaldehyde ")
self.assertEqual(specnote7.text, "2.5% paraformaldehyde ")
def test_cre_assay(self):
"""
@status: Tests that all cre assays are correctly displayed at the bottom
cre assays are Recombinase reporter and In situ reporter (transgenic)
"""
driver = self.driver
driver.get(PWI_URL)
# opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id("accids")
# put your J number in the box
accidbox.send_keys("J:105186")
accidbox.submit()
# finds the specimens link and clicks it
driver.find_element_by_link_text("Specimens").click()
wait.forAjax(driver)
# finds the specimen notes column and then the first 7 items
summarytable = driver.find_element_by_id("specimenSummaryTable")
assaytypes = summarytable.find_elements_by_css_selector("td:nth-child(3)")
assaytype1 = assaytypes[13]
assaytype2 = assaytypes[14]
assaytype3 = assaytypes[15]
assaytype4 = assaytypes[16]
assaytype5 = assaytypes[17]
assaytype6 = assaytypes[18]
assaytype7 = assaytypes[19]
# asserts the first 7 specimen notes are correct and in correct order
self.assertEqual(assaytype1.text, "In situ reporter (knock in)")
self.assertEqual(assaytype2.text, "In situ reporter (transgenic)")
self.assertEqual(assaytype3.text, "In situ reporter (transgenic)")
self.assertEqual(assaytype4.text, "In situ reporter (transgenic)")
self.assertEqual(assaytype5.text, "Recombinase reporter")
self.assertEqual(assaytype6.text, "Recombinase reporter")
self.assertEqual(assaytype7.text, "Recombinase reporter")
def test_age_note(self):
"""
@status: Tests that the age notes are correct
an age note is represented by a asterisk.
"""
driver = self.driver
driver.get(PWI_URL)
# opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id("accids")
# put your J number in the box
accidbox.send_keys("J:84605")
accidbox.submit()
# finds the specimens link and clicks it
driver.find_element_by_link_text("Specimens").click()
wait.forAjax(driver)
# finds the age note column and then the first 12 items
summarytable = driver.find_element_by_id("specimenSummaryTable")
agenotes = summarytable.find_elements_by_css_selector("td:nth-child(6)")
agenote1 = agenotes[0]
agenote2 = agenotes[1]
agenote3 = agenotes[2]
agenote4 = agenotes[3]
agenote5 = agenotes[4]
agenote6 = agenotes[5]
agenote7 = agenotes[6]
# asserts the first 7 age notes are correct and in correct order
self.assertEqual(agenote1.text, "* ")
self.assertEqual(agenote2.text, "* ")
self.assertEqual(agenote3.text, "* ")
self.assertEqual(agenote4.text, "* ")
self.assertEqual(agenote5.text, "* ")
self.assertEqual(agenote6.text, "* ")
self.assertEqual(agenote7.text, "* ")
def test_gene_column_sort(self):
"""
@status: Tests that the Gene column sort works correctly
Gene column:
* sort order is gene, then assay type
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/gxd")
genebox = driver.find_element_by_name('nomenclature')
# put your marker symbol
genebox.send_keys("shh")
genebox.send_keys(Keys.RETURN)
#find the Image tab
imagetab = driver.find_element_by_id("imagestab")
#click the image tab
imagetab.click()
wait.forAjax(driver)
time.sleep(.5)
imagesdata = driver.find_element_by_id("imagesdata")
genelist = imagesdata.find_elements_by_css_selector('td.yui-dt-col-gene')
items = genelist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["Arx", "Olig2", "Shh"])
geneheader = imagesdata.find_element_by_css_selector('th.yui-dt-col-gene')
#click the gene header column to sort
geneheader.click()
wait.forAjax(driver)
time.sleep(.5)
genelist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-gene')
items = genelist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["Arx", "Olig2", "Shh"])
def testAnnotationStageDetailLink(self):
"""
tests that when you click on the annotations link in the detail section it goes to the correct assay results; jlewis
"""
self.performSearch(term="thymus/parathyroid primordium", stage="19")
# select specific stage
activetree = self.driver.find_element_by_css_selector(".mgitreeview .active")
self.assertEqual(activetree.text,"thymus/parathyroid primordium")
wait.forAjax(self.driver)
# verify annotation count exists
annotCountTag = self.driver.find_element_by_css_selector(".resultsLink a")
annotCount = int(annotCountTag.text)
self.assertTrue(annotCount > 0, "annotation count not greater than zero")
# click link to go to results page
annotCountTag.click()
wait.forNewWindow(self.driver)
searchFor = self.driver.find_element_by_css_selector(".youSearchedFor")
self.assertEqual(self.driver.title, "Result Summary")
self.assertTrue("thymus/parathyroid primordium" in searchFor.text, "You searched for does not contain structure name")
body = self.driver.find_element_by_tag_name("body")
self.assertTrue( ("of %d" % annotCount) in body.text, "same annotation count not found on results summary")
def test_multispecs_diffassay(self):
"""
@status: Tests the display for image panes with multiple specimens from different assays
each specimen/assay should have it's own row per image
"""
driver = self.driver
driver.get(PWI_URL)
#opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id('accids')
# put your J number in the box
accidbox.send_keys("J:83696")
accidbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the specimens link and clicks it
driver.find_element_by_link_text("Exp Images").click()
wait.forAjax(driver)
#Locates the images table and finds the table headings
imagestable = driver.find_element_by_id("paneSummaryTable")
rows = imagestable.find_elements_by_css_selector('tr')
#displays each row of data for the first 18 rows
row1 = rows[1]
row2 = rows[2]
row3 = rows[3]
row4 = rows[4]
row5 = rows[5]
row6 = rows[6]
row7 = rows[7]
row8 = rows[8]
row9 = rows[9]
row10 = rows[10]
row11 = rows[11]
row12 = rows[12]
row13 = rows[13]
row14 = rows[14]
row15 = rows[15]
row16 = rows[16]
row17 = rows[17]
row18 = rows[18]
row19 = rows[19]
#asserts that the rows of data are correct for the first 18 rows
self.assertEqual(row1.text, 'MGI:3522445\n1 Syndecan-1 MGI:3522591 (Sdc1) RT-PCR')
self.assertEqual(row2.text, 'MGI:3522445\n1 Syndecan-2 MGI:3522592 (Sdc2) RT-PCR')
self.assertEqual(row3.text, 'MGI:3522445\n1 Syndecan-3 MGI:3522593 (Sdc3) RT-PCR')
self.assertEqual(row4.text, 'MGI:3522445\n1 Syndecan-4 MGI:3522594 (Sdc4) RT-PCR')
self.assertEqual(row5.text, 'MGI:3522448\n2 A 2A MGI:3522619 (Sdc1) Immunohistochemistry')
self.assertEqual(row6.text, "2A MGI:3522621 (Hspg2) Immunohistochemistry")
self.assertEqual(row7.text, "2A MGI:3522624 (Tubb3) Immunohistochemistry")
self.assertEqual(row8.text, "MGI:3522448\n2 B 2B,2B'' MGI:3522621 (Hspg2) Immunohistochemistry")
self.assertEqual(row9.text, "2B,2B'' MGI:3522624 (Tubb3) Immunohistochemistry")
self.assertEqual(row10.text, "MGI:3522448\n2 B' 2B',2B'' MGI:3522619 (Sdc1) Immunohistochemistry")
self.assertEqual(row11.text, "MGI:3522448\n2 B'' 2B',2B'' MGI:3522619 (Sdc1) Immunohistochemistry")
self.assertEqual(row12.text, "2B,2B'' MGI:3522621 (Hspg2) Immunohistochemistry")
self.assertEqual(row13.text, "2B,2B'' MGI:3522624 (Tubb3) Immunohistochemistry")
self.assertEqual(row14.text, "MGI:3522448\n2 C 2C,2C'' MGI:3522621 (Hspg2) Immunohistochemistry")
self.assertEqual(row15.text, "2C,2C'' MGI:3522624 (Tubb3) Immunohistochemistry")
self.assertEqual(row16.text, "MGI:3522448\n2 C' 2C',2C'' MGI:3522619 (Sdc1) Immunohistochemistry")
self.assertEqual(row17.text, "2C,2C'' MGI:3522624 (Tubb3) Immunohistochemistry")
self.assertEqual(row18.text, "MGI:3522448\n2 C'' 2C',2C'' MGI:3522619 (Sdc1) Immunohistochemistry")
self.assertEqual(row19.text, "2C,2C'' MGI:3522621 (Hspg2) Immunohistochemistry")
def testMinimalStageLinks(self):
"""
tests that all stage links exist in the term detail section and clicking them function correctly; this is for a case with only a few stages; jlewis
"""
self.performSearch(term="second polar body")
detailArea = self.driver.find_element_by_id("termDetailContent")
stageItems = detailArea.find_elements_by_class_name("stageSelector")
# add all link text to a list for "assertIn" test
stages = iterate.getTextAsList(stageItems)
self.assertEqual(stages, ["All", "1", "2", "3", "4"])
# click stage 1
stage1 = detailArea.find_element_by_link_text("1").click()
wait.forAjax(self.driver)
#verify EMAPS term is loaded for second polar body
detailItems = self.driver.find_elements_by_css_selector("#termDetailContent dd")
self.assertEqual(detailItems[2].text,"EMAPA:16034")
# verify stage is active
activeStage = self.driver.find_element_by_css_selector(".stageSelector.active")
self.assertEqual(activeStage.text,"1")
def test_images_noassay(self):
"""
@status: Tests the display for image panes with no attached assay
each image and figure displayed but no assay or specimen
"""
driver = self.driver
driver.get(PWI_URL)
#opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id('accids')
# put your J number in the box
accidbox.send_keys("J:102285")
accidbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the specimens link and clicks it
driver.find_element_by_link_text("Exp Images").click()
wait.forAjax(driver)
#Locates the images table and finds the table headings
imagestable = driver.find_element_by_id("paneSummaryTable")
rows = imagestable.find_elements_by_css_selector('tr')
#displays each row of data for the first 16 rows
row1 = rows[1]
row2 = rows[2]
row3 = rows[3]
row4 = rows[4]
row5 = rows[5]
row6 = rows[6]
row7 = rows[7]
row8 = rows[8]
row9 = rows[9]
row10 = rows[10]
row11 = rows[11]
row12 = rows[12]
row13 = rows[13]
row14 = rows[14]
row15 = rows[15]
row16 = rows[16]
#asserts that the rows of data are correct for the first 16 rows
self.assertEqual(row1.text, 'MGI:4453601\n2 b Fig. 1b MGI:4453599 (Tg(Scgb1a1-cre)1Tauc) In situ reporter (transgenic)')
self.assertEqual(row2.text, 'MGI:4453603\n3 a Fig. 3a MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row3.text, 'MGI:4453603\n3 c Fig. 3c MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row4.text, 'MGI:4453603\n3 e Fig. 3e MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row5.text, 'MGI:4453605\n4 a Fig. 4a MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row6.text, 'MGI:4453605\n4 b Fig. 4b MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row7.text, 'MGI:4453605\n4 c Fig. 4c MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row8.text, 'MGI:4453605\n4 d Fig. 4d MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row9.text, 'MGI:4453605\n4 e Fig. 4e MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row10.text, 'MGI:4453605\n4 f Fig. 4f MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row11.text, 'MGI:4453605\n4 g Fig. 4g MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row12.text, 'MGI:4453605\n4 h Fig. 4h MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row13.text, 'MGI:4453605\n4 i Fig. 4i MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row14.text, 'MGI:4453605\n4 j Fig. 4j MGI:4453606 (Tg(Scgb1a1-cre)1Tauc) Recombinase reporter')
self.assertEqual(row15.text, 'MGI:4453605\n4 k')
self.assertEqual(row16.text, 'MGI:4453605\n4 l')
def test_default_sort_treeview(self):
"""
@status: Tests that the terms are correctly sorted
The default sort for the tree view is smart alpha
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/vocab/gxd/anatomy/EMAPA:16042")
wait.forAjax(driver)
time.sleep(1)
termList = driver.find_elements_by_class_name("ygtvlabel")
terms = iterate.getTextAsList(termList)
print [x.text for x in termList]
def test_mrk_detail_build(self):
"""
@Status this test works
Checks the mouse build number on a marker detail page
"""
#displays the marker detail page for pax6
self.driver.get(PUBLIC_URL + "/marker/MGI:1096368")
#opens the Location & Maps section
self.driver.find_element_by_class_name("toggleImage").click()
wait.forAjax(self.driver)
#finds the build number at the top of the snp QF page
seqmapLabel = self.driver.find_element_by_class_name("detailData2").find_element_by_class_name("closed").find_element_by_css_selector("div.value")
#verifies GRCm38 is displayed in this section
self.assertIn("GRCm38", seqmapLabel.text)
def test_table_headers(self):
"""
@status: Tests that the Gene Ontology Classifications page in Tabular view, table headers are correct
Headers are: Aspect, Category, Classification Term, Context, Proteoform, Evidence, Inferred From, Reference(s)
"""
driver = self.driver
driver.get(config.FEWI_URL + "/marker")
genebox = driver.find_element_by_name('nomen')
# put your marker symbol
genebox.send_keys("Ccdc40")
genebox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the correct marker link and clicks it
driver.find_element_by_link_text("Ccdc40").click()
wait.forAjax(driver)
#Finds the All sequences link and clicks it
driver.find_element_by_class_name("goRibbon").find_element_by_link_text("26").click()
wait.forAjax(driver)
#Locates the marker header table and finds the table headings
tabularheaderlist = driver.find_element_by_id("dynamicdata")
items = tabularheaderlist.find_elements_by_tag_name("th")
searchTextItems = iterate.getTextAsList(items)
wait.forAjax(driver)
print searchTextItems
#verifies all the table headings are correct and in order
self.assertEqual(searchTextItems, ['Aspect','Category','Classification Term', 'Context', 'Proteoform', 'Evidence', 'Inferred From', 'Reference(s)'])
wait.forAjax(driver)
def test_hide_private_marker(self):
"""
@status: Tests that the dummy private allele Brca1<test1> does not display on public
"""
driver = self.driver
driver.get(config.PUBLIC_URL)
self.assertIn("Informatics", driver.title)
querytext = driver.find_element_by_name('query')
querytext.clear()
querytext.send_keys("Agit")# put your marker symbol
querytext.send_keys(Keys.RETURN) # click the submit button
wait.forAjax(driver)
missng = driver.find_element_by_class_name('redText').is_displayed()#verifies that the warning Could not find the independent term(s): is displaying
self.assertTrue(missng, 'oops, is not displaying warning message!')
def test_multispecs_sameassay_samepane(self):
"""
@status: Tests the display for image panes with multiple specimens from the same assay using the same image pane
each specimen should have it's own row
"""
driver = self.driver
driver.get(PWI_URL)
#opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id('accids')
# put your J number in the box
accidbox.send_keys("J:85638")
accidbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the specimens link and clicks it
driver.find_element_by_link_text("Exp Images").click()
wait.forAjax(driver)
#Locates the images table and finds the table headings
imagestable = driver.find_element_by_id("paneSummaryTable")
rows = imagestable.find_elements_by_css_selector('tr')
#displays each row of data for the first 13 rows
row1 = rows[1]
row2 = rows[2]
row3 = rows[3]
row4 = rows[4]
row5 = rows[5]
row6 = rows[6]
row7 = rows[7]
row8 = rows[8]
row9 = rows[9]
row10 = rows[10]
row11 = rows[11]
row12 = rows[12]
row13 = rows[13]
#asserts that the rows of data are correct for the first 13 rows
self.assertEqual(row1.text, 'MGI:5750634\n3 A MGI:5750650 (H13) Northern blot')
self.assertEqual(row2.text, 'MGI:5750637\n4 A 4A MGI:5750680 (H13) RNA in situ')
self.assertEqual(row3.text, 'MGI:5750637\n4 B 4B MGI:5750680 (H13) RNA in situ')
self.assertEqual(row4.text, 'MGI:5750637\n4 C 4C MGI:5750680 (H13) RNA in situ')
self.assertEqual(row5.text, 'MGI:5750638\n5 E5.5 5 E5.5 embryo, 5 E5.5 mother MGI:5750680 (H13) RNA in situ')
self.assertEqual(row6.text, 'MGI:5750638\n5 E6.5 5 E6.5 embryo, 5 E6.5 mother MGI:5750680 (H13) RNA in situ')
self.assertEqual(row7.text, 'MGI:5750638\n5 E7.5 5 E7.5 embryo, 5 E7.5 mother MGI:5750680 (H13) RNA in situ')
self.assertEqual(row8.text, 'MGI:5750638\n5 E8.5 5 E8.5 embryo, 5 E8.5 mother MGI:5750680 (H13) RNA in situ')
self.assertEqual(row9.text, 'MGI:5750638\n5 E9.5 5 E9.5 embryo, 5 E9.5 mother MGI:5750680 (H13) RNA in situ')
self.assertEqual(row10.text, 'MGI:5750639\n6 E10.5 6 E10.5 MGI:5750680 (H13) RNA in situ')
self.assertEqual(row11.text, 'MGI:5750639\n6 E11.5 6 E11.5 MGI:5750680 (H13) RNA in situ')
self.assertEqual(row12.text, 'MGI:5750639\n6 E13.5 6 E13.5 MGI:5750680 (H13) RNA in situ')
self.assertEqual(row13.text, 'MGI:5750639\n6 E14.5 6 E14.5 MGI:5750680 (H13) RNA in situ')
def test_parent_data(self):
"""
@status: Tests that the parent terms are correctly identified
In this case all 3 parent terms should be part-of
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/vocab/gxd/anatomy/EMAPA:16042")
wait.forAjax(driver)
time.sleep(1)
#identifies the table tags that contain parent terms
parent = driver.find_element_by_id("termPaneDetails").find_elements_by_tag_name("td")
#print [x.text for x in parent]
# verifies that the returned part terms are correct
self.assertEqual(parent[4].text, "part-of conceptus\npart-of egg cylinder\npart-of mouse")
def test_hide_private_allele(self):
"""
@status: Tests that the dummy private allele Brca1<test1> does not display on public
"""
driver = self.driver
driver.get(config.PUBLIC_URL)
self.assertIn("Informatics", driver.title)
querytext = driver.find_element_by_name('query')
querytext.clear()
querytext.send_keys("Brca1")# put your marker symbol
querytext.send_keys(Keys.RETURN) # click the submit button
brcalink = driver.find_element_by_link_text("Brca1") # Find the Brca1 link and click it
brcalink.click() # Find the all alleles and mutations link and click it
allallelelink = driver.find_element_by_link_text("89")
allallelelink.click()
wait.forAjax(driver)
# assert that there is no link for Brca1<test1>#testallele = driver.find_element_by_link_text('Brca1<sup>test1</sup>')
self.assertNotIn("test1", self.driver.page_source,"Test1 allele is displaying!")
def test_table_headers(self):
"""
@status: Tests that the Sequence Summary table headers are correct
Headers are: Select, Sequence, Type, Length, Strain/Species, Description from Sequence Provider, Clone Collection, Marker Symbol
"""
driver = self.driver
driver.get(config.FEWI_URL + "/marker")
genebox = driver.find_element_by_name("nomen")
# put your marker symbol
genebox.send_keys("Bloc1s2")
genebox.send_keys(Keys.RETURN)
time.sleep(3)
# finds the correct marker link and clicks it
driver.find_element_by_link_text("Bloc1s2").click()
wait.forAjax(driver)
# Finds the All sequences link and clicks it
driver.find_element_by_link_text("15").click()
wait.forAjax(driver)
# Locates the marker header table and finds the table headings
markerheaderlist = driver.find_element_by_class_name("summaryHeaderCat1")
items = markerheaderlist.find_elements_by_tag_name("div")
searchTextItems = iterate.getTextAsList(items)
wait.forAjax(driver)
# verifies all the table headings are correct and in order
self.assertEqual(searchTextItems, ["Symbol", "Name", "ID"])
wait.forAjax(driver)
# Locates the sequence summary table and finds the table headings
columnheaderlist = driver.find_elements_by_class_name("yui-dt-label")
searchTextItems = iterate.getTextAsList(columnheaderlist)
wait.forAjax(driver)
# verifies all the table headings are correct and in order
self.assertEqual(
searchTextItems,
[
"Select",
"Sequence",
"Type",
"Length",
"Strain/Species",
"Description From\nSequence Provider",
"Clone\nCollection",
"Marker\nSymbol",
],
)
def test_specimentype_column_sort(self):
"""
@status: Tests that the specimen type column sort works correctly
The order for the specimen type sort is the order in the EI menu:
*whole mount
*section
*section from whole mount
*optical section
*not specified
*blots
Reverse would be specified as:
*optical section
*section from whole mount
*section
*whole mount
*not specified
*blots
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/gxd")
genebox = driver.find_element_by_name('nomenclature')
# put your marker symbol
genebox.send_keys("hoxa13")
genebox.send_keys(Keys.RETURN)
#find the Image tab
imagetab = driver.find_element_by_id("imagestab")
#click the image tab
imagetab.click()
wait.forAjax(driver)
time.sleep(.5)
typelist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-hybridization')
items = typelist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["section", "section"])
specimenheader = driver.find_element_by_id("imagesdata").find_element_by_css_selector('th.yui-dt-col-hybridization')
#click the gene header column to sort
specimenheader.click()
wait.forAjax(driver)
time.sleep(.5)
assaylist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-hybridization')
items = assaylist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["whole mount"])
def test_old_gene_id(self):
"""
@status: Tests that an Old Gene ID search brings back the proper information
"""
driver = self.driver
driver.get(config.FEWI_URL)
searchbox = driver.find_element_by_id('searchToolTextArea')
# put your Old Gene ID in the quick search box
searchbox.send_keys("MGD-MRK-1672")
searchbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the Best Match information
buckets = driver.find_elements_by_class_name("qsBucket")
match_info = buckets[0].find_element_by_class_name("qsBucketRow1").find_elements_by_tag_name("td")
searchTextItems = iterate.getTextAsList(match_info)
wait.forAjax(driver)
print searchTextItems
#asserts that the Best Match data is correct for the ID searched
self.assertEqual(searchTextItems[7], 'ID : MGD-MRK-1672 and more detail...')
wait.forAjax(driver)
def test_mouse_anat_id(self):
"""
@status: Tests that an Adult Mouse Anatomy ID brings back the proper information
"""
driver = self.driver
driver.get(config.FEWI_URL)
searchbox = driver.find_element_by_id('searchToolTextArea')
# put your Adult Mouse Anatomy ID in the quick search box
searchbox.send_keys("MA:0000168")
searchbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the Best Match information
buckets = driver.find_elements_by_class_name("qsBucket")
match_info = buckets[2].find_element_by_class_name("qsBucketRow1").find_elements_by_tag_name("td")
searchTextItems = iterate.getTextAsList(match_info)
wait.forAjax(driver)
print searchTextItems
#asserts that the Best Match data is correct for the ID searched
self.assertEqual(searchTextItems[2], 'ID : MA:0000168 (Adult Mouse Anatomy)')
wait.forAjax(driver)
def test_ncbi_id(self):
"""
@status: Tests that a NCBI ID brings back the proper information
"""
driver = self.driver
driver.get(config.FEWI_URL)
searchbox = driver.find_element_by_id('searchToolTextArea')
# put your NCBI ID in the quick search box
searchbox.send_keys("20423")
searchbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the Best Match information
buckets = driver.find_elements_by_class_name("qsBucket")
match_info = buckets[2].find_elements_by_class_name("qsBucketRow2")[0].find_elements_by_tag_name("td")
searchTextItems = iterate.getTextAsList(match_info)
wait.forAjax(driver)
print searchTextItems
#asserts that the Best Match data is correct for the ID searched
self.assertEqual(searchTextItems[2], 'ID : 20423 (NCBI Gene Model)')
wait.forAjax(driver)
def test_escellline_lexicon_id(self):
"""
@status: Tests that an ES Cell Line ID(Lexicon) brings back the proper information
"""
driver = self.driver
driver.get(config.FEWI_URL)
searchbox = driver.find_element_by_id('searchToolTextArea')
# put your ES Cell Line ID in the quick search box
searchbox.send_keys("OST2298")
searchbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the Best Match information
buckets = driver.find_elements_by_class_name("qsBucket")
match_info = buckets[0].find_element_by_class_name("qsBucketRow1").find_elements_by_tag_name("td")
searchTextItems = iterate.getTextAsList(match_info)
wait.forAjax(driver)
print searchTextItems
#asserts that the Best Match data is correct for the ID searched
self.assertEqual(searchTextItems[7], 'Cell Line ID : OST2298 (Lexicon) and 2 more...')
wait.forAjax(driver)
def test_go_id(self):
"""
@status: Tests that an GO ID brings back the proper information
"""
driver = self.driver
driver.get(config.FEWI_URL)
searchbox = driver.find_element_by_id('searchToolTextArea')
# put your GO ID in the quick search box
searchbox.send_keys("GO:0005892")
searchbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the Best Match information
buckets = driver.find_elements_by_class_name("qsBucket")
match_info = buckets[0].find_element_by_class_name("qsBucketRow1").find_elements_by_tag_name("td")
searchTextItems = iterate.getTextAsList(match_info)
wait.forAjax(driver)
print searchTextItems
#asserts that the Best Match data is correct for the ID searched
self.assertEqual(searchTextItems[7], 'Function : acetylcholine-gated channel complex (GO:0005892) and more detail...')
wait.forAjax(driver)
def test_default_sort_genes(self):
"""
@status: Tests that the genes column sorts genes result correctly
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/gxd")
genebox = driver.find_element_by_name('nomenclature')
# put your marker symbol
genebox.send_keys("pax6")
genebox.send_keys(Keys.RETURN)
#find the Image tab
imagetab = driver.find_element_by_id("imagestab")
#click the image tab
imagetab.click()
wait.forAjax(driver)
time.sleep(.5)
genelist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-gene')
items = genelist[16].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["Gsx2", "Nkx2-1", "Pax6"])
def test_default_sort_specimentype(self):
"""
@status: Tests the sort order for specimen type using default sort
sort order is gene first, assay type secondary
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/gxd")
genebox = driver.find_element_by_name('nomenclature')
# put your marker symbol
genebox.send_keys("Tmem100")
genebox.send_keys(Keys.RETURN)
#find the Image tab
imagetab = driver.find_element_by_id("imagestab")
#click the image tab
imagetab.click()
wait.forAjax(driver)
time.sleep(.5)
typelist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-hybridization')
items = typelist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["section", "section from whole mount"])
def test_snp_qf(self):
"""
@Status this test works
Checks the dbSNp and mouse build numbers on the snp query form and snp summary page
"""
self.driver.get(PUBLIC_URL + "/snp/")
#finds the build number at the top of the snp QF page
formLabel = self.driver.find_element_by_css_selector("#form1 > div:nth-child(2)")
self.assertIn("dbSNP Build 142", formLabel.text)
genebox = self.driver.find_element_by_id("nomen")
#enters pax6 in the Gene Symbol/Name box
genebox.send_keys("pax6")
genebox.send_keys(Keys.RETURN)
wait.forAjax(self.driver)
#finds the snp build number in the heading of SNP ID column
snpidLabel = self.driver.find_element_by_id("snpSummaryTable").find_element_by_id("snp_id")
self.assertIn("(dbSNP Build 142)", snpidLabel.text)
#finds the GRC build number in the heading of Map Position column
mapLabel = self.driver.find_element_by_id("snpSummaryTable").find_element_by_id("map_position")
self.assertIn("(GRCm38)", mapLabel.text)
def test_default_sort_assaytype(self):
"""
@status: Tests the sort order for assay type using default sort
sort order is gene first, assay type secondary
"""
driver = self.driver
driver.get(config.PUBLIC_URL + "/gxd")
genebox = driver.find_element_by_name('nomenclature')
# put your marker symbol
genebox.send_keys("Igfbpl1")
genebox.send_keys(Keys.RETURN)
#find the Image tab
imagetab = driver.find_element_by_id("imagestab")
#click the image tab
imagetab.click()
wait.forAjax(driver)
time.sleep(.5)
assaylist = driver.find_element_by_id("imagesdata").find_elements_by_css_selector('td.yui-dt-col-assayType')
items = assaylist[0].find_elements_by_tag_name("li")
searchTextItems = iterate.getTextAsList(items)
self.assertEqual(searchTextItems, ["RNA in situ", "Immunohistochemistry", "Immunohistochemistry"])
def test_table_headers(self):
"""
@status: Tests that the summaries table headers are correct
"""
driver = self.driver
#opens the PWI marker form
driver.get(PWI_URL + '/#markerForm')
nomenbox = driver.find_element_by_id('nomen')
# put your marker symbol in the box
nomenbox.send_keys("gata1")
nomenbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the marker link and clicks it
driver.find_element_by_link_text("Gata1").click()
wait.forAjax(driver)
driver.find_element_by_link_text("GXD Lit Index").click()
wait.forAjax(driver)
#Locates the summary table and finds the table headings
headerlist = driver.find_element_by_id('indexRefsTable')
items = headerlist.find_elements_by_tag_name("th")
searchTextItems = iterate.getTextAsList(items)
wait.forAjax(driver)
#verifies all the table headings are correct and in order
self.assertEqual(searchTextItems, ['*','Reference','Priority','Conditional'])
def test_images_nospecimen(self):
"""
@status: Tests the display for image panes with no specimen label
each image, figure label, pane label, and assay displayed but no specimen label
"""
driver = self.driver
driver.get(PWI_URL)
#opens the PWI reference form
driver.find_element_by_link_text("Reference Form").click()
accidbox = driver.find_element_by_id('accids')
# put your J number in the box
accidbox.send_keys("J:9026")
accidbox.send_keys(Keys.RETURN)
time.sleep(3)
#finds the specimens link and clicks it
driver.find_element_by_link_text("Exp Images").click()
wait.forAjax(driver)
#Locates the images table and finds the table headings
imagestable = driver.find_element_by_id("paneSummaryTable")
rows = imagestable.find_elements_by_css_selector('tr')
#displays each row of data for the first 9 rows
row1 = rows[1]
row2 = rows[2]
row3 = rows[3]
row4 = rows[4]
row5 = rows[5]
row6 = rows[6]
row7 = rows[7]
row8 = rows[8]
row9 = rows[9]
#asserts that the rows of data are correct for the first 9 rows
self.assertEqual(row1.text, 'MGI:4441359\n1 A 2ar MGI:4441369 (Spp1) Northern blot')
self.assertEqual(row2.text, 'MGI:4441359\n1 A SPARC MGI:4441372 (Sparc) Northern blot')
self.assertEqual(row3.text, 'MGI:4441359\n1 B 2ar MGI:4441380 (Spp1) Northern blot')
self.assertEqual(row4.text, 'MGI:4441359\n1 B SPARC MGI:4441384 (Sparc) Northern blot')
self.assertEqual(row5.text, 'MGI:4441361\n2 a/e 2a,e MGI:4441386 (Spp1) RNA in situ')
self.assertEqual(row6.text, 'MGI:4441361\n2 b/f 2b,f MGI:4441386 (Spp1) RNA in situ')
self.assertEqual(row7.text, 'MGI:4441361\n2 d/h 2d,h - decidua, 2d,h - embryo MGI:4441386 (Spp1) RNA in situ')
self.assertEqual(row8.text, 'MGI:4441363\n3 a 3a MGI:4441386 (Spp1) RNA in situ')
self.assertEqual(row9.text, 'MGI:4441363\n3 d/e 3d MGI:4441386 (Spp1) RNA in situ')
