[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45653ba49df7/ Changeset: 45653ba49df7 User: jmchilton Date: 2014-12-06 04:35:44+00:00 Summary: Include diffs for all errors when testing - don't stop at first. Gives more details to aid testing (especially for tools with lots of outputs) and lets developer collect all correct test data files at once (when GALAXY_TEST_SAVE is set or using `planemo test` with --job_output_files argument) instead of needing to rerun the tool repeatedly. Affected #: 1 file diff -r e2bfb1e6e3c5845e4e1518e620dcf7fbcdc21a0c -r 45653ba49df7fb353dfd3dd4f9d30111818ff60b test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -61,6 +61,8 @@ messaage_template = "Incorrect number of outputs - expected %d, found %s." message = messaage_template % ( expected, actual ) raise Exception( message ) + found_exceptions = [] + for output_index, output_tuple in enumerate(testdef.outputs): # Get the correct hid name, outfile, attributes = output_tuple @@ -78,13 +80,18 @@ self.assertTrue( output_data is not None ) try: galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) - except Exception: - for job in jobs: - job_stdio = galaxy_interactor.get_job_stdio( job[ 'id' ] ) - for stream in ['stdout', 'stderr']: - if stream in job_stdio: - print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True ) - raise + except Exception as e: + if not found_exceptions: + # Only print this stuff out once. + for job in jobs: + job_stdio = galaxy_interactor.get_job_stdio( job[ 'id' ] ) + for stream in ['stdout', 'stderr']: + if stream in job_stdio: + print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True ) + found_exceptions.append(e) + if found_exceptions: + big_message = "\n".join(map(str, found_exceptions)) + raise AssertionError(big_message) @nottest https://bitbucket.org/galaxy/galaxy-central/commits/34ed52176b05/ Changeset: 34ed52176b05 User: jmchilton Date: 2014-12-06 04:35:44+00:00 Summary: Twill interactor for tests is broken - so I am deleting. It wasn't long for this world with a JavaScript tool form anyway - would be nice to implement a casperjs driven interactor though so the UI could be exercised for tests. Affected #: 1 file diff -r 45653ba49df7fb353dfd3dd4f9d30111818ff60b -r 34ed52176b054166d687c3a402391f0d40f339db test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -1,15 +1,11 @@ import os import re from StringIO import StringIO -from galaxy.tools.parameters import grouping from galaxy.tools import test from galaxy import eggs eggs.require( "requests" ) from galaxy import util from galaxy.util.odict import odict -import galaxy.model -from galaxy.model.orm import and_, desc -from functional import database_contexts from requests import get from requests import post from json import dumps @@ -407,120 +403,6 @@ return get( url, params=data ) -class GalaxyInteractorTwill( object ): - - def __init__( self, twill_test_case ): - self.twill_test_case = twill_test_case - - def verify_output( self, history, output_data, output_testdef, shed_tool_id, maxseconds ): - outfile = output_testdef.outfile - attributes = output_testdef.attributes - - hid = output_data.get( 'hid' ) - self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) - - def get_job_stream( self, history_id, output_data, stream ): - data_id = self.twill_test_case.security.encode_id( output_data.get( 'id' ) ) - return self.twill_test_case._get_job_stream_output( data_id, stream=stream, format=False ) - - def stage_data_async( self, test_data, history, shed_tool_id, async=True ): - name = test_data.get( 'name', None ) - if name: - async = False - self.twill_test_case.upload_file( test_data['fname'], - ftype=test_data['ftype'], - dbkey=test_data['dbkey'], - metadata=test_data['metadata'], - composite_data=test_data['composite_data'], - shed_tool_id=shed_tool_id, - wait=(not async) ) - if name: - hda_id = self.twill_test_case.get_history_as_data_list()[-1].get( 'id' ) - try: - self.twill_test_case.edit_hda_attribute_info( hda_id=str(hda_id), new_name=name ) - except: - print "### call to edit_hda failed for hda_id %s, new_name=%s" % (hda_id, name) - return lambda: self.twill_test_case.wait() - - def run_tool( self, testdef, test_history ): - # We need to handle the case where we've uploaded a valid compressed file since the upload - # tool will have uncompressed it on the fly. - - # Lose tons of information to accomodate legacy repeat handling. - all_inputs = {} - for key, value in testdef.inputs.iteritems(): - all_inputs[ key.split("|")[-1] ] = value - - # See if we have a grouping.Repeat element - repeat_name = None - for input_name, input_value in testdef.tool.inputs_by_page[0].items(): - if isinstance( input_value, grouping.Repeat ) and all_inputs.get( input_name, 1 ) not in [ 0, "0" ]: # default behavior is to test 1 repeat, for backwards compatibility - if not input_value.min: # If input_value.min == 1, the element is already on the page don't add new element. - repeat_name = input_name - break - - #check if we need to verify number of outputs created dynamically by tool - if testdef.tool.force_history_refresh: - job_finish_by_output_count = len( self.twill_test_case.get_history_as_data_list() ) - else: - job_finish_by_output_count = False - - inputs_tree = testdef.inputs - # # # HACK: Flatten single-value lists. Required when using expand_grouping - # #for key, value in inputs_tree.iteritems(): - # if isinstance(value, list) and len(value) == 1: - # inputs_tree[key] = value[0] - - # Strip out just a given page of inputs from inputs "tree". - def filter_page_inputs( n ): - page_input_keys = testdef.tool.inputs_by_page[ n ].keys() - return dict( [ (k, v) for k, v in inputs_tree.iteritems() if k.split("|")[0] or k.split("|")[0].resplit("_", 1)[0] in page_input_keys ] ) - - # Do the first page - page_inputs = filter_page_inputs( 0 ) - - # Run the tool - self.twill_test_case.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) - print "page_inputs (0)", page_inputs - # Do other pages if they exist - for i in range( 1, testdef.tool.npages ): - page_inputs = filter_page_inputs( i ) - self.twill_test_case.submit_form( **page_inputs ) - print "page_inputs (%i)" % i, page_inputs - - # Check the results ( handles single or multiple tool outputs ). Make sure to pass the correct hid. - # The output datasets from the tool should be in the same order as the testdef.outputs. - data_list = None - while data_list is None: - data_list = self.twill_test_case.get_history_as_data_list() - if job_finish_by_output_count and len( testdef.outputs ) > ( len( data_list ) - job_finish_by_output_count ): - data_list = None - return data_list - - def new_history( self ): - # Start with a new history - self.twill_test_case.logout() - self.twill_test_case.login( email='test@bx.psu.edu' ) - admin_user = database_contexts.galaxy_context.query( galaxy.model.User ).filter( galaxy.model.User.table.c.email == 'test@bx.psu.edu' ).one() - self.twill_test_case.new_history() - latest_history = database_contexts.galaxy_context.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted == False, - galaxy.model.History.table.c.user_id == admin_user.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() - assert latest_history is not None, "Problem retrieving latest_history from database" - if len( self.twill_test_case.get_hids_in_history( self.twill_test_case.get_latest_history()[ 'id' ] ) ) > 0: - raise AssertionError("ToolTestCase.do_it failed to create a new empty history") - return latest_history - - def delete_history( self, latest_history ): - self.twill_test_case.delete_history( id=self.twill_test_case.security.encode_id( latest_history.id ) ) - - def output_hid( self, output_data ): - return output_data.get( 'hid' ) - - GALAXY_INTERACTORS = { 'api': GalaxyInteractorApi, - 'twill': GalaxyInteractorTwill, } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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