Manually installing a Data Manager & running its tests
Hi all, I'm currently trying to manually install Dan's example Data Manager for the NCBI BLAST databases - but without using the Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blas... To be precise, I'm currently using a slightly modified version which we've moved into the Galaxy BLAST+ wrapper repository (thus far, only slight changes to folder names have been made from Dan's original): https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blast... https://github.com/peterjc/galaxy_blast/commit/21d7cff3e8dca13c4bd0f716a79a9... My goal is to be able to run the functional tests, $ ./run_functional_tests.sh -id data_manager_blast_db As with any other manually installed tool, I have added this data-manager to my tool_conf.xml.sample file (and for local testing via the GUI, the tool_conf.xml file as well): <tool file="ncbi_blastdb/blastdb.xml" /> Specific to data-managers, I have manually incorporated the additions to the central data_manager_conf.xml file (this would normally be merged at runtime if installed from the ToolShed): $ more data_manager_conf.xml <?xml version="1.0"?> <data_managers> <data_manager tool_file="ncbi_blastdb/blastdb.xml" id="data_manager_blast_db"> <data_table name="blastdb"> <output> <column name="value" /> <column name="name" /> <column name="path" output_ref="out_file" > <move type="directory"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">blastdb/${path}</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/blastdb/${path}/${nucleotide_alias_name}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> </data_table> </data_manager> </data_managers> Note the tool_file setting points correctly at the relative path within the tools folder, and the tool does define a test: $ more tools/ncbi_blastdb/blastdb.xml <tool id="data_manager_blast_db" name="Blast DB" version="0.0.2" tool_type="manage_data"> <description>Downloader</description> ... <tests> <test> <param name="blastdb_name" value="est"/> <param name="advanced_selector" value="basic"/> <output name="out_file" file="est_out.json"/> </test> </tests> ... $ ./run_functional_tests.sh -list | grep manager data_manager_blast_db Blast DB $ ./run_functional_tests.sh -id data_manager_blast_db ... galaxy.tools DEBUG 2014-04-11 15:59:00,780 Loaded tool id: data_manager_blast_db, version: 0.0.2 into tool panel. ... galaxy.tools.data_manager.manager DEBUG 2014-04-11 15:59:00,864 Loaded Data Manager: data_manager_blast_db ... Failure: ValueError (No such test TestForTool_data_manager_blast_db) ... ERROR ====================================================================== ERROR: Failure: ValueError (No such test TestForTool_data_manager_blast_db) ---------------------------------------------------------------------- Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/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_data_manager_blast_db ---------------------------------------------------------------------- I get the same error via TravisCI, e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/22782979 (This suggests using Twill vs the API does not matter) Am I missing something simple here? Thanks, Peter
Hi Peter, Looks like you are missing the -data_managers flag, try this: run_functional_tests.sh -data_managers -id data_manager_blast_db Let us know if you encounter more issues. Thanks, Dan On Apr 11, 2014, at 12:15 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I'm currently trying to manually install Dan's example Data Manager for the NCBI BLAST databases - but without using the Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blas...
To be precise, I'm currently using a slightly modified version which we've moved into the Galaxy BLAST+ wrapper repository (thus far, only slight changes to folder names have been made from Dan's original): https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blast... https://github.com/peterjc/galaxy_blast/commit/21d7cff3e8dca13c4bd0f716a79a9...
My goal is to be able to run the functional tests,
$ ./run_functional_tests.sh -id data_manager_blast_db
As with any other manually installed tool, I have added this data-manager to my tool_conf.xml.sample file (and for local testing via the GUI, the tool_conf.xml file as well):
<tool file="ncbi_blastdb/blastdb.xml" />
Specific to data-managers, I have manually incorporated the additions to the central data_manager_conf.xml file (this would normally be merged at runtime if installed from the ToolShed):
$ more data_manager_conf.xml <?xml version="1.0"?> <data_managers> <data_manager tool_file="ncbi_blastdb/blastdb.xml" id="data_manager_blast_db"> <data_table name="blastdb"> <output> <column name="value" /> <column name="name" /> <column name="path" output_ref="out_file" > <move type="directory"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">blastdb/${path}</target> </move>
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/blastdb/${path}/${nucleotide_alias_name}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> </data_table> </data_manager> </data_managers>
Note the tool_file setting points correctly at the relative path within the tools folder, and the tool does define a test:
$ more tools/ncbi_blastdb/blastdb.xml <tool id="data_manager_blast_db" name="Blast DB" version="0.0.2" tool_type="manage_data"> <description>Downloader</description> ... <tests> <test> <param name="blastdb_name" value="est"/> <param name="advanced_selector" value="basic"/> <output name="out_file" file="est_out.json"/> </test> </tests> ...
$ ./run_functional_tests.sh -list | grep manager data_manager_blast_db Blast DB
$ ./run_functional_tests.sh -id data_manager_blast_db ... galaxy.tools DEBUG 2014-04-11 15:59:00,780 Loaded tool id: data_manager_blast_db, version: 0.0.2 into tool panel. ... galaxy.tools.data_manager.manager DEBUG 2014-04-11 15:59:00,864 Loaded Data Manager: data_manager_blast_db ... Failure: ValueError (No such test TestForTool_data_manager_blast_db) ... ERROR
====================================================================== ERROR: Failure: ValueError (No such test TestForTool_data_manager_blast_db) ---------------------------------------------------------------------- Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/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_data_manager_blast_db
----------------------------------------------------------------------
I get the same error via TravisCI, e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/22782979
(This suggests using Twill vs the API does not matter)
Am I missing something simple here?
Thanks,
Peter
On Fri, Apr 11, 2014 at 5:29 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
Hi Peter,
Looks like you are missing the -data_managers flag, try this:
run_functional_tests.sh -data_managers -id data_manager_blast_db
Let us know if you encounter more issues.
Thanks,
Dan
Thank you! That was my silly mistake, it was clearly stated here: https://wiki.galaxyproject.org/Admin/Tools/DataManagers/Testing However, adding the switch seems to prevent testing traditional tools at the same time - is that deliberate? e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/22788397 Also note the test fails which I suspect is due to the database changing slightly? Mike is proposing to switch to a regex based test out the output JSON files for this tool... $ ./run_functional_tests.sh -data_managers -id data_manager_blast_db ... base.twilltestcase: DEBUG: Files diff for '/mnt/galaxy/galaxy-central/test-data/est_out.json' vs '/tmp/tmpIk35vy/tmpTNneBG/new_files_path_Q3kSF9/tmpl9xH_Qest_out.json' base.twilltestcase: INFO: ## files diff on /mnt/galaxy/galaxy-central/test-data/est_out.json and /tmp/tmpIk35vy/tmpTNneBG/new_files_path_Q3kSF9/tmpl9xH_Qest_out.json lines_diff=0, found diff = 2 --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 24.030s FAILED (failures=1) ... Thanks, Peter
On Fri, Apr 11, 2014 at 6:06 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Apr 11, 2014 at 5:29 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
Hi Peter,
Looks like you are missing the -data_managers flag, try this:
run_functional_tests.sh -data_managers -id data_manager_blast_db
Let us know if you encounter more issues.
Thanks,
Dan
Thank you! That was my silly mistake, it was clearly stated here: https://wiki.galaxyproject.org/Admin/Tools/DataManagers/Testing
However, adding the switch seems to prevent testing traditional tools at the same time - is that deliberate? e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/22788397
Also note the test fails which I suspect is due to the database changing slightly? Mike is proposing to switch to a regex based test out the output JSON files for this tool...
$ ./run_functional_tests.sh -data_managers -id data_manager_blast_db ... base.twilltestcase: DEBUG: Files diff for '/mnt/galaxy/galaxy-central/test-data/est_out.json' vs '/tmp/tmpIk35vy/tmpTNneBG/new_files_path_Q3kSF9/tmpl9xH_Qest_out.json' base.twilltestcase: INFO: ## files diff on /mnt/galaxy/galaxy-central/test-data/est_out.json and /tmp/tmpIk35vy/tmpTNneBG/new_files_path_Q3kSF9/tmpl9xH_Qest_out.json lines_diff=0, found diff = 2 --------------------- >> end captured logging << ---------------------
---------------------------------------------------------------------- Ran 1 test in 24.030s
FAILED (failures=1) ...
After a few missteps, I got this to run under TravisCI. This time the twill based test failed to download the est database (perhaps just a network glitch), but more interestingly this appears to show a bug with the API based testing (Hi John!): https://travis-ci.org/peterjc/galaxy_blast/builds/22938945 Running this locally, $ export GALAXY_TEST_DB_TEMPLATE=https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0117.sqli... $ export GALAXY_TEST_DEFAULT_INTERACTOR=api $ ./run_functional_tests.sh -data_managers -id data_manager_blast_db ... galaxy.jobs.handler DEBUG 2014-04-14 12:19:39,558 (1) Dispatching to local runner ERROR ====================================================================== ERROR: Blast DB ( data_manager_blast_db ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/test/functional/test_data_managers.py", line 99, in test_tool self.do_it( td ) File "/mnt/galaxy/galaxy-central/test/functional/test_data_managers.py", line 34, in do_it for assoc in reversed( test_history.user.data_manager_histories ): AttributeError: 'unicode' object has no attribute 'user' -------------------- >> begin captured logging << -------------------- galaxy.web.framework: INFO: Session authenticated using Galaxy master api key galaxy.web.framework: INFO: Session authenticated using Galaxy master api key galaxy.web.framework: INFO: Session authenticated using Galaxy master api key galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpE6lJPe/tmpNq68Jz/job_working_directory_5lfI0i/000/1 galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 1 test in 3.060s FAILED (errors=1) ... galaxy.jobs.handler ERROR 2014-04-14 12:19:39,895 Exception in monitor_step Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 154, in __monitor self.__monitor_step() File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/handler.py", line 264, in __monitor_step log.exception( "failure running job %d" % job.id ) ... File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 281, in connect return self.dbapi.connect(*cargs, **cparams) OperationalError: (OperationalError) unable to open database file None None ... Regards, Peter
participants (2)
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Daniel Blankenberg -
Peter Cock