first working selenium tests: formats yeast data and does a serach fo…

…r one of the gene names using the search box
GMOD · Jan 10, 2012 · fa4885a · fa4885a
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diff --git a/sample_data/json/.exists b/sample_data/json/.exists
diff --git a/sample_data/json/Makefile b/sample_data/json/Makefile
diff --git a/sample_data/raw/yeast.json b/sample_data/raw/yeast.json
@@ -0,0 +1,40 @@
+{
+  "description": "Yeast Example Database",
+  "db_adaptor": "Bio::DB::SeqFeature::Store",
+  "db_args": {
+      "-adaptor": "memory",
+      "-dir": "../raw/yeast_chr1+2"
+  },
+  "TRACK DEFAULTS": {
+    "class": "feature",
+    "autocomplete": "all"
+  },
+  "tracks": [
+    {
+      "track": "Genes",
+      "feature": ["gene"],
+      "class": "feature5",
+      "key": "Protein-coding genes",
+      "subfeatures": true,
+      "subfeature_classes": {
+        "CDS": "transcript-CDS"
+      },
+      "arrowheadClass": "transcript-arrowhead",
+      "category": "Genes"
+    },
+    {
+      "track": "Transcript",
+      "feature": ["mRNA"],
+      "description": 1,
+      "class": "transcript",
+      "subfeatures": true,
+      "subfeature_classes": {
+        "CDS": "transcript-CDS",
+        "UTR": "transcript-UTR"
+      },
+      "arrowheadClass": "transcript-arrowhead",
+      "key": "Exonerate predictions",
+      "category": "Genes"
+    }
+  ]
+}
diff --git a/test_harness.html b/test_harness.html
@@ -0,0 +1,76 @@
+<!DOCTYPE html
+	  PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+	  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+
+<!-- This HTML file is for use by the JBrowse integration tests only. -->
+
+  <head>
+    <title>JBrowse</title>
+    <link rel="stylesheet" type="text/css" href="jslib/dijit/themes/tundra/tundra.css"></link>
+    <link rel="stylesheet" type="text/css" href="jslib/dojo/resources/dojo.css"></link>
+    <link rel="stylesheet" type="text/css" href="genome.css"></link>
+    <style type="text/css">
+      html, body { height: 100%; width: 100%; padding: 0; border: 0; }
+    </style>
+
+    <script type="text/javascript" src="jslib/dojo/dojo.js" djConfig="isDebug: false"></script>
+    <script type="text/javascript" src="jslib/dojo/jbrowse_dojo.js" ></script>
+
+<!-- js_source_files -->
+<!-- the files between the "js_source_files" comments get replaced
+     when the JS gets minified (see the minification rule in the Makefile) -->
+    <script type="text/javascript" src="js/Browser.js"></script>
+    <script type="text/javascript" src="js/Util.js"></script>
+    <script type="text/javascript" src="js/NCList.js"></script>
+    <script type="text/javascript" src="js/LazyPatricia.js"></script>
+    <script type="text/javascript" src="js/LazyArray.js"></script>
+    <script type="text/javascript" src="js/Track.js"></script>
+    <script type="text/javascript" src="js/SequenceTrack.js"></script>
+    <script type="text/javascript" src="js/Layout.js"></script>
+    <script type="text/javascript" src="js/FeatureTrack.js"></script>
+    <script type="text/javascript" src="js/UITracks.js"></script>
+    <script type="text/javascript" src="js/ImageTrack.js"></script>
+    <script type="text/javascript" src="js/GenomeView.js"></script>
+<!-- js_source_files -->
+  </head>
+
+  <body>
+    <div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; border: 0;"></div>
+    <script type="text/javascript">
+    /* <![CDATA[ */
+           var queryParams = dojo.queryToObject(window.location.search.slice(1));
+
+           // load the proper refSeqs and trackInfo based on the data path passed as a query arg
+           var dataRoot = queryParams.data || 'data';
+           dojo.forEach( ['refSeqs.js','trackInfo.js'], function(file) {
+               dojo.xhrGet({
+                              url: dataRoot + '/' + file,
+                              handleAs: 'javascript',
+                              sync: true
+                           });
+           });
+
+           var bookmarkCallback = function(brwsr) {
+               return window.location.protocol
+                      + "//" + window.location.host
+                      + window.location.pathname
+                      + "?loc=" + brwsr.visibleRegion()
+                      + "&tracks=" + brwsr.visibleTracks();
+           }
+           var b = new Browser({
+                                   containerID: "GenomeBrowser",
+                                   refSeqs: refSeqs,
+                                   trackData: trackInfo,
+                                   defaultTracks: "DNA,gene,mRNA,noncodingRNA",
+                                   location: queryParams.loc,
+                                   tracks: queryParams.tracks,
+                                   bookmark: bookmarkCallback,
+                                   dataRoot: dataRoot + '/'
+                               });
+    /* ]]> */
+    </script>
+
+  </body>
+</html>
diff --git a/tests/selenium_tests/yeast_biodb_test.py b/tests/selenium_tests/yeast_biodb_test.py
@@ -0,0 +1,92 @@
+from selenium import webdriver
+from selenium.common.exceptions import NoSuchElementException
+from selenium.webdriver.common.keys import Keys
+from subprocess import check_call as call
+import os
+import shutil
+import time
+
+def test_yeast():
+    format_yeast()
+    browser = webdriver.Firefox() # Get local session of firefox
+    browser.get("file://%s/test_harness.html?data=sample_data/json/yeast" % os.getcwd() ) # Load page
+
+    # check a good browser title
+    assert "chrI" in browser.title
+
+    # check that we have the appropriate tracks
+    genes_track = assert_element( browser, '//div[@class="tracklist-label"]' )
+    assert genes_track.text == 'Protein-coding genes', "first track was called %s instead of %s" % (first_track.text, 'Protein-coding genes')
+
+    # do a test where we search for a certain gene using the search box
+    search_yal024c(browser)
+
+def search_yal024c(browser):
+
+    # check that a YAL024C feature label is not yet in the DOM
+    yal024_xpath = "//div[@class='feature-label'][contains(.,'YAL024C')]"
+    try:
+        browser.find_element_by_xpath( yal024_xpath )
+        assert 0, ( "YAL024C is already in the DOM at load time, something is wrong" )
+    except NoSuchElementException:
+        pass
+
+    # Find the query box and put YAL024C into it and hit enter
+    qbox = browser.find_element_by_id("location")
+    qbox.clear()
+    qbox.send_keys( "YAL024C" + Keys.RETURN )
+
+    # test that YAL024C appeared in the DOM (TODO: check that it's
+    # actually centered in the window), and that the protein-coding
+    # genes track is now selected
+    label = assert_element( browser, yal024_xpath )
+    assert label.text == 'YAL024C';
+
+    browser.close()
+    pass;
+
+def assert_element( browser, xpathExpression ):
+    try:
+        el = browser.find_element_by_xpath( xpathExpression )
+    except NoSuchElementException:
+        assert 0, ( "can't find %s" % xpathExpression )
+    return el
+
+def format_yeast():
+    os.chdir('sample_data/json')
+    os.environ['PATH'] = "../../bin:" + os.environ['PATH']
+    call( "rm -rf yeast/", shell=True )
+    call( "prepare-refseqs.pl --fasta ../raw/yeast_scaffolds/chr1.fa --fasta ../raw/yeast_scaffolds/chr2.fa  --out yeast/", shell=True )
+    call( "biodb-to-json.pl --conf ../raw/yeast.json --out yeast/", shell=True )
+    call( "generate-names.pl --dir yeast/", shell=True )
+    os.chdir('../..')
+
+
+# $ENV{PATH} = "../../bin:$ENV{PATH}";
+
+# chdir 'sample_data/json';
+
+# system 'rm -rf yeast/';
+# system qw( prepare-refseqs.pl
+#            --fasta ../raw/yeast_scaffolds/chr1.fa
+#            --fasta ../raw/yeast_scaffolds/chr2.fa
+#            --out yeast/
+#          );
+# system qw(
+#          );
+
+# # system qw( flatfile-to-json.pl
+# #            --gff ../raw/yeast_chr1+2/yeast_chr1+2.gff3
+# #            --tracklabel Genes
+# #            --cssClass feature5
+# #            --type gene
+# #            --
+# #            --out yeast/
+# #          );
+# #	flatfile-to-json.pl --gff ../raw/yeast_chr1+2/yeast_chr1+2.gff3 --autocomplete all --tracklabel Genes --getSubs --type gene --getLabel --urltemplate 'http://example.com/foo/genes/{id}' --out yeast/;
+# #	flatfile-to-json.pl --gff ../raw/yeast_chr1+2/yeast_chr1+2.gff3 --autocomplete all --tracklabel Repeats --getSubs --type repeat_region --getLabel --urltemplate 'http://example.com/foo/repeats/{id}' --out yeast/;
+
+# system qw( generate-names.pl --dir yeast/ );
+
+# ok 1;
+# done_testing;