class UserMember(Member):
relation = "%s/user" % RELATION_BASE_URL
title = attribute_alias('username')
label = attribute_alias('username')
username = terminal_attribute(str, 'username')
user_preferenceses = collection_attribute(IUserPreferences,
'user_preferenceses')
directory_user_id = terminal_attribute(str, 'directory_user_id')
class SpeciesMember(Member):
relation = 'http://plantscribe.org/relations/species'
title = attribute_alias('species_name')
species_name = terminal_attribute(str, 'species_name')
genus_name = terminal_attribute(str, 'genus_name')
cultivar = terminal_attribute(str, 'cultivar')
author = terminal_attribute(str, 'author')
class RackSpecsMember(Member):
relation = "%s/rack-specs" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
shape = member_attribute(IRackShape, 'shape')
manufacturer = member_attribute(IOrganization, 'manufacturer')
has_tubes = terminal_attribute(bool, 'has_tubes')
class BarcodePrintJobMember(Member):
relation = "%s/barcode" % RELATION_BASE_URL
title = attribute_alias('labels')
barcodes = terminal_attribute(str, 'barcodes')
labels = terminal_attribute(str, 'labels')
printer = terminal_attribute(str, 'printer')
type = terminal_attribute(str, 'type')
class ExperimentDesignRackMember(Member):
relation = "%s/experiment-design-rack" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
rack_shape = member_attribute(IRackShape, 'rack_layout.shape')
rack_layout = member_attribute(IRackLayout, 'rack_layout')
tags = collection_attribute(ITag, 'tags')
class MoleculeTypeMember(Member):
relation = "%s/molecule-type" % RELATION_BASE_URL
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
description = terminal_attribute(str, 'description')
thaw_time = terminal_attribute(float, 'thaw_time')
modifications = collection_attribute(IChemicalStructure, 'modifications')
class ProjectMember(Member):
relation = "%s/project" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
creation_date = terminal_attribute(datetime, 'creation_date')
leader = member_attribute(IUser, 'leader')
customer = member_attribute(IOrganization, 'customer')
subprojects = collection_attribute(ISubproject, 'subprojects')
class MyEntityParentMember(Member):
relation = 'http://test.org/myentity-parent'
# String terminal.
text = terminal_attribute(str, 'text')
# String terminal with different name in entity.
text_rc = terminal_attribute(str, 'text_ent')
#
text_alias = attribute_alias('text')
class ChemicalStructureMember(Member):
relation = "%s/chemical-structure" % RELATION_BASE_URL
molecule_designs = collection_attribute(IMoleculeDesign,
'molecule_designs')
structure_type = member_attribute(IChemicalStructureType, 'structure_type')
representation = terminal_attribute(str, 'representation')
structure_type_id = terminal_attribute(str, 'structure_type_id')
title = attribute_alias('representation')
class ContainerSpecsMember(Member):
relation = "%s/container-specs" % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
description = terminal_attribute(str, 'description')
max_volume = terminal_attribute(float, 'max_volume')
dead_volume = terminal_attribute(float, 'dead_volume')
manufacturer = member_attribute(IOrganization, 'manufacturer')
class SiteMember(Member):
relation = 'http://plantscribe.org/relations/site'
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
incidences = collection_attribute(IIncidence,
backref='site',
is_nested=True)
project = member_attribute(IProject, 'project')
class SpeciesMember(Member):
relation = "%s/species" % RELATION_BASE_URL
title = attribute_alias('common_name')
genus_name = terminal_attribute(str, 'genus_name')
species_name = terminal_attribute(str, 'species_name')
common_name = terminal_attribute(str, 'common_name')
acronym = terminal_attribute(str, 'acronym')
ncbi_tax_id = terminal_attribute(int, 'ncbi_tax_id')
class RackShapeMember(Member):
relation = "%s/rack-shape" % RELATION_BASE_URL
id = terminal_attribute(str, 'id') # rack shape IDs are *strings*.
name = terminal_attribute(str, 'name')
label = terminal_attribute(str, 'label')
number_rows = terminal_attribute(int, 'number_rows')
number_columns = terminal_attribute(int, 'number_columns')
title = attribute_alias('label')
class DeviceTypeMember(Member):
relation = "%s/device-type" % RELATION_BASE_URL
title = attribute_alias('label')
name = terminal_attribute(str, 'name')
label = terminal_attribute(str, 'label')
devices = collection_attribute(IDevice, 'devices', backref='type')
def update(self, member):
super(DeviceTypeMember, self).update(member)
self.get_entity().name = member.get_entity().name
self.label = member.label
class ExperimentMember(Member):
relation = '%s/experiment' % RELATION_BASE_URL
title = attribute_alias('label')
label = terminal_attribute(str, 'label')
source_rack = member_attribute(IRack, 'source_rack')
experiment_design = member_attribute(IExperimentDesign,
'experiment_design')
experiment_racks = collection_attribute(IExperimentRack,
'experiment_racks')
experiment_job = member_attribute(IExperimentJob, 'job')
experiment_metadata_type = \
member_attribute(IExperimentMetadataType,
'experiment_design.experiment_metadata.experiment_metadata_type')
def get_writer(self):
return get_writer(self.get_entity())
class GeneMember(Member):
relation = "%s/gene" % RELATION_BASE_URL
title = attribute_alias('locus_name')
accession = terminal_attribute(str, 'accession')
locus_name = terminal_attribute(str, 'locus_name')
# nice_name = terminal_attribute('nice_name')
species = member_attribute(ISpecies, 'species')
molecule_designs = \
collection_attribute(IMoleculeDesign,
'molecule_designs',
cardinality=CARDINALITIES.MANYTOMANY)
molecule_design_pools = \
collection_attribute(IMoleculeDesignPool,
'molecule_design_pools',
cardinality=CARDINALITIES.MANYTOMANY)
class StockInfoMember(Member):
relation = "%s/stock-info" % RELATION_BASE_URL
title = attribute_alias('id')
id = terminal_attribute(str, 'id') # stock info IDs are *strings*.
# FIXME: This should be called molecule_design_pool_id in the entity
molecule_design_pool_id = terminal_attribute(int,
'molecule_design_set_id')
total_tubes = terminal_attribute(int, 'total_tubes')
total_volume = terminal_attribute(float, 'total_volume')
maximum_volume = terminal_attribute(float, 'maximum_volume')
minimum_volume = terminal_attribute(float, 'minimum_volume')
concentration = terminal_attribute(float, 'concentration')
molecule_type = member_attribute(IMoleculeType, 'molecule_type')
molecule_design_pool = member_attribute(IMoleculeDesignPool,
'molecule_design_pool')
genes = collection_attribute(IGene, 'genes',
cardinality=CARDINALITIES.MANYTOMANY)
class IsoMember(Member):
relation = "%s/iso" % RELATION_BASE_URL
title = attribute_alias('label')
iso_type = terminal_attribute(str, 'label')
label = terminal_attribute(str, 'label')
status = terminal_attribute(str, 'status')
rack_layout = member_attribute(IRackLayout, 'rack_layout')
iso_job = member_attribute(IIsoJob, 'iso_job')
number_stock_racks = terminal_attribute(int, 'number_stock_racks')
molecule_design_pool_set = member_attribute(IMoleculeDesignPoolSet,
'molecule_design_pool_set')
optimizer_excluded_racks = terminal_attribute(str,
'optimizer_excluded_racks')
optimizer_requested_tubes = terminal_attribute(
str, 'optimizer_requested_tubes')
preparation_plates = collection_attribute(IPlate, 'preparation_plates')
aliquot_plates = collection_attribute(IPlate, 'aliquot_plates')
stock_racks = collection_attribute(IStockRack, 'stock_racks')
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
raise SyntaxError('Should not get here.')
else:
Member.update(self, data)
class ChemicalStructureTypeMember(Member):
relation = "%s/chemical-structure-type" % RELATION_BASE_URL
name = terminal_attribute(str, 'name')
label = terminal_attribute(str, 'label')
molecule_types = collection_attribute(IMoleculeType, 'molecule_types')
title = attribute_alias('label')
class LocationTypeMember(Member):
relation = "%s/location-type" % RELATION_BASE_URL
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
class ExperimentMetadataTypeMember(Member):
relation = '%s/experiment-metadata-type' % RELATION_BASE_URL
title = attribute_alias('display_name')
display_name = terminal_attribute(str, 'display_name')
class ExperimentMetadataMember(Member):
relation = '%s/experiment-metadata' % RELATION_BASE_URL
label = terminal_attribute(str, 'label')
title = attribute_alias('label')
ticket_number = terminal_attribute(int, 'ticket_number')
subproject = member_attribute(ISubproject, 'subproject')
number_replicates = terminal_attribute(int, 'number_replicates')
molecule_design_pool_set = member_attribute(IMoleculeDesignPoolSet,
'molecule_design_pool_set')
experiment_design = member_attribute(IExperimentDesign,
'experiment_design')
iso_request = member_attribute(ILabIsoRequest, 'lab_iso_request')
creation_date = terminal_attribute(datetime, 'creation_date')
experiment_metadata_type = member_attribute(IExperimentMetadataType,
'experiment_metadata_type')
def __getitem__(self, name):
if name == 'tags':
tags_dict = {}
design_racks = self.__get_design_racks()
for rack in design_racks:
for tp in rack.rack_layout.tagged_rack_position_sets:
for tag in tp.tags:
tags_dict[tag.get_entity().slug] = tag
tag_coll = get_root_collection(ITag)
tag_coll.filter = cntd(id=[tag.id for tag in tags_dict.values()])
result = tag_coll
elif name == 'experiment-design-racks':
result = self.__get_design_racks()
else:
result = Member.__getitem__(self, name)
return result
@classmethod
def create_from_entity(cls, entity):
if entity.ticket_number is None:
# Create a new ticket and attach the ticket number.
user = get_current_user()
ticket_creator = \
IsoRequestTicketCreator(requester=user,
experiment_metadata=entity)
entity.ticket_number = \
cls.__run_trac_tool(ticket_creator,
'Could not update the ticket: %s.')
return cls(entity)
def update(self, data):
if IDataElement.providedBy(data): # pylint: disable=E1101
# FIXME: This really should be a PATCH operation.
prx = DataElementAttributeProxy(data)
self_entity = self.get_entity()
changed_num_reps = prx.number_replicates != self.number_replicates
emt_id = prx.experiment_metadata_type.get('id')
changed_em_type = emt_id != self.experiment_metadata_type.id
if changed_em_type or changed_num_reps:
if changed_num_reps:
self_entity.number_replicates = prx.number_replicates
if changed_em_type:
self_entity.experiment_metadata_type = \
get_experiment_metadata_type(emt_id)
if not self_entity.experiment_design is None:
# invalidate data to force a fresh upload of the XLS file
self_entity.experiment_design.experiment_design_racks = []
self_entity.experiment_design.worklist_series = None
if not self_entity.lab_iso_request is None:
shape = self_entity.lab_iso_request.rack_layout.shape
new_layout = RackLayout(shape=shape)
self_entity.lab_iso_request.rack_layout = new_layout
self_entity.lab_iso_request.owner = ''
changed_sp = self_entity.subproject.id != prx.subproject.get('id')
if changed_sp:
new_sp = \
url_to_resource(prx.subproject.get('href')).get_entity()
self_entity.subproject = new_sp
self_entity.label = prx.label
# Perform appropriate Trac updates.
if not self_entity.lab_iso_request is None:
if self.iso_request.owner == STOCKMANAGEMENT_USER:
ticket_activator = IsoRequestTicketActivator(
experiment_metadata=self_entity)
self.__run_trac_tool(ticket_activator,
'Could not update the ticket: %s.')
else:
if changed_em_type or changed_num_reps:
trac_updater = IsoRequestTicketDescriptionRemover(
experiment_metadata=self_entity,
changed_num_replicates=changed_num_reps,
changed_em_type=changed_em_type)
else:
url = 'http://thelma/public//LOUICe.html#' \
+ self.path
iso_url = 'http://thelma/public//LOUICe.html#' \
+ self.iso_request.path
trac_updater = IsoRequestTicketDescriptionUpdater(
experiment_metadata=self_entity,
experiment_metadata_link=url,
iso_request_link=iso_url)
self.__run_trac_tool(trac_updater,
'Could not update the ticket: %s.')
else:
Member.update(self, data)
@classmethod
def __run_trac_tool(cls, tool, error_msg_text):
tool.run()
if not tool.transaction_completed():
exc_msg = str(tool.get_messages(logging_level=logging.ERROR))
raise HTTPBadRequest(error_msg_text % exc_msg).exception
return tool.return_value
def __get_design_racks(self):
if self.experiment_design is not None:
design_racks = self.experiment_design.experiment_design_racks
else: # order only type
design_racks = []
return design_racks
class CustomerMember(Member):
relation = 'http://plantscribe.org/relations/customer'
title = attribute_alias('last_name')
first_name = terminal_attribute(str, 'first_name')
last_name = terminal_attribute(str, 'last_name')
projects = collection_attribute(IProject, backref='customer')
class OrganizationMember(Member):
relation = "%s/organization" % RELATION_BASE_URL
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
class ItemStatusMember(Member):
id = terminal_attribute(str, 'id') # IDs are strings for item status
relation = "%s/item-status" % RELATION_BASE_URL
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
description = terminal_attribute(str, 'description')
class RackPositionMember(Member):
relation = "%s/rack-position" % RELATION_BASE_URL
label = terminal_attribute(str, 'label')
row_index = terminal_attribute(int, 'row_index')
column_index = terminal_attribute(int, 'column_index')
title = attribute_alias('label')
class ProjectMember(Member):
relation = 'http://plantscribe.org/relations/project'
title = attribute_alias('name')
name = terminal_attribute(str, 'name')
customer = member_attribute(ICustomer, 'customer')
sites = collection_attribute(ISite, backref='project', is_nested=True)
class UserPreferencesMember(Member):
relation = "%s/user-preferences" % RELATION_BASE_URL
title = attribute_alias('app_name')
label = attribute_alias('app_name')
app_name = terminal_attribute(str, 'app_name')
preferences = terminal_attribute(str, 'preferences')
