4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e032250c3f2e/ Changeset: e032250c3f2e User: jmchilton Date: 2014-08-27 22:32:26 Summary: Update readme for functional test tools directory. Affected #: 1 file diff -r a66a80701913bb99e8abd12235c1ca82dc508f57 -r e032250c3f2eef09002a00d6d1035de0928e58dd test/functional/tools/README.txt --- a/test/functional/tools/README.txt +++ b/test/functional/tools/README.txt @@ -1,3 +1,15 @@ -This directory contains tools only useful for testing the tool test framework -and demonstrating it features. Run the driver script 'run_functional_tests.sh' -with '-framework' as first argument to run through these tests. +This directory contains tools only useful for testing and +demonstrating aspects of the tool syntax. Run the test driver script +'run_tests.sh' with the '-framework' as first argument to run through +these tests. Pass in an '-id' along with one of these tool ids to test +a single tool. + +Some API tests use these tools to test various features of the API, +tool, and workflow subsystems. Pass the arugment +'-with_framework_test_tools' to 'run_tests.sh' in addition to '-api' +to ensure these tools get loaded during the testing process. + +Finally, to play around witht these tools interactively - simply +replace the 'universe_wsgi.ini' option 'tool_config_file' with: + +tool_config_file = test/functional/tools/samples_tool_conf.xml https://bitbucket.org/galaxy/galaxy-central/commits/14230488f497/ Changeset: 14230488f497 User: jmchilton Date: 2014-08-27 22:32:26 Summary: Add some more basic test tools for building simple workflows for testing. Affected #: 4 files diff -r e032250c3f2eef09002a00d6d1035de0928e58dd -r 14230488f49758d1abe748cd7500f9719a3390b6 test/functional/tools/for_workflows/cat.xml --- /dev/null +++ b/test/functional/tools/for_workflows/cat.xml @@ -0,0 +1,19 @@ +<tool id="cat" name="Concatenate datasets (for test workflows)"> + <description>tail-to-head</description> + <command> + cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + <repeat name="queries" title="Dataset"> + <param name="input2" type="data" label="Select" /> + </repeat> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + </tests> + <help> + </help> +</tool> diff -r e032250c3f2eef09002a00d6d1035de0928e58dd -r 14230488f49758d1abe748cd7500f9719a3390b6 test/functional/tools/for_workflows/cat_list.xml --- /dev/null +++ b/test/functional/tools/for_workflows/cat_list.xml @@ -0,0 +1,16 @@ +<tool id="cat_list" name="Concatenate dataset list (for test workflows)"> + <description>tail-to-head</description> + <command> + cat #for $q in $input1# $q #end for# > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset" multiple="true" /> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + </tests> + <help> + </help> +</tool> diff -r e032250c3f2eef09002a00d6d1035de0928e58dd -r 14230488f49758d1abe748cd7500f9719a3390b6 test/functional/tools/for_workflows/head.xml --- /dev/null +++ b/test/functional/tools/for_workflows/head.xml @@ -0,0 +1,13 @@ +<tool id="head" name="Select first"> + <description>lines from a dataset</description> + <command>head $input $lineNum > $out_file1</command> + <inputs> + <param name="lineNum" size="5" type="integer" value="10" label="Select first" help="lines"/> + <param format="txt" name="input" type="data" label="from"/> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <help> + </help> +</tool> diff -r e032250c3f2eef09002a00d6d1035de0928e58dd -r 14230488f49758d1abe748cd7500f9719a3390b6 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -23,4 +23,10 @@ <tool file="collection_mixed_param.xml" /><tool file="collection_two_paired.xml" /><tool file="collection_optional_param.xml" /> -</toolbox> \ No newline at end of file + + <!-- Tools interesting only for building up test workflows. --> + <tool file="for_workflows/cat.xml" /> + <tool file="for_workflows/cat_list.xml" /> + <tool file="for_workflows/head.xml" /> + +</toolbox> https://bitbucket.org/galaxy/galaxy-central/commits/c692332612dd/ Changeset: c692332612dd User: jmchilton Date: 2014-08-27 22:32:26 Summary: Remove workflow test that accidently depended on tool not in -central. Opps. Affected #: 3 files diff -r 14230488f49758d1abe748cd7500f9719a3390b6 -r c692332612dd5c8d7eff798cdba4f2e91d4ff5a1 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -11,7 +11,6 @@ # Simple workflow that takes an input and filters with random lines twice in a # row - first grabbing 8 lines at random and then 6. workflow_random_x2_str = resource_string( __name__, "test_workflow_2.ga" ) -workflow_two_paired_str = resource_string( __name__, "test_workflow_two_paired.ga" ) DEFAULT_HISTORY_TIMEOUT = 10 # Secs to wait on history to turn ok @@ -161,9 +160,6 @@ def load_random_x2_workflow( self, name ): return self.load_workflow( name, content=workflow_random_x2_str ) - def load_two_paired_workflow( self, name ): - return self.load_workflow( name, content=workflow_two_paired_str ) - def simple_workflow( self, name, **create_kwds ): workflow = self.load_workflow( name ) return self.create_workflow( workflow, **create_kwds ) diff -r 14230488f49758d1abe748cd7500f9719a3390b6 -r c692332612dd5c8d7eff798cdba4f2e91d4ff5a1 test/api/test_workflow_two_paired.ga --- a/test/api/test_workflow_two_paired.ga +++ /dev/null @@ -1,116 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "MultipairTest223", - "steps": { - "0": { - "annotation": "", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "f1" - } - ], - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 302.3333435058594, - "top": 330 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"collection_type\": \"paired\", \"name\": \"f1\"}", - "tool_version": null, - "type": "data_collection_input", - "user_outputs": [] - }, - "1": { - "annotation": "", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "f2" - } - ], - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": 288.3333435058594, - "top": 446 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"collection_type\": \"paired\", \"name\": \"f2\"}", - "tool_version": null, - "type": "data_collection_input", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "kind|f1": { - "id": 0, - "output_name": "output" - }, - "kind|f2": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "name": "collection_two_paired", - "outputs": [ - { - "name": "out1", - "type": "txt" - } - ], - "position": { - "left": 782.3333740234375, - "top": 200 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "collection_two_paired", - "tool_state": "{\"__page__\": 0, \"kind\": \"{\\\"f1\\\": null, \\\"f2\\\": null, \\\"collection_type\\\": \\\"paired\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0", - "type": "tool", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "cond1|input1": { - "id": 2, - "output_name": "out1" - } - }, - "inputs": [], - "name": "Concatenate datasets", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1239.3333740234375, - "top": 108.97916793823242 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "cat2", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond1\": \"{\\\"datatype\\\": \\\"txt\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file diff -r 14230488f49758d1abe748cd7500f9719a3390b6 -r c692332612dd5c8d7eff798cdba4f2e91d4ff5a1 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -149,26 +149,6 @@ run_workflow_response = self._post( "workflows", data=workflow_request ) self._assert_status_code_is( run_workflow_response, 403 ) - @skip_without_tool( "cat1" ) - @skip_without_tool( "collection_two_paired" ) - def test_run_workflow_collection_params( self ): - workflow = self.workflow_populator.load_two_paired_workflow( name="test_for_run_two_paired" ) - workflow_id = self.workflow_populator.create_workflow( workflow ) - history_id = self.dataset_populator.new_history() - hdca1 = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3", "4 5 6"] ).json() - hdca2 = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["7 8 9", "0 a b"] ).json() - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) - label_map = { "f1": self._ds_entry( hdca1 ), "f2": self._ds_entry( hdca2 ) } - workflow_request = dict( - history="hist_id=%s" % history_id, - workflow_id=workflow_id, - ds_map=self._build_ds_map( workflow_id, label_map ), - ) - run_workflow_response = self._post( "workflows", data=workflow_request ) - self._assert_status_code_is( run_workflow_response, 200 ) - self.dataset_populator.wait_for_history( history_id, assert_ok=True ) - self.assertEquals("1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content( history_id ) ) - def test_workflow_stability( self ): # Run this index stability test with following command: # ./run_tests.sh test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_stability https://bitbucket.org/galaxy/galaxy-central/commits/f36c6fc80e8c/ Changeset: f36c6fc80e8c User: jmchilton Date: 2014-08-27 22:32:26 Summary: Add workflow test demonstrating failure when multiple lists with different identifiers are using in workflows. Affected #: 3 files diff -r c692332612dd5c8d7eff798cdba4f2e91d4ff5a1 -r f36c6fc80e8cd2bc6a5c6f77f0806aa7271e65f0 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -160,6 +160,12 @@ def load_random_x2_workflow( self, name ): return self.load_workflow( name, content=workflow_random_x2_str ) + def load_workflow_from_resource( self, name, filename=None ): + if filename is None: + filename = "%s.ga" % name + content = resource_string( __name__, filename ) + return self.load_workflow( name, content=content ) + def simple_workflow( self, name, **create_kwds ): workflow = self.load_workflow( name ) return self.create_workflow( workflow, **create_kwds ) @@ -319,8 +325,14 @@ def list_identifiers( self, history_id, contents=None ): count = 3 if not contents else len( contents ) - hdas = self.__datasets( history_id, count=count, contents=contents ) - hda_to_identifier = lambda ( i, hda ): dict( name="data%d" % ( i + 1 ), src="hda", id=hda[ "id" ] ) + # Contents can be a list of strings (with name auto-assigned here) or a list of + # 2-tuples of form (name, dataset_content). + if contents and isinstance(contents[0], tuple): + hdas = self.__datasets( history_id, count=count, contents=[c[1] for c in contents] ) + hda_to_identifier = lambda ( i, hda ): dict( name=contents[i][0], src="hda", id=hda[ "id" ] ) + else: + hdas = self.__datasets( history_id, count=count, contents=contents ) + hda_to_identifier = lambda ( i, hda ): dict( name="data%d" % ( i + 1 ), src="hda", id=hda[ "id" ] ) element_identifiers = map( hda_to_identifier, enumerate( hdas ) ) return element_identifiers diff -r c692332612dd5c8d7eff798cdba4f2e91d4ff5a1 -r f36c6fc80e8cd2bc6a5c6f77f0806aa7271e65f0 test/api/test_workflow_matching_lists.ga --- /dev/null +++ b/test/api/test_workflow_matching_lists.ga @@ -0,0 +1,117 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "test_workflow_matching_lists", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "list1" + } + ], + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 139.833336353302, + "top": 162.33334398269653 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list\", \"name\": \"list1\"}", + "tool_version": null, + "type": "data_collection_input", + "user_outputs": [] + }, + "1": { + "annotation": "", + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "list2" + } + ], + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 141.864586353302, + "top": 272.3680577278137 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"collection_type\": \"list\", \"name\": \"list2\"}", + "tool_version": null, + "type": "data_collection_input", + "user_outputs": [] + }, + "2": { + "annotation": "", + "id": 2, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "queries_0|input2": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "name": "Concatenate datasets (for test workflows)", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 453.40974473953247, + "top": 203.4097294807434 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "3": { + "annotation": "", + "id": 3, + "input_connections": { + "input1": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Concatenate dataset list (for test workflows)", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 828.93061876297, + "top": 217.4201512336731 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat_list", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + }, + "uuid": "54aadd3b-9d2b-436a-acfa-246a8c251651" +} \ No newline at end of file diff -r c692332612dd5c8d7eff798cdba4f2e91d4ff5a1 -r f36c6fc80e8cd2bc6a5c6f77f0806aa7271e65f0 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -149,6 +149,26 @@ run_workflow_response = self._post( "workflows", data=workflow_request ) self._assert_status_code_is( run_workflow_response, 403 ) + @skip_without_tool( "cat" ) + @skip_without_tool( "cat_list" ) + def test_workflow_run_with_matching_lists( self ): + workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_matching_lists" ) + workflow_id = self.workflow_populator.create_workflow( workflow ) + history_id = self.dataset_populator.new_history() + hdca1 = self.dataset_collection_populator.create_list_in_history( history_id, contents=[("sample1-1", "1 2 3"), ("sample2-1", "7 8 9")] ).json() + hdca2 = self.dataset_collection_populator.create_list_in_history( history_id, contents=[("sample1-2", "4 5 6"), ("sample2-2", "0 a b")] ).json() + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + label_map = { "list1": self._ds_entry( hdca1 ), "list2": self._ds_entry( hdca2 ) } + workflow_request = dict( + history="hist_id=%s" % history_id, + workflow_id=workflow_id, + ds_map=self._build_ds_map( workflow_id, label_map ), + ) + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + self.assertEquals("1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content( history_id ) ) + def test_workflow_stability( self ): # Run this index stability test with following command: # ./run_tests.sh test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_stability Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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