4.1.1.1. datanator.api package

4.1.1.1.1. Subpackages

• 4.1.1.1.1.1. datanator.api.lib package
  • 4.1.1.1.1.1.1. Subpackages
    • 4.1.1.1.1.1.1.1. datanator.api.lib.complex package
      • 4.1.1.1.1.1.1.1.1. Submodules
      • 4.1.1.1.1.1.1.1.2. datanator.api.lib.complex.manager module
      • 4.1.1.1.1.1.1.1.3. Module contents
    • 4.1.1.1.1.1.1.2. datanator.api.lib.filter package
      • 4.1.1.1.1.1.1.2.1. Submodules
      • 4.1.1.1.1.1.1.2.2. datanator.api.lib.filter.manager module
      • 4.1.1.1.1.1.1.2.3. Module contents
    • 4.1.1.1.1.1.1.3. datanator.api.lib.metabolite package
      • 4.1.1.1.1.1.1.3.1. Submodules
      • 4.1.1.1.1.1.1.3.2. datanator.api.lib.metabolite.manager module
      • 4.1.1.1.1.1.1.3.3. Module contents
    • 4.1.1.1.1.1.1.4. datanator.api.lib.reaction package
      • 4.1.1.1.1.1.1.4.1. Submodules
      • 4.1.1.1.1.1.1.4.2. datanator.api.lib.reaction.manager module
      • 4.1.1.1.1.1.1.4.3. Module contents
    • 4.1.1.1.1.1.1.5. datanator.api.lib.search package
      • 4.1.1.1.1.1.1.5.1. Submodules
      • 4.1.1.1.1.1.1.5.2. datanator.api.lib.search.manager module
      • 4.1.1.1.1.1.1.5.3. Module contents
    • 4.1.1.1.1.1.1.6. datanator.api.lib.subunit package
      • 4.1.1.1.1.1.1.6.1. Submodules
      • 4.1.1.1.1.1.1.6.2. datanator.api.lib.subunit.manager module
      • 4.1.1.1.1.1.1.6.3. Module contents
  • 4.1.1.1.1.1.2. Submodules
  • 4.1.1.1.1.1.3. datanator.api.lib.data_manager module
  • 4.1.1.1.1.1.4. Module contents
• 4.1.1.1.1.2. datanator.api.query package
  • 4.1.1.1.1.2.1. Submodules
  • 4.1.1.1.1.2.2. datanator.api.query.dna_protein_interactions module
  • 4.1.1.1.1.2.3. datanator.api.query.metabolite_concentrations module
  • 4.1.1.1.1.2.4. datanator.api.query.protein_abundance module
  • 4.1.1.1.1.2.5. datanator.api.query.protein_protein_interactions module
  • 4.1.1.1.1.2.6. datanator.api.query.reaction_kinetics module
  • 4.1.1.1.1.2.7. datanator.api.query.text_search module
  • 4.1.1.1.1.2.8. Module contents

4.1.1.1.2. Submodules

4.1.1.1.3. datanator.api.serializer module

class datanator.api.serializer.CellCompartmentSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

exclude = ['search_vector', '_metadata', 'reaction']

model

alias of datanator.core.models.CellCompartment

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

class datanator.api.serializer.EntityInteractionOrPropertySerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['id', 'name', 'cross_references']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.EnvironmentSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['temperature', 'ph', 'media', 'growth_status', 'growth_system']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.GeneticsSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['taxon', 'variation']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.InteractionSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.EntityInteractionOrPropertySerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.EntityInteractionOrPropertySerializer

fields = ['id', 'name', 'cross_references', 'position', 'score', 'confidence']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.MetaboliteSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

exclude = ['simple_search_vector', 'complex_search_vector', 'parameter', 'reaction', '_is_name_ambiguous', 'concentration']

model

alias of datanator.core.models.Metabolite

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

class datanator.api.serializer.MetadataSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

fields = ['cell_compartment', 'taxon']

model

alias of datanator.core.models.Metadata

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

class datanator.api.serializer.ObservableSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['property', 'interaction', 'specie']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedComplexSpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

fields = ['metadata', 'specie']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedInteractionSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

fields = ['metadata', 'interaction']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedProteinSpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

fields = ['metadata', 'specie']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedResultMetadataSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['genetics', 'environment']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedResultSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['metadata']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedSpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

fields = ['metadata', 'specie']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ObservedValueSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ObservedResultSerializer

fields = ['metadata', 'observable', 'value', 'error', 'units']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.PolymerSpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.SpecieSerializer

class Meta

Bases: object

fields = ['id', 'name', 'cross_references', 'structure', 'sequence']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ProteinComplexSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

exclude = ['simple_search_vector']

model

alias of datanator.core.models.ProteinComplex

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

class datanator.api.serializer.ProteinComplexSpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.ProteinSpecieSerializer

class Meta

Bases: object

fields = ['id', 'name', 'cross_references', 'structure', 'sequence', 'uniprot_id', 'entrez_id', 'gene_name', 'length', 'mass', 'go_id', 'go_dsc', 'funcat_id', 'funcat_dsc', 'su_cmt', 'complex_cmt', 'disease_cmt', 'class_name', 'family_name', 'molecular_weight']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ProteinSpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.PolymerSpecieSerializer

class Meta

Bases: object

fields = ['id', 'name', 'cross_references', 'structure', 'sequence', 'uniprot_id', 'entrez_id', 'gene_name', 'length', 'mass']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ProteinSubunitSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

exclude = ['simple_search_vector', 'complex_search_vector']

model

alias of datanator.core.models.ProteinSubunit

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

class datanator.api.serializer.ReactionParticipantSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['specie', 'coefficient', 'order']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ReactionSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.InteractionSerializer

class Meta(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.InteractionSerializer

fields = ['id', 'name', 'cross_references', 'position', 'score', 'confidence', 'kinetic_law_id', 'reversible', 'participants']

opts = <marshmallow.schema.SchemaOpts object>

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.ResourceSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: flask_marshmallow.schema.Schema

class Meta

Bases: object

fields = ['namespace', 'id']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.SpecieSerializer(extra=None, only=None, exclude=(), prefix='', strict=None, many=False, context=None, load_only=(), dump_only=(), partial=False)

Bases: datanator.api.serializer.EntityInteractionOrPropertySerializer

class Meta

Bases: object

exclude = ['id']

fields = ['id', 'name', 'cross_references', 'structure']

opts = <marshmallow.schema.SchemaOpts object>

class datanator.api.serializer.StructureSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

exclude = ['metabolite', 'name', 'type']

model

alias of datanator.core.models.Structure

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

class datanator.api.serializer.TaxonSerializer(*args, **kwargs)

Bases: flask_marshmallow.sqla.ModelSchema

class Meta

Bases: object

exclude = ['search_vector', '_metadata', '_experimentmetadata']

model

alias of datanator.core.models.Taxon

sqla_session = <sqlalchemy.orm.scoping.scoped_session object>

opts = <flask_marshmallow.sqla.SchemaOpts object>

4.1.1.1.4. datanator.api.urls module

datanator.api.urls.get_version_endpoint(endpoint)

4.1.1.1.5. datanator.api.views module

Author:Saahith Pochiraju <saahith116@gmail.com> Date:2018-08-13 Copyright:2018, Karr Lab License:MIT

class datanator.api.views.Metabolite(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'metabolite'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.MetaboliteConcentration(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'metabolite_concentration'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.MetaboliteSearch(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'metabolite_search'

get(value)

mediatypes()

methods = {'GET'}

class datanator.api.views.ProteinAbundance(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'protein_abundance'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.ProteinComplex(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'protein_complex'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.ProteinComplexSearch(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'protein_complex_search'

get(value)

mediatypes()

methods = {'GET'}

class datanator.api.views.ProteinInteraction(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'protein_interaction'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.ProteinSubunit(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'protein_subunit'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.ProteinSubunitSearch(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'protein_subunit_search'

get(value)

mediatypes()

methods = {'GET'}

class datanator.api.views.Reaction(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'reaction'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.ReactionParameter(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'reaction_parameter'

get(id)

mediatypes()

methods = {'GET'}

class datanator.api.views.Search(api=None, *args, **kwargs)

Bases: flask_restplus.resource.Resource

endpoint = 'search'

get(value)

mediatypes()

methods = {'GET'}

datanator.api.views.output_json(data, code, headers=None)

4.1.1.1.6. Module contents