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JAL-1889 unit test tweaks for running on server
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 8 Nov 2018 15:24:06 +0000
(15:24 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 8 Nov 2018 15:24:06 +0000
(15:24 +0000)
test/jalview/ext/rbvi/chimera/ChimeraConnect.java
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test/jalview/gui/AlignViewportTest.java
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test/jalview/gui/AlignmentPanelTest.java
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test/jalview/io/IdentifyFileTest.java
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test/jalview/io/cache/JvCacheableInputBoxTest.java
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test/jalview/viewmodel/styles/ViewStyleTest.java
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diff --git
a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
index
4d904cf
..
99394dc
100644
(file)
--- a/
test/jalview/ext/rbvi/chimera/ChimeraConnect.java
+++ b/
test/jalview/ext/rbvi/chimera/ChimeraConnect.java
@@
-41,7
+41,7
@@
public class ChimeraConnect
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "External" })
public void testLaunchAndExit()
{
final StructureManager structureManager = new StructureManager(true);
public void testLaunchAndExit()
{
final StructureManager structureManager = new StructureManager(true);
diff --git
a/test/jalview/gui/AlignViewportTest.java
b/test/jalview/gui/AlignViewportTest.java
index
5ed0cac
..
7801250
100644
(file)
--- a/
test/jalview/gui/AlignViewportTest.java
+++ b/
test/jalview/gui/AlignViewportTest.java
@@
-277,7
+277,7
@@
public class AlignViewportTest
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, timeOut=2000)
public void testUpdateConservation_qualityOnly()
{
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
public void testUpdateConservation_qualityOnly()
{
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
@@
-292,7
+292,24
@@
public class AlignViewportTest
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+ /*
+ * wait for Conservation thread to complete
+ */
+ AlignViewport viewport = af.getViewport();
+ synchronized (this)
+ {
+ while (viewport.getAlignmentConservationAnnotation() != null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
assertEquals("More than one annotation found", 1, anns.length);
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
assertEquals("More than one annotation found", 1, anns.length);
diff --git
a/test/jalview/gui/AlignmentPanelTest.java
b/test/jalview/gui/AlignmentPanelTest.java
index
2819dbf
..
e84b87a
100644
(file)
--- a/
test/jalview/gui/AlignmentPanelTest.java
+++ b/
test/jalview/gui/AlignmentPanelTest.java
@@
-222,7
+222,7
@@
public class AlignmentPanelTest
/**
* Test that update layout reverts to original (unwrapped) values for endRes
/**
* Test that update layout reverts to original (unwrapped) values for endRes
- * and endSeq when switching from wrapped to unwrapped mode (JAL-2739)
+ * when switching from wrapped back to unwrapped mode (JAL-2739)
*/
@Test(groups = "Functional")
public void TestUpdateLayout_endRes()
*/
@Test(groups = "Functional")
public void TestUpdateLayout_endRes()
@@
-235,14
+235,14
@@
public class AlignmentPanelTest
af.alignPanel.getAlignViewport().setWrapAlignment(true);
af.alignPanel.updateLayout();
af.alignPanel.getAlignViewport().setWrapAlignment(true);
af.alignPanel.updateLayout();
- // endRes changes
+ // endRes has changed
assertNotEquals(ranges.getEndRes(), endres);
// unwrap
af.alignPanel.getAlignViewport().setWrapAlignment(false);
af.alignPanel.updateLayout();
assertNotEquals(ranges.getEndRes(), endres);
// unwrap
af.alignPanel.getAlignViewport().setWrapAlignment(false);
af.alignPanel.updateLayout();
- // endRes and endSeq back to original values
+ // endRes back to original value
assertEquals(ranges.getEndRes(), endres);
}
assertEquals(ranges.getEndRes(), endres);
}
diff --git
a/test/jalview/io/IdentifyFileTest.java
b/test/jalview/io/IdentifyFileTest.java
index
dd4f6ba
..
5be7968
100644
(file)
--- a/
test/jalview/io/IdentifyFileTest.java
+++ b/
test/jalview/io/IdentifyFileTest.java
@@
-94,7
+94,7
@@
public class IdentifyFileTest
{ "examples/plantfdx.fa", FileFormat.Fasta },
{ "examples/dna_interleaved.phy", FileFormat.Phylip },
{ "examples/2GIS.pdb", FileFormat.PDB },
{ "examples/plantfdx.fa", FileFormat.Fasta },
{ "examples/dna_interleaved.phy", FileFormat.Phylip },
{ "examples/2GIS.pdb", FileFormat.PDB },
- { "examples/rf00031_folded.stk", FileFormat.Stockholm },
+ { "examples/RF00031_folded.stk", FileFormat.Stockholm },
{ "examples/testdata/test.rnaml", FileFormat.Rnaml },
{ "examples/testdata/test.aln", FileFormat.Clustal },
{ "examples/testdata/test.pfam", FileFormat.Pfam },
{ "examples/testdata/test.rnaml", FileFormat.Rnaml },
{ "examples/testdata/test.aln", FileFormat.Clustal },
{ "examples/testdata/test.pfam", FileFormat.Pfam },
diff --git
a/test/jalview/io/cache/JvCacheableInputBoxTest.java
b/test/jalview/io/cache/JvCacheableInputBoxTest.java
index
dfd7973
..
010a4b2
100644
(file)
--- a/
test/jalview/io/cache/JvCacheableInputBoxTest.java
+++ b/
test/jalview/io/cache/JvCacheableInputBoxTest.java
@@
-55,10
+55,9
@@
public class JvCacheableInputBoxTest
cacheBox.updateCache();
try
{
cacheBox.updateCache();
try
{
- // This 1ms delay is essential to prevent the
- // assertion below from executing before
- // cacheBox.updateCache() finishes updating the cache
- Thread.sleep(100);
+ // This delay is to let
+ // cacheBox.updateCache() finish updating the cache
+ Thread.sleep(200);
} catch (InterruptedException e)
{
e.printStackTrace();
} catch (InterruptedException e)
{
e.printStackTrace();
diff --git
a/test/jalview/viewmodel/styles/ViewStyleTest.java
b/test/jalview/viewmodel/styles/ViewStyleTest.java
index
26c3574
..
2fcfe1a
100644
(file)
--- a/
test/jalview/viewmodel/styles/ViewStyleTest.java
+++ b/
test/jalview/viewmodel/styles/ViewStyleTest.java
@@
-114,6
+114,11
@@
public class ViewStyleTest
{
Class<?> type = field.getType();
{
Class<?> type = field.getType();
+ if (type.toString().contains("com_atlassian_clover"))
+ {
+ // instrumentation added for test coverage - ignore
+ return;
+ }
if (type.equals(boolean.class) || type.equals(Boolean.class))
{
boolean value = (Boolean) field.get(vs);
if (type.equals(boolean.class) || type.equals(Boolean.class))
{
boolean value = (Boolean) field.get(vs);