import subprocess from subprocess import check_call as call, PIPE import unittest import time from jbrowse_selenium import JBrowseTest class AbstractVolvoxBiodbTest( JBrowseTest ): data_dir = 'sample_data/json/volvox' def setUp( self ): super( AbstractVolvoxBiodbTest, self ).setUp() def test_volvox( self ): # select "ctgA from the dropdown self.select_refseq( 'ctgA' ) # check a good browser title assert "ctgA" in self.browser.title, "browser title is actually %s" % self.browser.title # do a test where we search for a certain gene using the search box self.search_f15() self.assert_no_js_errors() # test scrolling, make sure we get no js errors self.scroll() # test context menus self.context_menus() # test sequence track display self.sequence() # test that the frame usage track claims to have links to NCBI self.turn_on_track( 'HTMLFeatures - mRNAs' ) self.do_typed_query('ctgA:2,381..21,220') self.assert_element("//div[contains(@title,'Search for Apple3 at NCBI')]") self.turn_off_track( 'HTMLFeatures - mRNAs' ) # test bigwig self.bigwig() # test data export self.export() # test bam self.bam() # test cram self.cram() # test vcf self.vcf() # test CanvasFeatures tracks self.canvasfeatures() # test search tracks self.search_track() # test combination tracks self.combination() def canvasfeatures( self ): # turn on CanvasFeatures tracks and make sure they are created self.do_typed_query( 'Apple1' ) self.click_search_disambiguation('CanvasFeatures','Go') self.turn_on_track('CanvasFeatures - Protein-coding genes') self.assert_elements("//div[@id='track_Genes']//canvas") self.assert_elements("//div[@id='track_CDS']//canvas") self.assert_no_js_errors() self.turn_off_track('CanvasFeatures - mixed') # test left-clicking on CanvasFeatures track self.do_typed_query( 'ctgA:1049..9000' ) self.assert_no_element("//*[@class='dijitDialogTitle'][contains(text(), 'details')]") canvas = self.assert_element("//div[@id='track_Genes']/canvas") canvas.click() self.assert_element("//*[@class='dijitDialogTitle'][contains(text(), 'gene EDEN')]") self.close_dialog("gene EDEN") self.assert_no_element("//*[@class='dijitDialogTitle'][contains(text(), 'snippet')]") # test Canvas-features context menu functionality # right-click one of them self.actionchains() \ .context_click(canvas) \ .perform() self.menu_item_click("Popup with content snippet from string (feature EDEN)") self.assert_element("//*[@class='dijitDialogTitle'][contains(text(), 'from a JS callback')]") self.close_dialog('from a JS callback') # turn off canvasFeatures tracks so they're not cluttering everything up self.turn_off_track('CanvasFeatures - Protein-coding genes') def vcf( self ): self.do_typed_query('ctgA:18918..19070') self.turn_on_track('VCF - volvox-sorted') self.turn_on_track('VCF - additional') self.assert_elements("//div[@id='track_volvox_sorted_vcf']//canvas") self.assert_elements("//div[@id='track_volvox_vcf_test']//canvas") self.turn_off_track('VCF - volvox-sorted') self.turn_off_track('VCF - additional') def bam( self ): self.do_typed_query('ctgA:18918..19070') self.turn_on_track('volvox-sorted.bam') self.turn_on_track('volvox-sorted SNPs/Coverage') self.assert_elements("//div[@id='track_volvox_sorted_bam']//canvas") self.assert_elements("//div[@id='track_volvox_sorted_bam_coverage']//canvas") self.turn_off_track('volvox-sorted.bam') self.turn_off_track('volvox-sorted SNPs/Coverage') def cram( self ): self.do_typed_query('ctgA:18918..19070') self.turn_on_track('volvox-sorted.cram') self.assert_elements("//div[@id='track_volvox_sorted_cram']//canvas") self.turn_off_track('volvox-sorted.cram') def export( self ): self.do_typed_query('ctgA') self.turn_on_track( 'BigWig XY - volvox_microarray' ) trackname = 'volvox_microarray_bw_xyplot' self.export_track( trackname, 'Visible region','GFF3','View') self.close_dialog('export') self.export_track( trackname, 'Whole', 'bedGraph', 'Save' ) time.sleep( 0.5 * JBrowseTest.time_dilation ) self.export_track( trackname, 'Whole', 'Wiggle', 'Save' ) self.turn_off_track( 'BigWig XY - volvox_microarray' ) self.turn_on_track( 'HTMLFeatures - Example Features' ) trackname = 'ExampleFeatures' self.export_track( trackname, 'Visible region','GFF3','View') self.close_dialog('export') self.export_track( trackname, 'Visible region','BED','Save') self.turn_off_track( 'HTMLFeatures - Example Features' ) self.turn_on_track( 'CanvasFeatures - transcripts' ) trackname = 'Transcript' self.export_track( trackname, 'Visible region', 'GFF3', 'View') self.close_dialog('export') self.export_track( trackname, 'Visible region', 'BED', 'Save') self.turn_off_track( 'CanvasFeatures - transcripts' ) self.do_typed_query('ctgA:8379..31627') self.export_track( 'DNA', 'Visible region','FASTA','View') self.assert_no_js_errors() self.close_dialog('export') self.assert_no_js_errors() def bigwig( self ): self.turn_on_track('BigWig XY - volvox_microarray') self.assert_elements("//div[@id='track_volvox_microarray.bw_xyplot']//canvas") self.assert_no_js_errors() self.turn_on_track('BigWig Density - volvox_microarray') self.assert_elements("//div[@id='track_volvox_microarray.bw_density']//canvas") self.assert_no_js_errors() self.turn_off_track('BigWig XY - volvox_microarray') self.turn_off_track('BigWig Density - volvox_microarray') def sequence( self ): self.do_typed_query( '0..80' ) sequence_div_xpath_templ = "//table[contains(@class,'sequence')]//*[contains(.,'%s')]" sequence_div_xpath_1 = sequence_div_xpath_templ % 'aacaACGG' self.assert_element( sequence_div_xpath_1) self.turn_off_track( 'Reference sequence' ) self.assert_no_element( sequence_div_xpath_1 ) self.turn_on_track( 'Reference sequence' ) self.assert_element( sequence_div_xpath_1 ) self.do_typed_query( '1..20000') self.assert_no_element( sequence_div_xpath_1 ) self.do_typed_query( 'ctgA:19961..20040') self.assert_element( sequence_div_xpath_templ % 'ccgcgtgtagtc' ) def context_menus( self ): self.turn_on_track( 'HTMLFeatures - Features with right-click menus' ) self.do_typed_query( '20147..35574' ) # check that there is no dialog open self.assert_no_element("//*[@class='dijitDialogTitle'][contains(text(),'snippet')]") # get the example alignments features feature_elements = self.assert_elements("//div[@id='track_malformed_alignments']//div[contains(@class,'plus-feature4')]") time.sleep(1*JBrowseTest.time_dilation) # wait a second to make sure their click handlers are installed # right-click one of them self.actionchains() \ .context_click(feature_elements[int(len(feature_elements)/2)]) \ .perform() self.menu_item_click( 'Open popup' ) # check that the proper HTML snippet popped up in the dialog self.assert_element("//div[contains(@class,'dijitDialog')]//span[@class='amazingTestSnippet']") self.close_dialog('Random XHR') # check that the dialog closed self.assert_no_element("//*[@class='dijitDialogTitle'][contains(text(),'Random XHR')]") self.turn_off_track( 'HTMLFeatures - Features with right-click menus' ) def click( self ): self.turn_on_track('ChromHMM') self.assert_elements("//div[@id='track_ChromeHMM']//canvas") self.assert_no_js_errors() # test left-clicking on CanvasFeatures track self.do_typed_query( 'ctgA:20000..30000' ) self.assert_no_element("//*[@class='featureTooltip'][contains(text(), '15_Quies')]") canvas = self.assert_element("//div[@id='track_ChromHMM']/canvas") canvas.mouseover() self.assert_element("//*[@class='featureTooltip'][contains(text(), '15_Quies')]") self.turn_off_track('ChromHMM') def search_f15( self ): # check that a f15 feature label is not yet in the DOM xpath = "//div[contains(@class,'feature-label')]//*[contains(.,'f15')]" # check that f15 is not already in the DOM at load time self.assert_no_element( xpath ) self.do_typed_query( "f15" ) # click "Go" on the first row self.click_search_disambiguation('HTMLFeatures','Go') # test that f15 appeared in the DOM (TODO: check that it's # actually centered in the window), and that the protein-coding # genes track is now selected assert self.assert_element(xpath).text =='f15' self.turn_off_track('HTMLFeatures - Example Features') def search_track( self ): self.assert_element("#dropdownbutton_file").click() self.assert_element("//*[contains(@class,'dijitMenuTable')]//*[contains(@class,'dijitMenuItemLabel')][contains(text(),'Add sequence search')]").click() self.assert_element("//div[contains(@class,'dijitDialogPaneContent')]//input[@type='text'][contains(@class,'dijitInputInner')]").send_keys( "aaaccc" ) self.assert_element("//div[contains(@class,'dijitDialogPaneContent')]//span[contains(@class,'dijitButtonText')][text()='Search']").click() self.assert_element("//div[contains(@id, 'track_search_track')]//canvas") self.wait_for_dialog_disappearance() self.turn_off_track("Search reference sequence for") def combination( self ): self.assert_element("#dropdownbutton_file").click() self.assert_element("#menubar_combotrack_text").click() self.assert_element("//div[contains(@id, 'track_combination_track')]") self.turn_off_track("Combination Track") class VolvoxBiodbTest( AbstractVolvoxBiodbTest, unittest.TestCase ): pass if __name__ == '__main__': import unittest unittest.main()