errors with run_functional_tests.sh
Hi, We are currently installing galaxy on a server. By reading the galaxy wiki, we found the script run_functional_tests.sh (the principle is really handy!). Unfortunately, we encounter errors when we use it. I hope someone can help us. In reality, we encounter several types of errors ... The first is present in each run, for example for the execution follows: ./run_functional_tests.sh -id fastqc ... FastQC:Read QC ( fastqc ) > Test-1 ... galaxy.web.framework DEBUG 2013-03-01 09:42:10,466 ... galaxy.tools.actions.upload_common INFO 2013-03-01 09:42:13,357 tool upload1 created job id 1 ... galaxy.jobs DEBUG 2013-03-01 09:42:27,436 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-03-01 09:42:27,757 job 1 ended galaxy.tools.actions.upload_common INFO 2013-03-01 09:42:40,883 tool upload1 created job id 2 ... galaxy.jobs DEBUG 2013-03-01 09:42:52,000 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-03-01 09:42:52,311 job 2 ended galaxy.jobs.manager DEBUG 2013-03-01 09:42:55,285 (3) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-03-01 09:43:00,477 (3) Working directory for job is: /var/local/galaxy/galaxy-dist/database/job_working_directory/000/3 galaxy.jobs.handler DEBUG 2013-03-01 09:43:00,478 dispatching job 3 to local runner galaxy.jobs.handler INFO 2013-03-01 09:43:00,622 (3) Job dispatched galaxy.jobs.runners.local DEBUG 2013-03-01 09:43:00,727 Local runner: starting job 3 galaxy.jobs.runners.local DEBUG 2013-03-01 09:43:01,193 executing: python /var/local/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i "/tmp/tmp_YcL4J/database/files/000/dataset_1.dat" -d "/var/local/galaxy/galaxy-dist/database/job_working_directory/000/3/dataset_3_files" -o "/tmp/tmp_YcL4J/database/files/000/dataset_3.dat" -n "fastqcout" -f "fastq" -j "1000gsample.fastq" -e "/var/local/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc" -c "/tmp/tmp_YcL4J/database/files/000/dataset_2.dat" galaxy.jobs.runners.local DEBUG 2013-03-01 09:43:04,515 execution finished: python /var/local/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i "/tmp/tmp_YcL4J/database/files/000/dataset_1.dat" -d "/var/local/galaxy/galaxy-dist/database/job_working_directory/000/3/dataset_3_files" -o "/tmp/tmp_YcL4J/database/files/000/dataset_3.dat" -n "fastqcout" -f "fastq" -j "1000gsample.fastq" -e "/var/local/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc" -c "/tmp/tmp_YcL4J/database/files/000/dataset_2.dat" galaxy.jobs DEBUG 2013-03-01 09:43:04,578 Tool did not define exit code or stdio handling; checking stderr for success _galaxy.tools DEBUG 2013-03-01 09:43:04,814 Error opening galaxy.json file: [Errno 2] No such file or directory: '/var/local/galaxy/galaxy-dist/database/job_working_directory/000/3/galaxy.json'_ galaxy.jobs DEBUG 2013-03-01 09:43:04,899 job 3 ended ok ---------------------------------------------------------------------- Ran 1 test in 60.889s OK ... Exception OSError: (2, 'No such file or directory', '/tmp/tmp_YcL4J/database/tmp/tmpn5w0Ln') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w' at 0x18ffd5d0>> ignored According to other messages from the mailing list, my understanding is that this message should be ignored and we only have to consider the "OK" that says the test went well. Is that correct ? The other type of error we find is the following: ./run_functional_tests.sh -id cshl_fastx_clipper ... ERROR: Failure: ValueError (No such test TestForTool_cshl_fastx_clipper) ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/local/galaxy/galaxy-dist/eggs/nose-0.11.1-py2.6.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_cshl_fastx_clipper ---------------------------------------------------------------------- ... For some of these tools, the error seems logical given that the xml configuration tool does not contain test. However, for others like fastx_clipper, the test is described... So, why is there a problem with this kind of tools ? Finally, we have one last type of error, like this: ./run_functional_tests.sh -id sam_to_bam ... SAM-to-BAM ( sam_to_bam ) > Test-2 ... galaxy.web.framework DEBUG 2013-03-05 18:02:15,115 Error: this request returned None from get_history(): http://localhost:9051/user/logout galaxy.web.framework DEBUG 2013-03-05 18:02:15,159 Error: this request returned None from get_history(): http://localhost:9051/ ERROR ====================================================================== ERROR: SAM-to-BAM ( sam_to_bam ) > Test-2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/local/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/local/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 43, in do_it shed_tool_id=shed_tool_id ) File "/var/local/galaxy/galaxy-dist/test/base/twilltestcase.py", line 193, in upload_file tc.fv("1","dbkey", dbkey) File "/var/local/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 450, in formvalue set_form_control_value(control, value) File "/var/local/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/utils.py", line 190, in set_form_control_value raise ClientForm.ItemNotFoundError('cannot find value/label "%s" in list control' % (val,)) ItemNotFoundError: cannot find value/label "chrM" in list control -------------------- >> begin captured stdout << --------------------- --------------------- >> end captured stdout << ---------------------- -------------------- >> begin captured logging << -------------------- galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9051/user/logout galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9051/ --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 2 tests in 56.139s FAILED (errors=1) The first test is ok, but the second is failed. So, the dependence seems to be correctly installed, but the test doesn't pass, and I don't understand why... Thank you in advance for your help ! Florence
Hello, I'll respond inline, but your base understanding is correct. --Dave B. On 3/5/13 12:17:47.000, Florence Maurier wrote:
Hi,
We are currently installing galaxy on a server. By reading the galaxy wiki, we found the script run_functional_tests.sh (the principle is really handy!). Unfortunately, we encounter errors when we use it. I hope someone can help us.
In reality, we encounter several types of errors ... The first is present in each run, for example for the execution follows:
./run_functional_tests.sh -id fastqc ... FastQC:Read QC ( fastqc ) > Test-1 ... galaxy.web.framework DEBUG 2013-03-01 09:42:10,466 ... galaxy.tools.actions.upload_common INFO 2013-03-01 09:42:13,357 tool upload1 created job id 1 ... galaxy.jobs DEBUG 2013-03-01 09:42:27,436 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-03-01 09:42:27,757 job 1 ended
galaxy.tools.actions.upload_common INFO 2013-03-01 09:42:40,883 tool upload1 created job id 2 ... galaxy.jobs DEBUG 2013-03-01 09:42:52,000 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-03-01 09:42:52,311 job 2 ended
galaxy.jobs.manager DEBUG 2013-03-01 09:42:55,285 (3) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-03-01 09:43:00,477 (3) Working directory for job is: /var/local/galaxy/galaxy-dist/database/job_working_directory/000/3 galaxy.jobs.handler DEBUG 2013-03-01 09:43:00,478 dispatching job 3 to local runner galaxy.jobs.handler INFO 2013-03-01 09:43:00,622 (3) Job dispatched galaxy.jobs.runners.local DEBUG 2013-03-01 09:43:00,727 Local runner: starting job 3 galaxy.jobs.runners.local DEBUG 2013-03-01 09:43:01,193 executing: python /var/local/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i "/tmp/tmp_YcL4J/database/files/000/dataset_1.dat" -d "/var/local/galaxy/galaxy-dist/database/job_working_directory/000/3/dataset_3_files" -o "/tmp/tmp_YcL4J/database/files/000/dataset_3.dat" -n "fastqcout" -f "fastq" -j "1000gsample.fastq" -e "/var/local/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc" -c "/tmp/tmp_YcL4J/database/files/000/dataset_2.dat" galaxy.jobs.runners.local DEBUG 2013-03-01 09:43:04,515 execution finished: python /var/local/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i "/tmp/tmp_YcL4J/database/files/000/dataset_1.dat" -d "/var/local/galaxy/galaxy-dist/database/job_working_directory/000/3/dataset_3_files" -o "/tmp/tmp_YcL4J/database/files/000/dataset_3.dat" -n "fastqcout" -f "fastq" -j "1000gsample.fastq" -e "/var/local/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc" -c "/tmp/tmp_YcL4J/database/files/000/dataset_2.dat" galaxy.jobs DEBUG 2013-03-01 09:43:04,578 Tool did not define exit code or stdio handling; checking stderr for success _galaxy.tools DEBUG 2013-03-01 09:43:04,814 Error opening galaxy.json file: [Errno 2] No such file or directory: '/var/local/galaxy/galaxy-dist/database/job_working_directory/000/3/galaxy.json'_
galaxy.jobs DEBUG 2013-03-01 09:43:04,899 job 3 ended ok ---------------------------------------------------------------------- Ran 1 test in 60.889s OK ... Exception OSError: (2, 'No such file or directory', '/tmp/tmp_YcL4J/database/tmp/tmpn5w0Ln') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w' at 0x18ffd5d0>> ignored
According to other messages from the mailing list, my understanding is that this message should be ignored and we only have to consider the "OK" that says the test went well. Is that correct ?
Yes, the error messages you see there are irrelevant, and can be safely ignored. As you deduced, the functional test passed.
The other type of error we find is the following: ./run_functional_tests.sh -id cshl_fastx_clipper ... ERROR: Failure: ValueError (No such test TestForTool_cshl_fastx_clipper) ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/local/galaxy/galaxy-dist/eggs/nose-0.11.1-py2.6.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_cshl_fastx_clipper ---------------------------------------------------------------------- ... For some of these tools, the error seems logical given that the xml configuration tool does not contain test. However, for others like fastx_clipper, the test is described... So, why is there a problem with this kind of tools ?
In the case of fastx_clipper, the test definition is commented out, and therefore not found in the toolbox.
Finally, we have one last type of error, like this: ./run_functional_tests.sh -id sam_to_bam ... SAM-to-BAM ( sam_to_bam ) > Test-2 ... galaxy.web.framework DEBUG 2013-03-05 18:02:15,115 Error: this request returned None from get_history(): http://localhost:9051/user/logout galaxy.web.framework DEBUG 2013-03-05 18:02:15,159 Error: this request returned None from get_history(): http://localhost:9051/ ERROR
====================================================================== ERROR: SAM-to-BAM ( sam_to_bam ) > Test-2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/local/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/local/galaxy/galaxy-dist/test/functional/test_toolbox.py", line 43, in do_it shed_tool_id=shed_tool_id ) File "/var/local/galaxy/galaxy-dist/test/base/twilltestcase.py", line 193, in upload_file tc.fv("1","dbkey", dbkey) File "/var/local/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 450, in formvalue set_form_control_value(control, value) File "/var/local/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/utils.py", line 190, in set_form_control_value raise ClientForm.ItemNotFoundError('cannot find value/label "%s" in list control' % (val,)) ItemNotFoundError: cannot find value/label "chrM" in list control -------------------- >> begin captured stdout << ---------------------
--------------------- >> end captured stdout << ---------------------- -------------------- >> begin captured logging << -------------------- galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9051/user/logout galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): http://localhost:9051/ --------------------- >> end captured logging << ---------------------
---------------------------------------------------------------------- Ran 2 tests in 56.139s
FAILED (errors=1)
The first test is ok, but the second is failed. So, the dependence seems to be correctly installed, but the test doesn't pass, and I don't understand why...
This type of error is usually due to the test specifying a locally cached data file not present in the data table used by the tool being tested. You can find more information on local data setup at: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup In this case, the test is expecting to find an entry for chrM in sam_fa_indices.loc, which is the mitochondrial DNA for equCab2, indexed with SAM. That index is present on our rsync server at: rsync://datacache.g2.bx.psu.edu/indexes/equCab2_chrM/sam_index/
Thank you in advance for your help !
Florence ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Dave Bouvier -
Florence Maurier