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jctrotterjctrotter
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updated JBrowseTests
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‎jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java‎

Lines changed: 71 additions & 171 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
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import org.junit.Test;
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import org.labkey.serverapi.reader.Readers;
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import org.labkey.test.BaseWebDriverTest;
24+
import org.labkey.test.Locator;
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import org.labkey.test.TestFileUtils;
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import org.labkey.test.TestTimeoutException;
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import org.labkey.test.components.ext4.Window;
@@ -67,7 +68,18 @@ public void testSteps() throws Exception
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{
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setUpTest();
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70-
testOutputFileProcessing();
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testDemoUi();
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//testOutputFileProcessing();
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}
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private void testDemoUi()
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{
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beginAt("/home/jbrowse-jbrowse.view");
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waitAndClick(Locator.tagWithClass("span", "MuiButton-label"));
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waitAndClick(Locator.tagWithClass("span", "MuiButton-label").containing("Open track selector"));
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7183
}
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@Override
@@ -81,187 +93,75 @@ protected void setUpTest() throws Exception
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_containerHelper.createProject(getProjectName(), "Sequence Analysis");
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_containerHelper.enableModule("JBrowse");
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84-
//TODO
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//download/setup jbrowse scripts
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// File scriptDir = Files.createTempDir();
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// downloadInstallScripts(scriptDir);
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//
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// goToAdminConsole();
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// waitAndClickAndWait(Locator.linkContainingText("jbrowse admin"));
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// Ext4FieldRef.waitForField(this, "Script Directory");
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// Ext4FieldRef.getForLabel(this, "Script Directory").setValue(scriptDir.toString());
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// click(Ext4Helper.Locators.ext4ButtonEnabled("Save Settings"));
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// waitAndClickAndWait(Ext4Helper.Locators.ext4ButtonEnabled("OK"));
95-
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//create genome and add resources
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Integer genomeId = SequenceTest.createReferenceGenome(this, _completedPipelineJobs);
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_completedPipelineJobs++; //keep track of pipeline jobs
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_completedPipelineJobs = SequenceTest.addReferenceGenomeTracks(this, getProjectName(), SequenceTest.TEST_GENOME_NAME, genomeId, _completedPipelineJobs);
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}
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103-
private void downloadInstallScripts(File scriptDir) throws Exception
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{
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URL url = new URL("http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=98");
106-
File zip = new File(scriptDir, "jbrowse.zip");
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108-
try (InputStream is = url.openStream();BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(zip)))
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{
110-
IOUtils.copy(is, out);
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}
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113-
unzipToDirectory(zip, scriptDir);
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zip.delete();
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//now attempt to run/install script:
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File unzipDir = new File(scriptDir, "JBrowse-1.11.5");
118-
if (SystemUtils.IS_OS_WINDOWS)
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{
120-
execute(Arrays.asList("perl", "bin\\cpanm", "--notest", "-l", "extlib\\", "--installdeps", "."), unzipDir);
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}
122-
else
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{
124-
//just run the shell script
125-
execute(Arrays.asList("setup.sh"), unzipDir);
126-
}
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}
128-
129-
private void unzipToDirectory(File sourceZip, File unzipDir) throws IOException
130-
{
131-
try (ZipInputStream zis = new ZipInputStream(new FileInputStream(sourceZip));BufferedInputStream is = new BufferedInputStream(zis))
132-
{
133-
ZipEntry entry;
134-
while (null != (entry = zis.getNextEntry()))
135-
{
136-
if (entry.isDirectory())
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{
138-
File newDir = new File(unzipDir, entry.getName());
139-
newDir.mkdir();
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continue;
141-
}
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143-
//log("Expanding " + entry.getName());
144-
145-
File destFile = new File(unzipDir, entry.getName());
146-
destFile.getParentFile().mkdirs();
147-
destFile.createNewFile();
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149-
try (BufferedOutputStream os = new BufferedOutputStream(new FileOutputStream(destFile)))
150-
{
151-
IOUtils.copy(is, os);
152-
zis.closeEntry();
153-
}
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}
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}
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}
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158-
public String execute(List<String> params, File workingDir) throws Exception
159-
{
160-
StringBuffer output = new StringBuffer();
161-
log("\t" + StringUtils.join(params, " "));
162-
163-
ProcessBuilder pb = new ProcessBuilder(params);
164-
pb.environment().put("PATH", System.getenv("PATH"));
165-
pb.directory(workingDir);
166-
log("using working dir: " + workingDir.getPath());
167-
pb.redirectErrorStream(true);
168-
169-
Process p = null;
170-
try
171-
{
172-
p = pb.start();
173-
174-
try (BufferedReader procReader = Readers.getReader(p.getInputStream()))
175-
{
176-
String line;
177-
while ((line = procReader.readLine()) != null)
178-
{
179-
output.append(line);
180-
output.append(System.getProperty("line.separator"));
181-
182-
log(line);
183-
}
184-
}
185-
186-
int returnCode = p.waitFor();
187-
if (returnCode != 0)
188-
{
189-
throw new Exception("process exited with non-zero value: " + returnCode);
190-
}
191-
}
192-
finally
193-
{
194-
if (p != null)
195-
{
196-
p.destroy();
197-
}
198-
}
199-
200-
return output.toString();
201-
}
202-
203103
@Override
204104
public List<String> getAssociatedModules()
205105
{
206106
return Arrays.asList("jbrowse");
207107
}
208108

209-
private void testOutputFileProcessing() throws Exception
210-
{
211-
goToProjectHome();
212-
213-
//import BAM, VCF, BED, GFF
214-
File dataDir = TestFileUtils.getSampleData("sequenceAnalysis/genomeAnnotations");
215-
for (File f : dataDir.listFiles())
216-
{
217-
SequenceTest.addOutputFile(this, f, SequenceTest.TEST_GENOME_NAME, f.getName(), "Gene Annotations", "This is an output file", false);
218-
}
219-
220-
File testBam = new File(SequenceTest._sampleData, "test.bam");
221-
SequenceTest.addOutputFile(this, testBam, SequenceTest.TEST_GENOME_NAME, "TestBAM", "BAM File", "This is an output file", false);
222-
223-
//create session w/ some of these, verify
224-
log("creating initial jbrowse session");
225-
beginAt("/sequenceanalysis/" + getContainerId() + "/begin.view");
226-
waitAndClickAndWait(LabModuleHelper.getNavPanelItem("Output Files:", null));
227-
228-
DataRegionTable dr = new DataRegionTable("query", this);
229-
dr.uncheckAll();
230-
dr.checkCheckbox(0);
231-
dr.clickHeaderMenu("More Actions", false, "View In JBrowse");
232-
233-
String sessionName = "TestSession1";
234-
new Window.WindowFinder(getDriver()).withTitle("Create/Modify JBrowse Session").waitFor();
235-
Ext4FieldRef.getForLabel(this, "Name").setValue(sessionName);
236-
Ext4FieldRef.getForLabel(this, "Description").setValue("This is the first session");
237-
waitAndClick(Ext4Helper.Locators.ext4ButtonEnabled("Submit"));
238-
new Window.WindowFinder(getDriver()).withTitle("Success").waitFor();
239-
waitAndClickAndWait(Ext4Helper.Locators.ext4ButtonEnabled("OK"));
240-
_completedPipelineJobs++;
241-
waitForPipelineJobsToComplete(_completedPipelineJobs, "Create New Session", false);
242-
243-
//add additional file to session, verify
244-
//TODO: first cache timestamps on JSON resources. we expect these to be untouched
245-
246-
beginAt("/sequenceanalysis/" + getContainerId() + "/begin.view");
247-
waitAndClickAndWait(LabModuleHelper.getNavPanelItem("Output Files:", null));
248-
249-
dr = new DataRegionTable("query", this);
250-
dr.uncheckAll();
251-
dr.checkCheckbox(1);
252-
dr.checkCheckbox(2);
253-
dr.clickHeaderMenu("More Actions", false, "View In JBrowse");
254-
new Window.WindowFinder(getDriver()).withTitle("Create/Modify JBrowse Session").waitFor();
255-
Ext4FieldRef.getForBoxLabel(this, "Add To Existing Session").setChecked(true);
256-
Ext4FieldRef.waitForField(this, "Session");
257-
Ext4ComboRef.getForLabel(this, "Session").setComboByDisplayValue(sessionName);
258-
waitAndClick(Ext4Helper.Locators.ext4ButtonEnabled("Submit"));
259-
new Window.WindowFinder(getDriver()).withTitle("Success").waitFor();
260-
waitAndClickAndWait(Ext4Helper.Locators.ext4ButtonEnabled("OK"));
261-
_completedPipelineJobs++;
262-
waitForPipelineJobsToComplete(_completedPipelineJobs, "Add To Existing Session", false);
263-
264-
//TODO: reprocess one of these JSONFiles. make sure original files are deleted + session reprocessed
265-
beginAt("/sequenceanalysis/" + getContainerId() + "/begin.view");
266-
}
109+
// private void testOutputFileProcessing() throws Exception
110+
// {
111+
// goToProjectHome();
112+
//
113+
// //import BAM, VCF, BED, GFF
114+
// File dataDir = TestFileUtils.getSampleData("sequenceAnalysis/genomeAnnotations");
115+
// for (File f : dataDir.listFiles())
116+
// {
117+
// SequenceTest.addOutputFile(this, f, SequenceTest.TEST_GENOME_NAME, f.getName(), "Gene Annotations", "This is an output file", false);
118+
// }
119+
//
120+
// File testBam = new File(SequenceTest._sampleData, "test.bam");
121+
// SequenceTest.addOutputFile(this, testBam, SequenceTest.TEST_GENOME_NAME, "TestBAM", "BAM File", "This is an output file", false);
122+
//
123+
// //create session w/ some of these, verify
124+
// log("creating initial jbrowse session");
125+
// beginAt("/sequenceanalysis/" + getContainerId() + "/begin.view");
126+
// waitAndClickAndWait(LabModuleHelper.getNavPanelItem("Output Files:", null));
127+
//
128+
// DataRegionTable dr = new DataRegionTable("query", this);
129+
// dr.uncheckAll();
130+
// dr.checkCheckbox(0);
131+
// dr.clickHeaderMenu("More Actions", false, "View In JBrowse");
132+
//
133+
// String sessionName = "TestSession1";
134+
// new Window.WindowFinder(getDriver()).withTitle("Create/Modify JBrowse Session").waitFor();
135+
// Ext4FieldRef.getForLabel(this, "Name").setValue(sessionName);
136+
// Ext4FieldRef.getForLabel(this, "Description").setValue("This is the first session");
137+
// waitAndClick(Ext4Helper.Locators.ext4ButtonEnabled("Submit"));
138+
// new Window.WindowFinder(getDriver()).withTitle("Success").waitFor();
139+
// waitAndClickAndWait(Ext4Helper.Locators.ext4ButtonEnabled("OK"));
140+
// _completedPipelineJobs++;
141+
// waitForPipelineJobsToComplete(_completedPipelineJobs, "Create New Session", false);
142+
//
143+
// //add additional file to session, verify
144+
// //TODO: first cache timestamps on JSON resources. we expect these to be untouched
145+
//
146+
// beginAt("/sequenceanalysis/" + getContainerId() + "/begin.view");
147+
// waitAndClickAndWait(LabModuleHelper.getNavPanelItem("Output Files:", null));
148+
//
149+
// dr = new DataRegionTable("query", this);
150+
// dr.uncheckAll();
151+
// dr.checkCheckbox(1);
152+
// dr.checkCheckbox(2);
153+
// dr.clickHeaderMenu("More Actions", false, "View In JBrowse");
154+
// new Window.WindowFinder(getDriver()).withTitle("Create/Modify JBrowse Session").waitFor();
155+
// Ext4FieldRef.getForBoxLabel(this, "Add To Existing Session").setChecked(true);
156+
// Ext4FieldRef.waitForField(this, "Session");
157+
// Ext4ComboRef.getForLabel(this, "Session").setComboByDisplayValue(sessionName);
158+
// waitAndClick(Ext4Helper.Locators.ext4ButtonEnabled("Submit"));
159+
// new Window.WindowFinder(getDriver()).withTitle("Success").waitFor();
160+
// waitAndClickAndWait(Ext4Helper.Locators.ext4ButtonEnabled("OK"));
161+
// _completedPipelineJobs++;
162+
// waitForPipelineJobsToComplete(_completedPipelineJobs, "Add To Existing Session", false);
163+
//
164+
// //TODO: reprocess one of these JSONFiles. make sure original files are deleted + session reprocessed
165+
// beginAt("/sequenceanalysis/" + getContainerId() + "/begin.view");
166+
// }
267167
}

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