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adds log4j zip file
[jalview.git]
/
test
/
jalview
/
io
/
CrossRef2xmlTests.java
diff --git
a/test/jalview/io/CrossRef2xmlTests.java
b/test/jalview/io/CrossRef2xmlTests.java
index
b3db4de
..
2b8a62f
100644
(file)
--- a/
test/jalview/io/CrossRef2xmlTests.java
+++ b/
test/jalview/io/CrossRef2xmlTests.java
@@
-45,6
+45,7
@@
import junit.extensions.PA;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
import org.testng.annotations.Test;
@Test(singleThreaded = true)
@@
-59,6
+60,14
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @DataProvider(name = "initialAccessions")
+ static Object[][] getAccessions()
+ {
+ return new String[][] { { "UNIPROT", "P00338" },
+ { "UNIPROT", "Q8Z9G6" },
+ { "ENSEMBLGENOMES", "CAD01290" } };
+ }
+
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
@@
-66,8
+75,13
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
*
* @throws Exception
*/
*
* @throws Exception
*/
- @Test(groups = { "Operational" }, enabled = true)
- public void testRetrieveAndShowCrossref() throws Exception
+ @Test(
+ groups =
+ { "Operational" },
+ dataProvider = "initialAccessions",
+ enabled = true)
+ public void testRetrieveAndShowCrossref(String forSource,
+ String forAccession) throws Exception
{
List<String> failedDBRetr = new ArrayList<>();
{
List<String> failedDBRetr = new ArrayList<>();
@@
-97,8
+111,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
List<String> keyseq = new ArrayList<>();
Map<String, File> savedProjects = new HashMap<>();
List<String> keyseq = new ArrayList<>();
Map<String, File> savedProjects = new HashMap<>();
- for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
- {
+// for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+// {
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
int pass1 = 0, pass2 = 0, pass3 = 0;
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
int pass1 = 0, pass2 = 0, pass3 = 0;
@@
-108,7
+122,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
// { pass 2 = 0 { pass 3 = 0 } }
do
{
// { pass 2 = 0 { pass 3 = 0 } }
do
{
- String first = did[0] + " " + did[1];
+ String first = forSource + " " + forAccession;//did[0] + " " + did[1];
AlignFrame af = null;
boolean dna;
AlignmentI retral;
AlignFrame af = null;
boolean dna;
AlignmentI retral;
@@
-120,7
+134,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
// retrieve dbref
List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
// retrieve dbref
List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
- did[0], did[1]);
+ forSource, forAccession);
+ // did[0], did[1]);
if (afs.size() == 0)
{
failedDBRetr.add("Didn't retrieve " + first);
if (afs.size() == 0)
{
failedDBRetr.add("Didn't retrieve " + first);
@@
-416,7
+431,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
pass1++;
}
} while (pass1 < 3);
pass1++;
}
} while (pass1 < 3);
- }
+
if (failedXrefMenuItems.size() > 0)
{
for (String s : failedXrefMenuItems)
if (failedXrefMenuItems.size() > 0)
{
for (String s : failedXrefMenuItems)