def test_00_metadata_edit(self):
"""test_metadata_edit: Testing metadata editing"""
sa_session = database_contexts.galaxy_context
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()
# 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 index( self, trans, deleted='False', **kwd ):
"""
GET /api/histories
GET /api/histories/deleted
Displays a collection (list) of histories.
"""
#TODO: query (by name, date, etc.)
rval = []
deleted = string_as_bool( deleted )
try:
if trans.user:
query = trans.sa_session.query(trans.app.model.History ).filter_by( user=trans.user, deleted=deleted ).order_by(
desc(trans.app.model.History.table.c.update_time)).all()
for history in query:
item = history.get_api_value(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
rval.append( item )
elif trans.galaxy_session.current_history:
#No user, this must be session authentication with an anonymous user.
history = trans.galaxy_session.current_history
item = history.get_api_value(value_mapper={'id':trans.security.encode_id})
item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) )
rval.append(item)
except Exception, e:
rval = "Error in history API"
log.error( rval + ": %s" % str(e) )
trans.response.status = 500
def test_00_metadata_edit( self ):
"""test_metadata_edit: Testing metadata editing"""
sa_session = database_contexts.galaxy_context
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 disk_usage( self, trans, **kwd ):
file_path = trans.app.config.file_path
disk_usage = self.get_disk_usage( file_path )
min_file_size = 2**32 # 4 Gb
file_size_str = nice_size( min_file_size )
datasets = trans.sa_session.query( model.Dataset ) \
.filter( and_( model.Dataset.table.c.purged == False,
model.Dataset.table.c.file_size > min_file_size ) ) \
.order_by( desc( model.Dataset.table.c.file_size ) )
return file_path, disk_usage, datasets, file_size_str
def disk_usage( self, trans, **kwd ):
file_path = trans.app.config.file_path
disk_usage = self.get_disk_usage( file_path )
min_file_size = 2**32 # 4 Gb
file_size_str = nice_size( min_file_size )
datasets = trans.sa_session.query( model.Dataset ) \
.filter( and_( model.Dataset.table.c.purged == False,
model.Dataset.table.c.file_size > min_file_size ) ) \
.order_by( desc( model.Dataset.table.c.file_size ) )
return file_path, disk_usage, datasets, file_size_str
def most_recent( self, trans, user=None, deleted=False ):
user = user or trans.user
if not user:
return None if trans.history.deleted else trans.history
#TODO: dup with by_user - should return query from there and call first and not all
history_model = trans.model.History
query = ( trans.sa_session.query( history_model )
.filter( history_model.user == user )
.order_by( orm.desc( history_model.table.c.update_time ) ) )
if not deleted:
query = query.filter( history_model.deleted == False )
return query.first()
def most_recent(self, trans, user=None, deleted=False):
user = user or trans.user
if not user:
return None if trans.history.deleted else trans.history
#TODO: dup with by_user - should return query from there and call first and not all
history_model = trans.model.History
query = (trans.sa_session.query(history_model).filter(
history_model.user == user).order_by(
orm.desc(history_model.table.c.update_time)))
if not deleted:
query = query.filter(history_model.deleted == False)
return query.first()
def new_history( self ):
# Start with a new history
self.twill_test_case.logout()
self.twill_test_case.login( email='*****@*****.**' )
admin_user = database_contexts.galaxy_context.query( galaxy.model.User ).filter( galaxy.model.User.table.c.email == '*****@*****.**' ).one()
self.twill_test_case.new_history()
latest_history = database_contexts.galaxy_context.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 latest_history is not None, "Problem retrieving latest_history from database"
if len( self.twill_test_case.get_history_as_data_list() ) > 0:
raise AssertionError("ToolTestCase.do_it failed")
return latest_history
def by_user( self, trans, user=None, include_deleted=False, only_deleted=False ):
"""
Get all the histories for a given user (defaulting to `trans.user`)
ordered by update time and filtered on whether they've been deleted.
"""
# handle default and/or anonymous user (which still may not have a history yet)
user = user or trans.user
if not user:
current_history = trans.get_history()
return [ current_history ] if current_history else []
history_model = trans.model.History
query = ( trans.sa_session.query( history_model )
.filter( history_model.user == user )
.order_by( orm.desc( history_model.table.c.update_time ) ) )
if only_deleted:
query = query.filter( history_model.deleted == True )
elif not include_deleted:
query = query.filter( history_model.deleted == False )
return query.all()
def by_user( self, trans, user=None, include_deleted=False, only_deleted=False ):
"""
Get all the histories for a given user (defaulting to `trans.user`)
ordered by update time and filtered on whether they've been deleted.
"""
# handle default and/or anonymous user (which still may not have a history yet)
user = user or trans.user
if not user:
current_history = trans.get_history()
return [ current_history ] if current_history else []
history_model = trans.model.History
query = ( trans.sa_session.query( history_model )
.filter( history_model.user == user )
.order_by( orm.desc( history_model.table.c.update_time ) ) )
if only_deleted:
query = query.filter( history_model.deleted == True )
elif not include_deleted:
query = query.filter( history_model.deleted == False )
return query.all()
def new_history(self):
# Start with a new history
self.twill_test_case.logout()
self.twill_test_case.login(email='*****@*****.**')
admin_user = database_contexts.galaxy_context.query(
galaxy.model.User).filter(
galaxy.model.User.table.c.email == '*****@*****.**').one()
self.twill_test_case.new_history()
latest_history = database_contexts.galaxy_context.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 latest_history is not None, "Problem retrieving latest_history from database"
if len(
self.twill_test_case.get_hids_in_history(
self.twill_test_case.get_latest_history()['id'])) > 0:
raise AssertionError(
"ToolTestCase.do_it failed to create a new empty history")
return latest_history
def index(self, trans, deleted='False', **kwd):
"""
GET /api/histories
GET /api/histories/deleted
Displays a collection (list) of histories.
"""
#TODO: query (by name, date, etc.)
rval = []
deleted = string_as_bool(deleted)
try:
if trans.user:
query = trans.sa_session.query(
trans.app.model.History
).filter_by(user=trans.user, deleted=deleted).order_by(
desc(trans.app.model.History.table.c.update_time)).all()
for history in query:
item = history.get_api_value(
value_mapper={'id': trans.security.encode_id})
item['url'] = url_for('history',
id=trans.security.encode_id(
history.id))
rval.append(item)
elif trans.galaxy_session.current_history:
#No user, this must be session authentication with an anonymous user.
history = trans.galaxy_session.current_history
item = history.get_api_value(
value_mapper={'id': trans.security.encode_id})
item['url'] = url_for('history',
id=trans.security.encode_id(history.id))
rval.append(item)
except Exception, e:
rval = "Error in history API"
log.error(rval + ": %s" % str(e))
trans.response.status = 500