Roberto -
Sorry for consistently taking so long to respond to these parallelism
inquires - you are doing awesome work but I am just constantly swamped
- I'll try to do more testing today.
I can confirm both of those tests fail - it has nothing to do with your setup.
compare_bam_as_sam was added here:
https://github.com/galaxyproject/galaxy/commit/a38bae5cca98177eacaa3cdbeb74d3722263f377
It looks like I added a failing test to demonstrate metadata
generation was broken - and I was going to follow up on it and never
did.
parallelism_bam_filter_reads only ever existed in my fork on github
right? I am not sure why it failed - but you had some clues and I was
going to try to follow up. Once it is working I will open a pull
request for it.
If you are working on tests that is great - but I would focus on the
tests that work as examples. Some relevant ones may be:
test/functional/tools/parallelism_optional.xml
test/functional/tools/parallelism.xml
test/functional/tools/metadata_bam.xml
test/functional/tools/metadata_bcf.xml
These can be executed one at a time with:
./run_tests.sh -framework -id tool_id
... where tool id is the id in the tool XML file (which for these
tools usually match the basename of the file without the .xml
extension).
Will try to get to the pull requests today.
Thanks a bunch for your patience.
-John
On Mon, May 11, 2015 at 6:51 AM, Roberto Alonso CIPF ralo...@cipf.es wrote:
Hello,
I am designing some test and I have a problem, it works under the Galaxy web
environment, but it doesn't work when I try to use it as a test case. Indeed
I am trying other tests and they fail as well.
My test ./run_tests.sh -framework -id parallelism_bam_filter_reads says the
next:
==
ERROR: filter reads ( parallelism_bam_filter_reads ) Test-1
--
Traceback (most recent call last):
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 268, in
test_tool
self.do_it( td )
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 55, in
do_it
raise e
RunToolException: Error creating a job for these tool inputs - {u'type':
u'error', u'data': {u'input': u'History does not include a dataset of the
required format / build'}}
And the other test ./run_tests.sh -framework -id compare_bam_as_sam
==
ERROR: compare_bam_as_sam ( compare_bam_as_sam ) Test-1
--
Traceback (most recent call last):
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 268, in
test_tool
self.do_it( td )
File /home/ralonso/galaxy/test/functional/test_toolbox.py, line 37, in
do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
File /home/ralonso/galaxy/test/base/interactor.py, line 38, in
stage_data_in_history
upload_wait()
File /home/ralonso/galaxy/test/base/interactor.py, line 279, in wait
while not self.__history_ready( history_id ):
File /home/ralonso/galaxy/test/base/interactor.py, line 297, in
__history_ready
return self._state_ready( state, error_msg=History in error state. )
File /home/ralonso/galaxy/test/base/interactor.py, line 356, in
_state_ready
raise Exception( error_msg )
Exception: History in error state.
begin captured logging
Besides than it tries to migrate the database each time I try a test case
and it takes too long. I have seen that you can use --db postgres but it
doesn't work, I think this option should be user with --dockerize (that is
not my case).
would you have any idea of what is going on?
Best regards
--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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