def test_00_metadata_edit( self ):
"""test_metadata_edit: Testing metadata editing"""
self.logout()
self.login( email='*****@*****.**', username='******' )
admin_user = sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.email=='*****@*****.**' ) \
.one()
self.new_history( name='Test Metadata Edit' )
history1 = sa_session.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()
self.upload_file( '1.bed' )
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
.first()
self.home()
# Due to twill not being able to handle the permissions forms, we'll eliminate
# DefaultHistoryPermissions prior to uploading a dataset so that the permission
# form will not be displayed on ted edit attributes page.
for dp in latest_hda.dataset.actions:
sa_session.delete( dp )
sa_session.flush()
sa_session.refresh( latest_hda.dataset )
self.check_history_for_string( '1.bed' )
self.check_metadata_for_string( '1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=str( latest_hda.hid ) )
"""test editing attributes"""
self.edit_hda_attribute_info( hda_id=str( latest_hda.id ),
new_name='Testdata',
new_info="Uploaded my file",
new_dbkey='hg16',
new_startcol='6' )
self.check_metadata_for_string( 'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=str( latest_hda.hid ) )
"""test Auto-detecting attributes"""
self.auto_detect_metadata( hda_id=str( latest_hda.id ) )
self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=str( latest_hda.hid ) )
"""test converting formats"""
self.convert_format( hda_id=str( latest_hda.id ), target_type='gff' )
self.check_metadata_for_string( '"gff" selected="yes"', hid=str( latest_hda.hid ) )
"""test changing data type"""
self.change_datatype( hda_id=str( latest_hda.id ), datatype='gff3' )
self.check_metadata_for_string( 'gff3', hid=str( latest_hda.hid ) )
self.delete_history( id=self.security.encode_id( history1.id ) )
self.logout()
def test_999_reset_data_for_later_test_runs( self ):
"""Reseting data to enable later test runs to pass"""
# Logged in as regular_user2
self.logout()
self.login( email=admin_user.email )
##################
# Purge all libraries
##################
for library in [ library1, library2 ]:
self.delete_library_item( 'library_admin',
self.security.encode_id( library.id ),
self.security.encode_id( library.id ),
library.name,
item_type='library' )
self.purge_library( self.security.encode_id( library.id ), library.name )
##################
# Eliminate all non-private roles
##################
for role in [ role1, role2 ]:
self.mark_role_deleted( self.security.encode_id( role.id ), role.name )
self.purge_role( self.security.encode_id( role.id ), role.name )
# Manually delete the role from the database
refresh( role )
sa_session.delete( role )
sa_session.flush()
##################
# Eliminate all groups
##################
for group in [ group1 ]:
self.mark_group_deleted( self.security.encode_id( group.id ), group.name )
self.purge_group( self.security.encode_id( group.id ), group.name )
# Manually delete the group from the database
refresh( group )
sa_session.delete( group )
sa_session.flush()
##################
# Make sure all users are associated only with their private roles
##################
for user in [ admin_user, regular_user1, regular_user2, regular_user3 ]:
refresh( user )
if len( user.roles) != 1:
raise AssertionError( '%d UserRoleAssociations are associated with %s ( should be 1 )' % ( len( user.roles ), user.email ) )
def test_get_DNAseHSS_flanked_genes( self ):
self.logout()
self.login( email='*****@*****.**' )
admin_user = sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.email=='*****@*****.**' ) \
.one()
self.new_history( name='DNAseHSS_flanked_genes' )
history1 = sa_session.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()
track_params = dict(
db="hg17",
hgta_group="regulation",
hgta_table="dukeDnaseCd4Sites",
hgta_track="dukeDnaseCd4Sites",
hgta_regionType="range",
position="chr22",
hgta_outputType="bed",
sendToGalaxy="1"
)
output_params = dict(
fbQual="whole",
)
# Test 1
self.run_ucsc_main( track_params, output_params )
self.wait()
self.verify_dataset_correctness('DNAseHSS.dat')
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
.first()
# Due to twill not being able to handle the permissions forms, we'll eliminate
# DefaultHistoryPermissions prior to uploading a dataset so that the permission
# form will not be displayed on ted edit attributes page.
for dp in latest_hda.dataset.actions:
sa_session.delete( dp )
sa_session.flush()
sa_session.refresh( latest_hda.dataset )
self.edit_hda_attribute_info( str( latest_hda.id ), new_name="DNAse HS" )
self.check_metadata_for_string( "DNAse HS" )
track_params = dict(
db="hg17",
hgta_group="genes",
hgta_table="knownGene",
hgta_track="knownGene",
hgta_regionType="range",
position="chr22",
hgta_outputType="bed",
sendToGalaxy="1"
)
output_params = dict(
fbQual="whole",
)
# Test 2
self.run_ucsc_main( track_params, output_params )
self.wait()
self.verify_dataset_correctness('hg17chr22KnownGenes.dat')
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
.first()
for dp in latest_hda.dataset.actions:
sa_session.delete( dp )
sa_session.flush()
sa_session.refresh( latest_hda.dataset )
self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Genes" )
self.check_metadata_for_string( "Genes" )
# Test 3
self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" )
self.wait()
self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' )
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
.first()
for dp in latest_hda.dataset.actions:
sa_session.delete( dp )
sa_session.flush()
sa_session.refresh( latest_hda.dataset )
self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Flanks" )
self.check_metadata_for_string( "Flanks" )
# Test 4
self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none" )
self.wait()
# We cannot verify this dataset, because this tool spits out data in a non-deterministic order
#self.verify_dataset_correctness( 'joinFlanksDNAse.dat' )
# Test 5
self.run_tool( 'Filter1', input="4", cond="c17==1000" )
self.wait()
self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' )
self.delete_history( self.security.encode_id( history1.id ) )
self.logout()