SD2 Data Catalog
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Using the Python Package
API Reference
Usage Scenarios
Finding and Discovering Data
User-Led Annotations
Building Data Catalog-Aware ETL Pipelines
Advanced Topics
Managing the Data Catalog
Developing the Schema
Developing the Python Package
Related Projects
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SD2 Data Catalog
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_
__init__() (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.sample.store.SampleStore method)
_mongodb (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
A
abaco_dir (datacatalog.stores.agave.StorageSystem attribute)
abspath() (in module datacatalog.pathmappings.stores)
(in module datacatalog.stores.agave)
(in module datacatalog.stores.managed)
add_document() (datacatalog.linkedstores.basestore.softdelete.SoftDelete method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
add_link() (datacatalog.linkedstores.basestore.linkmanager.LinkageManager method)
add_update_document() (datacatalog.linkedstores.basestore.store.LinkedStore method)
(datacatalog.linkedstores.file.store.FileStore method)
(datacatalog.linkedstores.process.store.ProcessStore method)
(datacatalog.linkedstores.reference.store.ReferenceStore method)
ADMIN_EVENTS (datacatalog.managers.pipelinejobs.jobmanager.JobManager attribute)
admin_template() (in module datacatalog.linkedstores.basestore.admin)
ADMIN_TOKEN_KEY (in module datacatalog.settings.crypt)
ADMIN_TOKEN_LIFETIME (in module datacatalog.settings.crypt)
ADMIN_TOKEN_SECRET (in module datacatalog.settings.crypt)
ag_files_list() (in module datacatalog.agavehelpers)
agave_dir() (datacatalog.stores.agave.StorageSystem method)
agave_notifications() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
agave_path (datacatalog.stores.pathmapping.PathMapping attribute)
agave_path_uri (datacatalog.stores.pathmapping.PathMapping attribute)
agave_path_uri() (datacatalog.stores.agave.StorageSystem class method)
AgaveClient (class in datacatalog.linkedstores.basestore.agaveclient)
AgaveError
,
[1]
AgaveEvents (class in datacatalog.linkedstores.pipelinejob.mappings)
AgaveHelper (class in datacatalog.agavehelpers)
AgaveHelperError
,
[1]
,
[2]
AgaveHelperException
agavejobs (datacatalog.linkedstores.pipelinejob.mappings.AgaveEvents attribute)
Aggregation (class in datacatalog.views.aggregations)
all_settings() (in module datacatalog.settings)
annotation (datacatalog.managers.annotations.anno.AssociatedAnnotation attribute)
annotation_uuid (datacatalog.managers.annotations.anno.AnnotationResponse attribute)
AnnotationDocument (class in datacatalog.linkedstores.annotation.annotation)
AnnotationError
AnnotationManager (class in datacatalog.managers.annotations.anno)
AnnotationManagerSchema (class in datacatalog.managers.annotations.anno)
AnnotationResponse (class in datacatalog.managers.annotations.anno)
annotations (datacatalog.managers.annotations.anno.DeletedRecordCounts attribute)
AnnotationSchema (class in datacatalog.linkedstores.annotation.annotation)
AnnotationStore (class in datacatalog.linkedstores.annotation.store)
AnnotationUpdateFailure
archive_uri() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
ArchiveIndexRequest (class in datacatalog.managers.pipelinejobs.indexrequest)
array_from_string() (in module datacatalog.settings.helpers)
as_dict() (datacatalog.extensible.ExtensibleAttrDict method)
(datacatalog.linkedstores.basestore.extensible.ExtensibleAttrDict method)
associate() (datacatalog.linkedstores.association.store.AssociationStore method)
AssociatedAnnotation (class in datacatalog.managers.annotations.anno)
Association (class in datacatalog.linkedstores.association.document)
association (datacatalog.managers.annotations.anno.AssociatedAnnotation attribute)
association_uuid (datacatalog.managers.annotations.anno.AnnotationResponse attribute)
AssociationDocument (class in datacatalog.linkedstores.association.document)
AssociationError
associations (datacatalog.managers.annotations.anno.DeletedRecordCounts attribute)
AssociationSchema (class in datacatalog.linkedstores.association.document)
AssociationStore (class in datacatalog.linkedstores.association.store)
attach() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
author (datacatalog.views.aggregations.Aggregation attribute)
B
BASEREF (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
BATCH_PAUSE (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
BATCH_RANDOM (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
BATCH_SIZE (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
BATCH_WINDOW (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
binary_uuid_to_text() (in module datacatalog.identifiers.typeduuid.typeduuid)
Biofab (class in datacatalog.formats.biofab.convert)
BLACKLIST (datacatalog.stores.managed.ManagedStore attribute)
build_graph() (in module datacatalog.linkedstores.pipelinejob.graphfsm)
build_jsondocs() (in module datacatalog.definitions.schemas)
build_templates() (in module datacatalog.definitions.schemas)
build_webhook() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
C
Caltech (class in datacatalog.formats.caltech.convert)
camel_to_snake() (in module datacatalog.utils)
cancel() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
canonicalize_actor() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
canonicalize_app() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
canonicalize_execution() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
canonicalize_job() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
canonicalize_system() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
catalog_uuid() (in module datacatalog.identifiers.typeduuid.typeduuid)
catalog_uuid_from_v1_uuid() (in module datacatalog.identifiers.typeduuid.typeduuid)
CatalogDatabaseError
CatalogDataError
CatalogError
,
[1]
CatalogManager (class in datacatalog.managers.catalog)
(class in datacatalog.managers.catalog.catalog)
CatalogManagerError
,
[1]
CatalogQueryError
,
[1]
CatalogUpdateFailure
,
[1]
CatalogUUID (class in datacatalog.identifiers.typeduuid.uuidtypes)
ChallengeDocument (class in datacatalog.linkedstores.challenge_problem.store)
ChallengeStore (class in datacatalog.linkedstores.challenge_problem.store)
ChallengeUpdateFailure
CHECKSUM_BLOCKSIZE (datacatalog.linkedstores.fixity.indexer.FixityIndexer attribute)
checksum_xxhash() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
classify_component() (datacatalog.linkedstores.pipeline.serializer.SerializedPipeline class method)
clean_fields() (datacatalog.linkedstores.sample.store.SampleStore method)
code (datacatalog.linkedstores.basestore.exceptions.CatalogDatabaseError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogDataError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogQueryError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogUpdateFailure attribute)
(datacatalog.linkedstores.basestore.store.CatalogError attribute)
(datacatalog.linkedstores.basestore.store.CatalogQueryError attribute)
(datacatalog.linkedstores.basestore.store.CatalogUpdateFailure attribute)
coll (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
COLL_PARAMS (datacatalog.managers.pipelinejobs.ManagedPipelineJob attribute)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob attribute)
COLLECTION (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
comment (datacatalog.filetypes.filetype.FileType attribute)
COMPONENT_KEYS (datacatalog.linkedstores.pipeline.serializer.SerializedPipeline attribute)
COMPOSED_SCHEMAS (in module datacatalog.jsonschemas.schemas)
config (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping attribute)
CONNECTS_FROM_MAX_LENGTH (datacatalog.linkedstores.association.document.AssociationDocument attribute)
CONNECTS_FROM_UUIDTYPES (datacatalog.linkedstores.association.document.AssociationDocument attribute)
CONNECTS_TO_MAX_LENGTH (datacatalog.linkedstores.association.document.AssociationDocument attribute)
CONNECTS_TO_UUIDTYPES (datacatalog.linkedstores.association.document.AssociationDocument attribute)
contextualize() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
ConversionError
convert() (datacatalog.formats.biofab.convert.Biofab method)
(datacatalog.formats.caltech.convert.Caltech method)
(datacatalog.formats.converter.Converter method)
(datacatalog.formats.ginkgo.convert.Ginkgo method)
(datacatalog.formats.marshall.convert.Marshall method)
(datacatalog.formats.sample_attributes.convert.SampleAttributes method)
(datacatalog.formats.transcriptic.convert.Transcriptic method)
convert_file() (in module datacatalog.formats.runner)
Converter (class in datacatalog.formats.converter)
CorePipelinesConfig (class in datacatalog.managers.pipelinejobs.config)
create() (datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
(datacatalog.slots.client.Slot method)
createView() (in module datacatalog.mongo.manage_views)
current_admin_username() (in module datacatalog.tenancy.funcs)
current_project() (in module datacatalog.tenancy.funcs)
current_tapis_user() (datacatalog.managers.common.Manager method)
current_tenant() (in module datacatalog.tenancy.funcs)
current_tenant_uri() (in module datacatalog.tenancy.funcs)
current_time() (in module datacatalog.utils)
current_username() (in module datacatalog.tenancy.funcs)
D
data_merge() (in module datacatalog.dicthelpers)
data_merge_diff() (in module datacatalog.dicthelpers)
datacatalog (module)
datacatalog.agavehelpers (module)
datacatalog.compositions (module)
datacatalog.compositions.catalog (module)
datacatalog.compositions.catalog.schemas (module)
datacatalog.compositions.sample_set (module)
datacatalog.compositions.sample_set.schemas (module)
datacatalog.definitions (module)
datacatalog.definitions.schemas (module)
datacatalog.dicthelpers (module)
datacatalog.extensible (module)
datacatalog.filetypes (module)
datacatalog.filetypes.anytype (module)
datacatalog.filetypes.filetype (module)
datacatalog.filetypes.infer (module)
datacatalog.filetypes.listing (module)
datacatalog.filetypes.mime (module)
datacatalog.filetypes.rules (module)
datacatalog.filetypes.ruleset (module)
datacatalog.filetypes.schemas (module)
datacatalog.filetypes.unknown (module)
datacatalog.filetypes.validate (module)
datacatalog.formats (module)
datacatalog.formats.biofab (module)
datacatalog.formats.biofab.convert (module)
datacatalog.formats.caltech (module)
datacatalog.formats.caltech.convert (module)
datacatalog.formats.classify (module)
datacatalog.formats.converter (module)
datacatalog.formats.ginkgo (module)
datacatalog.formats.ginkgo.convert (module)
datacatalog.formats.ginkgo.mappings (module)
datacatalog.formats.marshall (module)
datacatalog.formats.marshall.convert (module)
datacatalog.formats.runner (module)
datacatalog.formats.sample_attributes (module)
datacatalog.formats.sample_attributes.convert (module)
datacatalog.formats.schemas (module)
datacatalog.formats.transcriptic (module)
datacatalog.formats.transcriptic.convert (module)
datacatalog.githelpers (module)
datacatalog.hashable (module)
datacatalog.hashable.jsoncache (module)
datacatalog.hashable.picklecache (module)
datacatalog.identifiers (module)
datacatalog.identifiers.abaco (module)
datacatalog.identifiers.abaco.actorid (module)
datacatalog.identifiers.abaco.examples (module)
datacatalog.identifiers.abaco.execid (module)
datacatalog.identifiers.abaco.hashid (module)
datacatalog.identifiers.abaco.nonceid (module)
datacatalog.identifiers.abaco.schemas (module)
datacatalog.identifiers.agave (module)
datacatalog.identifiers.agave.appid (module)
datacatalog.identifiers.agave.examples (module)
datacatalog.identifiers.agave.schemas (module)
datacatalog.identifiers.agave.uuids (module)
datacatalog.identifiers.agave.uuidtypes (module)
datacatalog.identifiers.identifier (module)
datacatalog.identifiers.interestinganimal (module)
datacatalog.identifiers.schemas (module)
datacatalog.identifiers.tacc (module)
datacatalog.identifiers.tacc.schemas (module)
datacatalog.identifiers.tacc.username (module)
datacatalog.identifiers.tests (module)
datacatalog.identifiers.tests.test_typed_uuid (module)
datacatalog.identifiers.typeduuid (module)
datacatalog.identifiers.typeduuid.convert (module)
datacatalog.identifiers.typeduuid.examples (module)
datacatalog.identifiers.typeduuid.schemas (module)
datacatalog.identifiers.typeduuid.typeduuid (module)
datacatalog.identifiers.typeduuid.uuidtypes (module)
datacatalog.jsonschemas (module)
datacatalog.jsonschemas.encoders (module)
datacatalog.jsonschemas.exceptions (module)
datacatalog.jsonschemas.formatchecker (module)
datacatalog.jsonschemas.objects (module)
datacatalog.jsonschemas.objects.pjso (module)
datacatalog.jsonschemas.schema (module)
datacatalog.jsonschemas.schemas (module)
datacatalog.jsonschemas.validate (module)
datacatalog.jsonschemas.version (module)
datacatalog.linkages (module)
datacatalog.linkedstores (module)
datacatalog.linkedstores.annotation (module)
datacatalog.linkedstores.annotation.annotation (module)
datacatalog.linkedstores.annotation.inline (module)
datacatalog.linkedstores.annotation.schemas (module)
datacatalog.linkedstores.annotation.store (module)
datacatalog.linkedstores.annotations (module)
datacatalog.linkedstores.annotations.exceptions (module)
datacatalog.linkedstores.annotations.tag (module)
datacatalog.linkedstores.annotations.tag.document (module)
datacatalog.linkedstores.annotations.tag.schemas (module)
datacatalog.linkedstores.annotations.tag.store (module)
datacatalog.linkedstores.annotations.text (module)
datacatalog.linkedstores.annotations.text.document (module)
datacatalog.linkedstores.annotations.text.schemas (module)
datacatalog.linkedstores.annotations.text.store (module)
datacatalog.linkedstores.association (module)
datacatalog.linkedstores.association.document (module)
datacatalog.linkedstores.association.exceptions (module)
datacatalog.linkedstores.association.schemas (module)
datacatalog.linkedstores.association.store (module)
datacatalog.linkedstores.basestore (module)
datacatalog.linkedstores.basestore.admin (module)
datacatalog.linkedstores.basestore.agaveclient (module)
datacatalog.linkedstores.basestore.diff (module)
datacatalog.linkedstores.basestore.documentschema (module)
datacatalog.linkedstores.basestore.exceptions (module)
datacatalog.linkedstores.basestore.extensible (module)
datacatalog.linkedstores.basestore.heritableschema (module)
datacatalog.linkedstores.basestore.linkmanager (module)
datacatalog.linkedstores.basestore.managedfields (module)
datacatalog.linkedstores.basestore.merge (module)
datacatalog.linkedstores.basestore.mongomerge (module)
datacatalog.linkedstores.basestore.ratelimit (module)
datacatalog.linkedstores.basestore.record (module)
datacatalog.linkedstores.basestore.schemas (module)
datacatalog.linkedstores.basestore.softdelete (module)
datacatalog.linkedstores.basestore.store (module)
datacatalog.linkedstores.basestore.strategies (module)
datacatalog.linkedstores.challenge_problem (module)
datacatalog.linkedstores.challenge_problem.mappings (module)
datacatalog.linkedstores.challenge_problem.mappings.gdrive (module)
datacatalog.linkedstores.challenge_problem.mappings.gdrive.errors (module)
datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive (module)
datacatalog.linkedstores.challenge_problem.mappings.gdrive.google_utils (module)
datacatalog.linkedstores.challenge_problem.mappings.gdrive.quickstart_service (module)
datacatalog.linkedstores.challenge_problem.schemas (module)
datacatalog.linkedstores.challenge_problem.store (module)
datacatalog.linkedstores.experiment (module)
datacatalog.linkedstores.experiment.mappings (module)
datacatalog.linkedstores.experiment.mappings.gdrive (module)
datacatalog.linkedstores.experiment.mappings.gdrive.errors (module)
datacatalog.linkedstores.experiment.mappings.gdrive.gdrive (module)
datacatalog.linkedstores.experiment.mappings.gdrive.google_utils (module)
datacatalog.linkedstores.experiment.mappings.gdrive.quickstart_service (module)
datacatalog.linkedstores.experiment.schemas (module)
datacatalog.linkedstores.experiment.store (module)
datacatalog.linkedstores.experiment_design (module)
datacatalog.linkedstores.experiment_design.mappings (module)
datacatalog.linkedstores.experiment_design.mappings.gdrive (module)
datacatalog.linkedstores.experiment_design.mappings.gdrive.errors (module)
datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive (module)
datacatalog.linkedstores.experiment_design.mappings.gdrive.google_utils (module)
datacatalog.linkedstores.experiment_design.mappings.gdrive.quickstart_service (module)
datacatalog.linkedstores.experiment_design.schemas (module)
datacatalog.linkedstores.experiment_design.store (module)
datacatalog.linkedstores.file (module)
datacatalog.linkedstores.file.schemas (module)
datacatalog.linkedstores.file.store (module)
datacatalog.linkedstores.fixity (module)
datacatalog.linkedstores.fixity.exceptions (module)
datacatalog.linkedstores.fixity.indexer (module)
datacatalog.linkedstores.fixity.schema (module)
datacatalog.linkedstores.fixity.schemas (module)
datacatalog.linkedstores.fixity.store (module)
datacatalog.linkedstores.measurement (module)
datacatalog.linkedstores.measurement.schemas (module)
datacatalog.linkedstores.measurement.store (module)
datacatalog.linkedstores.pipeline (module)
datacatalog.linkedstores.pipeline.exceptions (module)
datacatalog.linkedstores.pipeline.schema (module)
datacatalog.linkedstores.pipeline.schemas (module)
datacatalog.linkedstores.pipeline.serializer (module)
datacatalog.linkedstores.pipeline.store (module)
datacatalog.linkedstores.pipelinejob (module)
datacatalog.linkedstores.pipelinejob.exceptions (module)
datacatalog.linkedstores.pipelinejob.fsm (module)
datacatalog.linkedstores.pipelinejob.graphfsm (module)
datacatalog.linkedstores.pipelinejob.job (module)
datacatalog.linkedstores.pipelinejob.mappings (module)
datacatalog.linkedstores.pipelinejob.schema (module)
datacatalog.linkedstores.pipelinejob.schemas (module)
datacatalog.linkedstores.pipelinejob.store (module)
datacatalog.linkedstores.process (module)
datacatalog.linkedstores.process.schemas (module)
datacatalog.linkedstores.process.store (module)
datacatalog.linkedstores.product (module)
datacatalog.linkedstores.product.schemas (module)
datacatalog.linkedstores.product.store (module)
datacatalog.linkedstores.reference (module)
datacatalog.linkedstores.reference.schemas (module)
datacatalog.linkedstores.reference.store (module)
datacatalog.linkedstores.sample (module)
datacatalog.linkedstores.sample.schemas (module)
datacatalog.linkedstores.sample.store (module)
datacatalog.linkedstores.structured_request (module)
datacatalog.linkedstores.structured_request.document (module)
datacatalog.linkedstores.structured_request.schemas (module)
datacatalog.linkedstores.structured_request.store (module)
datacatalog.logger (module)
datacatalog.managers (module)
datacatalog.managers.annotations (module)
datacatalog.managers.annotations.anno (module)
datacatalog.managers.catalog (module)
datacatalog.managers.catalog.catalog (module)
datacatalog.managers.common (module)
datacatalog.managers.pipelinejobs (module)
datacatalog.managers.pipelinejobs.clients (module)
datacatalog.managers.pipelinejobs.config (module)
datacatalog.managers.pipelinejobs.exceptions (module)
datacatalog.managers.pipelinejobs.indexer (module)
datacatalog.managers.pipelinejobs.indexrequest (module)
datacatalog.managers.pipelinejobs.instanced (module)
datacatalog.managers.pipelinejobs.jobmanager (module)
datacatalog.managers.pipelinejobs.reactor (module)
datacatalog.managers.pipelinejobs.store (module)
datacatalog.managers.sampleset (module)
datacatalog.managers.sampleset.processor (module)
datacatalog.mongo (module)
datacatalog.mongo.encodeauthn (module)
datacatalog.mongo.manage_views (module)
datacatalog.mongo.mongo (module)
datacatalog.pathmappings (module)
datacatalog.pathmappings.levels (module)
datacatalog.pathmappings.stores (module)
datacatalog.settings (module)
datacatalog.settings.callbacks (module)
datacatalog.settings.crypt (module)
datacatalog.settings.debug (module)
datacatalog.settings.dockerfile (module)
datacatalog.settings.helpers (module)
datacatalog.settings.identifiers (module)
datacatalog.settings.jsonschema (module)
datacatalog.settings.mongo (module)
datacatalog.settings.organization (module)
datacatalog.slots (module)
datacatalog.slots.client (module)
datacatalog.slots.constants (module)
datacatalog.slots.dbkey (module)
datacatalog.slots.logger (module)
datacatalog.slots.record (module)
datacatalog.slots.settings (module)
datacatalog.slots.status (module)
datacatalog.stores (module)
datacatalog.stores.agave (module)
datacatalog.stores.exceptions (module)
datacatalog.stores.level (module)
datacatalog.stores.managed (module)
datacatalog.stores.pathmapping (module)
datacatalog.stores.stores (module)
datacatalog.tenancy (module)
datacatalog.tenancy.classes (module)
datacatalog.tenancy.funcs (module)
datacatalog.tenancy.projects (module)
datacatalog.tenancy.schemas (module)
datacatalog.tenancy.tenants (module)
datacatalog.tokens (module)
datacatalog.tokens.admin (module)
datacatalog.tokens.classes (module)
datacatalog.tokens.exceptions (module)
datacatalog.tokens.salt (module)
datacatalog.tokens.token (module)
datacatalog.utils (module)
datacatalog.views (module)
datacatalog.views.aggregations (module)
datacatalog.views.challenge_problem_view (module)
datacatalog.views.experiment_design_view (module)
datacatalog.views.experiment_flow_incomplete_jobs_view (module)
datacatalog.views.experiment_flow_jobs_view (module)
datacatalog.views.experiment_pending_flow_jobs_view (module)
datacatalog.views.experiment_rnaseq_jobs_view (module)
datacatalog.views.experiment_view (module)
datacatalog.views.file_view (module)
datacatalog.views.jobs_view (module)
datacatalog.views.measurement_view (module)
datacatalog.views.metadatajob_view (module)
datacatalog.views.pipelinejob_view (module)
datacatalog.views.pipelinejobs_table (module)
datacatalog.views.product_view (module)
datacatalog.views.sample_view (module)
datacatalog.views.science_table (module)
datacatalog.views.science_view (module)
datacatalog.views.upload_view (module)
DateTimeEncoder (class in datacatalog.jsonschemas.encoders)
db (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
db_connection() (in module datacatalog.mongo.mongo)
debug (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
debug_mode() (datacatalog.linkedstores.basestore.store.LinkedStore method)
decode_authn_string() (in module datacatalog.mongo.encodeauthn)
decode_path() (in module datacatalog.utils)
default() (datacatalog.jsonschemas.encoders.DateTimeEncoder method)
DEFAULT_DOCUMENT_NAME (datacatalog.linkedstores.basestore.documentschema.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.heritableschema.HeritableDocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.HeritableDocumentSchema attribute)
(datacatalog.managers.annotations.anno.AnnotationManagerSchema attribute)
DEFAULT_FILTERS_NAME (datacatalog.linkedstores.basestore.documentschema.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.heritableschema.HeritableDocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.HeritableDocumentSchema attribute)
DEFAULT_SIZE (datacatalog.linkedstores.fixity.indexer.FixityIndexer attribute)
Definition (class in datacatalog.definitions.schemas)
delete() (datacatalog.agavehelpers.AgaveHelper method)
(datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
(datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
delete_association() (datacatalog.managers.annotations.anno.AnnotationManager method)
delete_by_uuid() (datacatalog.managers.catalog.catalog.CatalogManager method)
(datacatalog.managers.catalog.CatalogManager method)
delete_document() (datacatalog.linkedstores.basestore.softdelete.SoftDelete method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
DELETE_FIELD (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
(datacatalog.linkedstores.annotations.tag.document.TagAnnotationDocument attribute)
(datacatalog.linkedstores.annotations.tag.document.TagAnnotationSchema attribute)
(datacatalog.linkedstores.annotations.text.document.TextAnnotation attribute)
(datacatalog.linkedstores.annotations.text.document.TextAnnotationDocument attribute)
(datacatalog.linkedstores.annotations.text.document.TextAnnotationSchema attribute)
(datacatalog.linkedstores.association.document.AssociationDocument attribute)
(datacatalog.linkedstores.association.document.AssociationSchema attribute)
(datacatalog.linkedstores.basestore.documentschema.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.softdelete.SoftDelete attribute)
(datacatalog.linkedstores.basestore.store.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.LinkedStore attribute)
(datacatalog.linkedstores.structured_request.document.StructuredRequestDocument attribute)
DeletedRecordCounts (class in datacatalog.managers.annotations.anno)
derivation_from_inputs() (datacatalog.managers.common.Manager method)
description (datacatalog.stores.agave.StorageSystem attribute)
(datacatalog.views.aggregations.Aggregation attribute)
designs_from_challenges() (datacatalog.managers.common.Manager method)
detect_encoding() (in module datacatalog.utils)
dict_compare() (in module datacatalog.dicthelpers)
dict_merge() (in module datacatalog.dicthelpers)
DictionaryMergeError
diff_list() (in module datacatalog.linkedstores.basestore.diff)
diff_remove_long_lists() (in module datacatalog.linkedstores.basestore.diff)
dirname() (datacatalog.agavehelpers.AgaveHelper method)
dissociate() (datacatalog.linkedstores.association.store.AssociationStore method)
do_validate() (datacatalog.identifiers.identifier.IdentifierFactory method)
document() (datacatalog.linkedstores.basestore.diff.DocumentDiff method)
document_schema (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
DocumentAgaveClient (class in datacatalog.linkedstores.basestore.agaveclient)
DocumentDiff (class in datacatalog.linkedstores.basestore.diff)
DocumentSchema (class in datacatalog.linkedstores.basestore.documentschema)
(class in datacatalog.linkedstores.basestore.store)
dropView() (in module datacatalog.mongo.manage_views)
DuplicateJobError
DuplicateKeyError
DuplicatePipelineError
dynamic_import() (in module datacatalog.utils)
E
elapsed (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
encode_connection_string() (in module datacatalog.mongo.encodeauthn)
encode_files() (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
encode_name() (in module datacatalog.linkedstores.process.store)
(in module datacatalog.linkedstores.reference.store)
encode_path() (in module datacatalog.utils)
encode_title_as_id() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
EventResponse (class in datacatalog.linkedstores.pipelinejob.fsm)
exists() (datacatalog.agavehelpers.AgaveHelper method)
ExperimentDesignDocument (class in datacatalog.linkedstores.experiment_design.store)
ExperimentDesignStore (class in datacatalog.linkedstores.experiment_design.store)
ExperimentDesignUpdateFailure
ExperimentDocument (class in datacatalog.linkedstores.experiment.store)
ExperimentReferenceError
,
[1]
,
[2]
ExperimentReferenceMapping (class in datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive)
(class in datacatalog.linkedstores.experiment.mappings.gdrive.gdrive)
(class in datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive)
experiments_from_designs() (datacatalog.managers.common.Manager method)
experiments_from_experiments() (datacatalog.managers.common.Manager method)
ExperimentStore (class in datacatalog.linkedstores.experiment.store)
ExperimentUpdateFailure
ExtensibleAttrDict (class in datacatalog.extensible)
(class in datacatalog.linkedstores.basestore.extensible)
F
fail() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
failures (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping attribute)
file_agave_url() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
file_job_relative_path() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
file_or_ref_identifier() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
file_or_ref_uuid() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
FileDocument (class in datacatalog.linkedstores.file.store)
FILENAME (datacatalog.formats.biofab.convert.Biofab attribute)
(datacatalog.formats.caltech.convert.Caltech attribute)
(datacatalog.formats.converter.Converter attribute)
(datacatalog.formats.ginkgo.convert.Ginkgo attribute)
(datacatalog.formats.marshall.convert.Marshall attribute)
(datacatalog.formats.sample_attributes.convert.SampleAttributes attribute)
(datacatalog.formats.transcriptic.convert.Transcriptic attribute)
FileRecord (class in datacatalog.linkedstores.file.store)
files_from_designs() (datacatalog.managers.common.Manager method)
files_from_experiments() (datacatalog.managers.common.Manager method)
files_from_measurements() (datacatalog.managers.common.Manager method)
files_from_samples() (datacatalog.managers.common.Manager method)
filescache (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping attribute)
FileStore (class in datacatalog.linkedstores.file.store)
FileType (class in datacatalog.filetypes.filetype)
FileTypeComment (class in datacatalog.filetypes.filetype)
FileTypeError
FileTypeLabel (class in datacatalog.filetypes.filetype)
FileTypeLabelDoc (class in datacatalog.filetypes.schemas)
FILETYPES (in module datacatalog.filetypes.ruleset)
FileUpdateFailure
filter_actor_def() (datacatalog.linkedstores.pipeline.serializer.SerializedPipeline method)
filter_app_job_def() (datacatalog.linkedstores.pipeline.serializer.SerializedPipeline method)
filter_component() (datacatalog.linkedstores.pipeline.serializer.SerializedPipeline class method)
filter_dict() (in module datacatalog.dicthelpers)
filter_keys() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
find_one_by_id() (datacatalog.linkedstores.basestore.store.LinkedStore method)
find_one_by_identifier() (datacatalog.linkedstores.basestore.store.LinkedStore method)
find_one_by_uuid() (datacatalog.linkedstores.basestore.store.LinkedStore method)
finish() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
fix_assets_path() (in module datacatalog.settings.helpers)
FixityDocument (class in datacatalog.linkedstores.fixity.schema)
FixityDuplicateError
FixityIndexer (class in datacatalog.linkedstores.fixity.indexer)
FixityStore (class in datacatalog.linkedstores.fixity.store)
FixtyNotFoundError
FixtyUpdateFailure
flatten() (in module datacatalog.dicthelpers)
flatten_dict() (in module datacatalog.dicthelpers)
formatChecker (class in datacatalog.formats.converter)
(class in datacatalog.jsonschemas.formatchecker)
FORMATS (in module datacatalog.formats.classify)
from_agave_uri() (in module datacatalog.agavehelpers)
fsm_state_png() (datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
G
generate() (datacatalog.identifiers.identifier.IdentifierFactory method)
(in module datacatalog.identifiers.abaco.actorid)
(in module datacatalog.identifiers.abaco.execid)
(in module datacatalog.identifiers.abaco.hashid)
(in module datacatalog.identifiers.abaco.nonceid)
(in module datacatalog.identifiers.interestinganimal)
(in module datacatalog.identifiers.typeduuid.typeduuid)
generate_salt() (in module datacatalog.tokens.salt)
generate_string_id() (datacatalog.linkedstores.file.store.FileStore class method)
generate_string_id_v2_0() (datacatalog.linkedstores.file.store.FileStore class method)
generator_from_inputs() (datacatalog.managers.common.Manager method)
get() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
get_admin_key() (in module datacatalog.tokens.admin)
get_admin_lifetime() (in module datacatalog.tokens.admin)
get_admin_token() (in module datacatalog.tokens.admin)
get_aggregations() (in module datacatalog.views.aggregations)
get_all_schemas() (in module datacatalog.jsonschemas.schemas)
get_archive_path() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
get_by_identifier() (datacatalog.managers.common.Manager method)
get_by_uuid() (datacatalog.managers.common.Manager method)
get_by_uuids() (datacatalog.managers.common.Manager method)
get_checksum() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
get_class() (datacatalog.jsonschemas.schema.JSONSchemaBaseObject method)
get_class_object() (in module datacatalog.jsonschemas.objects.pjso)
get_class_object_from_dict() (in module datacatalog.jsonschemas.objects.pjso)
get_class_object_from_file() (in module datacatalog.jsonschemas.objects.pjso)
get_class_object_from_uri() (in module datacatalog.jsonschemas.objects.pjso)
get_classifier_schema() (datacatalog.formats.converter.Converter method)
get_collection() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
get_converter() (in module datacatalog.formats.classify)
get_converters() (in module datacatalog.formats.classify)
get_created() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
get_definitions() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_diff() (in module datacatalog.linkedstores.basestore.diff)
get_document_schemas() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_drive_service() (in module datacatalog.linkedstores.challenge_problem.mappings.gdrive.google_utils)
(in module datacatalog.linkedstores.experiment.mappings.gdrive.google_utils)
(in module datacatalog.linkedstores.experiment_design.mappings.gdrive.google_utils)
get_event_document_schemas() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_events() (datacatalog.linkedstores.pipelinejob.fsm.JobStateMachine class method)
get_fields() (datacatalog.linkedstores.basestore.store.LinkedStore method)
get_filename() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
get_files() (in module datacatalog.linkedstores.challenge_problem.mappings.gdrive.google_utils)
(in module datacatalog.linkedstores.experiment.mappings.gdrive.google_utils)
(in module datacatalog.linkedstores.experiment_design.mappings.gdrive.google_utils)
get_fingerprint() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
get_fsm_schema_events() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_fsm_schema_states() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_identifiers() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
get_index_request() (in module datacatalog.managers.pipelinejobs.indexrequest)
get_indexes() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
get_job_document_schemas() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_linearized_values() (datacatalog.linkedstores.basestore.store.LinkedStore method)
get_links() (datacatalog.linkedstores.basestore.linkmanager.LinkageManager method)
get_links_from_identifier() (datacatalog.managers.common.Manager method)
get_logger() (in module datacatalog.logger)
(in module datacatalog.slots.logger)
get_machine() (in module datacatalog.linkedstores.pipelinejob.graphfsm)
get_machine_state() (in module datacatalog.linkedstores.pipelinejob.graphfsm)
get_modified() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
get_mongo_uri() (in module datacatalog.mongo.mongo)
get_primitives() (in module datacatalog.linkedstores.pipelinejob.schemas)
get_project_name_schema() (in module datacatalog.tenancy.schemas)
get_remote_uri() (in module datacatalog.githelpers)
get_required() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
get_schema() (datacatalog.formats.converter.Converter method)
get_schemas() (in module datacatalog.compositions.catalog.schemas)
(in module datacatalog.compositions.sample_set.schemas)
(in module datacatalog.definitions.schemas)
(in module datacatalog.filetypes.schemas)
(in module datacatalog.formats.schemas)
(in module datacatalog.identifiers.abaco.actorid)
(in module datacatalog.identifiers.abaco.execid)
(in module datacatalog.identifiers.abaco.nonceid)
(in module datacatalog.identifiers.abaco.schemas)
(in module datacatalog.identifiers.agave.appid)
(in module datacatalog.identifiers.agave.schemas)
(in module datacatalog.identifiers.agave.uuids)
(in module datacatalog.identifiers.schemas)
(in module datacatalog.identifiers.tacc.schemas)
(in module datacatalog.identifiers.tacc.username)
(in module datacatalog.identifiers.typeduuid.schemas)
(in module datacatalog.linkedstores.annotation.schemas)
(in module datacatalog.linkedstores.annotations.tag.schemas)
(in module datacatalog.linkedstores.annotations.text.schemas)
(in module datacatalog.linkedstores.association.schemas)
(in module datacatalog.linkedstores.basestore.schemas)
(in module datacatalog.linkedstores.challenge_problem.schemas)
(in module datacatalog.linkedstores.experiment.schemas)
(in module datacatalog.linkedstores.experiment_design.schemas)
(in module datacatalog.linkedstores.file.schemas)
(in module datacatalog.linkedstores.fixity.schemas)
(in module datacatalog.linkedstores.measurement.schemas)
(in module datacatalog.linkedstores.pipeline.schemas)
(in module datacatalog.linkedstores.pipelinejob.schemas)
(in module datacatalog.linkedstores.process.schemas)
(in module datacatalog.linkedstores.product.schemas)
(in module datacatalog.linkedstores.reference.schemas)
(in module datacatalog.linkedstores.sample.schemas)
(in module datacatalog.linkedstores.structured_request.schemas)
(in module datacatalog.tenancy.schemas)
get_serialized_document() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
get_sha1() (in module datacatalog.githelpers)
get_sha1_short() (in module datacatalog.githelpers)
get_size() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
get_states() (datacatalog.linkedstores.pipelinejob.fsm.JobStateMachine class method)
get_storage_system() (datacatalog.agavehelpers.AgaveHelper method)
get_system_record() (datacatalog.stores.agave.StorageSystem method)
get_tapis_user() (datacatalog.managers.common.Manager method)
get_tenant_id_schema() (in module datacatalog.tenancy.schemas)
get_token() (in module datacatalog.tokens.token)
get_token_fields() (datacatalog.linkedstores.basestore.store.LinkedStore method)
get_type() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
get_type_optimized() (in module datacatalog.filetypes.mime)
get_typeduuid() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
(datacatalog.linkedstores.file.store.FileStore method)
(datacatalog.linkedstores.fixity.store.FixityStore method)
(datacatalog.linkedstores.pipeline.store.PipelineStore method)
(datacatalog.linkedstores.process.store.ProcessStore method)
(datacatalog.linkedstores.reference.store.ReferenceStore method)
get_uuid_fields() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
get_uuid_from_identifier() (datacatalog.managers.common.Manager method)
get_uuid_type() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.LinkedStore method)
get_uuidtype() (datacatalog.managers.common.ManagerBase class method)
(in module datacatalog.identifiers.typeduuid.typeduuid)
get_valid_link_types() (datacatalog.linkedstores.basestore.linkmanager.LinkageManager method)
get_version() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
gethistory() (datacatalog.linkedstores.pipelinejob.job.PipelineJob method)
getView() (in module datacatalog.mongo.manage_views)
Ginkgo (class in datacatalog.formats.ginkgo.convert)
GINKGO_LAB_IDS (datacatalog.formats.ginkgo.mappings.SampleContentsFilter attribute)
GoogleSheetsError
,
[1]
,
[2]
H
handle() (datacatalog.linkedstores.pipelinejob.fsm.JobStateMachine method)
(datacatalog.linkedstores.pipelinejob.job.PipelineJob method)
(datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
(datacatalog.managers.pipelinejobs.ManagedPipelineJobInstance method)
(datacatalog.managers.pipelinejobs.instanced.ManagedPipelineJobInstance method)
(datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
HeritableDocumentSchema (class in datacatalog.linkedstores.basestore.heritableschema)
(class in datacatalog.linkedstores.basestore.store)
history() (datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
HistoryEntry (class in datacatalog.linkedstores.pipelinejob.job)
HistoryEventDocument (class in datacatalog.linkedstores.pipelinejob.schema)
home_dir (datacatalog.stores.agave.StorageSystem attribute)
hpc_dir (datacatalog.stores.agave.StorageSystem attribute)
hpc_path (datacatalog.stores.pathmapping.PathMapping attribute)
hpc_path_uri() (datacatalog.stores.pathmapping.PathMapping method)
I
id_to_key() (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
id_to_title() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
id_to_uri() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
Identifier (class in datacatalog.identifiers.identifier)
IdentifierFactory (class in datacatalog.identifiers.identifier)
identifiers (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
IdentifierSchema (class in datacatalog.identifiers.abaco.hashid)
(class in datacatalog.identifiers.schemas)
import_submodules() (in module datacatalog.utils)
IncorrectConfiguration
,
[1]
,
[2]
INDENT (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
(in module datacatalog.linkedstores.pipeline.serializer)
index() (datacatalog.linkedstores.file.store.FileStore method)
(datacatalog.linkedstores.fixity.store.FixityStore method)
(datacatalog.managers.pipelinejobs.ManagedPipelineJobInstance method)
(datacatalog.managers.pipelinejobs.instanced.ManagedPipelineJobInstance method)
(datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
index_if_exists() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
indexed() (datacatalog.managers.pipelinejobs.instanced.ManagedPipelineJobInstance method)
(datacatalog.managers.pipelinejobs.ManagedPipelineJobInstance method)
(datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
Indexer (class in datacatalog.managers.pipelinejobs.indexer)
IndexingError
IndexType (class in datacatalog.managers.pipelinejobs.indexrequest)
infer() (in module datacatalog.filetypes.mime)
(in module datacatalog.filetypes.rules)
infer_filetype() (in module datacatalog.filetypes.infer)
INIT_LINK_PARAMS (datacatalog.managers.pipelinejobs.ManagedPipelineJob attribute)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob attribute)
init_stores() (datacatalog.managers.common.Manager class method)
InlineAnnotationDocument (class in datacatalog.linkedstores.annotation.inline)
InlineAnnotationSchema (class in datacatalog.linkedstores.annotation.inline)
InlineAnnotationStore (class in datacatalog.linkedstores.annotation.inline)
instanced_directory() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
int_or_none() (in module datacatalog.settings.helpers)
internal_get_admin_token() (in module datacatalog.tokens.admin)
InvalidAdminToken
,
[1]
InvalidIdentifierType
InvalidIdentifierValue
InvalidIndexingRequest
InvalidToken
is_primitive() (in module datacatalog.dicthelpers)
isdir() (datacatalog.agavehelpers.AgaveHelper method)
isfile() (datacatalog.agavehelpers.AgaveHelper method)
islink() (datacatalog.agavehelpers.AgaveHelper method)
J
JobCreateFailure
JobDocument (class in datacatalog.linkedstores.pipelinejob.schema)
JobError
JobManager (class in datacatalog.managers.pipelinejobs.jobmanager)
jobs_from_any() (datacatalog.managers.common.Manager method)
JobStateMachine (class in datacatalog.linkedstores.pipelinejob.fsm)
JobUpdateFailure
json (datacatalog.hashable.jsoncache.Serialized attribute)
json() (datacatalog.linkedstores.basestore.diff.DocumentDiff method)
json_diff() (in module datacatalog.dicthelpers)
json_merge() (in module datacatalog.linkedstores.basestore.merge)
JSONSCHEMA_SPEC (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
JSONSchemaBaseObject (class in datacatalog.jsonschemas.schema)
JSONSchemaCollection (class in datacatalog.identifiers.abaco.hashid)
jupyter_dir (datacatalog.stores.agave.StorageSystem attribute)
jupyter_path (datacatalog.stores.pathmapping.PathMapping attribute)
jupyter_path_uri() (datacatalog.stores.agave.StorageSystem class method)
jupyterhub_path (datacatalog.stores.pathmapping.PathMapping attribute)
jupyterhub_path_uri (datacatalog.stores.pathmapping.PathMapping attribute)
K
kids_from_parents() (datacatalog.managers.common.Manager method)
kind (datacatalog.managers.pipelinejobs.indexrequest.ArchiveIndexRequest attribute)
(datacatalog.managers.pipelinejobs.indexrequest.IndexType attribute)
(datacatalog.managers.pipelinejobs.indexrequest.ProductIndexRequest attribute)
L
label (datacatalog.filetypes.filetype.FileType attribute)
left_only (datacatalog.linkages.LinkEdgesDiff attribute)
Level (class in datacatalog.stores.level)
level_for_filepath() (in module datacatalog.pathmappings.levels)
level_for_prefix() (in module datacatalog.pathmappings.levels)
level_from_lineage() (datacatalog.managers.common.Manager method)
levels_for_filepath() (datacatalog.stores.managed.ManagedStores class method)
levels_for_prefix() (datacatalog.stores.managed.ManagedStores class method)
limit() (datacatalog.linkedstores.basestore.ratelimit.RateLimiter method)
lineage_from_uuid() (datacatalog.managers.common.Manager method)
linearize_dict() (in module datacatalog.dicthelpers)
link() (datacatalog.managers.catalog.catalog.CatalogManager method)
(datacatalog.managers.catalog.CatalogManager method)
(datacatalog.managers.common.Manager method)
LINK_FIELDS (datacatalog.linkedstores.annotations.tag.store.TagAnnotationStore attribute)
(datacatalog.linkedstores.annotations.text.store.TextAnnotationStore attribute)
(datacatalog.linkedstores.association.store.AssociationStore attribute)
(datacatalog.linkedstores.basestore.store.LinkedStore attribute)
(datacatalog.linkedstores.challenge_problem.store.ChallengeStore attribute)
(datacatalog.linkedstores.experiment.store.ExperimentStore attribute)
(datacatalog.linkedstores.experiment_design.store.ExperimentDesignStore attribute)
(datacatalog.linkedstores.file.store.FileStore attribute)
(datacatalog.linkedstores.fixity.store.FixityStore attribute)
(datacatalog.linkedstores.measurement.store.MeasurementStore attribute)
(datacatalog.linkedstores.pipeline.store.PipelineStore attribute)
(datacatalog.linkedstores.pipelinejob.store.PipelineJobStore attribute)
(datacatalog.linkedstores.process.store.ProcessStore attribute)
(datacatalog.linkedstores.reference.store.ReferenceStore attribute)
(datacatalog.linkedstores.sample.store.SampleStore attribute)
(datacatalog.managers.pipelinejobs.ManagedPipelineJob attribute)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob attribute)
Linkage (class in datacatalog.linkages)
linkage_from_inputs() (datacatalog.managers.common.Manager method)
LINKAGE_POLICIES (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
LinkageError
LinkageManager (class in datacatalog.linkedstores.basestore.linkmanager)
LinkageManagerError
LinkEdges (class in datacatalog.linkages)
LinkEdgesDiff (class in datacatalog.linkages)
LinkedStore (class in datacatalog.linkedstores.basestore.store)
list_job_archive_path() (datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
list_merge() (in module datacatalog.dicthelpers)
listall() (in module datacatalog.filetypes.anytype)
(in module datacatalog.filetypes.listing)
(in module datacatalog.filetypes.mime)
(in module datacatalog.filetypes.rules)
(in module datacatalog.filetypes.unknown)
listall_comments() (in module datacatalog.filetypes.listing)
listall_labels() (in module datacatalog.filetypes.listing)
listdir() (datacatalog.agavehelpers.AgaveHelper method)
listdir_agave_lustre() (datacatalog.agavehelpers.AgaveHelper method)
listdir_agave_native() (datacatalog.agavehelpers.AgaveHelper method)
listdir_agave_posix() (datacatalog.agavehelpers.AgaveHelper method)
listify_uuid() (datacatalog.managers.common.ManagerBase class method)
(in module datacatalog.identifiers.typeduuid.typeduuid)
load() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
LOG_JSONDIFF_UPDATES (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
(datacatalog.linkedstores.fixity.store.FixityStore attribute)
logcoll (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
LogFormatter (class in datacatalog.logger)
LookupNotPopulated
,
[1]
,
[2]
M
main() (in module datacatalog.linkedstores.challenge_problem.mappings.gdrive.quickstart_service)
(in module datacatalog.linkedstores.experiment.mappings.gdrive.quickstart_service)
(in module datacatalog.linkedstores.experiment_design.mappings.gdrive.quickstart_service)
MANAGED_FIELDS (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
ManagedField (class in datacatalog.linkedstores.basestore.managedfields)
ManagedFieldError
ManagedPipelineJob (class in datacatalog.managers.pipelinejobs)
(class in datacatalog.managers.pipelinejobs.store)
ManagedPipelineJobError
,
[1]
ManagedPipelineJobInstance (class in datacatalog.managers.pipelinejobs)
(class in datacatalog.managers.pipelinejobs.instanced)
ManagedStore (class in datacatalog.stores.managed)
ManagedStoreError
ManagedStores (class in datacatalog.stores.managed)
Manager (class in datacatalog.managers.common)
ManagerBase (class in datacatalog.managers.common)
ManagerError
map() (datacatalog.stores.pathmapping.PathMappings class method)
mapped_posix_path() (datacatalog.agavehelpers.AgaveHelper method)
MappingNotFound
,
[1]
,
[2]
Marshall (class in datacatalog.formats.marshall.convert)
mcache() (in module datacatalog.hashable.jsoncache)
(in module datacatalog.hashable.picklecache)
MeasurementDocument (class in datacatalog.linkedstores.measurement.store)
measurements_from_challenges() (datacatalog.managers.common.Manager method)
measurements_from_designs() (datacatalog.managers.common.Manager method)
measurements_from_experiments() (datacatalog.managers.common.Manager method)
measurements_from_measurements() (datacatalog.managers.common.Manager method)
measurements_from_samples() (datacatalog.managers.common.Manager method)
MeasurementStore (class in datacatalog.linkedstores.measurement.store)
MeasurementUpdateFailure
MEMBERS (datacatalog.managers.pipelinejobs.indexrequest.IndexType attribute)
(datacatalog.stores.level.Level attribute)
MERGE_DICT_OPTS (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
MERGE_LIST_OPTS (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
METADATA_ARG_NAMES (datacatalog.managers.pipelinejobs.ManagedPipelineJob attribute)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob attribute)
microseconds() (in module datacatalog.utils)
mkdir() (datacatalog.agavehelpers.AgaveHelper method)
mock() (datacatalog.identifiers.identifier.IdentifierFactory method)
(in module datacatalog.identifiers.abaco.actorid)
(in module datacatalog.identifiers.abaco.execid)
(in module datacatalog.identifiers.abaco.hashid)
(in module datacatalog.identifiers.abaco.nonceid)
(in module datacatalog.identifiers.interestinganimal)
(in module datacatalog.identifiers.typeduuid.typeduuid)
msec_precision() (in module datacatalog.linkedstores.basestore.store)
(in module datacatalog.utils)
msg (datacatalog.linkedstores.basestore.exceptions.CatalogDatabaseError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogDataError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogQueryError attribute)
(datacatalog.linkedstores.basestore.exceptions.CatalogUpdateFailure attribute)
(datacatalog.linkedstores.basestore.store.CatalogError attribute)
(datacatalog.linkedstores.basestore.store.CatalogQueryError attribute)
(datacatalog.linkedstores.basestore.store.CatalogUpdateFailure attribute)
N
name (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
(datacatalog.stores.agave.StorageSystem attribute)
names() (datacatalog.tenancy.projects.Projects method)
(datacatalog.tenancy.tenants.Tenants method)
NEVER_INDEX_FIELDS (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
(datacatalog.linkedstores.pipelinejob.store.PipelineJobStore attribute)
new() (datacatalog.linkedstores.pipelinejob.job.PipelineJob method)
new_keyname() (in module datacatalog.slots.dbkey)
new_reply() (datacatalog.linkedstores.annotations.text.store.TextAnnotationStore method)
new_slot() (in module datacatalog.slots.record)
new_tag() (datacatalog.linkedstores.annotations.tag.store.TagAnnotationStore method)
new_text() (datacatalog.linkedstores.annotations.text.store.TextAnnotationStore method)
NoClassifierError
normalize() (in module datacatalog.pathmappings.stores)
(in module datacatalog.utils)
normpath() (in module datacatalog.pathmappings.stores)
(in module datacatalog.utils)
O
otherindexes (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
owner (datacatalog.stores.agave.StorageSystem attribute)
P
page_size (datacatalog.stores.agave.StorageSystem attribute)
PARAMS (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
(datacatalog.linkedstores.annotation.annotation.AnnotationDocument attribute)
(datacatalog.linkedstores.annotation.inline.InlineAnnotationDocument attribute)
(datacatalog.linkedstores.annotations.tag.document.TagAnnotationDocument attribute)
(datacatalog.linkedstores.annotations.text.document.TextAnnotationDocument attribute)
(datacatalog.linkedstores.association.document.AssociationDocument attribute)
(datacatalog.linkedstores.basestore.record.Record attribute)
(datacatalog.linkedstores.file.store.FileRecord attribute)
(datacatalog.linkedstores.pipelinejob.fsm.EventResponse attribute)
(datacatalog.linkedstores.structured_request.document.StructuredRequestDocument attribute)
(datacatalog.managers.pipelinejobs.ManagedPipelineJob attribute)
(datacatalog.managers.pipelinejobs.ManagedPipelineJobInstance attribute)
(datacatalog.managers.pipelinejobs.indexrequest.ArchiveIndexRequest attribute)
(datacatalog.managers.pipelinejobs.indexrequest.ProductIndexRequest attribute)
(datacatalog.managers.pipelinejobs.instanced.ManagedPipelineJobInstance attribute)
(datacatalog.managers.pipelinejobs.jobmanager.JobManager attribute)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob attribute)
parent_from_inputs() (datacatalog.managers.common.Manager method)
parse_boolean() (in module datacatalog.settings.helpers)
PathMapping (class in datacatalog.stores.pathmapping)
PathMappings (class in datacatalog.stores.pathmapping)
paths_to_agave_uris() (datacatalog.agavehelpers.AgaveHelper method)
patterns_field (datacatalog.managers.pipelinejobs.indexrequest.IndexType attribute)
payload (datacatalog.hashable.picklecache.Serialized attribute)
pet_name() (in module datacatalog.identifiers.interestinganimal)
PipelineCreateFailure
PipelineDocument (class in datacatalog.linkedstores.pipeline.schema)
PipelineJob (class in datacatalog.linkedstores.pipelinejob.job)
PipelineJobError
PipelineJobsConfig (class in datacatalog.managers.pipelinejobs.config)
PipelineJobStore (class in datacatalog.linkedstores.pipelinejob.store)
PipelinesConfig (class in datacatalog.managers.pipelinejobs.config)
PipelineStore (class in datacatalog.linkedstores.pipeline.store)
PipelineUpdateFailure
PjsCacheMiss
populate() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
pre_merge_filter() (in module datacatalog.linkedstores.basestore.mongomerge)
prefix_for_level() (in module datacatalog.pathmappings.levels)
prefixes_for_level() (datacatalog.stores.managed.ManagedStores class method)
PRIMITIVE_SCHEMAS (in module datacatalog.jsonschemas.schemas)
process() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
process_agave_httperror() (in module datacatalog.agavehelpers)
process_experiment() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
process_files() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
process_measurements() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
process_samples() (datacatalog.managers.sampleset.processor.SampleSetProcessor method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
ProcessDocument (class in datacatalog.linkedstores.process.store)
ProcessRecord (class in datacatalog.linkedstores.process.store)
ProcessStore (class in datacatalog.linkedstores.process.store)
ProcessUpdateFailure
ProductDocument (class in datacatalog.linkedstores.product.store)
ProductIndexRequest (class in datacatalog.managers.pipelinejobs.indexrequest)
ProductStore (class in datacatalog.linkedstores.product.store)
ProductUpdateFailure
Project (class in datacatalog.tenancy.projects)
PROJECT (datacatalog.formats.caltech.convert.Caltech attribute)
(datacatalog.formats.converter.Converter attribute)
(datacatalog.formats.marshall.convert.Marshall attribute)
project_names() (datacatalog.tenancy.projects.Projects method)
ProjectName (class in datacatalog.tenancy.classes)
ProjectNameSchema (class in datacatalog.tenancy.schemas)
Projects (class in datacatalog.tenancy.projects)
projects (datacatalog.formats.caltech.convert.Caltech attribute)
(datacatalog.formats.converter.Converter attribute)
(datacatalog.formats.marshall.convert.Marshall attribute)
PROPERTIES_TEMPLATE (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
PUBLIC_USER (datacatalog.managers.annotations.anno.AnnotationManager attribute)
Q
query() (datacatalog.linkedstores.basestore.store.LinkedStore method)
R
random_string() (in module datacatalog.identifiers.identifier)
random_uuid5() (in module datacatalog.identifiers.typeduuid.typeduuid)
RateLimiter (class in datacatalog.linkedstores.basestore.ratelimit)
RateLimitExceeded
ReactorManagedPipelineJob (class in datacatalog.managers.pipelinejobs)
(class in datacatalog.managers.pipelinejobs.reactor)
read() (datacatalog.slots.client.Slot method)
READONLY_FIELDS (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
ready (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping attribute)
ready() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
(datacatalog.slots.client.Slot method)
Record (class in datacatalog.linkedstores.basestore.record)
record_uuid (datacatalog.managers.annotations.anno.AnnotationResponse attribute)
ReferenceDocument (class in datacatalog.linkedstores.reference.store)
ReferenceRecord (class in datacatalog.linkedstores.reference.store)
ReferenceStore (class in datacatalog.linkedstores.reference.store)
ReferenceUpdateFailure
refs_from_data_dict() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
relativize() (in module datacatalog.pathmappings.stores)
remaining (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
remaining_calls (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
remaining_time (datacatalog.linkedstores.basestore.ratelimit.RateLimiter attribute)
remove_link() (datacatalog.linkedstores.basestore.linkmanager.LinkageManager method)
render_graph() (in module datacatalog.linkedstores.pipelinejob.graphfsm)
replace_document() (datacatalog.linkedstores.basestore.store.LinkedStore method)
reset() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
reset_limit() (datacatalog.linkedstores.basestore.ratelimit.RateLimiter method)
resolve_derived_references() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
RESOLVE_ORDER (datacatalog.managers.common.Manager attribute)
RESOLVE_RE (datacatalog.managers.common.Manager attribute)
resource() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
RETURN_DOC_FILTERS (datacatalog.linkedstores.basestore.documentschema.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.DocumentSchema attribute)
right_merge() (datacatalog.linkages.LinkEdges method)
(in module datacatalog.dicthelpers)
right_only (datacatalog.linkages.LinkEdgesDiff attribute)
root_dir (datacatalog.stores.agave.StorageSystem attribute)
root_prefix() (in module datacatalog.pathmappings.stores)
run() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
S
safen_path() (in module datacatalog.utils)
Salt (class in datacatalog.tokens.classes)
SampleAttributes (class in datacatalog.formats.sample_attributes.convert)
SampleCatalogDocument (class in datacatalog.compositions.catalog.schemas)
SampleContentsFilter (class in datacatalog.formats.ginkgo.mappings)
SampleDocument (class in datacatalog.linkedstores.sample.store)
samples_from_experiments() (datacatalog.managers.common.Manager method)
samples_from_samples() (datacatalog.managers.common.Manager method)
SampleSetDocument (class in datacatalog.compositions.sample_set.schemas)
SampleSetProcessor (class in datacatalog.managers.sampleset)
(class in datacatalog.managers.sampleset.processor)
SampleSetProcessorError
SampleStore (class in datacatalog.linkedstores.sample.store)
SampleUpdateFailure
sanitize() (datacatalog.managers.common.ManagerBase class method)
schema (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
SCHEMA_BASEURL (in module datacatalog.settings.jsonschema)
schema_name (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
SCHEMA_REFERENCE (in module datacatalog.settings.jsonschema)
SCHEMAS (in module datacatalog.jsonschemas.schemas)
self_from_ids() (datacatalog.managers.common.Manager method)
self_from_inputs() (datacatalog.managers.common.Manager method)
SEPARATORS (in module datacatalog.linkedstores.pipeline.serializer)
serialize_data() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
Serialized (class in datacatalog.hashable.jsoncache)
(class in datacatalog.hashable.picklecache)
SerializedPipeline (class in datacatalog.linkedstores.pipeline.serializer)
session (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
set_archive_path() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
set_callbacks() (datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
set_from_string() (in module datacatalog.settings.helpers)
set_private_keys() (datacatalog.linkedstores.basestore.store.LinkedStore method)
set_token() (datacatalog.linkedstores.file.store.FileRecord method)
set_type_and_name() (datacatalog.stores.agave.StorageSystem method)
setup() (datacatalog.linkedstores.basestore.store.LinkedStore method)
(datacatalog.managers.pipelinejobs.ManagedPipelineJob method)
(datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
(datacatalog.managers.pipelinejobs.store.ManagedPipelineJob method)
(datacatalog.managers.sampleset.SampleSetProcessor method)
(datacatalog.managers.sampleset.processor.SampleSetProcessor method)
short_name (datacatalog.stores.agave.StorageSystem attribute)
single_index_request() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
Slot (class in datacatalog.slots.client)
SlotNotReady
SoftDelete (class in datacatalog.linkedstores.basestore.softdelete)
SORT_KEYS (datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
(in module datacatalog.linkedstores.pipeline.serializer)
ssh_host (datacatalog.stores.agave.StorageSystem attribute)
STANDARD (datacatalog.logger.LogFormatter attribute)
states (datacatalog.linkedstores.pipelinejob.fsm.JobStateMachine attribute)
status() (datacatalog.slots.client.Slot method)
STORAGE_SYSTEM (datacatalog.stores.level.Level attribute)
StorageSystem (class in datacatalog.stores.agave)
store_for_level() (datacatalog.stores.managed.ManagedStores class method)
(in module datacatalog.pathmappings.levels)
store_for_prefix() (datacatalog.stores.managed.ManagedStores class method)
STORE_SCHEMAS (in module datacatalog.jsonschemas.schemas)
StoreInterface (class in datacatalog.linkedstores.annotation.store)
(class in datacatalog.linkedstores.annotations.tag.store)
(class in datacatalog.linkedstores.annotations.text.store)
(class in datacatalog.linkedstores.association.store)
(class in datacatalog.linkedstores.basestore.store)
(class in datacatalog.linkedstores.challenge_problem.store)
(class in datacatalog.linkedstores.experiment.store)
(class in datacatalog.linkedstores.experiment_design.store)
(class in datacatalog.linkedstores.file.store)
(class in datacatalog.linkedstores.fixity.store)
(class in datacatalog.linkedstores.measurement.store)
(class in datacatalog.linkedstores.pipeline.store)
(class in datacatalog.linkedstores.pipelinejob.store)
(class in datacatalog.linkedstores.process.store)
(class in datacatalog.linkedstores.product.store)
(class in datacatalog.linkedstores.reference.store)
(class in datacatalog.linkedstores.sample.store)
(class in datacatalog.linkedstores.structured_request.store)
STORES (datacatalog.stores.managed.ManagedStores attribute)
stores() (datacatalog.stores.managed.ManagedStores class method)
stores_for_filepath() (datacatalog.stores.managed.ManagedStores class method)
Strategy (class in datacatalog.linkedstores.basestore.strategies)
StrategyError
StructuredRequestDocument (class in datacatalog.linkedstores.structured_request.document)
StructuredRequestSchema (class in datacatalog.linkedstores.structured_request.document)
StructuredRequestStore (class in datacatalog.linkedstores.structured_request.store)
sync() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
(datacatalog.tenancy.projects.Projects class method)
(datacatalog.tenancy.tenants.Tenants class method)
sync_listing() (datacatalog.managers.pipelinejobs.indexer.Indexer method)
system_id (datacatalog.stores.agave.StorageSystem attribute)
T
TagAnnotation (class in datacatalog.linkedstores.annotations.tag.document)
TagAnnotationDocument (class in datacatalog.linkedstores.annotations.tag.document)
TagAnnotationSchema (class in datacatalog.linkedstores.annotations.tag.document)
TagAnnotationStore (class in datacatalog.linkedstores.annotations.tag.store)
tags_list() (datacatalog.managers.annotations.anno.AnnotationManager method)
Tenant (class in datacatalog.tenancy.tenants)
TENANT (datacatalog.formats.caltech.convert.Caltech attribute)
(datacatalog.formats.converter.Converter attribute)
(datacatalog.formats.marshall.convert.Marshall attribute)
tenant_ids() (datacatalog.tenancy.tenants.Tenants method)
TenantIdSchema (class in datacatalog.tenancy.schemas)
TenantName (class in datacatalog.tenancy.classes)
Tenants (class in datacatalog.tenancy.tenants)
TenantURL (class in datacatalog.tenancy.classes)
test() (datacatalog.formats.converter.Converter method)
(in module datacatalog.mongo.manage_views)
test_classify_object_uuid() (in module datacatalog.identifiers.tests.test_typed_uuid)
test_classify_text_uuid() (in module datacatalog.identifiers.tests.test_typed_uuid)
test_create() (in module datacatalog.identifiers.tests.test_typed_uuid)
text_uuid_to_binary() (in module datacatalog.identifiers.typeduuid.typeduuid)
(in module datacatalog.utils)
TextAnnotation (class in datacatalog.linkedstores.annotations.text.document)
TextAnnotationDocument (class in datacatalog.linkedstores.annotations.text.document)
TextAnnotationSchema (class in datacatalog.linkedstores.annotations.text.document)
TextAnnotationStore (class in datacatalog.linkedstores.annotations.text.store)
time_stamp() (datacatalog.linkedstores.basestore.documentschema.DocumentSchema class method)
(datacatalog.linkedstores.basestore.store.DocumentSchema class method)
(in module datacatalog.linkedstores.basestore.store)
(in module datacatalog.utils)
title_to_id() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
title_to_uri() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
to_dict() (datacatalog.jsonschemas.schema.JSONSchemaBaseObject method)
(datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
(datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
(datacatalog.linkedstores.pipelinejob.job.HistoryEntry method)
(datacatalog.linkedstores.pipelinejob.job.PipelineJob method)
to_file_type() (in module datacatalog.filetypes.filetype)
to_json() (datacatalog.linkedstores.pipeline.serializer.SerializedPipeline method)
to_jsonschema() (datacatalog.jsonschemas.schema.JSONSchemaBaseObject method)
Token (class in datacatalog.tokens.classes)
token (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping attribute)
TOKEN_FIELDS (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
tokenpath (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping attribute)
Transcriptic (class in datacatalog.formats.transcriptic.convert)
transitions (datacatalog.linkedstores.pipelinejob.fsm.JobStateMachine attribute)
type (datacatalog.stores.agave.StorageSystem attribute)
TYPED_UUID_FIELD (datacatalog.linkedstores.basestore.documentschema.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.DocumentSchema attribute)
TYPED_UUID_TYPE (datacatalog.linkedstores.basestore.documentschema.DocumentSchema attribute)
(datacatalog.linkedstores.basestore.store.DocumentSchema attribute)
TypedCatalogUUID (class in datacatalog.identifiers.typeduuid.typeduuid)
TypedUUID (class in datacatalog.identifiers.typeduuid.uuidtypes)
U
undelete() (datacatalog.linkedstores.basestore.softdelete.SoftDelete method)
UnknownJob
UnknownPipeline
UnknownReference
unlink() (datacatalog.managers.catalog.catalog.CatalogManager method)
(datacatalog.managers.catalog.CatalogManager method)
(datacatalog.managers.common.Manager method)
UNMANAGED_SCHEMAS (in module datacatalog.jsonschemas.schemas)
UnsupportedMapping
,
[1]
,
[2]
update() (datacatalog.managers.pipelinejobs.jobmanager.JobManager method)
update_attrs() (datacatalog.linkedstores.basestore.store.LinkedStore method)
update_comment() (datacatalog.jsonschemas.schema.JSONSchemaBaseObject method)
update_document() (datacatalog.linkedstores.basestore.store.LinkedStore method)
update_id() (datacatalog.identifiers.typeduuid.uuidtypes.CatalogUUID method)
(datacatalog.jsonschemas.schema.JSONSchemaBaseObject method)
(datacatalog.linkedstores.basestore.documentschema.DocumentSchema method)
(datacatalog.linkedstores.basestore.store.DocumentSchema method)
update_request_or_add_stub() (datacatalog.linkedstores.structured_request.store.StructuredRequestStore method)
update_request_status_for_etl() (datacatalog.linkedstores.structured_request.store.StructuredRequestStore method)
update_request_status_for_experiment() (datacatalog.linkedstores.structured_request.store.StructuredRequestStore method)
update_request_with_status() (datacatalog.linkedstores.structured_request.store.StructuredRequestStore method)
updated (datacatalog.linkedstores.basestore.diff.DocumentDiff attribute)
updated() (datacatalog.linkedstores.fixity.indexer.FixityIndexer method)
uri_to_id() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
uri_to_key() (datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
uri_to_title() (datacatalog.linkedstores.challenge_problem.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
(datacatalog.linkedstores.experiment_design.mappings.gdrive.gdrive.ExperimentReferenceMapping method)
Username (class in datacatalog.tenancy.classes)
uuid_fields (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
uuid_from_properties() (datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
uuid_to_hashid() (in module datacatalog.identifiers.typeduuid.typeduuid)
uuid_type (datacatalog.linkedstores.basestore.store.LinkedStore attribute)
,
[1]
UUIDType (in module datacatalog.identifiers.agave.uuidtypes)
V
validate() (datacatalog.formats.converter.Converter method)
(datacatalog.identifiers.identifier.IdentifierFactory method)
(in module datacatalog.identifiers.abaco.actorid)
(in module datacatalog.identifiers.abaco.execid)
(in module datacatalog.identifiers.abaco.hashid)
(in module datacatalog.identifiers.abaco.nonceid)
(in module datacatalog.identifiers.agave.appid)
(in module datacatalog.identifiers.interestinganimal)
(in module datacatalog.identifiers.tacc.username)
(in module datacatalog.identifiers.typeduuid.typeduuid)
(in module datacatalog.jsonschemas.validate)
validate_admin_token() (in module datacatalog.linkedstores.basestore.store)
(in module datacatalog.tokens.admin)
validate_file_to_schema() (in module datacatalog.utils)
validate_input() (datacatalog.formats.converter.Converter method)
validate_label() (in module datacatalog.filetypes.validate)
validate_pipeline_uuid() (datacatalog.linkedstores.pipelinejob.store.PipelineJobStore method)
validate_project_id() (datacatalog.tenancy.projects.Projects method)
validate_tapis_username() (datacatalog.managers.common.Manager method)
validate_tenant_id() (datacatalog.tenancy.tenants.Tenants method)
validate_token() (in module datacatalog.linkedstores.basestore.store)
(in module datacatalog.tokens.token)
validate_type() (in module datacatalog.identifiers.typeduuid.typeduuid)
validate_uuid() (datacatalog.managers.common.Manager method)
validate_uuid5() (in module datacatalog.identifiers.typeduuid.typeduuid)
value (datacatalog.slots.client.Slot attribute)
VERBOSE (datacatalog.logger.LogFormatter attribute)
VERSION (datacatalog.formats.biofab.convert.Biofab attribute)
(datacatalog.formats.caltech.convert.Caltech attribute)
(datacatalog.formats.converter.Converter attribute)
(datacatalog.formats.ginkgo.convert.Ginkgo attribute)
(datacatalog.formats.marshall.convert.Marshall attribute)
(datacatalog.formats.sample_attributes.convert.SampleAttributes attribute)
(datacatalog.formats.transcriptic.convert.Transcriptic attribute)
(datacatalog.jsonschemas.schema.JSONSchemaBaseObject attribute)
view_name (datacatalog.views.aggregations.Aggregation attribute)
view_on (datacatalog.views.aggregations.Aggregation attribute)
W
work_dir (datacatalog.stores.agave.StorageSystem attribute)
write() (datacatalog.slots.client.Slot method)
write_key() (datacatalog.linkedstores.basestore.store.LinkedStore method)
X
XXHASH32_SEED (datacatalog.linkedstores.fixity.indexer.FixityIndexer attribute)
XXHASH64_SEED (datacatalog.linkedstores.fixity.indexer.FixityIndexer attribute)
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