Class jalview.bin.CommandLineOperations

all > jalview.bin > CommandLineOperations
28

tests
0

failures
0

ignored
32.757s

duration
100%

successful

Tests

Test Duration Result
reportCurrentWorkingDirectory 0.001s passed
testAllInputOperations[0](CMD [-color zappo] executed successfully!, Failed command : -color zappo) 0s passed
testAllInputOperations[10](CMD [-noquestionnaire] executed successfully!, Failed command : -noquestionnaire) 0s passed
testAllInputOperations[1](CMD [-props test/jalview/io/testProps.jvprops] executed successfully!, Failed command : -props File) 0s passed
testAllInputOperations[2](CMD [-sortbytree] executed successfully!, Failed command : -sortbytree) 0s passed
testAllInputOperations[3](CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!, Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws) 0s passed
testAllInputOperations[4](CMD [-open examples/uniref50.fa] executed successfully!, Failed command : -open examples/uniref50.fa) 0s passed
testAllInputOperations[5](CMD [-nosortbytree] executed successfully!, Failed command : -nosortbytree) 0s passed
testAllInputOperations[6](CMD [-features examples/testdata/plantfdx.features] executed successfully!, Failed command : -features examples/testdata/plantfdx.features) 0s passed
testAllInputOperations[7](CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!, Failed command : -annotations examples/testdata/plantfdx.annotations) 0s passed
testAllInputOperations[8](CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!, Failed command : -tree examples/testdata/uniref50_test_tree) 0s passed
testAllInputOperations[9](CMD [-nousagestats] executed successfully!, Failed command : -nousagestats) 0s passed
testHeadlessModeOutputOperations[0](nodisplay -open examples/uniref50.fa, -eps, test/jalview/bin/test_uniref50_out.eps, true, 4096, 9000) 2.141s passed
testHeadlessModeOutputOperations[10](headless -open examples/uniref50.fa, -msf, test/jalview/bin/test_uniref50_out.msf, true, 2096, 9000) 2.041s passed
testHeadlessModeOutputOperations[11](headless -open examples/uniref50.fa, -pileup, test/jalview/bin/test_uniref50_out.aln, true, 2096, 9000) 2.030s passed
testHeadlessModeOutputOperations[12](headless -open examples/uniref50.fa, -pir, test/jalview/bin/test_uniref50_out.pir, true, 2096, 9000) 2.025s passed
testHeadlessModeOutputOperations[13](headless -open examples/uniref50.fa, -pfam, test/jalview/bin/test_uniref50_out.pfam, true, 2096, 9000) 2.005s passed
testHeadlessModeOutputOperations[14](headless -open examples/uniref50.fa, -blc, test/jalview/bin/test_uniref50_out.blc, true, 2096, 9000) 2.051s passed
testHeadlessModeOutputOperations[15](headless -open examples/uniref50.fa, -jalview, test/jalview/bin/test_uniref50_out.jvp, true, 2096, 9000) 2.066s passed
testHeadlessModeOutputOperations[1](nodisplay -open examples/uniref50.fa, -eps, test/jalview/bin/test_uniref50_out.eps, false, 4096, 9000) 2.007s passed
testHeadlessModeOutputOperations[2](nogui -open examples/uniref50.fa, -eps, test/jalview/bin/test_uniref50_out.eps, true, 4096, 9000) 2.079s passed
testHeadlessModeOutputOperations[3](nogui -open examples/uniref50.fa, -eps, test/jalview/bin/test_uniref50_out.eps, false, 4096, 9000) 2.021s passed
testHeadlessModeOutputOperations[4](headless -open examples/uniref50.fa, -eps, test/jalview/bin/test_uniref50_out.eps, true, 4096, 9000) 2.042s passed
testHeadlessModeOutputOperations[5](headless -open examples/uniref50.fa, -svg, test/jalview/bin/test_uniref50_out.svg, false, 4096, 9000) 2.048s passed
testHeadlessModeOutputOperations[6](headless -open examples/uniref50.fa, -png, test/jalview/bin/test_uniref50_out.png, true, 4096, 9000) 2.043s passed
testHeadlessModeOutputOperations[7](headless -open examples/uniref50.fa, -html, test/jalview/bin/test_uniref50_out.html, true, 4096, 9000) 2.016s passed
testHeadlessModeOutputOperations[8](headless -open examples/uniref50.fa, -fasta, test/jalview/bin/test_uniref50_out.mfa, true, 2096, 9000) 2.096s passed
testHeadlessModeOutputOperations[9](headless -open examples/uniref50.fa, -clustal, test/jalview/bin/test_uniref50_out.aln, true, 2096, 9000) 2.045s passed

Standard output

Test CWD is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDBC-JOB1

Standard error

ERROR - Exception when trying to start Rest Job.
java.lang.NullPointerException
	at jalview.ws.rest.RestJobThread.doPost(RestJobThread.java:202)
	at jalview.ws.rest.RestJobThread.StartJob(RestJobThread.java:435)
	at jalview.ws.AWSThread.run(AWSThread.java:117)
Exception in thread "Thread-34" java.lang.NullPointerException
	at jalview.ws.JobStateSummary.updateJobPanelState(JobStateSummary.java:162)
	at jalview.ws.AWSThread.run(AWSThread.java:177)