Index

A

ACQUISITION_PARAMETER_DATA_FILE (data_set_manager.models.Node attribute) add_child() (data_set_manager.models.Node method) ALL_FIELDS (data_set_manager.models.Attribute attribute) AnnotatedNode (class in data_set_manager.models) AnnotatedNode.DoesNotExist AnnotatedNode.MultipleObjectsReturned annotatednode_set (data_set_manager.models.Assay attribute) (data_set_manager.models.Attribute attribute) (data_set_manager.models.Node attribute) (data_set_manager.models.Study attribute) AnnotatedNodeRegistry (class in data_set_manager.models) AnnotatedNodeRegistry.DoesNotExist AnnotatedNodeRegistry.MultipleObjectsReturned annotatednoderegistry_set (data_set_manager.models.Assay attribute) (data_set_manager.models.Study attribute) ARRAY_DATA_FILE (data_set_manager.models.Node attribute) ARRAY_DATA_MATRIX_FILE (data_set_manager.models.Node attribute) ARRAY_DESIGN_FILE (data_set_manager.models.Node attribute) ARRAY_DESIGN_FILE_REF (data_set_manager.models.Node attribute) Assay (class in data_set_manager.models) assay (data_set_manager.models.AnnotatedNode attribute) (data_set_manager.models.AnnotatedNodeRegistry attribute) (data_set_manager.models.AttributeDefinition attribute) (data_set_manager.models.AttributeOrder attribute) (data_set_manager.models.Node attribute) ASSAY (data_set_manager.models.Node attribute)

Assay.DoesNotExist Assay.MultipleObjectsReturned assay_nodes() (data_set_manager.models.Study method) assay_set (data_set_manager.models.Study attribute) ASSAYS (data_set_manager.models.Node attribute) Attribute (class in data_set_manager.models) attribute (data_set_manager.models.AnnotatedNode attribute) Attribute.DoesNotExist Attribute.MultipleObjectsReturned attribute_set (data_set_manager.models.Node attribute) AttributeDefinition (class in data_set_manager.models) AttributeDefinition.DoesNotExist AttributeDefinition.MultipleObjectsReturned attributedefinition_set (data_set_manager.models.Assay attribute) (data_set_manager.models.Study attribute) AttributeOrder (class in data_set_manager.models) AttributeOrder.DoesNotExist AttributeOrder.MultipleObjectsReturned attributeorder_set (data_set_manager.models.Assay attribute) (data_set_manager.models.Study attribute)

C

CHARACTERISTICS (data_set_manager.models.Attribute attribute) children (data_set_manager.models.Node attribute) children_set (data_set_manager.models.Node attribute) collection (data_set_manager.models.Contact attribute) (data_set_manager.models.Publication attribute) COMMENT (data_set_manager.models.Attribute attribute)

Contact (class in data_set_manager.models) Contact.DoesNotExist Contact.MultipleObjectsReturned contact_set (data_set_manager.models.NodeCollection attribute)

D

data_set_manager.models (module) data_set_manager.tests (module) DATA_TRANSFORMATION (data_set_manager.models.Node attribute) delete_datafile() (file_store.models.FileStoreItem method) DERIVED_ARRAY_DATA_FILE (data_set_manager.models.Node attribute) DERIVED_ARRAY_DATA_MATRIX_FILE (data_set_manager.models.Node attribute) DERIVED_DATA_FILE (data_set_manager.models.Node attribute)

DERIVED_SPECTRAL_DATA_FILE (data_set_manager.models.Node attribute) Design (class in data_set_manager.models) Design.DoesNotExist Design.MultipleObjectsReturned design_set (data_set_manager.models.Study attribute) DownloadError

E

exists() (file_store.models.SymlinkedFileSystemStorage method)

EXTRACT (data_set_manager.models.Node attribute)

F

Factor (class in data_set_manager.models) Factor.DoesNotExist Factor.MultipleObjectsReturned factor_set (data_set_manager.models.Study attribute) FACTOR_VALUE (data_set_manager.models.Attribute attribute) file_path() (in module file_store.models) file_server.urls (module) file_store.models (module) file_store.tasks (module) file_store.tests (module) file_store.views (module)

FILES (data_set_manager.models.Node attribute) FileStoreCache (class in file_store.models) FileStoreItem (class in file_store.models) FileStoreItem.DoesNotExist FileStoreItem.MultipleObjectsReturned FileStoreItemManagerTest (class in file_store.tests) FileStoreItemTest (class in file_store.tests) FileStoreModuleTest (class in file_store.tests) filetype (file_store.models.FileStoreItem attribute) FREE_INDUCTION_DECAY_DATA_FILE (data_set_manager.models.Node attribute)

G

GEL_ELECTROPHORESIS_ASSAY (data_set_manager.models.Node attribute) genome_builds_for_files() (data_set_manager.models.NodeManager method) get_absolute_path() (file_store.models.FileStoreItem method) get_assay_count() (data_set_manager.models.Investigation method) get_description() (data_set_manager.models.Investigation method) get_extension_from_path() (in module file_store.models) get_file_extension() (file_store.models.FileStoreItem method) (in module file_store.models) get_file_object() (file_store.models.FileStoreItem method) (in module file_store.models) get_file_size() (file_store.models.FileStoreItem method) (in module file_store.models) get_filetype() (file_store.models.FileStoreItem method)

get_filetype_display() (file_store.models.FileStoreItem method) get_full_url() (file_store.models.FileStoreItem method) get_identifier() (data_set_manager.models.Investigation method) get_next_by_creation_date() (data_set_manager.models.AnnotatedNodeRegistry method) get_next_by_modification_date() (data_set_manager.models.AnnotatedNodeRegistry method) get_previous_by_creation_date() (data_set_manager.models.AnnotatedNodeRegistry method) get_previous_by_modification_date() (data_set_manager.models.AnnotatedNodeRegistry method) get_study_count() (data_set_manager.models.Investigation method) get_temp_dir() (in module file_store.models) get_title() (data_set_manager.models.Investigation method)

H

HYBRIDIZATION_ASSAY (data_set_manager.models.Node attribute)

I

IMAGE_FILE (data_set_manager.models.Node attribute) initialize_attribute_order() (in module data_set_manager.models) Investigation (class in data_set_manager.models) investigation (data_set_manager.models.NodeCollection attribute) (data_set_manager.models.Ontology attribute) (data_set_manager.models.Study attribute) Investigation.DoesNotExist

Investigation.MultipleObjectsReturned is_attribute() (data_set_manager.models.Attribute method) is_local() (file_store.models.FileStoreItem method) (in module file_store.models) is_permanent() (in module file_store.models) is_symlinked() (file_store.models.FileStoreItem method)

L

LABEL (data_set_manager.models.Attribute attribute) LABELED_EXTRACT (data_set_manager.models.Node attribute)

logger (in module data_set_manager.models)

M

MATERIAL_TYPE (data_set_manager.models.Attribute attribute)

MS_ASSAY (data_set_manager.models.Node attribute)

N

NMR_ASSAY (data_set_manager.models.Node attribute) Node (class in data_set_manager.models) node (data_set_manager.models.AnnotatedNode attribute) (data_set_manager.models.Attribute attribute) (data_set_manager.models.ProtocolReference attribute) Node.DoesNotExist Node.MultipleObjectsReturned node_set (data_set_manager.models.Assay attribute) (data_set_manager.models.Study attribute) NodeCollection (class in data_set_manager.models)

NodeCollection.DoesNotExist NodeCollection.MultipleObjectsReturned nodecollection_ptr (data_set_manager.models.Investigation attribute) (data_set_manager.models.Study attribute) NodeManager (class in data_set_manager.models) NON_ONTOLOGY_FIELDS (data_set_manager.models.Attribute attribute) NORMALIZATION (data_set_manager.models.Node attribute) normalize_date() (data_set_manager.models.NodeCollection method)

O

objects (data_set_manager.models.AnnotatedNode attribute) (data_set_manager.models.AnnotatedNodeRegistry attribute) (data_set_manager.models.Assay attribute) (data_set_manager.models.Attribute attribute) (data_set_manager.models.AttributeDefinition attribute) (data_set_manager.models.AttributeOrder attribute) (data_set_manager.models.Contact attribute) (data_set_manager.models.Design attribute) (data_set_manager.models.Factor attribute) (data_set_manager.models.Investigation attribute) (data_set_manager.models.Node attribute) (data_set_manager.models.NodeCollection attribute) (data_set_manager.models.Ontology attribute) (data_set_manager.models.Protocol attribute) (data_set_manager.models.ProtocolComponent attribute) (data_set_manager.models.ProtocolParameter attribute) (data_set_manager.models.ProtocolReference attribute) (data_set_manager.models.ProtocolReferenceParameter attribute) (data_set_manager.models.Publication attribute) (data_set_manager.models.Study attribute) (file_store.models.FileStoreItem attribute) Ontology (class in data_set_manager.models) Ontology.DoesNotExist

Ontology.MultipleObjectsReturned ontology_set (data_set_manager.models.Investigation attribute)

P

parents (data_set_manager.models.Node attribute) parents_set (data_set_manager.models.Node attribute) PEPTIDE_ASSIGNMENT_FILE (data_set_manager.models.Node attribute) pre_isarchive_file (data_set_manager.models.Investigation attribute) PROTEIN_ASSIGNMENT_FILE (data_set_manager.models.Node attribute) Protocol (class in data_set_manager.models) protocol (data_set_manager.models.ProtocolComponent attribute) (data_set_manager.models.ProtocolParameter attribute) (data_set_manager.models.ProtocolReference attribute) Protocol.DoesNotExist Protocol.MultipleObjectsReturned protocol_reference (data_set_manager.models.ProtocolReferenceParameter attribute) protocol_set (data_set_manager.models.Study attribute) ProtocolComponent (class in data_set_manager.models) ProtocolComponent.DoesNotExist ProtocolComponent.MultipleObjectsReturned protocolcomponent_set (data_set_manager.models.Protocol attribute) (data_set_manager.models.Study attribute) ProtocolParameter (class in data_set_manager.models)

ProtocolParameter.DoesNotExist ProtocolParameter.MultipleObjectsReturned protocolparameter_set (data_set_manager.models.Protocol attribute) (data_set_manager.models.Study attribute) ProtocolReference (class in data_set_manager.models) ProtocolReference.DoesNotExist ProtocolReference.MultipleObjectsReturned protocolreference_set (data_set_manager.models.Node attribute) (data_set_manager.models.Protocol attribute) ProtocolReferenceParameter (class in data_set_manager.models) ProtocolReferenceParameter.DoesNotExist ProtocolReferenceParameter.MultipleObjectsReturned protocolreferenceparameter_set (data_set_manager.models.ProtocolReference attribute) PTM_ASSIGNMENT_FILE (data_set_manager.models.Node attribute) Publication (class in data_set_manager.models) Publication.DoesNotExist Publication.MultipleObjectsReturned publication_set (data_set_manager.models.NodeCollection attribute)

R

RAW_DATA_FILE (data_set_manager.models.Node attribute) RAW_SPECTRAL_DATA_FILE (data_set_manager.models.Node attribute)

rename_datafile() (file_store.models.FileStoreItem method)

S

SAMPLE (data_set_manager.models.Node attribute) SCAN (data_set_manager.models.Node attribute) set_filetype() (file_store.models.FileStoreItem method) setUp() (file_store.tests.FileStoreItemManagerTest method) (file_store.tests.FileStoreItemTest method) (file_store.tests.FileStoreModuleTest method) sharename (file_store.models.FileStoreItem attribute) SimpleTest (class in data_set_manager.tests) SOURCE (data_set_manager.models.Node attribute) source (file_store.models.FileStoreItem attribute)

SPOT_PICKING_FILE (data_set_manager.models.Node attribute) Study (class in data_set_manager.models) study (data_set_manager.models.AnnotatedNode attribute) (data_set_manager.models.AnnotatedNodeRegistry attribute) (data_set_manager.models.Assay attribute) (data_set_manager.models.AttributeDefinition attribute) (data_set_manager.models.AttributeOrder attribute) (data_set_manager.models.Design attribute) (data_set_manager.models.Factor attribute) (data_set_manager.models.Node attribute) (data_set_manager.models.NodeCollection attribute) (data_set_manager.models.Protocol attribute) (data_set_manager.models.ProtocolComponent attribute) (data_set_manager.models.ProtocolParameter attribute) Study.DoesNotExist Study.MultipleObjectsReturned study_set (data_set_manager.models.Investigation attribute) symlink_datafile() (file_store.models.FileStoreItem method) SymlinkedFileSystemStorage (class in file_store.models)

T

test_basic_addition() (data_set_manager.tests.SimpleTest method) test_empty_file_source_map_translation() (file_store.tests.FileStoreItemManagerTest method) test_file_path() (file_store.tests.FileStoreModuleTest method) test_file_path_parens() (file_store.tests.FileStoreModuleTest method) test_file_source_map_translation() (file_store.tests.FileStoreItemManagerTest method) test_get_file_extension() (file_store.tests.FileStoreItemTest method) test_get_file_object() (file_store.tests.FileStoreModuleTest method) test_get_file_object_2() (file_store.tests.FileStoreModuleTest method)

test_get_file_type() (file_store.tests.FileStoreItemTest method) test_get_full_url_remote_file() (file_store.tests.FileStoreItemTest method) test_get_temp_dir() (file_store.tests.FileStoreModuleTest method) test_set_file_type_automatically() (file_store.tests.FileStoreItemTest method) test_set_unkown_file_type() (file_store.tests.FileStoreItemTest method) test_set_valid_file_type() (file_store.tests.FileStoreItemTest method) TYPES (data_set_manager.models.Attribute attribute) (data_set_manager.models.Node attribute)

U

uuid (file_store.models.FileStoreItem attribute)