data_set_manager Package

admin Module

models Module

Created on May 10, 2012

@author: nils

class data_set_manager.models.AnnotatedNode(*args, **kwargs)

Bases: django.db.models.base.Model

AnnotatedNode(id, node_id, attribute_id, study_id, assay_id, node_uuid, node_file_uuid, node_type, node_name, attribute_type, attribute_subtype, attribute_value, attribute_value_unit, node_species, node_genome_build, node_analysis_uuid, node_subanalysis, node_workflow_output, is_annotation)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception AnnotatedNode.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

AnnotatedNode.assay

AnnotatedNode.attribute

AnnotatedNode.node

AnnotatedNode.objects = <django.db.models.manager.Manager object at 0x7f298be3b850>

AnnotatedNode.study

class data_set_manager.models.AnnotatedNodeRegistry(*args, **kwargs)

Bases: django.db.models.base.Model

AnnotatedNodeRegistry(id, study_id, assay_id, node_type, creation_date, modification_date)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception AnnotatedNodeRegistry.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

AnnotatedNodeRegistry.assay

AnnotatedNodeRegistry.get_next_by_creation_date(*moreargs, **morekwargs)

AnnotatedNodeRegistry.get_next_by_modification_date(*moreargs, **morekwargs)

AnnotatedNodeRegistry.get_previous_by_creation_date(*moreargs, **morekwargs)

AnnotatedNodeRegistry.get_previous_by_modification_date(*moreargs, **morekwargs)

AnnotatedNodeRegistry.objects = <django.db.models.manager.Manager object at 0x7f298be32bd0>

AnnotatedNodeRegistry.study

class data_set_manager.models.Assay(*args, **kwargs)

Bases: django.db.models.base.Model

Study Assay (ISA-Tab Spec 4.1.3.5)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Assay.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Assay.annotatednode_set

Assay.annotatednoderegistry_set

Assay.attributedefinition_set

Assay.attributeorder_set

Assay.node_set

Assay.objects = <django.db.models.manager.Manager object at 0x7f298bec8850>

Assay.study

class data_set_manager.models.Attribute(*args, **kwargs)

Bases: django.db.models.base.Model

Attribute(id, node_id, type, subtype, value, value_unit, value_accession, value_source)

ALL_FIELDS = ['id', 'type', 'subtype', 'value', 'value_unit', 'value_accession', 'value_source', 'node']

CHARACTERISTICS = 'Characteristics'

COMMENT = 'Comment'

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

Attribute.FACTOR_VALUE = 'Factor Value'

Attribute.LABEL = 'Label'

Attribute.MATERIAL_TYPE = 'Material Type'

exception Attribute.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Attribute.NON_ONTOLOGY_FIELDS = ['id', 'type', 'subtype', 'value', 'value_unit', 'node']

Attribute.TYPES = set(['Comment', 'Characteristics', 'Material Type', 'Factor Value', 'Label'])

Attribute.annotatednode_set

Attribute.is_attribute(string)

Attribute.node

Attribute.objects = <django.db.models.manager.Manager object at 0x7f298be27850>

class data_set_manager.models.AttributeDefinition(*args, **kwargs)

Bases: django.db.models.base.Model

AttributeDefinition(id, study_id, assay_id, type, subtype, value, definition, value_accession, value_source)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception AttributeDefinition.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

AttributeDefinition.assay

AttributeDefinition.objects = <django.db.models.manager.Manager object at 0x7f298be27ed0>

AttributeDefinition.study

class data_set_manager.models.AttributeOrder(*args, **kwargs)

Bases: django.db.models.base.Model

AttributeOrder(id, study_id, assay_id, solr_field, rank, is_exposed, is_facet, is_active, is_internal)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception AttributeOrder.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

AttributeOrder.assay

AttributeOrder.objects = <django.db.models.manager.Manager object at 0x7f298be32510>

AttributeOrder.study

class data_set_manager.models.Contact(*args, **kwargs)

Bases: django.db.models.base.Model

Investigation or Study Contact (ISA-Tab Spec 4.1.2.3, 4.1.3.7)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Contact.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Contact.collection

Contact.objects = <django.db.models.manager.Manager object at 0x7f298beb3b10>

class data_set_manager.models.Design(*args, **kwargs)

Bases: django.db.models.base.Model

Study Design Descriptor (ISA-Tab Spec 4.1.3.2)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Design.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Design.objects = <django.db.models.manager.Manager object at 0x7f298bebbd90>

Design.study

class data_set_manager.models.Factor(*args, **kwargs)

Bases: django.db.models.base.Model

Study Factor (ISA-Tab Spec 4.1.3.4)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Factor.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Factor.objects = <django.db.models.manager.Manager object at 0x7f298bec81d0>

Factor.study

class data_set_manager.models.Investigation(*args, **kwargs)

Bases: data_set_manager.models.NodeCollection

Investigation(id, uuid, identifier, title, description, submission_date, release_date, nodecollection_ptr_id, isarchive_file, pre_isarchive_file)

exception DoesNotExist

Bases: data_set_manager.models.DoesNotExist

exception Investigation.MultipleObjectsReturned

Bases: data_set_manager.models.MultipleObjectsReturned

Investigation.get_assay_count()

Investigation.get_description()

Investigation.get_identifier()

Investigation.get_study_count()

Investigation.get_title()

Investigation.nodecollection_ptr

Investigation.objects = <django.db.models.manager.Manager object at 0x7f298beb3f90>

Investigation.ontology_set

Investigation.pre_isarchive_file = None

easily retrieves the proper NodeCollection fields

Investigation.study_set

class data_set_manager.models.Node(*args, **kwargs)

Bases: django.db.models.base.Model

Node(id, uuid, study_id, assay_id, type, name, file_uuid, genome_build, species, is_annotation, analysis_uuid, subanalysis, workflow_output)

ACQUISITION_PARAMETER_DATA_FILE = 'Aquisition Parameter Data File'

ARRAY_DATA_FILE = 'Array Data File'

ARRAY_DATA_MATRIX_FILE = 'Array Data Matrix File'

ARRAY_DESIGN_FILE = 'Array Design File'

ARRAY_DESIGN_FILE_REF = 'Array Design File REF'

ASSAY = 'Assay Name'

ASSAYS = set(['Hybridization Assay Name', 'Gel Electrophoresis Assay Name', 'Assay Name', 'NMR Assay Name', 'MS Assay Name'])

DATA_TRANSFORMATION = 'Data Transformation Name'

DERIVED_ARRAY_DATA_FILE = 'Derived Array Data File'

DERIVED_ARRAY_DATA_MATRIX_FILE = 'Derived Array Data Matrix File'

DERIVED_DATA_FILE = 'Derived Data File'

DERIVED_SPECTRAL_DATA_FILE = 'Derived Spectral Data File'

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

Node.EXTRACT = 'Extract Name'

Node.FILES = set(['Array Data File', 'Protein Assignment File', 'Array Data Matrix File', 'Array Design File REF', 'Post Translational Modification Assignment File', 'Free Induction Decay Data File', 'Raw Spectral Data File', 'Spot Picking File', 'Derived Spectral Data File', 'Peptide Assignment File', 'Derived Array Data Matrix File', 'Array Design File', 'Aquisition Parameter Data File', 'Derived Data File', 'Raw Data File', 'Image File', 'Derived Array Data File'])

Node.FREE_INDUCTION_DECAY_DATA_FILE = 'Free Induction Decay Data File'

Node.GEL_ELECTROPHORESIS_ASSAY = 'Gel Electrophoresis Assay Name'

Node.HYBRIDIZATION_ASSAY = 'Hybridization Assay Name'

Node.IMAGE_FILE = 'Image File'

Node.LABELED_EXTRACT = 'Labeled Extract Name'

Node.MS_ASSAY = 'MS Assay Name'

exception Node.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Node.NMR_ASSAY = 'NMR Assay Name'

Node.NORMALIZATION = 'Normalization Name'

Node.PEPTIDE_ASSIGNMENT_FILE = 'Peptide Assignment File'

Node.PROTEIN_ASSIGNMENT_FILE = 'Protein Assignment File'

Node.PTM_ASSIGNMENT_FILE = 'Post Translational Modification Assignment File'

Node.RAW_DATA_FILE = 'Raw Data File'

Node.RAW_SPECTRAL_DATA_FILE = 'Raw Spectral Data File'

Node.SAMPLE = 'Sample Name'

Node.SCAN = 'Scan Name'

Node.SOURCE = 'Source Name'

Node.SPOT_PICKING_FILE = 'Spot Picking File'

Node.TYPES = set(['Derived Array Data File', 'Labeled Extract Name', 'Spot Picking File', 'Scan Name', 'Free Induction Decay Data File', 'Hybridization Assay Name', 'Derived Spectral Data File', 'Peptide Assignment File', 'Image File', 'Array Design File', 'Aquisition Parameter Data File', 'Derived Data File', 'Raw Data File', 'Data Transformation Name', 'Normalization Name', 'Extract Name', 'Protein Assignment File', 'Array Data File', 'Array Design File REF', 'Sample Name', 'MS Assay Name', 'NMR Assay Name', 'Raw Spectral Data File', 'Source Name', 'Array Data Matrix File', 'Derived Array Data Matrix File', 'Assay Name', 'Post Translational Modification Assignment File', 'Gel Electrophoresis Assay Name'])

Node.add_child(node)

Node.annotatednode_set

Node.assay

Node.attribute_set

Node.children

Node.children_set

Node.objects = <data_set_manager.models.NodeManager object at 0x7f298be12a90>

Node.parents

Node.parents_set

Node.protocolreference_set

Node.study

class data_set_manager.models.NodeCollection(*args, **kwargs)

Bases: django.db.models.base.Model

Base class for Investigation and Study

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception NodeCollection.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

NodeCollection.contact_set

NodeCollection.investigation

NodeCollection.normalize_date(dateString)

Normalizes date strings in dd/mm/yyyy format to yyyy-mm-dd.

Returns normalized date string if in expected unnormalized format or unnormalized date string.

NodeCollection.objects = <django.db.models.manager.Manager object at 0x7f298beb30d0>

NodeCollection.publication_set

NodeCollection.study

class data_set_manager.models.NodeManager

Bases: django.db.models.manager.Manager

genome_builds_for_files(file_uuids, default_fallback=True)

Returns a dictionary that groups file nodes based on their genome build information.

class data_set_manager.models.Ontology(*args, **kwargs)

Bases: django.db.models.base.Model

Ontology Source Reference (ISA-Tab Spec 4.1.1)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Ontology.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Ontology.investigation

Ontology.objects = <django.db.models.manager.Manager object at 0x7f298bebb410>

class data_set_manager.models.Protocol(*args, **kwargs)

Bases: django.db.models.base.Model

Study Protocol (ISA-Tab Spec 4.1.3.6)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Protocol.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Protocol.objects = <django.db.models.manager.Manager object at 0x7f298bec8f50>

Protocol.protocolcomponent_set

Protocol.protocolparameter_set

Protocol.protocolreference_set

Protocol.study

class data_set_manager.models.ProtocolComponent(*args, **kwargs)

Bases: django.db.models.base.Model

ProtocolComponent(id, study_id, protocol_id, name, type, type_accession, type_source)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception ProtocolComponent.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

ProtocolComponent.objects = <django.db.models.manager.Manager object at 0x7f298be12ad0>

ProtocolComponent.protocol

ProtocolComponent.study

class data_set_manager.models.ProtocolParameter(*args, **kwargs)

Bases: django.db.models.base.Model

ProtocolParameter(id, study_id, protocol_id, name, name_accession, name_source)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception ProtocolParameter.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

ProtocolParameter.objects = <django.db.models.manager.Manager object at 0x7f298be12510>

ProtocolParameter.protocol

ProtocolParameter.study

class data_set_manager.models.ProtocolReference(*args, **kwargs)

Bases: django.db.models.base.Model

ProtocolReference(id, node_id, protocol_id, performer, performer_uuid, date, comment)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception ProtocolReference.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

ProtocolReference.node

ProtocolReference.objects = <django.db.models.manager.Manager object at 0x7f298be3be50>

ProtocolReference.protocol

ProtocolReference.protocolreferenceparameter_set

class data_set_manager.models.ProtocolReferenceParameter(*args, **kwargs)

Bases: django.db.models.base.Model

ProtocolReferenceParameter(id, protocol_reference_id, name, value, value_unit, value_accession, value_source)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception ProtocolReferenceParameter.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

ProtocolReferenceParameter.objects = <django.db.models.manager.Manager object at 0x7f298be47410>

ProtocolReferenceParameter.protocol_reference

class data_set_manager.models.Publication(*args, **kwargs)

Bases: django.db.models.base.Model

Investigation or Study Publication (ISA-Tab Spec 4.1.2.2, 4.1.3.3)

exception DoesNotExist

Bases: django.core.exceptions.ObjectDoesNotExist

exception Publication.MultipleObjectsReturned

Bases: django.core.exceptions.MultipleObjectsReturned

Publication.collection

Publication.objects = <django.db.models.manager.Manager object at 0x7f298beb3510>

class data_set_manager.models.Study(*args, **kwargs)

Bases: data_set_manager.models.NodeCollection

Study(id, uuid, identifier, title, description, submission_date, release_date, nodecollection_ptr_id, investigation_id, file_name)

exception DoesNotExist

Bases: data_set_manager.models.DoesNotExist

exception Study.MultipleObjectsReturned

Bases: data_set_manager.models.MultipleObjectsReturned

Study.annotatednode_set

Study.annotatednoderegistry_set

Study.assay_nodes()

Study.assay_set

Study.attributedefinition_set

Study.attributeorder_set

Study.design_set

Study.factor_set

Study.investigation

Study.node_set

Study.nodecollection_ptr

Study.objects = <django.db.models.manager.Manager object at 0x7f298bebb9d0>

Study.protocol_set

Study.protocolcomponent_set

Study.protocolparameter_set

data_set_manager.models.initialize_attribute_order(study, assay)

Initializes the AttributeOrder table after all nodes for the given study and assay have been indexed by Solr.

Parameters:

• study (Study) – Study object to query for in AnnotatedNode.
• assay (Assay) – Assay object to query for in AnnotatedNode.

Returns:

Number of attributes that were indexed.

data_set_manager.models.logger = <celery.utils.log.SigSafeLogger object at 0x7f298be88d90>

General: - xyz_term = accession number of an ontology term - xyz_source = reference to the ontology where xyz_term originates (defined in the investigation)

tasks Module

tests Module

This file demonstrates writing tests using the unittest module. These will pass when you run “manage.py test”.

Replace this with more appropriate tests for your application.

class data_set_manager.tests.SimpleTest(methodName='runTest')

Bases: django.test.testcases.TestCase

test_basic_addition()

Tests that 1 + 1 always equals 2.

views Module