--- /dev/null
+{"$schema":"http://json-schema.org/draft-04/schema#","id":"http://jsonschema.net","type":"object","properties":{"seqs":{"id":"http://jsonschema.net/seqs","type":"array","items":{"id":"http://jsonschema.net/seqs/0","type":"object","properties":{"name":{"id":"http://jsonschema.net/seqs/0/name","type":"string","description":"Sequence name"},"start":{"id":"http://jsonschema.net/seqs/0/start","type":"integer","description":"Start residue position"},"svid":{"id":"http://jsonschema.net/seqs/0/svid","type":"string","description":"Serial version id for sequence object"},"end":{"id":"http://jsonschema.net/seqs/0/end","type":"integer","description":"End residue position"},"id":{"id":"http://jsonschema.net/seqs/0/id","type":"string","description":"Sequence unique identifier"},"seq":{"id":"http://jsonschema.net/seqs/0/seq","type":"string","description":"Sequence Residues"},"order":{"id":"http://jsonschema.net/seqs/0/order","type":"integer","description":"Sequence order in an alignment space"}},"required":["name","start","svid","end","id","seq"]},"required":["0"],"description":"Sequences in the Alignemnt","minItems":"1","maxItems":"*"},"appSettings":{"id":"http://jsonschema.net/appSettings","type":"object","properties":{"globalColorScheme":{"id":"http://jsonschema.net/appSettings/globalColorScheme","type":"string","description":"Global colour schem for the alignment"},"webStartUrl":{"id":"http://jsonschema.net/appSettings/webStartUrl","type":"string","description":"Jalview specific setting which points to a url for launching Jalview"},"application":{"id":"http://jsonschema.net/appSettings/application","type":"string","description":"Application which generated the Json"},"showSeqFeatures":{"id":"http://jsonschema.net/appSettings/showSeqFeatures","type":"string","description":"Determines if sequence features are visible or not"},"version":{"id":"http://jsonschema.net/appSettings/version","type":"string","description":"Verion of the application which generated the JSON"},"hiddenCols":{"id":"http://jsonschema.net/appSettings/hiddenCols","type":"string","description":"Delimited lists of hidden colums ranges i.e [2-3,5-5,11-23]"}},"description":"Application specific settings"},"seqGroups":{"id":"http://jsonschema.net/seqGroups","type":"array","items":[{"id":"http://jsonschema.net/seqGroups/0","type":"object","properties":{"displayText":{"id":"http://jsonschema.net/seqGroups/0/displayText","type":"boolean","description":"Determines if the texts of the group is displayed or not"},"startRes":{"id":"http://jsonschema.net/seqGroups/0/startRes","type":"integer","description":"Start residue position for a given group"},"groupName":{"id":"http://jsonschema.net/seqGroups/0/groupName","type":"string","description":"Group name"},"endRes":{"id":"http://jsonschema.net/seqGroups/0/endRes","type":"integer","description":"End residue position for a given group"},"colourText":{"id":"http://jsonschema.net/seqGroups/0/colourText","type":"boolean","description":"Determines if the Residues text for the group is coloured"},"seqsHash":{"id":"http://jsonschema.net/seqGroups/0/seqsHash","type":"array","items":[],"minItems":"0","maxItems":"*","description":"The id's of the sequences which belongs to the group"},"svid":{"id":"http://jsonschema.net/seqGroups/0/svid","type":"string","description":"Serial version id for a given group"},"showNonconserved":{"id":"http://jsonschema.net/seqGroups/0/showNonconserved","type":"boolean","description":"Determines if non conserved regions of a group is shown or not"},"colourScheme":{"id":"http://jsonschema.net/seqGroups/0/colourScheme","type":"string","description":"Colour Scheme for the sequence group"},"displayBoxes":{"id":"http://jsonschema.net/seqGroups/0/displayBoxes","type":"boolean","description":"Determines if the group border should be visible or not"}}}],"description":"Sequence groups in the Alignment","minItems":"0","maxItems":"*"},"alignAnnotation":{"id":"http://jsonschema.net/alignAnnotation","type":"array","items":{"id":"http://jsonschema.net/alignAnnotation/0","type":"object","properties":{"svid":{"id":"http://jsonschema.net/alignAnnotation/0/svid","type":"string","description":"Serial version id for the annotation object"},"annotations":{"id":"http://jsonschema.net/alignAnnotation/0/annotations","type":"array","items":[{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/displayCharacter","type":"string","description":"Display character to denote the given annotation"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/value","type":"integer","description":"Value of the annotation"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/0/secondaryStructure","type":"string","description":"Secondary structure symbol for the given annotation"}}},{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/displayCharacter","type":"string"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/value","type":"integer"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/1/secondaryStructure","type":"string"}}},{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2","type":"object","properties":{"displayCharacter":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/displayCharacter","type":"string"},"value":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/value","type":"integer"},"secondaryStructure":{"id":"http://jsonschema.net/alignAnnotation/0/annotations/2/secondaryStructure","type":"string"}}}]},"description":{"id":"http://jsonschema.net/alignAnnotation/0/description","type":"string","description":"Description of the Alignment Annotation"},"label":{"id":"http://jsonschema.net/alignAnnotation/0/label","type":"string","description":"Label for the Annotation"}}},"description":"Alignment Annotations","minItems":"0","maxItems":"*"},"svid":{"id":"http://jsonschema.net/svid","type":"string","description":"Serial version id"},"seqFeatures":{"id":"http://jsonschema.net/seqFeatures","type":"array","items":{"id":"http://jsonschema.net/seqFeatures/0","type":"object","properties":{"fillColor":{"id":"http://jsonschema.net/seqFeatures/0/fillColor","type":"string","description":"Fill colour"},"score":{"id":"http://jsonschema.net/seqFeatures/0/score","type":"integer","description":"Score"},"sequenceRef":{"id":"http://jsonschema.net/seqFeatures/0/sequenceRef","type":"string","description":"Reference to the Sequence in the alignement (More like a foreign key)"},"featureGroup":{"id":"http://jsonschema.net/seqFeatures/0/featureGroup","type":"string","description":"Feature Group"},"svid":{"id":"http://jsonschema.net/seqFeatures/0/svid","type":"string","description":"Serial version id for the SeqFeature object"},"description":{"id":"http://jsonschema.net/seqFeatures/0/description","type":"string","description":"Description of Feature"},"xStart":{"id":"http://jsonschema.net/seqFeatures/0/xStart","type":"integer","description":"Start residue position for the sequence feature"},"xEnd":{"id":"http://jsonschema.net/seqFeatures/0/xEnd","type":"integer","description":"End residue position for the sequence feature"},"type":{"id":"http://jsonschema.net/seqFeatures/0/type","type":"string","description":"The name of the SequenceFeature"}}},"minItems":"0","maxItems":"*","description":"Sequence Features within the alignment"}},"required":["seqs","appSettings","seqGroups","alignAnnotation","svid","seqFeatures"]}
\ No newline at end of file
import java.io.InputStreamReader;
import org.testng.Assert;
-import org.testng.AssertJUnit;
+import org.testng.FileAssert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class CommandLineOperations
String _cmd = "java "
+ (withAwt ? "-Djava.awt.headless=true" : "")
+ " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
- System.out.println("###############Jalview CMD: " + _cmd + cmd);
+ System.out.println("############ Testing Jalview CMD: " + _cmd + cmd);
Process ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
BufferedReader outputReader = new BufferedReader(new InputStreamReader(
ls2_proc.getInputStream()));
Worker worker = new Worker(ls2_proc);
worker.start();
worker.join(timeout);
- System.out.println("Output: ");
- String ln = null;
- while ((ln = outputReader.readLine()) != null)
+ // System.out.println("Output: ");
+ // String ln = null;
+ // while ((ln = outputReader.readLine()) != null)
+ // {
+ // System.out.println(ln);
+ // }
+ //
+ // System.out.println("Error: ");
+ // while ((ln = errorReader.readLine()) != null)
+ // {
+ // System.out.println(ln);
+ // }
+ return worker;
+ }
+
+ @BeforeTest
+ public void initialize()
+ {
+ new CommandLineOperations();
+ }
+
+ @Test(dataProvider = "headlessModeOutputParams")
+ public void testHeadlessModeOutputs(String harg, String type,
+ String fileName, boolean withAWT, int expectedMinFileSize)
+ {
+ String cmd = harg + type + " " + fileName;
+ // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+ File file = new File(fileName);
+ Worker worker = null;
+ try
{
- System.out.println(ln);
+ worker = jalviewDesktopRunner(withAWT, cmd, 9000);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
}
- System.out.println("Error: ");
- while ((ln = errorReader.readLine()) != null)
+ FileAssert.assertFile(file, "Didn't create an output" + type
+ + " file.[" + harg + "]");
+ FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
+ if (worker != null && worker.exit == null)
{
- System.out.println(ln);
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
+ Assert.fail("Jalview did not exit after "
+ + type
+ + " generation (try running test again to verify - timeout at 9000ms). ["
+ + harg + "]");
}
- return worker;
+ new File(fileName).delete();
}
- @Test
- public void testHeadlessModeEPS() throws Exception
+ @DataProvider(name = "headlessModeOutputParams")
+ public static Object[][] headlessModeOutput()
{
- String[] headlessArgs = new String[]
- { "nodisplay", "headless", "nogui" };
- for (String _harg : headlessArgs)
+ return new Object[][]
{
- boolean _switch = false, withAwt = false;
- do
- {
- if (_switch)
- {
- withAwt = true;
- }
- _switch = true;
- String jalview_input = "examples/uniref50.fa";
- String jalview_output = "test_uniref50_out.eps";
- String cmd = "" + _harg + " -open " + jalview_input + " -eps "
- + jalview_output;
- String harg = _harg
- + (withAwt ? "-Djava.awt.headless=true"
- : " NO AWT.HEADLESS");
- System.out.println("Testing with Headless argument: '" + harg
- + "'\n");
- Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
- AssertJUnit.assertTrue("Didn't create an output EPS file.[" + harg
- + "]", new File("test_uniref50_out.eps").exists());
- AssertJUnit.assertTrue(
- "Didn't create an EPS file with any content[" + harg + "]",
- new File("test_uniref50_out.eps").length() > 4096);
- if (worker.exit == null)
- {
- worker.interrupt();
- Thread.currentThread().interrupt();
- worker.process.destroy();
- Assert.fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["
- + harg + "]");
- }
- } while (!withAwt);
- }
+ { "nodisplay -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", true, 4096 },
+ { "nodisplay -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", false, 4096 },
+ { "headless -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", true, 4096 },
+ { "headless -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", false, 4096 },
+ { "nogui -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", true, 4096 },
+ { "nogui -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", false, 4096 },
+ { "headless -open examples/uniref50.fa", " -svg",
+ "test_uniref50_out.svg", true, 4096 },
+ { "headless -open examples/uniref50.fa", " -svg",
+ "test_uniref50_out.svg", false, 4096 },
+ { "headless -open examples/uniref50.fa", " -png",
+ "test_uniref50_out.png", true, 4096 },
+ { "headless -open examples/uniref50.fa", " -png",
+ "test_uniref50_out.png", false, 4096 },
+ { "headless -open examples/uniref50.fa", " -html",
+ "test_uniref50_out.html", true, 4096 },
+ { "headless -open examples/uniref50.fa", " -html",
+ "test_uniref50_out.html", false, 4096 },
+ { "headless -open examples/uniref50.fa", " -fasta",
+ "test_uniref50_out.mfa", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -fasta",
+ "test_uniref50_out.mfa", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -clustal",
+ "test_uniref50_out.aln", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -clustal",
+ "test_uniref50_out.aln", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -msf",
+ "test_uniref50_out.msf", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -msf",
+ "test_uniref50_out.msf", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -pileup",
+ "test_uniref50_out.aln", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -pileup",
+ "test_uniref50_out.aln", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -pir",
+ "test_uniref50_out.pir", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -pir",
+ "test_uniref50_out.pir", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -pfam",
+ "test_uniref50_out.pfam", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -pfam",
+ "test_uniref50_out.pfam", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -blc",
+ "test_uniref50_out.blc", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -blc",
+ "test_uniref50_out.blc", false, 2096 },
+ { "headless -open examples/uniref50.fa", " -jalview",
+ "test_uniref50_out.jvp", true, 2096 },
+ { "headless -open examples/uniref50.fa", " -jalview",
+ "test_uniref50_out.jvp", false, 2096 },
+ };
}
- // @Test
- // public void testJalview2XMLDataset() throws Exception
- // {
- // String jalview_input = "examples/uniref50.fa";
- // String jalview_output = "test_uniref50_out.eps";
- // String cmd = ""+" -open "+ jalview_input + " -eps " + jalview_output;
- // //String harg = _harg+(withAwt ?
- // "-Djava.awt.headless=true":" NO AWT.HEADLESS");
- // System.out.println("Testing with Headless argument: '"+harg+"'\n");
- // Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
- // assertTrue("Didn't create an output EPS file.["+harg+"]", new
- // File("test_uniref50_out.eps").exists());
- // assertTrue("Didn't create an EPS file with any content["+harg+"]", new
- // File("test_uniref50_out.eps").length()>4096);
- // if (worker.exit == null){
- // worker.interrupt();
- // Thread.currentThread().interrupt();
- // worker.process.destroy();
- // fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]");
- // }
- // }
+
+
}
git://source.jalview.org / jalview.git / commitdiff