galaxy/test/unit/test_galaxy_mapping.py

# -*- coding: utf-8 -*-
import unittest
import galaxy.model.mapping as mapping
import uuid


class MappingTests( unittest.TestCase ):

    def test_annotations( self ):
        model = self.model

        u = model.User( email="annotator@example.com", password="password" )
        self.persist( u )

        def persist_and_check_annotation( annotation_class, **kwds ):
            annotated_association = annotation_class()
            annotated_association.annotation = "Test Annotation"
            annotated_association.user = u
            for key, value in kwds.iteritems():
                setattr(annotated_association, key, value)
            self.persist( annotated_association )
            self.expunge()
            stored_annotation = self.query( annotation_class ).all()[0]
            assert stored_annotation.annotation == "Test Annotation"
            assert stored_annotation.user.email == "annotator@example.com"

        sw = model.StoredWorkflow()
        sw.user = u
        self.persist( sw )
        persist_and_check_annotation( model.StoredWorkflowAnnotationAssociation, stored_workflow=sw )

        workflow = model.Workflow()
        workflow.stored_workflow = sw
        self.persist( workflow )

        ws = model.WorkflowStep()
        ws.workflow = workflow
        self.persist( ws )
        persist_and_check_annotation( model.WorkflowStepAnnotationAssociation, workflow_step=ws )

        h = model.History( name="History for Annotation", user=u)
        self.persist( h )
        persist_and_check_annotation( model.HistoryAnnotationAssociation, history=h )

        d1 = model.HistoryDatasetAssociation( extension="txt", history=h, create_dataset=True, sa_session=model.session )
        self.persist( d1 )
        persist_and_check_annotation( model.HistoryDatasetAssociationAnnotationAssociation, hda=d1 )

        page = model.Page()
        page.user = u
        self.persist( page )
        persist_and_check_annotation( model.PageAnnotationAssociation, page=page )

        visualization = model.Visualization()
        visualization.user = u
        self.persist( visualization )
        persist_and_check_annotation( model.VisualizationAnnotationAssociation, visualization=visualization )

        dataset_collection = model.DatasetCollection( collection_type="paired" )
        history_dataset_collection = model.HistoryDatasetCollectionAssociation( collection=dataset_collection )
        self.persist( history_dataset_collection )
        persist_and_check_annotation( model.HistoryDatasetCollectionAnnotationAssociation, history_dataset_collection=history_dataset_collection )

        library_dataset_collection = model.LibraryDatasetCollectionAssociation( collection=dataset_collection )
        self.persist( library_dataset_collection )
        persist_and_check_annotation( model.LibraryDatasetCollectionAnnotationAssociation, library_dataset_collection=library_dataset_collection )

    def test_ratings( self ):
        model = self.model

        u = model.User( email="rater@example.com", password="password" )
        self.persist( u )

        def persist_and_check_rating( rating_class, **kwds ):
            rating_association = rating_class()
            rating_association.rating = 5
            rating_association.user = u
            for key, value in kwds.iteritems():
                setattr(rating_association, key, value)
            self.persist( rating_association )
            self.expunge()
            stored_annotation = self.query( rating_class ).all()[0]
            assert stored_annotation.rating == 5
            assert stored_annotation.user.email == "rater@example.com"

        sw = model.StoredWorkflow()
        sw.user = u
        self.persist( sw )
        persist_and_check_rating( model.StoredWorkflowRatingAssociation, stored_workflow=sw )

        h = model.History( name="History for Rating", user=u)
        self.persist( h )
        persist_and_check_rating( model.HistoryRatingAssociation, history=h )

        d1 = model.HistoryDatasetAssociation( extension="txt", history=h, create_dataset=True, sa_session=model.session )
        self.persist( d1 )
        persist_and_check_rating( model.HistoryDatasetAssociationRatingAssociation, hda=d1 )

        page = model.Page()
        page.user = u
        self.persist( page )
        persist_and_check_rating( model.PageRatingAssociation, page=page )

        visualization = model.Visualization()
        visualization.user = u
        self.persist( visualization )
        persist_and_check_rating( model.VisualizationRatingAssociation, visualization=visualization )

        dataset_collection = model.DatasetCollection( collection_type="paired" )
        history_dataset_collection = model.HistoryDatasetCollectionAssociation( collection=dataset_collection )
        self.persist( history_dataset_collection )
        persist_and_check_rating( model.HistoryDatasetCollectionRatingAssociation, history_dataset_collection=history_dataset_collection )

        library_dataset_collection = model.LibraryDatasetCollectionAssociation( collection=dataset_collection )
        self.persist( library_dataset_collection )
        persist_and_check_rating( model.LibraryDatasetCollectionRatingAssociation, library_dataset_collection=library_dataset_collection )

    def test_display_name( self ):

        def assert_display_name_converts_to_unicode( item, name ):
            assert not isinstance( item.name, unicode )
            assert isinstance( item.get_display_name(), unicode )
            assert item.get_display_name() == name

        ldda = self.model.LibraryDatasetDatasetAssociation( name='ldda_name' )
        assert_display_name_converts_to_unicode( ldda, 'ldda_name' )

        hda = self.model.HistoryDatasetAssociation( name='hda_name' )
        assert_display_name_converts_to_unicode( hda, 'hda_name' )

        history = self.model.History( name='history_name' )
        assert_display_name_converts_to_unicode( history, 'history_name' )

        library = self.model.Library( name='library_name' )
        assert_display_name_converts_to_unicode( library, 'library_name' )

        library_folder = self.model.LibraryFolder( name='library_folder' )
        assert_display_name_converts_to_unicode( library_folder, 'library_folder' )

        history = self.model.History(
            name=u'Hello₩◎ґʟⅾ'
        )
        assert isinstance( history.name, unicode )
        assert isinstance( history.get_display_name(), unicode )
        assert history.get_display_name() == u'Hello₩◎ґʟⅾ'

    def test_tags( self ):
        model = self.model

        my_tag = model.Tag(name="Test Tag")
        u = model.User( email="tagger@example.com", password="password" )
        self.persist( my_tag, u )

        def tag_and_test( taggable_object, tag_association_class, backref_name ):
            assert len( getattr(self.query( model.Tag ).filter( model.Tag.name == "Test Tag" ).all()[0], backref_name) ) == 0

            tag_association = tag_association_class()
            tag_association.tag = my_tag
            taggable_object.tags = [ tag_association ]
            self.persist( tag_association, taggable_object )

            assert len( getattr(self.query( model.Tag ).filter( model.Tag.name == "Test Tag" ).all()[0], backref_name) ) == 1

        sw = model.StoredWorkflow()
        sw.user = u
        tag_and_test( sw, model.StoredWorkflowTagAssociation, "tagged_workflows" )

        h = model.History( name="History for Tagging", user=u)
        tag_and_test( h, model.HistoryTagAssociation, "tagged_histories" )

        d1 = model.HistoryDatasetAssociation( extension="txt", history=h, create_dataset=True, sa_session=model.session )
        tag_and_test( d1, model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations" )

        page = model.Page()
        page.user = u
        tag_and_test( page, model.PageTagAssociation, "tagged_pages" )

        visualization = model.Visualization()
        visualization.user = u
        tag_and_test( visualization, model.VisualizationTagAssociation, "tagged_visualizations" )

        dataset_collection = model.DatasetCollection( collection_type="paired" )
        history_dataset_collection = model.HistoryDatasetCollectionAssociation( collection=dataset_collection )
        tag_and_test( history_dataset_collection, model.HistoryDatasetCollectionTagAssociation, "tagged_history_dataset_collections" )

        library_dataset_collection = model.LibraryDatasetCollectionAssociation( collection=dataset_collection )
        tag_and_test( library_dataset_collection, model.LibraryDatasetCollectionTagAssociation, "tagged_library_dataset_collections" )

    def test_collections_in_histories(self):
        model = self.model

        u = model.User( email="mary@example.com", password="password" )
        h1 = model.History( name="History 1", user=u)
        d1 = model.HistoryDatasetAssociation( extension="txt", history=h1, create_dataset=True, sa_session=model.session )
        d2 = model.HistoryDatasetAssociation( extension="txt", history=h1, create_dataset=True, sa_session=model.session )

        c1 = model.DatasetCollection(collection_type="pair")
        hc1 = model.HistoryDatasetCollectionAssociation(history=h1, collection=c1, name="HistoryCollectionTest1")

        dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="left")
        dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="right")

        self.persist( u, h1, d1, d2, c1, hc1, dce1, dce2 )

        loaded_dataset_collection = self.query( model.HistoryDatasetCollectionAssociation ).filter( model.HistoryDatasetCollectionAssociation.name == "HistoryCollectionTest1" ).first().collection
        self.assertEquals(len(loaded_dataset_collection.elements), 2)
        assert loaded_dataset_collection.collection_type == "pair"
        assert loaded_dataset_collection[ "left" ] == dce1
        assert loaded_dataset_collection[ "right" ] == dce2

    def test_collections_in_library_folders(self):
        model = self.model

        u = model.User( email="mary2@example.com", password="password" )
        lf = model.LibraryFolder( name="RootFolder" )
        l = model.Library( name="Library1", root_folder=lf )
        ld1 = model.LibraryDataset( )
        ld2 = model.LibraryDataset( )

        ldda1 = model.LibraryDatasetDatasetAssociation( extension="txt", library_dataset=ld1 )
        ldda2 = model.LibraryDatasetDatasetAssociation( extension="txt", library_dataset=ld1 )

        c1 = model.DatasetCollection(collection_type="pair")
        dce1 = model.DatasetCollectionElement(collection=c1, element=ldda1)
        dce2 = model.DatasetCollectionElement(collection=c1, element=ldda2)
        self.persist( u, l, lf, ld1, ld2, c1, ldda1, ldda2, dce1, dce2 )

        # TODO:
        # loaded_dataset_collection = self.query( model.DatasetCollection ).filter( model.DatasetCollection.name == "LibraryCollectionTest1" ).first()
        # self.assertEquals(len(loaded_dataset_collection.datasets), 2)
        # assert loaded_dataset_collection.collection_type == "pair"

    def test_default_disk_usage( self ):
        model = self.model

        u = model.User( email="disk_default@test.com", password="password" )
        self.persist( u )
        u.adjust_total_disk_usage( 1 )
        u_id = u.id
        self.expunge()
        user_reload = model.session.query( model.User ).get( u_id )
        assert user_reload.disk_usage == 1

    def test_basic( self ):
        model = self.model

        original_user_count = len( model.session.query( model.User ).all() )

        # Make some changes and commit them
        u = model.User( email="james@foo.bar.baz", password="password" )
        # gs = model.GalaxySession()
        h1 = model.History( name="History 1", user=u)
        # h1.queries.append( model.Query( "h1->q1" ) )
        # h1.queries.append( model.Query( "h1->q2" ) )
        h2 = model.History( name=( "H" * 1024 ) )
        self.persist( u, h1, h2 )
        # q1 = model.Query( "h2->q1" )
        metadata = dict( chromCol=1, startCol=2, endCol=3 )
        d1 = model.HistoryDatasetAssociation( extension="interval", metadata=metadata, history=h2, create_dataset=True, sa_session=model.session )
        # h2.queries.append( q1 )
        # h2.queries.append( model.Query( "h2->q2" ) )
        self.persist( d1 )

        # Check
        users = model.session.query( model.User ).all()
        assert len( users ) == original_user_count + 1
        user = [user for user in users if user.email == "james@foo.bar.baz"][0]
        assert user.email == "james@foo.bar.baz"
        assert user.password == "password"
        assert len( user.histories ) == 1
        assert user.histories[0].name == "History 1"
        hists = model.session.query( model.History ).all()
        hist0 = [history for history in hists if history.name == "History 1"][0]
        hist1 = [history for history in hists if history.name == "H" * 255][0]
        assert hist0.name == "History 1"
        assert hist1.name == ( "H" * 255 )
        assert hist0.user == user
        assert hist1.user is None
        assert hist1.datasets[0].metadata.chromCol == 1
        # The filename test has moved to objecstore
        # id = hist1.datasets[0].id
        # assert hist1.datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id )
        # Do an update and check
        hist1.name = "History 2b"
        self.expunge()
        hists = model.session.query( model.History ).all()
        hist0 = [history for history in hists if history.name == "History 1"][0]
        hist1 = [history for history in hists if history.name == "History 2b"][0]
        assert hist0.name == "History 1"
        assert hist1.name == "History 2b"
        # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like.

    def test_jobs( self ):
        model = self.model
        u = model.User( email="jobtest@foo.bar.baz", password="password" )
        job = model.Job()
        job.user = u
        job.tool_id = "cat1"

        self.persist( u, job )

        loaded_job = model.session.query( model.Job ).filter( model.Job.user == u ).first()
        assert loaded_job.tool_id == "cat1"

    def test_job_metrics( self ):
        model = self.model
        u = model.User( email="jobtest@foo.bar.baz", password="password" )
        job = model.Job()
        job.user = u
        job.tool_id = "cat1"

        job.add_metric( "gx", "galaxy_slots", 5 )
        job.add_metric( "system", "system_name", "localhost" )

        self.persist( u, job )

        task = model.Task( job=job, working_directory="/tmp", prepare_files_cmd="split.sh" )
        task.add_metric( "gx", "galaxy_slots", 5 )
        task.add_metric( "system", "system_name", "localhost" )

        big_value = ":".join( [ "%d" % i for i in range( 2000 ) ] )
        task.add_metric( "env", "BIG_PATH", big_value )
        self.persist( task )
        # Ensure big values truncated
        assert len( task.text_metrics[ 1 ].metric_value ) <= 1023

    def test_tasks( self ):
        model = self.model
        u = model.User( email="jobtest@foo.bar.baz", password="password" )
        job = model.Job()
        task = model.Task( job=job, working_directory="/tmp", prepare_files_cmd="split.sh" )
        job.user = u
        self.persist( u, job, task )

        loaded_task = model.session.query( model.Task ).filter( model.Task.job == job ).first()
        assert loaded_task.prepare_input_files_cmd == "split.sh"

    def test_history_contents( self ):
        model = self.model
        u = model.User( email="contents@foo.bar.baz", password="password" )
        # gs = model.GalaxySession()
        h1 = model.History( name="HistoryContentsHistory1", user=u)

        self.persist( u, h1, expunge=False )

        d1 = self.new_hda( h1, name="1" )
        d2 = self.new_hda( h1, name="2", visible=False )
        d3 = self.new_hda( h1, name="3", deleted=True )
        d4 = self.new_hda( h1, name="4", visible=False, deleted=True )

        self.session().flush()

        def contents_iter_names(**kwds):
            history = model.context.query( model.History ).filter(
                model.History.name == "HistoryContentsHistory1"
            ).first()
            return list( map( lambda hda: hda.name, history.contents_iter( **kwds ) ) )

        self.assertEquals(contents_iter_names(), [ "1", "2", "3", "4" ])
        assert contents_iter_names( deleted=False ) == [ "1", "2" ]
        assert contents_iter_names( visible=True ) == [ "1", "3" ]
        assert contents_iter_names( visible=False ) == [ "2", "4" ]
        assert contents_iter_names( deleted=True, visible=False ) == [ "4" ]

        assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ] ) == [ "1", "2", "3", "4" ]
        assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ], max_in_filter_length=1 ) == [ "1", "2", "3", "4" ]

        assert contents_iter_names( ids=[ d1.id, d3.id ] ) == [ "1", "3" ]

    def test_workflows( self ):
        model = self.model
        user = model.User(
            email="testworkflows@bx.psu.edu",
            password="password"
        )

        def workflow_from_steps(steps):
            stored_workflow = model.StoredWorkflow()
            stored_workflow.user = user
            workflow = model.Workflow()
            workflow.steps = steps
            workflow.stored_workflow = stored_workflow
            return workflow

        child_workflow = workflow_from_steps([])
        self.persist( child_workflow )

        workflow_step_1 = model.WorkflowStep()
        workflow_step_1.order_index = 0
        workflow_step_1.type = "data_input"
        workflow_step_2 = model.WorkflowStep()
        workflow_step_2.order_index = 1
        workflow_step_2.type = "subworkflow"
        workflow_step_2.subworkflow = child_workflow

        workflow = workflow_from_steps([workflow_step_1, workflow_step_2])
        self.persist( workflow )

        assert workflow_step_1.id is not None
        h1 = model.History( name="WorkflowHistory1", user=user)

        invocation_uuid = uuid.uuid1()

        workflow_invocation = model.WorkflowInvocation()
        workflow_invocation.uuid = invocation_uuid
        workflow_invocation.history = h1

        workflow_invocation_step1 = model.WorkflowInvocationStep()
        workflow_invocation_step1.workflow_invocation = workflow_invocation
        workflow_invocation_step1.workflow_step = workflow_step_1

        subworkflow_invocation = model.WorkflowInvocation()
        workflow_invocation.attach_subworkflow_invocation_for_step(workflow_step_2, subworkflow_invocation)

        workflow_invocation_step2 = model.WorkflowInvocationStep()
        workflow_invocation_step2.workflow_invocation = workflow_invocation
        workflow_invocation_step2.workflow_step = workflow_step_2

        workflow_invocation.workflow = workflow

        d1 = self.new_hda( h1, name="1" )
        workflow_request_dataset = model.WorkflowRequestToInputDatasetAssociation()
        workflow_request_dataset.workflow_invocation = workflow_invocation
        workflow_request_dataset.workflow_step = workflow_step_1
        workflow_request_dataset.dataset = d1
        self.persist( workflow_invocation )
        assert workflow_request_dataset is not None
        assert workflow_invocation.id is not None

        history_id = h1.id
        self.expunge()

        loaded_invocation = self.query( model.WorkflowInvocation ).get( workflow_invocation.id )
        assert loaded_invocation.uuid == invocation_uuid, "%s != %s" % (loaded_invocation.uuid, invocation_uuid)
        assert loaded_invocation
        assert loaded_invocation.history.id == history_id

        step_1, step_2 = loaded_invocation.workflow.steps

        assert not step_1.subworkflow
        assert step_2.subworkflow
        assert len( loaded_invocation.steps ) == 2

        subworkflow_invocation_assoc = loaded_invocation.get_subworkflow_invocation_association_for_step(step_2)
        assert subworkflow_invocation_assoc is not None
        assert isinstance(subworkflow_invocation_assoc.subworkflow_invocation, model.WorkflowInvocation)
        assert isinstance(subworkflow_invocation_assoc.parent_workflow_invocation, model.WorkflowInvocation)

        assert subworkflow_invocation_assoc.subworkflow_invocation.history.id == history_id

    def new_hda( self, history, **kwds ):
        return history.add_dataset( self.model.HistoryDatasetAssociation( create_dataset=True, sa_session=self.model.session, **kwds ) )

    @classmethod
    def setUpClass(cls):
        # Start the database and connect the mapping
        cls.model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True, object_store=MockObjectStore() )
        assert cls.model.engine is not None

    @classmethod
    def query( cls, type ):
        return cls.model.session.query( type )

    @classmethod
    def persist(cls, *args, **kwargs):
        session = cls.session()
        flush = kwargs.get('flush', True)
        for arg in args:
            session.add( arg )
            if flush:
                session.flush()
        if kwargs.get('expunge', not flush):
            cls.expunge()
        return arg  # Return last or only arg.

    @classmethod
    def session(cls):
        return cls.model.session

    @classmethod
    def expunge(cls):
        cls.model.session.flush()
        cls.model.session.expunge_all()


class MockObjectStore(object):

    def __init__(self):
        pass

    def size(self, dataset):
        return 42

    def exists(self, *args, **kwds):
        return True

    def get_filename(self, *args, **kwds):
        return "dataest_14.dat"


def get_suite():
    suite = unittest.TestSuite()
    suite.addTest( MappingTests( "test_basic" ) )
    return suite