def test_genes_tab_headers(self):
'''
@status this test verifies all the table headers on the genes tab are correct and in the correct order.
'''
my_select = self.driver.find_element_by_xpath("//select[starts-with(@id, 'field_0_')]")#identifies the select field and picks the gene symbols option
for option in my_select.find_elements_by_tag_name("option"):
if option.text == 'Gene Symbol(s) or ID(s)':
option.click()
break
self.driver.find_element_by_name("formly_3_input_input_0").send_keys("Gata1")#indentifies the input field and enters gata1
wait.forAngular(self.driver)
self.driver.find_element_by_id("searchButton").click()
#identify the Genes tab and verify the tab's text
gene_tab = self.driver.find_element_by_css_selector("ul.nav.nav-tabs > li.uib-tab.nav-item.ng-scope.ng-isolate-scope:nth-child(2) > a.nav-link.ng-binding")
print gene_tab.text
self.assertEqual(gene_tab.text, "Genes (6)", "Genes tab is not visible!")
gene_tab.click()
gene_table_headers = self.driver.find_element_by_id("geneTable").find_element_by_css_selector("tr")
items = gene_table_headers.find_elements_by_tag_name("th")
searchTermItems = iterate.getTextAsList(items)
self.assertEqual(searchTermItems[0], "Organism")
self.assertEqual(searchTermItems[1], "Gene Symbol")
self.assertEqual(searchTermItems[2], "Genetic Location")
self.assertEqual(searchTermItems[3], "Genome Coordinates")
self.assertEqual(searchTermItems[4], "Associated Human Diseases (Source)")
self.assertEqual(searchTermItems[5], "Abnormal Mouse Phenotypes\nReported in these Systems")
self.assertEqual(searchTermItems[6], "References in MGI")
self.assertEqual(searchTermItems[7], "Mice With Mutations\nIn this Gene (IMSR)")
def press_tab(self):
"""
press enter key on previous_element
"""
current_element = self._get_current_element()
current_element.send_keys(Keys.TAB)
wait.forAngular(self.driver)
def testAnnotationResults(self):
"""
tests that when you click a term from the tree the annotation results changes to just that node results
@status: test works
@todo: add comments
"""
self.performSearch(term="brain")
# select specific stage
activetree = self.driver.find_element_by_css_selector(".mgitreeview .active")
self.assertEqual(activetree.text,"brain")
# verify count of results for the EMAPA term
term1CountTag = self.driver.find_element_by_css_selector(".resultsLink a")
term1Count = int(term1CountTag.text)
# assert positive count
self.assertGreater(term1Count,0)
# navigate to a term from the tree
self.driver.find_element_by_css_selector(".mgitreeview").find_element_by_link_text("brain blood vessel").click()
wait.forAngular(self.driver)
# verify count of results for the stage specific term2 term
term2CountTag = self.driver.find_element_by_css_selector(".resultsLink a")
term2Count = int(term2CountTag.text)
# assert positive count
self.assertGreater(term2Count,0)
# verify the count is different from the first term
self.assertNotEqual(term1Count, term2Count)
def test_genes_tab_doids(self):
'''
@status this test verifies the correct DO IDs are returned for this query.
@bug: under construction
'''
my_select = self.driver.find_element_by_xpath("//select[starts-with(@id, 'field_0_')]")#identifies the select field and picks the gene symbols option
for option in my_select.find_elements_by_tag_name("option"):
if option.text == 'Gene Symbol(s) or ID(s)':
option.click()
break
self.driver.find_element_by_name("formly_3_input_input_0").send_keys("Gata1")#identifies the input field and enters gata1
wait.forAngular(self.driver)
self.driver.find_element_by_id("searchButton").click()
wait.forAngular(self.driver)
#identify the Genes tab and verify the tab's text
gene_tab = self.driver.find_element_by_css_selector("ul.nav.nav-tabs > li.uib-tab.nav-item.ng-scope.ng-isolate-scope:nth-child(3) > a.nav-link.ng-binding")
self.assertEqual(gene_tab.text, "Diseases (3)", "Diseases tab is not visible!")
gene_tab.click()
gene_table = Table(self.driver.find_element_by_id("diseaseTable"))
cells = gene_table.get_column_cells("DO ID")
print iterate.getTextAsList(cells)
#displays each row of gene data
doid1 = cells[1]
doid2 = cells[2]
doid3 = cells[3]
#asserts that the correct genes in the correct order are returned
self.assertEqual(doid1.text, 'DOID:14250')
self.assertEqual(doid2.text, 'DOID:4971')
self.assertEqual(doid3.text, 'DOID:1588')
def enter_shortcut(self, keys):
"""
send keys to previous_element
"""
current_element = self._get_current_element()
current_element.send_keys(keys)
wait.forAngular(self.driver)
def testDeleteIndex(self):
"""
@Status tests that an index record can be deleted
"""
driver = self.driver
form = self.form
form.enter_value('jnumid', '225216')
# click the Tab key
form.press_tab()
#finds the citation field
citation = form.get_value('citation')
print citation
self.assertEqual(citation, 'Alvarez-Saavedra M, Nat Commun 2014;5():4181')
#finds the marker field
form.enter_value('marker_symbol', 'Bmp2')
marker_symbol = form.get_value('marker_symbol')
form.press_tab()
print marker_symbol
self.assertEqual(marker_symbol, 'Bmp2')
#find the table field to check
table_element = driver.find_element_by_id("indexGrid")
table = Table(table_element)
#puts an X in the Prot-sxn by age 7.5 box
cell = table.get_cell("prot-sxn", "7.5")
cell.click()
wait.forAngular(driver)
self.assertEqual(cell.text, 'X', "the cell is not checked")
form.click_modify()
form.click_delete()#click the delete button
def testAnnotationStageResults(self):
"""
tests that when you click a term for a specific stage from the tree the annotation results changes to just that node results; jlewis
@status: test works
"""
self.performSearch(term="bowman's capsule%", stage=26)
# verify tree is highlighting correct term
activetree = self.driver.find_element_by_css_selector(".mgitreeview .active")
self.assertEqual(activetree.text,"Bowman's capsule of mature renal corpuscle")
# verify there is a count of results for the EMAPS term
term1CountTag = self.driver.find_element_by_css_selector(".resultsLink a")
term1Count = int(term1CountTag.text)
# assert positive count
self.assertGreater(term1Count,0)
# navigate to a child term from the tree
self.driver.find_element_by_css_selector(".mgitreeview").find_element_by_link_text("urinary space of mature renal corpuscle").click()
wait.forAngular(self.driver)
# verify count of results for the stage specific term2 term
term2CountTag = self.driver.find_element_by_css_selector(".resultsLink a")
term2Count = int(term2CountTag.text)
# assert zero count (as-of data on 8/18/2016)
self.assertEqual(term2Count,0)
# verify the count is different from the first term
self.assertNotEqual(term1Count, term2Count)
def testAnnotationDetailLink(self):
"""
tests that when you click on the annotations link in the detail section it goes to the correct assay results
"""
self.performSearch(term="brain blood vessel")
# select specific stage
activetree = self.driver.find_element_by_css_selector(".mgitreeview .active")
self.assertEqual(activetree.text,"brain blood vessel")
wait.forAngular(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("brain blood vessel" 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 testGreaterThanEqualDateSearch(self):
"""
@Status tests that searching by greater than or equal to created by date gives the correct results
"""
form = self.form
form.enter_value('_priority_key', 'Medium')
form.press_tab()
form.enter_value('_conditionalmutants_key', 'Conditional (minor)')
form.press_tab()
form.enter_value('is_coded', 'Yes')
form.press_tab()
form.enter_value('creation_date', ">=11/10/2015")
form.press_tab()
wait.forAngular(self.driver)
form.click_search()#click the search button
#find the search results table
results_table = self.driver.find_element_by_id("resultsTable")
table = Table(results_table)
#Iterate and print the search results headers
header_cells = table.get_header_cells()
print iterate.getTextAsList(header_cells)
# print row 1
cells = table.get_row_cells(1)
print iterate.getTextAsList(cells)
#print column 1
symbols_cells = table.get_column_cells('Marker')
symbols = iterate.getTextAsList(symbols_cells)
self.assertEqual(symbols, ['Marker', 'Acta2', 'Aqp2', 'Emcn', 'Postn', 'Tagln', 'Upk1b', 'Upk3a', 'Upk3b'])
def testBetweenDateSearch(self):
"""
@Status tests that searching by inclusive dates gives the correct results
"""
form = self.form
form.enter_value('_priority_key', 'Medium')
form.press_tab()
form.enter_value('_conditionalmutants_key', 'Conditional')
form.press_tab()
form.enter_value('is_coded', 'Yes')
form.press_tab()
form.enter_value('creation_date', "10/01/2015..12/01/2015")
form.press_tab()
wait.forAngular(self.driver)
form.click_search()#click the search button
#find the search results table
results_table = self.driver.find_element_by_id("resultsTable")
table = Table(results_table)
#Iterate and print the search results headers
header_cells = table.get_header_cells()
print iterate.getTextAsList(header_cells)
# print row 1
cells = table.get_row_cells(1)
print iterate.getTextAsList(cells)
#print column 1
symbols_cells = table.get_column_cells('Marker')
symbols = iterate.getTextAsList(symbols_cells)
self.assertEqual(symbols, ['Marker', 'Flrt3', 'Ntn1', 'Pecam1', 'Slit1', 'Tlx1'])
def testSearchIndex(self):
"""
@Status tests that an index record(s) can be searched
"""
driver = self.driver
form = self.form
#find the Index grid
table_element = driver.find_element_by_id("indexGrid")
table = Table(table_element)
#puts an X in the Prot-wm by age 7 box
cell = table.get_cell("prot-wm", "7")
cell.click()
#puts an X in the Prot-wm by age 8 box
cell = table.get_cell("prot-wm", "8")
cell.click()
wait.forAngular(driver)
form.click_search()#click the search button
#find the search results table
results_table = driver.find_element_by_id("resultsTable")
table = Table(results_table)
#Iterate and print the search results headers
header_cells = table.get_header_cells()
print iterate.getTextAsList(header_cells)
# print row 1
cells = table.get_row_cells(1)
print iterate.getTextAsList(cells)
#print column 1
symbols_cells = table.get_column_cells('Marker')
symbols = iterate.getTextAsList(symbols_cells)
self.assertEqual(symbols, ['Marker','Adgre1', 'Cdh5', 'Cdx4', 'Eng', 'Fgf8', 'Foxa2', 'Gata6', 'Itga2b', 'Kdr', 'Kdr', 'Kdr', 'Kdr', 'Lrp2', 'Nanog', 'Pdgfra', 'Pecam1', 'Pou3f1', 'Ptprc', 'T', 'T', 'Tal1', 'Tek'])
def testMultipleMrkSearch(self):
"""
@Status tests that a multiple marker search works
@bug test needs to be written
"""
driver = self.driver
form = self.form
form.enter_value('marker_symbol', 't')
form.press_tab()
wait.forAngular(driver)
# verify that display with two markers is shown
mrkrows = driver.find_elements_by_css_selector(".markerSelections td")
print mrkrows
markers = [r.text for r in mrkrows]
self.assertEqual(len(markers), 2)
self.assertEqual(markers[0], "T, brachyury, Chr 17, Band")
self.assertEqual(markers[1], "t, t-complex, Chr 17, Band")
#form.press_enter()
mrkrows[0].click()
wait.forAngular(driver)
# marker T should be selected
marker_symbol = form.get_value('marker_symbol')
self.assertEqual(marker_symbol, 'T')
def testClipboardShortcut(self):
"""
@status confirm the shortcut keys(CTRL + ALT + k) resets the clipboard input box
"""
actions = ActionChains(self.driver)
#search for the term tail
self.performSearch(term="tail")
result = self.driver.find_element_by_id("termResultList").find_element_by_css_selector("mark")
result.click()
wait.forAngular(self.driver)
#clear all items in the clipboard
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
#Add 18 into the add to clipboard field
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("18")
clipbox.send_keys(Keys.RETURN)
clipdata = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipdata.find_elements_by_css_selector("li")
searchTreeItems = iterate.getTextAsList(items)
#assert that TS18 tail is displayed in the clipboard
self.assertEqual(["TS18; tail"], searchTreeItems)
#clear the clipboard using the shortcut keys
actions.key_down(Keys.CONTROL).key_down(Keys.ALT).send_keys('k').key_up(Keys.CONTROL).key_up(Keys.ALT).perform()
time.sleep(5)
clipdata = self.driver.find_element_by_id("emapClipBoardContent")
items = clipdata.find_elements_by_css_selector("li")
searchTreeItems = iterate.getTextAsList(items)
#Assert that the clipboard is empty
self.assertEqual([], searchTreeItems)
def test_diseases_tab_headers(self):
'''
@status this test verifies the headings on the disease tab are correct and in the correct order.
@bug: under construction
'''
my_select = self.driver.find_element_by_xpath("//select[starts-with(@id, 'field_0_')]")#identifies the select field and picks the gene symbols option
for option in my_select.find_elements_by_tag_name("option"):
if option.text == 'Gene Symbol(s) or ID(s)':
option.click()
break
self.driver.find_element_by_name("formly_3_input_input_0").send_keys("Gata1")#indentifies the input field and enters gata1
wait.forAngular(self.driver)
self.driver.find_element_by_id("searchButton").click()
#identify the Genes tab and verify the tab's text
disease_tab = self.driver.find_element_by_css_selector("ul.nav.nav-tabs > li.uib-tab.nav-item.ng-scope.ng-isolate-scope:nth-child(3) > a.nav-link.ng-binding")
print disease_tab.text
self.assertEqual(disease_tab.text, "Diseases (3)", "Diseases tab is not visible!")
disease_tab.click()
gene_table_headers = self.driver.find_element_by_id("diseaseTable").find_element_by_css_selector("tr")
items = gene_table_headers.find_elements_by_tag_name("th")
searchTermItems = iterate.getTextAsList(items)
self.assertEqual(searchTermItems[0], "Disease")
self.assertEqual(searchTermItems[1], "DO ID")
self.assertEqual(searchTermItems[2], "OMIM ID(s)")
self.assertEqual(searchTermItems[3], "Mouse Models")
self.assertEqual(searchTermItems[4], "Associated Genes from Mouse Models")
self.assertEqual(searchTermItems[5], "Associated Human Genes (Source)")
self.assertEqual(searchTermItems[6], "References using\nMouse Models")
def testStageLinks(self):
"""
tests that all stage links exist in the term detail section and clicking them function correctly
"""
self.performSearch(term="mouse")
detailArea = self.driver.find_element_by_id("termDetailContent")
stageItems = detailArea.find_elements_by_class_name("stageSelector")
# add all li text to a list for "assertIn" test
stages = iterate.getTextAsList(stageItems)
self.assertEqual(stages, ["All","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28"])
# click stage 10
stage10 = detailArea.find_element_by_link_text("10").click()
wait.forAngular(self.driver)
#verify EMAPS term is loaded for mouse
detailItems = self.driver.find_elements_by_css_selector("#termDetailContent dd")
self.assertEqual(detailItems[2].text, "EMAPA:2576510")
# verify stage is active
activeStage = self.driver.find_element_by_css_selector(".stageSelector.active")
self.assertEqual(activeStage.text, "10")
def testdeleteoneclipboard(self):
"""
@status tests you can delete one item from the clipboard.
"""
self.performSearch(term="emb%")
result = self.driver.find_element_by_id("termResultList").find_elements_by_link_text("embryo")
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("4-5")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS4; embryo", "TS5; embryo"], searchTreeItems)
items[1].click()
wait.forAngular(self.driver)
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]/img").click()
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS4; embryo"], searchTreeItems)
def testNonNumberStage(self):
"""
@status trying to add a stage to the clip board using a non-numeric number.
"""
self.performSearch(term="epiblast")
result = self.driver.find_element_by_id("termResultList").find_element_by_css_selector("mark")
result.click()
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("seven")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
errdisplay = self.driver.find_element_by_id("errorMessage")
self.assertTrue(errdisplay.is_displayed(), "Error message not displaying")
def testSpecificStageTree(self):
"""
tests that tree view changes to show just tree of term selected.
@status: test works
@todo: add comments
"""
self.performSearch(term="embryo")
# select specific stage
stage20 = self.driver.find_element_by_id("stageList").find_element_by_link_text("20")
stage20.click()
wait.forAngular(self.driver)
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "embryo")
self.assertEqual(items[1].text, "Theiler Stage 20 (11.5-13.0 dpc)")
self.assertEqual(items[2].text, "EMAPS:1603920")
def testParentStage(self):
"""
tests that if parent link is clicked remain in the current stage.
@status: works fine
@todo: add comments
"""
self.performSearch(term="3rd ventricle%")
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "3rd ventricle")
self.assertEqual(items[1].text, "Theiler Stages 14-28")
self.assertEqual(items[2].text, "EMAPA:16900")
self.assertEqual(items[3].text, "diencephalic vesicle, third ventricle")
self.assertEqual(items[4].text.split("\n"), ["is-a brain ventricle","part-of diencephalon","part-of future diencephalon"])
stage15 = self.driver.find_element_by_id("stageList").find_element_by_link_text("15")
stage15.click()
wait.forAngular(self.driver)
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "3rd ventricle")
self.assertEqual(items[1].text, "Theiler Stage 15 (9.0-10.25 dpc)")
self.assertEqual(items[2].text, "EMAPS:1690015")
self.assertEqual(items[3].text, "diencephalic vesicle, third ventricle")
self.assertEqual(items[4].text.split("\n"), ["is-a brain ventricle","part-of diencephalon"])
parent = self.driver.find_element_by_id("termDetailContent").find_element_by_class_name("detailPageListData")
parent.find_element_by_link_text("diencephalon").click()
wait.forAngular(self.driver)
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "diencephalon")
self.assertEqual(items[1].text, "Theiler Stage 15 (9.0-10.25 dpc)")
self.assertEqual(items[2].text, "EMAPS:1689615")
self.assertEqual(items[3].text.split("\n"), ["part-of future forebrain"])
activestage = self.driver.find_element_by_css_selector(".stageselector.active")
self.assertEqual(activestage.text,"15")
def testClipboardBasicSort(self):
"""
@status tests that a basic sort works by displaying the clip board results in smart alpha order.
"""
self.performSearch(term="emb%")
result = self.driver.find_element_by_id("termResultList").find_elements_by_link_text("embryo")
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("5-7")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS5; embryo","TS6; embryo","TS7; embryo"], searchTreeItems)
clipbox.clear()
# do a new search for endoderm
self.performSearch(term="endoderm")
result = self.driver.find_element_by_id("termResultList").find_elements_by_link_text("endoderm")
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("6-8")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS5; embryo","TS6; embryo","TS7; embryo","TS6; endoderm","TS7; endoderm","TS8; endoderm"], searchTreeItems)
sort = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardSort")
sort.click()
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS5; embryo","TS6; embryo","TS6; endoderm","TS7; embryo","TS7; endoderm","TS8; endoderm"], searchTreeItems)
def performSearch(self,
term="",
stage=""):
"""
Submit the EMAPA search form
with the supplied parameters
"""
termSearch = self.driver.find_element_by_id("termSearch")
termSearch.clear()
termSearch.send_keys(term)
stageSearch = self.driver.find_element_by_id("stageSearch")
stageSearch.clear()
stageSearch.send_keys(stage)
stageSearch.send_keys(Keys.RETURN)
# wait for all AJAX behavior to complete
wait.forAngular(self.driver)
def testDashStages(self):
"""
@status adding stages to the clip board separated by a dash.
"""
self.performSearch(term="neck")
result = self.driver.find_element_by_id("termResultList").find_element_by_css_selector("mark")
result.click()
wait.forAngular(self.driver)
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("22-25")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS22; neck", "TS23; neck", "TS24; neck", "TS25; neck"], searchTreeItems)
def testDuplicateStage(self):
"""
@status trying to add a duplicate term/stage to the clip board.
"""
self.performSearch(term="brain")
result = self.driver.find_element_by_id("termResultList").find_element_by_css_selector("mark")
result.click()
wait.forAngular(self.driver)
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("18,19,20,20,21,22,23,24,25")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS18; brain", "TS19; brain", "TS20; brain", "TS21; brain", "TS22; brain", "TS23; brain", "TS24; brain", "TS25; brain"], searchTreeItems)
def testWildcardStage(self):
"""
@status adding all stages to clip board using a *.
"""
self.performSearch(term="epiblast")
result = self.driver.find_element_by_id("termResultList").find_element_by_css_selector("mark")
result.click()
wait.forAngular(self.driver)
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("*")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS6; epiblast", "TS7; epiblast", "TS8; epiblast"], searchTreeItems)
def testCommaStages(self):
"""
@status adding stages to the clipboard separated by commas.
"""
self.performSearch(term="epithelium")
result = self.driver.find_element_by_id("termResultList").find_element_by_css_selector("mark")
result.click()
wait.forAngular(self.driver)
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("15,16,17,19")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS15; epithelium", "TS16; epithelium", "TS17; epithelium", "TS19; epithelium"], searchTreeItems)
def test_genes_tab_genes(self):
'''
@status this test verifies the correct genes are returned for this query.
'''
my_select = self.driver.find_element_by_xpath("//select[starts-with(@id, 'field_0_')]")#identifies the select field and picks the gene symbols option
for option in my_select.find_elements_by_tag_name("option"):
if option.text == 'Gene Symbol(s) or ID(s)':
option.click()
break
self.driver.find_element_by_name("formly_3_input_input_0").send_keys("Gata1")#identifies the input field and enters gata1
wait.forAngular(self.driver)
self.driver.find_element_by_id("searchButton").click()
wait.forAngular(self.driver)
#identify the Genes tab and verify the tab's text
gene_tab = self.driver.find_element_by_css_selector("ul.nav.nav-tabs > li.uib-tab.nav-item.ng-scope.ng-isolate-scope:nth-child(2) > a.nav-link.ng-binding")
print gene_tab.text
self.assertEqual(gene_tab.text, "Genes (6)", "Genes tab is not visible!")
gene_tab.click()
gene_table = Table(self.driver.find_element_by_id("geneTable"))
cells = gene_table.get_column_cells("Gene Symbol")
print iterate.getTextAsList(cells)
#displays each row of gene data
gene1 = cells[1]
gene2 = cells[2]
gene3 = cells[3]
gene4 = cells[4]
gene5 = cells[5]
gene6 = cells[6]
#asserts that the correct genes in the correct order are returned
self.assertEqual(gene1.text, 'Gata1')
self.assertEqual(gene2.text, 'GATA1')
self.assertEqual(gene3.text, 'Tg(Gata1)#Mym')
self.assertEqual(gene4.text, 'Tg(Gata1*)#Mym')
self.assertEqual(gene5.text, 'Tg(Gata1*V205G)1Mym')
self.assertEqual(gene6.text, 'Tg(HBB-Gata1)G4Phi')
def testDeleteMultClipboard(self):
"""
@status tests you can delete multiple items from the clipboard.
"""
self.performSearch(term="neck")
clear = self.driver.find_element_by_id("clipboardFunctions").find_element_by_id("clipboardClear")
clear.click()
wait.forAngular(self.driver)
clipbox = self.driver.find_element_by_id("clipboardInput")
clipbox.send_keys("23-27")
clipbox.send_keys(Keys.RETURN)
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
# add all li text to a list for "assertIn" test
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS23; neck","TS24; neck","TS25; neck","TS26; neck","TS27; neck"], searchTreeItems)
# TS24; neck
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]").click()
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]/img").click()
wait.forAngular(self.driver)
# TS25; neck
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]").click()
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]/img").click()
wait.forAngular(self.driver)
# TS26; neck
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]").click()
self.driver.find_element_by_xpath("//*[@id='clipboard']/li[2]/img").click()
wait.forAngular(self.driver)
clipsort = self.driver.find_element_by_id("emapClipBoardContent").find_element_by_id("clipboard")
items = clipsort.find_elements_by_css_selector("li")
searchTreeItems = iterate.getTextAsList(items)
self.assertEqual(["TS23; neck","TS27; neck"], searchTreeItems)
def test_genes_tab_diseases(self):
'''
@status this test verifies the correct diseases are returned for this query.
'''
my_select = self.driver.find_element_by_xpath("//select[starts-with(@id, 'field_0_')]")#identifies the select field and picks the gene symbols option
for option in my_select.find_elements_by_tag_name("option"):
if option.text == 'Gene Symbol(s) or ID(s)':
option.click()
break
self.driver.find_element_by_name("formly_3_input_input_0").send_keys("Gata1")#identifies the input field and enters gata1
wait.forAngular(self.driver)
self.driver.find_element_by_id("searchButton").click()
wait.forAngular(self.driver)
#identify the Genes tab and verify the tab's text
gene_tab = self.driver.find_element_by_css_selector("ul.nav.nav-tabs > li.uib-tab.nav-item.ng-scope.ng-isolate-scope:nth-child(2) > a.nav-link.ng-binding")
self.assertEqual(gene_tab.text, "Genes (6)", "Genes tab is not visible!")
gene_tab.click()
gene_table = Table(self.driver.find_element_by_id("geneTable"))
cells = gene_table.get_column_cells("Associated Human Diseases (Source)")
print iterate.getTextAsList(cells)
#displays each row of gene data
disease1 = cells[1]
disease2 = cells[2]
disease3 = cells[3]
disease4 = cells[4]
disease5 = cells[5]
disease6 = cells[6]
#asserts that the correct genes in the correct order are returned
self.assertEqual(disease1.text, 'myelofibrosis\nthrombocytopenia')
self.assertEqual(disease2.text, 'Down syndrome\nthrombocytopenia')
self.assertEqual(disease3.text, '')
self.assertEqual(disease4.text, '')
self.assertEqual(disease5.text, 'thrombocytopenia')
self.assertEqual(disease6.text, '')
def testDetailParent(self):
"""
tests that term detail updates including valid parents.
@status: test works
@todo: needs comments
"""
self.performSearch(term="cortical renal tubule")
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "cortical renal tubule")
self.assertEqual(items[1].text, "Theiler Stages 22-28")
self.assertEqual(items[2].text, "EMAPA:18976")
self.assertEqual(items[3].text, "kidney cortex tubule, renal cortex tubule")
self.assertEqual(items[4].text.split("\n"), ["part-of developing capillary loop stage nephron group","part-of early nephron","part-of late tubule","part-of mature nephron","part-of maturing nephron","part-of renal cortex","part-of stage IV immature nephron"])
stage24 = self.driver.find_element_by_id("stageList").find_element_by_link_text("24")
stage24.click()
wait.forAngular(self.driver)
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "cortical renal tubule")
self.assertEqual(items[1].text, "Theiler Stage 24 (16.0-16.99 dpc)")
self.assertEqual(items[2].text, "EMAPS:1897624")
self.assertEqual(items[3].text, "kidney cortex tubule, renal cortex tubule")
self.assertEqual(items[4].text.split("\n"), ["part-of developing capillary loop stage nephron group","part-of early nephron","part-of late tubule","part-of maturing nephron","part-of renal cortex"])
stage22 = self.driver.find_element_by_id("stageList").find_element_by_link_text("22")
stage22.click()
wait.forAngular(self.driver)
term_det = self.driver.find_element_by_id("termDetailContent")
items = term_det.find_elements_by_tag_name("dd")
self.assertEqual(items[0].text, "cortical renal tubule")
self.assertEqual(items[1].text, "Theiler Stage 22 (13.5-15.0 dpc)")
self.assertEqual(items[2].text, "EMAPS:1897622")
self.assertEqual(items[3].text, "kidney cortex tubule, renal cortex tubule")
self.assertEqual(items[4].text.split("\n"), ["part-of developing capillary loop stage nephron group","part-of early nephron","part-of late tubule","part-of maturing nephron","part-of renal cortex","part-of stage IV immature nephron"])
def testClickingNode(self):
"""
tests that if a term is clicked, the detail updates,
and also that node expands
"""
self.performSearch(term="mouse")
# click tissue node in tree
tree = self.driver.find_element_by_id("emapaTree")
tissueNode = tree.find_element_by_link_text("tissue")
tissueNode.click()
wait.forAngular(self.driver)
# verify term detail changed
detail = self.driver.find_element_by_id("termDetailContent")
ddItems = detail.find_elements_by_tag_name("dd")
# verify EMAPA ID for 'tissue' is displayed
self.assertEqual(ddItems[2].text, "EMAPA:35868")
# verify tree has expanded to include children of tissue
tree = self.driver.find_element_by_id("emapaTree")
self.assertTrue("epithelium" in tree.text, "epithelium should be in tree view")
self.assertTrue("muscle tissue" in tree.text, "muscle tissue should be in tree view")