3 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/2aafaa6a9159/ Changeset: 2aafaa6a9159 User: jmchilton Date: 2014-05-28 18:58:33 Summary: Remove invalid comment. Affected #: 1 file

diff -r 23aac3b3c0e2cfe784d8c5dfd94cc3b6ccff7b7c -r 2aafaa6a915977f2f5970e01ccfbf51dc3db7c14 static/scripts/galaxy.tools.js --- a/static/scripts/galaxy.tools.js +++ b/static/scripts/galaxy.tools.js @@ -30,7 +30,7 @@ 'min_option_count': 2 // Don't show multiple select switch if only // one dataset available. }, - 'select_collection': { // NOT YET IMPLEMENTED + 'select_collection': { 'icon_class': 'fa-folder-o', 'select_by': 'Run tool in parallel across dataset collection', 'allow_remap': false

https://bitbucket.org/galaxy/galaxy-central/commits/a763290e92ad/ Changeset: a763290e92ad User: jmchilton Date: 2014-05-28 18:58:33 Summary: Improvements to workflow extraction tests. Affected #: 1 file

diff -r 2aafaa6a915977f2f5970e01ccfbf51dc3db7c14 -r a763290e92adb2215f4cba507e3eb9fe52618d2c test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -75,11 +75,12 @@

@skip_without_tool( "cat1" ) def test_extract_from_history( self ): + # Run the simple test workflow and extract it back out from history workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) workflow_request, history_id = self._setup_workflow_run( workflow ) contents_response = self._get( "histories/%s/contents" % history_id ) self._assert_status_code_is( contents_response, 200 ) - hda_ids = map( lambda c: c[ "hid" ], contents_response.json() ) + input_hids = map( lambda c: c[ "hid" ], contents_response.json() )

run_workflow_response = self._post( "workflows", data=workflow_request ) self._assert_status_code_is( run_workflow_response, 200 ) @@ -89,23 +90,16 @@ jobs_response = self._get( "jobs", data=data ) self._assert_status_code_is( jobs_response, 200 ) cat1_job_id = jobs_response.json()[ 0 ][ "id" ] - - contents_response = self._get( "history/%s/contents", data=data ) - create_from_data = dict( + downloaded_workflow = self._extract_and_download_workflow( from_history_id=history_id, - dataset_ids=dumps( hda_ids ), + dataset_ids=dumps( input_hids ), job_ids=dumps( [ cat1_job_id ] ), workflow_name="test import from history", ) - create_workflow_response = self._post( "workflows", data=create_from_data ) - self._assert_status_code_is( create_workflow_response, 200 ) - - new_workflow_id = create_workflow_response.json()[ "id" ] - download_response = self._get( "workflows/%s/download" % new_workflow_id ) - self._assert_status_code_is( download_response, 200 ) - downloaded_workflow = download_response.json() self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) assert len( downloaded_workflow[ "steps" ] ) == 3 + self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 ) + self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 )

@skip_without_tool( "collection_paired_test" ) def test_extract_workflows_with_dataset_collections( self ): @@ -241,7 +235,8 @@ def _get_steps_of_type( self, downloaded_workflow, type, expected_len=None ): steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == type ] if expected_len is not None: - assert len( steps ) == expected_len + n = len( steps ) + assert n == expected_len, "Expected %d steps of type %s, found %d" % ( expected_len, type, n ) return steps

@skip_without_tool( "random_lines1" )

https://bitbucket.org/galaxy/galaxy-central/commits/7fd77febf6bb/ Changeset: 7fd77febf6bb User: jmchilton Date: 2014-05-28 18:58:33 Summary: Workflow extraction test from copied datasets. Detailed some bugs I found in the test case and recorded them here https://trello.com/c/mKzLbM2P. Affected #: 1 file

diff -r a763290e92adb2215f4cba507e3eb9fe52618d2c -r 7fd77febf6bb8aa7a6acde9c3a31429f7b1ee99f test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -1,6 +1,7 @@ from base import api from json import dumps from json import loads +import operator import time from .helpers import WorkflowPopulator from .helpers import DatasetPopulator @@ -75,21 +76,11 @@

@skip_without_tool( "cat1" ) def test_extract_from_history( self ): + history_id = self.dataset_populator.new_history() # Run the simple test workflow and extract it back out from history - workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) - workflow_request, history_id = self._setup_workflow_run( workflow ) + cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id ) contents_response = self._get( "histories/%s/contents" % history_id ) - self._assert_status_code_is( contents_response, 200 ) - input_hids = map( lambda c: c[ "hid" ], contents_response.json() ) - - 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 ) - data = dict( history_id=history_id, tool_id="cat1" ) - jobs_response = self._get( "jobs", data=data ) - self._assert_status_code_is( jobs_response, 200 ) - cat1_job_id = jobs_response.json()[ 0 ][ "id" ] + input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] ) downloaded_workflow = self._extract_and_download_workflow( from_history_id=history_id, dataset_ids=dumps( input_hids ), @@ -97,9 +88,74 @@ workflow_name="test import from history", ) self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) + self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) + + def test_extract_with_copied_inputs( self ): + old_history_id = self.dataset_populator.new_history() + # Run the simple test workflow and extract it back out from history + self.__setup_and_run_cat1_workflow( history_id=old_history_id ) + + history_id = self.dataset_populator.new_history() + + # Bug cannot mess up hids or these don't extract correctly. See Trello card here: + # https://trello.com/c/mKzLbM2P + # # create dummy dataset to complicate hid mapping + # self.dataset_populator.new_dataset( history_id, content="dummydataset" ) + # offset = 1 + + offset = 0 + old_contents = self._get( "histories/%s/contents" % old_history_id ).json() + for old_dataset in old_contents: + payload = dict( + source="hda", + content=old_dataset["id"] + ) + response = self._post( "histories/%s/contents/datasets" % history_id, payload ) + self._assert_status_code_is( response, 200 ) + new_contents = self._get( "histories/%s/contents" % history_id ).json() + input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) + cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] ) + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_ids=dumps( input_hids ), + job_ids=dumps( [ cat1_job_id ] ), + workflow_name="test import from history", + ) + self.__assert_looks_like_cat1_example_workflow( downloaded_workflow ) + + def __assert_looks_like_cat1_example_workflow( self, downloaded_workflow ): assert len( downloaded_workflow[ "steps" ] ) == 3 - self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 ) - self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 ) + input_steps = self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 ) + tool_step = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 )[ 0 ] + + input1 = tool_step[ "input_connections" ][ "input1" ] + input2 = tool_step[ "input_connections" ][ "queries_0|input2" ] + + print downloaded_workflow + self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] ) + self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] ) + + def __setup_and_run_cat1_workflow( self, history_id ): + workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) + workflow_request, history_id = self._setup_workflow_run( workflow, history_id=history_id ) + 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, timeout=10 ) + return self.__cat_job_id( history_id ) + + def __cat_job_id( self, history_id ): + data = dict( history_id=history_id, tool_id="cat1" ) + jobs_response = self._get( "jobs", data=data ) + self._assert_status_code_is( jobs_response, 200 ) + cat1_job_id = jobs_response.json()[ 0 ][ "id" ] + return cat1_job_id + + def __job_id( self, history_id, dataset_id ): + url = "histories/%s/contents/%s/provenance" % ( history_id, dataset_id ) + prov_response = self._get( url, data=dict( follow=False ) ) + self._assert_status_code_is( prov_response, 200 ) + return prov_response.json()[ "job_id" ]

@skip_without_tool( "collection_paired_test" ) def test_extract_workflows_with_dataset_collections( self ): @@ -237,7 +293,7 @@ if expected_len is not None: n = len( steps ) assert n == expected_len, "Expected %d steps of type %s, found %d" % ( expected_len, type, n ) - return steps + return sorted( steps, key=operator.itemgetter("id") )

@skip_without_tool( "random_lines1" ) def test_run_replace_params_by_tool( self ): @@ -316,7 +372,7 @@ # renamed to 'the_new_name'. assert "the_new_name" in map( lambda hda: hda[ "name" ], contents )

- def _setup_workflow_run( self, workflow ): + def _setup_workflow_run( self, workflow, history_id=None ): uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) workflow_inputs = self._workflow_inputs( uploaded_workflow_id ) step_1 = step_2 = None @@ -326,7 +382,8 @@ step_1 = key if label == "WorkflowInput2": step_2 = key - history_id = self.dataset_populator.new_history() + if not history_id: + history_id = self.dataset_populator.new_history() hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" ) hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" ) workflow_request = dict(

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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