def get_clipboard_items(self, _user_key):
result = self.clipboard_dao.get_clipboard_items(_user_key)
# convert to domain object
result.items = convert_models(result.items, EMAPAClipboardItem)
return result
def get_valid_markers_by_symbol(self, symbol):
"""
Retrieve list of valid markers by symbol
"""
search_query = SearchQuery()
search_query.set_param('symbol', symbol)
# restrict to official and withdrawn
search_query.set_param('_marker_status_keys', [1,2])
# only search mouse
search_query.set_param('_organism_keys', [1])
search_results = self.marker_dao.search(search_query)
markers = search_results.items
batchLoadAttribute(markers, 'current_markers')
batchLoadAttribute(markers, 'featuretype_vocterms')
ValidMarkerSortHelper().sort(markers)
# convert db models to domain objects
search_results.items = convert_models(markers, SmallMarker)
return search_results
def search(self, search_query):
search_result = self.mgitype_dao.search(search_query)
# convert results to domain objects
search_result.items = convert_models(search_result.items, MGITypeDomain)
return search_result
def get_by_jnumber(self, jnumber):
"""
Retrieve a single reference by jnumber (without J: prefix)
returns SmallReference
"""
jnum_id = parse_jnumber(jnumber)
reference = self.get_by_jnum_id(jnum_id)
return convert_models(reference, SmallReference)
def get_by_key(self, _index_key):
gxdindex_record = self.gxdindex_dao.get_by_key(_index_key)
if not gxdindex_record:
raise NotFoundError("No GxdIndexRecord for _index_key=%d" % _index_key)
# convert to domain object
return convert_models(gxdindex_record, IndexRecordDomain)
def delete(self, _user_key):
"""
Delete MGIUser object
"""
user = self.user_dao.get_by_key(_user_key)
if not user:
raise NotFoundError("No MGIUser for _user_key=%d" % _user_key)
self.user_dao.delete(user)
return convert_models(user, UserDomain)
def search(self, search_query):
"""
Search using a SearchQuery
"""
search_result = self.user_dao.search(search_query)
# convert results to domain objects
users = search_result.items
search_result.items = convert_models(users, UserDomain)
return search_result
def search(self, search_query):
"""
Search using a SearchQuery
"""
search_results = self.gxdindex_dao.search(search_query)
# load data to be displayed
gxdindex_records = search_results.items
# convert results to gxd index domain objects
search_results.items = convert_models(gxdindex_records, IndexRecordSearchResultDomain)
return search_results
def update(self, key, args):
"""
update user with and argument object
"""
user = self.user_dao.get_by_key(key)
if not user:
raise NotFoundError("No MGIUser for _user_key=%d" % key)
user.login = args['login']
user.name = args['name']
user._usertype_key = args['_usertype_key']
user._userstatus_key = args['_userstatus_key']
#user._modifiedby_key = current_user._modifiedby_key
self.user_dao.update(user)
return convert_models(user, UserDomain)
def create(self, args):
"""
Create user with an argument object
"""
user = MGIUser()
# get the next primary key
user._user_key = self.user_dao.get_next_key()
# set MGIUser values
user.login = args['login']
user.name = args['name']
user._usertype_key = args['_usertype_key']
user._userstatus_key = args['_userstatus_key']
#user._createdby_key = current_user._user_key
#user._modifiedby_key = current_user._modifiedby_key
self.user_dao.create(user)
return convert_models(user, UserDomain)
def update(self, key, indexrecord_domain, current_user):
"""
Update GxdIndexRecord with and argument object
"""
gxdindex_record = self.gxdindex_dao.get_by_key(key)
if not gxdindex_record:
raise NotFoundError("No GxdIndexRecord for _index_key=%d" % key)
self.validate_input(indexrecord_domain)
# set GxdIndexRecord values
gxdindex_record._refs_key = indexrecord_domain._refs_key
gxdindex_record._marker_key = indexrecord_domain._marker_key
gxdindex_record._priority_key = indexrecord_domain._priority_key
gxdindex_record._conditionalmutants_key = indexrecord_domain._conditionalmutants_key
gxdindex_record.comments = indexrecord_domain.comments
gxdindex_record._modifiedby_key = current_user._user_key
# TODO(kstone): get SQLAlchemy to do this automatically
gxdindex_record.modification_date = datetime.now()
gxdindex_record.indexstages = []
for indexstage_input in indexrecord_domain.indexstages:
indexstage = GxdIndexStage()
indexstage._index_key = gxdindex_record._index_key
indexstage._indexassay_key = indexstage_input._indexassay_key
indexstage._stageid_key = indexstage_input._stageid_key
indexstage._createdby_key = current_user._user_key
indexstage._modifiedby_key = current_user._user_key
gxdindex_record.indexstages.append(indexstage)
self.gxdindex_dao.update(gxdindex_record)
return convert_models(gxdindex_record, IndexRecordDomain)
def create(self, indexrecord_domain, current_user):
"""
Create GxdIndexRecord with an argument object
"""
self.validate_input(indexrecord_domain)
gxdindex_record = GxdIndexRecord()
# get the next primary key
gxdindex_record._index_key = self.gxdindex_dao.get_next_key()
# set GxdIndexRecord values
gxdindex_record._refs_key = indexrecord_domain._refs_key
gxdindex_record._marker_key = indexrecord_domain._marker_key
gxdindex_record._priority_key = indexrecord_domain._priority_key
gxdindex_record._conditionalmutants_key = indexrecord_domain._conditionalmutants_key
gxdindex_record.comments = indexrecord_domain.comments
gxdindex_record._createdby_key = current_user._user_key
gxdindex_record._modifiedby_key = current_user._user_key
if indexrecord_domain.indexstages:
# add the GxdIndexStage(s)
gxdindex_record.indexstages = []
for indexstage_input in indexrecord_domain.indexstages:
indexstage = GxdIndexStage()
indexstage._index_key = gxdindex_record._index_key
indexstage._indexassay_key = indexstage_input._indexassay_key
indexstage._stageid_key = indexstage_input._stageid_key
indexstage._createdby_key = current_user._user_key
indexstage._modifiedby_key = current_user._user_key
gxdindex_record.indexstages.append(indexstage)
self.gxdindex_dao.create(gxdindex_record)
return convert_models(gxdindex_record, IndexRecordDomain)
def current_user(self):
return convert_models(current_user, UserDomain)
def get_by_key(self, _user_key):
user = self.user_dao.get_by_key(_user_key)
if not user:
raise NotFoundError("No MGIUser for _user_key=%d" % _user_key)
return convert_models(user, UserDomain)
