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: ralonso@cipf.es
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/a38bae5cca98177eacaa3cdbeb74d... 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 <ralonso@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: ralonso@cipf.es
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Hello, don't worry John, I understand that there are plenty of things before this and also there is the Galaxy conference, so I can wait, no problem. I will go through the things that you suggest. Best regards On 22 May 2015 at 16:11, John Chilton <jmchilton@gmail.com> wrote:
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/a38bae5cca98177eacaa3cdbeb74d...
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
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
On Mon, May 11, 2015 at 6:51 AM, Roberto Alonso CIPF <ralonso@cipf.es> wrote: 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: ralonso@cipf.es
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- 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: ralonso@cipf.es
participants (2)
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John Chilton -
Roberto Alonso CIPF