def test_045_change_permissions_on_current_history(self):
"""Testing changing permissions on the current history"""
# Logged in as regular_user3
self.logout()
self.login(email=admin_user.email)
# Current history is history4
self.new_history()
global history5
history5 = (
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()
)
assert history5 is not None, "Problem retrieving history5 from database"
self.rename_history(self.security.encode_id(history5.id), history5.name, new_name=urllib.quote("history 5"))
# Current history is hostory5
sa_session.refresh(history5)
# Due to the limitations of twill ( not functional with the permissions forms ), we're forced
# to do this manually. At this point, we just want to restrict the access permission on history5
# to the admin_user
global access_action
access_action = galaxy.model.Dataset.permitted_actions.DATASET_ACCESS.action
dhp = galaxy.model.DefaultHistoryPermissions(history5, access_action, admin_user_private_role)
sa_session.add(dhp)
sa_session.flush()
sa_session.refresh(history5)
global history5_default_permissions
history5_default_permissions = [dhp.action for dhp in history5.default_permissions]
# Sort for later comparison
history5_default_permissions.sort()
self.upload_file("1.bed", dbkey="hg18")
history5_dataset1 = None
for hda in history5.datasets:
if hda.name == "1.bed":
history5_dataset1 = hda.dataset
break
assert history5_dataset1 is not None, "Problem retrieving history5_dataset1 from the database"
# The permissions on the dataset should be restricted from sharing with anyone due to the
# inherited history permissions
dataset_permissions = [a.action for a in history5_dataset1.actions]
dataset_permissions.sort()
if dataset_permissions != history5_default_permissions:
err_msg = (
"Dataset permissions for history5_dataset1 (%s) were not correctly inherited from history permissions (%s)"
% (str(dataset_permissions), str(history5_default_permissions))
)
raise AssertionError, err_msg
# Make sure when we logout and login, the history default permissions are preserved
self.logout()
self.login(email=admin_user.email)
sa_session.refresh(history5)
current_history_permissions = [dhp.action for dhp in history5.default_permissions]
current_history_permissions.sort()
if current_history_permissions != history5_default_permissions:
raise AssertionError, "With logout and login, the history default permissions are not preserved"
def test_085_reset_data_for_later_test_runs(self):
"""Reseting data to enable later test runs to to be valid"""
# logged in as admin_user
# Clean up admin_user
# Unshare history3 - shared with regular_user1, regular_user2, regular_user3
self.unshare_history(self.security.encode_id(history3.id), self.security.encode_id(regular_user1.id))
self.unshare_history(self.security.encode_id(history3.id), self.security.encode_id(regular_user2.id))
self.unshare_history(self.security.encode_id(history3.id), self.security.encode_id(regular_user3.id))
# Unshare history4 - shared with regular_user2, regular_user3
self.unshare_history(self.security.encode_id(history4.id), self.security.encode_id(regular_user2.id))
self.unshare_history(self.security.encode_id(history4.id), self.security.encode_id(regular_user3.id))
# Unshare history5 - shared with regular_user1
self.unshare_history(self.security.encode_id(history5.id), self.security.encode_id(regular_user1.id))
# Delete histories
self.delete_history(id=self.security.encode_id(history3.id))
self.delete_history(id=self.security.encode_id(history3_clone2.id))
self.delete_history(id=self.security.encode_id(history3_clone3.id))
self.delete_history(id=self.security.encode_id(history4.id))
self.delete_history(id=self.security.encode_id(history5.id))
# Eliminate Sharing role for: [email protected], [email protected]
self.mark_role_deleted(self.security.encode_id(sharing_role.id), sharing_role.name)
self.purge_role(self.security.encode_id(sharing_role.id), sharing_role.name)
# Manually delete the sharing role from the database
sa_session.refresh(sharing_role)
sa_session.delete(sharing_role)
sa_session.flush()
# Clean up regular_user_1
self.logout()
self.login(email=regular_user1.email)
self.delete_history(id=self.security.encode_id(history3_clone1.id))
self.delete_history(id=self.security.encode_id(history5_clone1.id))
def delete_request_type_permissions( id ):
rtps = sa_session.query( galaxy.model.RequestTypePermissions ) \
.filter( and_( galaxy.model.RequestTypePermissions.table.c.request_type_id==id ) ) \
.order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) )
for rtp in rtps:
sa_session.delete( rtp )
sa_session.flush()
def test_010_user_reqistration_single_user_info_forms( self ):
''' Testing user registration with a single user info form '''
# lets delete the 'Researcher' user info form
self.login( '*****@*****.**' )
form_two_latest = get_latest_form(form_two_name)
form_two_latest.current.deleted = True
sa_session.add( form_two_latest.current )
sa_session.flush()
self.home()
self.visit_page('forms/manage?sort=create_time&f-deleted=True')
self.check_page_for_string(form_two_latest.name)
self.logout()
# user a new user with 'Student' user info form
form_one = get_latest_form(form_one_name)
user_info_values=['Educational', 'Penn State', True]
self.create_user_with_info( '*****@*****.**', 'testuser', 'test12',
user_info_forms='single',
user_info_form_id=form_one.id,
user_info_values=user_info_values )
self.home()
self.visit_page( "user/show_info" )
self.check_page_for_string( "Manage User Information" )
self.check_page_for_string( user_info_values[0] )
self.check_page_for_string( user_info_values[1] )
self.check_page_for_string( '<input type="checkbox" name="field_2" value="true" checked>' )
def delete_request_type_permissions(id):
rtps = sa_session.query( galaxy.model.RequestTypePermissions ) \
.filter( and_( galaxy.model.RequestTypePermissions.table.c.request_type_id==id ) ) \
.order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) )
for rtp in rtps:
sa_session.delete(rtp)
sa_session.flush()
def test_010_user_reqistration_single_user_info_forms(self):
''' Testing user registration with a single user info form '''
# lets delete the 'Researcher' user info form
self.login('*****@*****.**')
form_two_latest = get_latest_form(form_two_name)
form_two_latest.current.deleted = True
sa_session.add(form_two_latest.current)
sa_session.flush()
self.home()
self.visit_page('forms/manage?sort=create_time&f-deleted=True')
self.check_page_for_string(form_two_latest.name)
self.logout()
# user a new user with 'Student' user info form
form_one = get_latest_form(form_one_name)
user_info_values = ['Educational', 'Penn State', True]
self.create_user_with_info('*****@*****.**',
'testuser',
'test12',
user_info_forms='single',
user_info_form_id=form_one.id,
user_info_values=user_info_values)
self.home()
self.visit_page("user/show_info")
self.check_page_for_string("Manage User Information")
self.check_page_for_string(user_info_values[0])
self.check_page_for_string(user_info_values[1])
self.check_page_for_string(
'<input type="checkbox" name="field_2" value="true" checked>')
def test_020_create_user_as_admin( self ):
''' Testing creating users as an admin '''
self.logout()
self.login( '*****@*****.**' )
form_one = get_latest_form(form_one_name)
user_info_values=['Educational', 'Penn State', True]
self.create_user_with_info( '*****@*****.**', 'testuser', 'test13',
user_info_forms='single',
user_info_form_id=form_one.id,
user_info_values=user_info_values )
self.logout()
self.login( '*****@*****.**' )
user = sa_session.query( galaxy.model.User ) \
.filter( and_( galaxy.model.User.table.c.email=='*****@*****.**' ) ).first()
self.home()
page = "admin/users?id=%s&operation=information&f-deleted=False" % self.security.encode_id( user.id )
self.visit_page( page )
self.check_page_for_string( 'Manage User Information' )
self.check_page_for_string( '*****@*****.**' )
self.check_page_for_string( user_info_values[0] )
self.check_page_for_string( user_info_values[1] )
self.check_page_for_string( '<input type="checkbox" name="field_2" value="true" checked>' )
# lets delete the 'Student' user info form
self.login( '*****@*****.**' )
form_one_latest = get_latest_form(form_one_name)
form_one_latest.current.deleted = True
sa_session.add( form_one_latest.current )
sa_session.flush()
self.home()
self.visit_page('forms/manage?sort=create_time&f-deleted=True')
self.check_page_for_string(form_one_latest.name)
self.logout()
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_00_metadata_edit( self ):
"""test_metadata_edit: Testing metadata editing"""
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='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_020_create_user_as_admin(self):
''' Testing creating users as an admin '''
self.logout()
self.login('*****@*****.**')
form_one = get_latest_form(form_one_name)
user_info_values = ['Educational', 'Penn State', True]
self.create_user_with_info('*****@*****.**',
'testuser',
'test13',
user_info_forms='single',
user_info_form_id=form_one.id,
user_info_values=user_info_values)
self.logout()
self.login('*****@*****.**')
user = sa_session.query( galaxy.model.User ) \
.filter( and_( galaxy.model.User.table.c.email=='*****@*****.**' ) ).first()
self.home()
page = "admin/users?id=%s&operation=information&f-deleted=False" % self.security.encode_id(
user.id)
self.visit_page(page)
self.check_page_for_string('Manage User Information')
self.check_page_for_string('*****@*****.**')
self.check_page_for_string(user_info_values[0])
self.check_page_for_string(user_info_values[1])
self.check_page_for_string(
'<input type="checkbox" name="field_2" value="true" checked>')
# lets delete the 'Student' user info form
self.login('*****@*****.**')
form_one_latest = get_latest_form(form_one_name)
form_one_latest.current.deleted = True
sa_session.add(form_one_latest.current)
sa_session.flush()
self.home()
self.visit_page('forms/manage?sort=create_time&f-deleted=True')
self.check_page_for_string(form_one_latest.name)
self.logout()
def delete_obj( obj ):
sa_session.delete( obj )
sa_session.flush()
def mark_obj_deleted(obj):
obj.deleted = True
sa_session.add(obj)
sa_session.flush()
def mark_obj_deleted( obj ):
obj.deleted = True
sa_session.add( obj )
sa_session.flush()
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()
def delete_user_roles(user):
for ura in user.roles:
sa_session.delete(ura)
sa_session.flush()
def flush(obj):
sa_session.add(obj)
sa_session.flush()
def delete_user_roles( user ):
for ura in user.roles:
sa_session.delete( ura )
sa_session.flush()
def delete_obj(obj):
sa_session.delete(obj)
sa_session.flush()
def flush( obj ):
sa_session.add( obj )
sa_session.flush()
