Table of Contents
Omics.Client¶A low-level client representing Amazon Omics
This is the Amazon Omics API Reference . For an introduction to the service, see What is Amazon Omics? in the Amazon Omics Developer Guide .
import boto3
client = boto3.client('omics')
These are the available methods:
batch_delete_read_set()can_paginate()cancel_annotation_import_job()cancel_run()cancel_variant_import_job()close()create_annotation_store()create_reference_store()create_run_group()create_sequence_store()create_variant_store()create_workflow()delete_annotation_store()delete_reference()delete_reference_store()delete_run()delete_run_group()delete_sequence_store()delete_variant_store()delete_workflow()get_annotation_import_job()get_annotation_store()get_paginator()get_read_set()get_read_set_activation_job()get_read_set_export_job()get_read_set_import_job()get_read_set_metadata()get_reference()get_reference_import_job()get_reference_metadata()get_reference_store()get_run()get_run_group()get_run_task()get_sequence_store()get_variant_import_job()get_variant_store()get_waiter()get_workflow()list_annotation_import_jobs()list_annotation_stores()list_read_set_activation_jobs()list_read_set_export_jobs()list_read_set_import_jobs()list_read_sets()list_reference_import_jobs()list_reference_stores()list_references()list_run_groups()list_run_tasks()list_runs()list_sequence_stores()list_tags_for_resource()list_variant_import_jobs()list_variant_stores()list_workflows()start_annotation_import_job()start_read_set_activation_job()start_read_set_export_job()start_read_set_import_job()start_reference_import_job()start_run()start_variant_import_job()tag_resource()untag_resource()update_annotation_store()update_run_group()update_variant_store()update_workflow()batch_delete_read_set(**kwargs)¶Deletes one or more read sets.
See also: AWS API Documentation
Request Syntax
response = client.batch_delete_read_set(
ids=[
'string',
],
sequenceStoreId='string'
)
[REQUIRED]
The read sets' IDs.
[REQUIRED]
The read sets' sequence store ID.
dict
Response Syntax
{
'errors': [
{
'code': 'string',
'id': 'string',
'message': 'string'
},
]
}
Response Structure
(dict) --
errors (list) --
Errors returned by individual delete operations.
(dict) --
An error from a batch read set operation.
code (string) --
The error's code.
id (string) --
The error's ID.
message (string) --
The error's message.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptioncan_paginate(operation_name)¶Check if an operation can be paginated.
create_foo, and you'd normally invoke the
operation as client.create_foo(**kwargs), if the
create_foo operation can be paginated, you can use the
call client.get_paginator("create_foo").True if the operation can be paginated,
False otherwise.cancel_annotation_import_job(**kwargs)¶Cancels an annotation import job.
See also: AWS API Documentation
Request Syntax
response = client.cancel_annotation_import_job(
jobId='string'
)
[REQUIRED]
The job's ID.
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptioncancel_run(**kwargs)¶Cancels a run.
See also: AWS API Documentation
Request Syntax
response = client.cancel_run(
id='string'
)
[REQUIRED]
The run's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptioncancel_variant_import_job(**kwargs)¶Cancels a variant import job.
See also: AWS API Documentation
Request Syntax
response = client.cancel_variant_import_job(
jobId='string'
)
[REQUIRED]
The job's ID.
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionclose()¶Closes underlying endpoint connections.
create_annotation_store(**kwargs)¶Creates an annotation store.
See also: AWS API Documentation
Request Syntax
response = client.create_annotation_store(
description='string',
name='string',
reference={
'referenceArn': 'string'
},
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
storeFormat='GFF'|'TSV'|'VCF',
storeOptions={
'tsvStoreOptions': {
'annotationType': 'GENERIC'|'CHR_POS'|'CHR_POS_REF_ALT'|'CHR_START_END_ONE_BASE'|'CHR_START_END_REF_ALT_ONE_BASE'|'CHR_START_END_ZERO_BASE'|'CHR_START_END_REF_ALT_ZERO_BASE',
'formatToHeader': {
'string': 'string'
},
'schema': [
{
'string': 'LONG'|'INT'|'STRING'|'FLOAT'|'DOUBLE'|'BOOLEAN'
},
]
}
},
tags={
'string': 'string'
}
)
The genome reference for the store's annotations.
Note
This is a Tagged Union structure. Only one of the following top level keys can be set: referenceArn.
The reference's ARN.
Server-side encryption (SSE) settings for the store.
An encryption key ARN.
The encryption type.
[REQUIRED]
The annotation file format of the store.
File parsing options for the annotation store.
Note
This is a Tagged Union structure. Only one of the following top level keys can be set: tsvStoreOptions.
File settings for a TSV store.
The store's annotation type.
The store's header key to column name mapping.
The store's schema.
Tags for the store.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'storeFormat': 'GFF'|'TSV'|'VCF',
'storeOptions': {
'tsvStoreOptions': {
'annotationType': 'GENERIC'|'CHR_POS'|'CHR_POS_REF_ALT'|'CHR_START_END_ONE_BASE'|'CHR_START_END_REF_ALT_ONE_BASE'|'CHR_START_END_ZERO_BASE'|'CHR_START_END_REF_ALT_ZERO_BASE',
'formatToHeader': {
'string': 'string'
},
'schema': [
{
'string': 'LONG'|'INT'|'STRING'|'FLOAT'|'DOUBLE'|'BOOLEAN'
},
]
}
}
}
Response Structure
(dict) --
creationTime (datetime) --
When the store was created.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
status (string) --
The store's status.
storeFormat (string) --
The annotation file format of the store.
storeOptions (dict) --
The store's file parsing options.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: tsvStoreOptions. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
tsvStoreOptions (dict) --
File settings for a TSV store.
annotationType (string) --
The store's annotation type.
formatToHeader (dict) --
The store's header key to column name mapping.
schema (list) --
The store's schema.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptioncreate_reference_store(**kwargs)¶Creates a reference store.
See also: AWS API Documentation
Request Syntax
response = client.create_reference_store(
clientToken='string',
description='string',
name='string',
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
tags={
'string': 'string'
}
)
[REQUIRED]
A name for the store.
Server-side encryption (SSE) settings for the store.
An encryption key ARN.
The encryption type.
Tags for the store.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
}
Response Structure
(dict) --
arn (string) --
The store's ARN.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
sseConfig (dict) --
The store's SSE settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptioncreate_run_group(**kwargs)¶Creates a run group.
See also: AWS API Documentation
Request Syntax
response = client.create_run_group(
maxCpus=123,
maxDuration=123,
maxRuns=123,
name='string',
requestId='string',
tags={
'string': 'string'
}
)
[REQUIRED]
A request ID for the group.
This field is autopopulated if not provided.
Tags for the group.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
arn (string) --
The group's ARN.
id (string) --
The group's ID.
tags (dict) --
Tags for the run group.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptioncreate_sequence_store(**kwargs)¶Creates a sequence store.
See also: AWS API Documentation
Request Syntax
response = client.create_sequence_store(
clientToken='string',
description='string',
name='string',
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
tags={
'string': 'string'
}
)
[REQUIRED]
A name for the store.
Server-side encryption (SSE) settings for the store.
An encryption key ARN.
The encryption type.
Tags for the store.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
}
Response Structure
(dict) --
arn (string) --
The store's ARN.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
sseConfig (dict) --
The store's SSE settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptioncreate_variant_store(**kwargs)¶Creates a variant store.
See also: AWS API Documentation
Request Syntax
response = client.create_variant_store(
description='string',
name='string',
reference={
'referenceArn': 'string'
},
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
tags={
'string': 'string'
}
)
[REQUIRED]
The genome reference for the store's variants.
Note
This is a Tagged Union structure. Only one of the following top level keys can be set: referenceArn.
The reference's ARN.
Server-side encryption (SSE) settings for the store.
An encryption key ARN.
The encryption type.
Tags for the store.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
}
Response Structure
(dict) --
creationTime (datetime) --
When the store was created.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
status (string) --
The store's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptioncreate_workflow(**kwargs)¶Creates a workflow.
See also: AWS API Documentation
Request Syntax
response = client.create_workflow(
definitionUri='string',
definitionZip=b'bytes',
description='string',
engine='WDL'|'NEXTFLOW',
main='string',
name='string',
parameterTemplate={
'string': {
'description': 'string',
'optional': True|False
}
},
requestId='string',
storageCapacity=123,
tags={
'string': 'string'
}
)
A parameter template for the workflow.
A workflow parameter.
The parameter's description.
Whether the parameter is optional.
[REQUIRED]
A request ID for the workflow.
This field is autopopulated if not provided.
Tags for the workflow.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
arn (string) --
The workflow's ARN.
id (string) --
The workflow's ID.
status (string) --
The workflow's status.
tags (dict) --
The workflow's tags.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptiondelete_annotation_store(**kwargs)¶Deletes an annotation store.
See also: AWS API Documentation
Request Syntax
response = client.delete_annotation_store(
force=True|False,
name='string'
)
[REQUIRED]
The store's name.
dict
Response Syntax
{
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
}
Response Structure
(dict) --
status (string) --
The store's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptiondelete_reference(**kwargs)¶Deletes a genome reference.
See also: AWS API Documentation
Request Syntax
response = client.delete_reference(
id='string',
referenceStoreId='string'
)
[REQUIRED]
The reference's ID.
[REQUIRED]
The reference's store ID.
dict
Response Syntax
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptiondelete_reference_store(**kwargs)¶Deletes a genome reference store.
See also: AWS API Documentation
Request Syntax
response = client.delete_reference_store(
id='string'
)
[REQUIRED]
The store's ID.
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptiondelete_run(**kwargs)¶Deletes a workflow run.
See also: AWS API Documentation
Request Syntax
response = client.delete_run(
id='string'
)
[REQUIRED]
The run's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptiondelete_run_group(**kwargs)¶Deletes a workflow run group.
See also: AWS API Documentation
Request Syntax
response = client.delete_run_group(
id='string'
)
[REQUIRED]
The run group's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptiondelete_sequence_store(**kwargs)¶Deletes a sequence store.
See also: AWS API Documentation
Request Syntax
response = client.delete_sequence_store(
id='string'
)
[REQUIRED]
The sequence store's ID.
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptiondelete_variant_store(**kwargs)¶Deletes a variant store.
See also: AWS API Documentation
Request Syntax
response = client.delete_variant_store(
force=True|False,
name='string'
)
[REQUIRED]
The store's name.
dict
Response Syntax
{
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
}
Response Structure
(dict) --
status (string) --
The store's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptiondelete_workflow(**kwargs)¶Deletes a workflow.
See also: AWS API Documentation
Request Syntax
response = client.delete_workflow(
id='string'
)
[REQUIRED]
The workflow's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_annotation_import_job(**kwargs)¶Gets information about an annotation import job.
See also: AWS API Documentation
Request Syntax
response = client.get_annotation_import_job(
jobId='string'
)
[REQUIRED]
The job's ID.
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destinationName': 'string',
'formatOptions': {
'tsvOptions': {
'readOptions': {
'comment': 'string',
'encoding': 'string',
'escape': 'string',
'escapeQuotes': True|False,
'header': True|False,
'lineSep': 'string',
'quote': 'string',
'quoteAll': True|False,
'sep': 'string'
}
},
'vcfOptions': {
'ignoreFilterField': True|False,
'ignoreQualField': True|False
}
},
'id': 'string',
'items': [
{
'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'source': 'string'
},
],
'roleArn': 'string',
'runLeftNormalization': True|False,
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'statusMessage': 'string',
'updateTime': datetime(2015, 1, 1)
}
Response Structure
When the job completed.
When the job was created.
The job's destination annotation store.
Formatting options for a file.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: tsvOptions, vcfOptions. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
Options for a TSV file.
The file's read options.
The file's comment character.
The file's encoding.
A character for escaping quotes in the file.
Whether quotes need to be escaped in the file.
Whether the file has a header row.
A line separator for the file.
The file's quote character.
Whether all values need to be quoted, or just those that contain quotes.
The file's field separator.
Options for a VCF file.
The file's ignore filter field setting.
The file's ignore qual field setting.
The job's ID.
The job's imported items.
Details about an imported annotation item.
The item's job status.
The source file's location in Amazon S3.
The job's service role ARN.
The job's left normalization setting.
The job's status.
The job's status message.
When the job was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionget_annotation_store(**kwargs)¶Gets information about an annotation store.
See also: AWS API Documentation
Request Syntax
response = client.get_annotation_store(
name='string'
)
[REQUIRED]
The store's name.
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'statusMessage': 'string',
'storeArn': 'string',
'storeFormat': 'GFF'|'TSV'|'VCF',
'storeOptions': {
'tsvStoreOptions': {
'annotationType': 'GENERIC'|'CHR_POS'|'CHR_POS_REF_ALT'|'CHR_START_END_ONE_BASE'|'CHR_START_END_REF_ALT_ONE_BASE'|'CHR_START_END_ZERO_BASE'|'CHR_START_END_REF_ALT_ZERO_BASE',
'formatToHeader': {
'string': 'string'
},
'schema': [
{
'string': 'LONG'|'INT'|'STRING'|'FLOAT'|'DOUBLE'|'BOOLEAN'
},
]
}
},
'storeSizeBytes': 123,
'tags': {
'string': 'string'
},
'updateTime': datetime(2015, 1, 1)
}
Response Structure
When the store was created.
The store's description.
The store's ID.
The store's name.
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
The reference's ARN.
The store's server-side encryption (SSE) settings.
An encryption key ARN.
The encryption type.
The store's status.
A status message.
The store's ARN.
The store's annotation file format.
The store's parsing options.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: tsvStoreOptions. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
File settings for a TSV store.
The store's annotation type.
The store's header key to column name mapping.
The store's schema.
The store's size in bytes.
The store's tags.
When the store was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionget_paginator(operation_name)¶Create a paginator for an operation.
create_foo, and you'd normally invoke the
operation as client.create_foo(**kwargs), if the
create_foo operation can be paginated, you can use the
call client.get_paginator("create_foo").client.can_paginate method to
check if an operation is pageable.get_read_set(**kwargs)¶Gets a file from a read set.
See also: AWS API Documentation
Request Syntax
response = client.get_read_set(
file='SOURCE1'|'SOURCE2'|'INDEX',
id='string',
partNumber=123,
sequenceStoreId='string'
)
[REQUIRED]
The read set's ID.
[REQUIRED]
The part number to retrieve.
[REQUIRED]
The read set's sequence store ID.
dict
Response Syntax
{
'payload': StreamingBody()
}
Response Structure
(dict) --
payload (StreamingBody) --
The read set file payload.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.RangeNotSatisfiableExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_read_set_activation_job(**kwargs)¶Gets information about a read set activation job.
See also: AWS API Documentation
Request Syntax
response = client.get_read_set_activation_job(
id='string',
sequenceStoreId='string'
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's sequence store ID.
dict
Response Syntax
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'sequenceStoreId': 'string',
'sources': [
{
'readSetId': 'string',
'status': 'NOT_STARTED'|'IN_PROGRESS'|'FINISHED'|'FAILED',
'statusMessage': 'string'
},
],
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string'
}
Response Structure
(dict) --
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
sequenceStoreId (string) --
The job's sequence store ID.
sources (list) --
The job's sources.
(dict) --
A source for a read set activation job.
readSetId (string) --
The source's read set ID.
status (string) --
The source's status.
statusMessage (string) --
The source's status message.
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_read_set_export_job(**kwargs)¶Gets information about a read set export job.
See also: AWS API Documentation
Request Syntax
response = client.get_read_set_export_job(
id='string',
sequenceStoreId='string'
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's sequence store ID.
dict
Response Syntax
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destination': 'string',
'id': 'string',
'readSets': [
{
'id': 'string',
'status': 'NOT_STARTED'|'IN_PROGRESS'|'FINISHED'|'FAILED',
'statusMessage': 'string'
},
],
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string'
}
Response Structure
(dict) --
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destination (string) --
The job's destination in Amazon S3.
id (string) --
The job's ID.
readSets (list) --
The job's read sets.
(dict) --
Details about a read set.
id (string) --
The set's ID.
status (string) --
The set's status.
statusMessage (string) --
The set's status message.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_read_set_import_job(**kwargs)¶Gets information about a read set import job.
See also: AWS API Documentation
Request Syntax
response = client.get_read_set_import_job(
id='string',
sequenceStoreId='string'
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's sequence store ID.
dict
Response Syntax
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'roleArn': 'string',
'sequenceStoreId': 'string',
'sources': [
{
'description': 'string',
'generatedFrom': 'string',
'name': 'string',
'referenceArn': 'string',
'sampleId': 'string',
'sourceFileType': 'FASTQ'|'BAM'|'CRAM',
'sourceFiles': {
'source1': 'string',
'source2': 'string'
},
'status': 'NOT_STARTED'|'IN_PROGRESS'|'FINISHED'|'FAILED',
'statusMessage': 'string',
'subjectId': 'string',
'tags': {
'string': 'string'
}
},
],
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string'
}
Response Structure
(dict) --
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
sequenceStoreId (string) --
The job's sequence store ID.
sources (list) --
The job's sources.
(dict) --
A source for an import read set job.
description (string) --
The source's description.
generatedFrom (string) --
Where the source originated.
name (string) --
The source's name.
referenceArn (string) --
The source's genome reference ARN.
sampleId (string) --
The source's sample ID.
sourceFileType (string) --
The source's file type.
sourceFiles (dict) --
The source files' location in Amazon S3.
source1 (string) --
The location of the first file in Amazon S3.
source2 (string) --
The location of the second file in Amazon S3.
status (string) --
The source's status.
statusMessage (string) --
The source's status message.
subjectId (string) --
The source's subject ID.
tags (dict) --
The source's tags.
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_read_set_metadata(**kwargs)¶Gets details about a read set.
See also: AWS API Documentation
Request Syntax
response = client.get_read_set_metadata(
id='string',
sequenceStoreId='string'
)
[REQUIRED]
The read set's ID.
[REQUIRED]
The read set's sequence store ID.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'fileType': 'FASTQ'|'BAM'|'CRAM',
'files': {
'index': {
'contentLength': 123,
'partSize': 123,
'totalParts': 123
},
'source1': {
'contentLength': 123,
'partSize': 123,
'totalParts': 123
},
'source2': {
'contentLength': 123,
'partSize': 123,
'totalParts': 123
}
},
'id': 'string',
'name': 'string',
'referenceArn': 'string',
'sampleId': 'string',
'sequenceInformation': {
'alignment': 'string',
'generatedFrom': 'string',
'totalBaseCount': 123,
'totalReadCount': 123
},
'sequenceStoreId': 'string',
'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED',
'subjectId': 'string'
}
Response Structure
(dict) --
arn (string) --
The read set's ARN.
creationTime (datetime) --
When the read set was created.
description (string) --
The read set's description.
fileType (string) --
The read set's file type.
files (dict) --
The read set's files.
index (dict) --
The files' index.
contentLength (integer) --
The file's content length.
partSize (integer) --
The file's part size.
totalParts (integer) --
The file's total parts.
source1 (dict) --
The location of the first file in Amazon S3.
contentLength (integer) --
The file's content length.
partSize (integer) --
The file's part size.
totalParts (integer) --
The file's total parts.
source2 (dict) --
The location of the second file in Amazon S3.
contentLength (integer) --
The file's content length.
partSize (integer) --
The file's part size.
totalParts (integer) --
The file's total parts.
id (string) --
The read set's ID.
name (string) --
The read set's name.
referenceArn (string) --
The read set's genome reference ARN.
sampleId (string) --
The read set's sample ID.
sequenceInformation (dict) --
The read set's sequence information.
alignment (string) --
The sequence's alignment setting.
generatedFrom (string) --
Where the sequence originated.
totalBaseCount (integer) --
The sequence's total base count.
totalReadCount (integer) --
The sequence's total read count.
sequenceStoreId (string) --
The read set's sequence store ID.
status (string) --
The read set's status.
subjectId (string) --
The read set's subject ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_reference(**kwargs)¶Gets a reference file.
See also: AWS API Documentation
Request Syntax
response = client.get_reference(
file='SOURCE'|'INDEX',
id='string',
partNumber=123,
range='string',
referenceStoreId='string'
)
[REQUIRED]
The reference's ID.
[REQUIRED]
The part number to retrieve.
[REQUIRED]
The reference's store ID.
dict
Response Syntax
{
'payload': StreamingBody()
}
Response Structure
(dict) --
payload (StreamingBody) --
The reference file payload.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.RangeNotSatisfiableExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_reference_import_job(**kwargs)¶Gets information about a reference import job.
See also: AWS API Documentation
Request Syntax
response = client.get_reference_import_job(
id='string',
referenceStoreId='string'
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's reference store ID.
dict
Response Syntax
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'referenceStoreId': 'string',
'roleArn': 'string',
'sources': [
{
'description': 'string',
'name': 'string',
'sourceFile': 'string',
'status': 'NOT_STARTED'|'IN_PROGRESS'|'FINISHED'|'FAILED',
'statusMessage': 'string',
'tags': {
'string': 'string'
}
},
],
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES',
'statusMessage': 'string'
}
Response Structure
(dict) --
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
referenceStoreId (string) --
The job's reference store ID.
roleArn (string) --
The job's service role ARN.
sources (list) --
The job's sources.
(dict) --
An genome reference source.
description (string) --
The source's description.
name (string) --
The source's name.
sourceFile (string) --
The source file's location in Amazon S3.
status (string) --
The source's status.
statusMessage (string) --
The source's status message.
tags (dict) --
The source's tags.
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_reference_metadata(**kwargs)¶Gets information about a genome reference's metadata.
See also: AWS API Documentation
Request Syntax
response = client.get_reference_metadata(
id='string',
referenceStoreId='string'
)
[REQUIRED]
The reference's ID.
[REQUIRED]
The reference's reference store ID.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'files': {
'index': {
'contentLength': 123,
'partSize': 123,
'totalParts': 123
},
'source': {
'contentLength': 123,
'partSize': 123,
'totalParts': 123
}
},
'id': 'string',
'md5': 'string',
'name': 'string',
'referenceStoreId': 'string',
'status': 'ACTIVE'|'DELETING'|'DELETED',
'updateTime': datetime(2015, 1, 1)
}
Response Structure
(dict) --
arn (string) --
The reference's ARN.
creationTime (datetime) --
When the reference was created.
description (string) --
The reference's description.
files (dict) --
The reference's files.
index (dict) --
The files' index.
contentLength (integer) --
The file's content length.
partSize (integer) --
The file's part size.
totalParts (integer) --
The file's total parts.
source (dict) --
The source file's location in Amazon S3.
contentLength (integer) --
The file's content length.
partSize (integer) --
The file's part size.
totalParts (integer) --
The file's total parts.
id (string) --
The reference's ID.
md5 (string) --
The reference's MD5 checksum.
name (string) --
The reference's name.
referenceStoreId (string) --
The reference's reference store ID.
status (string) --
The reference's status.
updateTime (datetime) --
When the reference was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_reference_store(**kwargs)¶Gets information about a reference store.
See also: AWS API Documentation
Request Syntax
response = client.get_reference_store(
id='string'
)
[REQUIRED]
The store's ID.
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
}
Response Structure
The store's ARN.
When the store was created.
The store's description.
The store's ID.
The store's name.
The store's server-side encryption (SSE) settings.
An encryption key ARN.
The encryption type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_run(**kwargs)¶Gets information about a workflow run.
See also: AWS API Documentation
Request Syntax
response = client.get_run(
export=[
'DEFINITION',
],
id='string'
)
The run's export format.
[REQUIRED]
The run's ID.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'definition': 'string',
'digest': 'string',
'id': 'string',
'logLevel': 'OFF'|'FATAL'|'ERROR'|'ALL',
'name': 'string',
'outputUri': 'string',
'parameters': {...}|[...]|123|123.4|'string'|True|None,
'priority': 123,
'resourceDigests': {
'string': 'string'
},
'roleArn': 'string',
'runGroupId': 'string',
'runId': 'string',
'startTime': datetime(2015, 1, 1),
'startedBy': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'statusMessage': 'string',
'stopTime': datetime(2015, 1, 1),
'storageCapacity': 123,
'tags': {
'string': 'string'
},
'workflowId': 'string',
'workflowType': 'PRIVATE'
}
Response Structure
(dict) --
arn (string) --
The run's ARN.
creationTime (datetime) --
When the run was created.
definition (string) --
The run's definition.
digest (string) --
The run's digest.
id (string) --
The run's ID.
logLevel (string) --
The run's log level.
name (string) --
The run's name.
outputUri (string) --
The run's output URI.
parameters (document) --
The run's parameters.
priority (integer) --
The run's priority.
resourceDigests (dict) --
The run's resource digests.
roleArn (string) --
The run's service role ARN.
runGroupId (string) --
The run's group ID.
runId (string) --
The run's ID.
startTime (datetime) --
When the run started.
startedBy (string) --
Who started the run.
status (string) --
The run's status.
statusMessage (string) --
The run's status message.
stopTime (datetime) --
The run's stop time.
storageCapacity (integer) --
The run's storage capacity.
tags (dict) --
The run's tags.
workflowId (string) --
The run's workflow ID.
workflowType (string) --
The run's workflow type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_run_group(**kwargs)¶Gets information about a workflow run group.
See also: AWS API Documentation
Request Syntax
response = client.get_run_group(
id='string'
)
[REQUIRED]
The group's ID.
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'maxCpus': 123,
'maxDuration': 123,
'maxRuns': 123,
'name': 'string',
'tags': {
'string': 'string'
}
}
Response Structure
The group's ARN.
When the group was created.
The group's ID.
The group's maximum number of CPUs to use.
The group's maximum run duration.
The maximum number of concurrent runs for the group.
The group's name.
The group's tags.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_run_task(**kwargs)¶Gets information about a workflow run task.
See also: AWS API Documentation
Request Syntax
response = client.get_run_task(
id='string',
taskId='string'
)
[REQUIRED]
The task's ID.
[REQUIRED]
The task's ID.
dict
Response Syntax
{
'cpus': 123,
'creationTime': datetime(2015, 1, 1),
'logStream': 'string',
'memory': 123,
'name': 'string',
'startTime': datetime(2015, 1, 1),
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
'statusMessage': 'string',
'stopTime': datetime(2015, 1, 1),
'taskId': 'string'
}
Response Structure
(dict) --
cpus (integer) --
The task's CPU usage.
creationTime (datetime) --
When the task was created.
logStream (string) --
The task's log stream.
memory (integer) --
The task's memory setting.
name (string) --
The task's name.
startTime (datetime) --
The task's start time.
status (string) --
The task's status.
statusMessage (string) --
The task's status message.
stopTime (datetime) --
The task's stop time.
taskId (string) --
The task's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_sequence_store(**kwargs)¶Gets information about a sequence store.
See also: AWS API Documentation
Request Syntax
response = client.get_sequence_store(
id='string'
)
[REQUIRED]
The store's ID.
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
}
Response Structure
The store's ARN.
When the store was created.
The store's description.
The store's ID.
The store's name.
The store's server-side encryption (SSE) settings.
An encryption key ARN.
The encryption type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionget_variant_import_job(**kwargs)¶Gets information about a variant import job.
See also: AWS API Documentation
Request Syntax
response = client.get_variant_import_job(
jobId='string'
)
[REQUIRED]
The job's ID.
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destinationName': 'string',
'id': 'string',
'items': [
{
'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'source': 'string'
},
],
'roleArn': 'string',
'runLeftNormalization': True|False,
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'statusMessage': 'string',
'updateTime': datetime(2015, 1, 1)
}
Response Structure
When the job completed.
When the job was created.
The job's destination variant store.
The job's ID.
The job's items.
Details about an imported variant item.
The item's job status.
The source file's location in Amazon S3.
The job's service role ARN.
The job's left normalization setting.
The job's status.
The job's status message.
When the job was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionget_variant_store(**kwargs)¶Gets information about a variant store.
See also: AWS API Documentation
Request Syntax
response = client.get_variant_store(
name='string'
)
[REQUIRED]
The store's name.
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'statusMessage': 'string',
'storeArn': 'string',
'storeSizeBytes': 123,
'tags': {
'string': 'string'
},
'updateTime': datetime(2015, 1, 1)
}
Response Structure
When the store was created.
The store's description.
The store's ID.
The store's name.
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
The reference's ARN.
The store's server-side encryption (SSE) settings.
An encryption key ARN.
The encryption type.
The store's status.
The store's status message.
The store's ARN.
The store's size in bytes.
The store's tags.
When the store was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionget_waiter(waiter_name)¶Returns an object that can wait for some condition.
get_workflow(**kwargs)¶Gets information about a workflow.
See also: AWS API Documentation
Request Syntax
response = client.get_workflow(
export=[
'DEFINITION',
],
id='string',
type='PRIVATE'
)
The export format for the workflow.
[REQUIRED]
The workflow's ID.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'definition': 'string',
'description': 'string',
'digest': 'string',
'engine': 'WDL'|'NEXTFLOW',
'id': 'string',
'main': 'string',
'name': 'string',
'parameterTemplate': {
'string': {
'description': 'string',
'optional': True|False
}
},
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED',
'statusMessage': 'string',
'storageCapacity': 123,
'tags': {
'string': 'string'
},
'type': 'PRIVATE'
}
Response Structure
(dict) --
arn (string) --
The workflow's ARN.
creationTime (datetime) --
When the workflow was created.
definition (string) --
The workflow's definition.
description (string) --
The workflow's description.
digest (string) --
The workflow's digest.
engine (string) --
The workflow's engine.
id (string) --
The workflow's ID.
main (string) --
The path of the main definition file for the workflow.
name (string) --
The workflow's name.
parameterTemplate (dict) --
The workflow's parameter template.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
status (string) --
The workflow's status.
statusMessage (string) --
The workflow's status message.
storageCapacity (integer) --
The workflow's storage capacity.
tags (dict) --
The workflow's tags.
type (string) --
The workflow's type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_annotation_import_jobs(**kwargs)¶Retrieves a list of annotation import jobs.
See also: AWS API Documentation
Request Syntax
response = client.list_annotation_import_jobs(
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'storeName': 'string'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
A filter to apply to the list.
A status to filter on.
A store name to filter on.
IDs of annotation import jobs to retrieve.
dict
Response Syntax
{
'annotationImportJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destinationName': 'string',
'id': 'string',
'roleArn': 'string',
'runLeftNormalization': True|False,
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'updateTime': datetime(2015, 1, 1)
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
annotationImportJobs (list) --
A list of jobs.
(dict) --
An annotation import job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destinationName (string) --
The job's destination annotation store.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
runLeftNormalization (boolean) --
The job's left normalization setting.
status (string) --
The job's status.
updateTime (datetime) --
When the job was updated.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionlist_annotation_stores(**kwargs)¶Retrieves a list of annotation stores.
See also: AWS API Documentation
Request Syntax
response = client.list_annotation_stores(
filter={
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
A filter to apply to the list.
A status to filter on.
IDs of stores to list.
dict
Response Syntax
{
'annotationStores': [
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'statusMessage': 'string',
'storeArn': 'string',
'storeFormat': 'GFF'|'TSV'|'VCF',
'storeSizeBytes': 123,
'updateTime': datetime(2015, 1, 1)
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
annotationStores (list) --
A list of stores.
(dict) --
An annotation store.
creationTime (datetime) --
The store's creation time.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
status (string) --
The store's status.
statusMessage (string) --
The store's status message.
storeArn (string) --
The store's ARN.
storeFormat (string) --
The store's file format.
storeSizeBytes (integer) --
The store's size in bytes.
updateTime (datetime) --
When the store was updated.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionlist_read_set_activation_jobs(**kwargs)¶Retrieves a list of read set activation jobs.
See also: AWS API Documentation
Request Syntax
response = client.list_read_set_activation_jobs(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
maxResults=123,
nextToken='string',
sequenceStoreId='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
The filter's status.
[REQUIRED]
The read set's sequence store ID.
dict
Response Syntax
{
'activationJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
activationJobs (list) --
A list of jobs.
(dict) --
A read set activation job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_read_set_export_jobs(**kwargs)¶Retrieves a list of read set export jobs.
See also: AWS API Documentation
Request Syntax
response = client.list_read_set_export_jobs(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
maxResults=123,
nextToken='string',
sequenceStoreId='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A status to filter on.
[REQUIRED]
The jobs' sequence store ID.
dict
Response Syntax
{
'exportJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destination': 'string',
'id': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
exportJobs (list) --
A list of jobs.
(dict) --
Details about a read set export job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destination (string) --
The job's destination in Amazon S3.
id (string) --
The job's ID.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_read_set_import_jobs(**kwargs)¶Retrieves a list of read set import jobs.
See also: AWS API Documentation
Request Syntax
response = client.list_read_set_import_jobs(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
maxResults=123,
nextToken='string',
sequenceStoreId='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A status to filter on.
[REQUIRED]
The jobs' sequence store ID.
dict
Response Syntax
{
'importJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'roleArn': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
importJobs (list) --
A list of jobs.
(dict) --
An import read set job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_read_sets(**kwargs)¶Retrieves a list of read sets.
See also: AWS API Documentation
Request Syntax
response = client.list_read_sets(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string',
'referenceArn': 'string',
'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'
},
maxResults=123,
nextToken='string',
sequenceStoreId='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A name to filter on.
A genome reference ARN to filter on.
A status to filter on.
[REQUIRED]
The jobs' sequence store ID.
dict
Response Syntax
{
'nextToken': 'string',
'readSets': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'fileType': 'FASTQ'|'BAM'|'CRAM',
'id': 'string',
'name': 'string',
'referenceArn': 'string',
'sampleId': 'string',
'sequenceInformation': {
'alignment': 'string',
'generatedFrom': 'string',
'totalBaseCount': 123,
'totalReadCount': 123
},
'sequenceStoreId': 'string',
'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED',
'subjectId': 'string'
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
readSets (list) --
A list of read sets.
(dict) --
A read set.
arn (string) --
The read set's ARN.
creationTime (datetime) --
When the read set was created.
description (string) --
The read set's description.
fileType (string) --
The read set's file type.
id (string) --
The read set's ID.
name (string) --
The read set's name.
referenceArn (string) --
The read set's genome reference ARN.
sampleId (string) --
The read set's sample ID.
sequenceInformation (dict) --
Details about a sequence.
alignment (string) --
The sequence's alignment setting.
generatedFrom (string) --
Where the sequence originated.
totalBaseCount (integer) --
The sequence's total base count.
totalReadCount (integer) --
The sequence's total read count.
sequenceStoreId (string) --
The read set's sequence store ID.
status (string) --
The read set's status.
subjectId (string) --
The read set's subject ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_reference_import_jobs(**kwargs)¶Retrieves a list of reference import jobs.
See also: AWS API Documentation
Request Syntax
response = client.list_reference_import_jobs(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
maxResults=123,
nextToken='string',
referenceStoreId='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A status to filter on.
[REQUIRED]
The job's reference store ID.
dict
Response Syntax
{
'importJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'referenceStoreId': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
importJobs (list) --
A lis of jobs.
(dict) --
An import reference job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
referenceStoreId (string) --
The job's reference store ID.
roleArn (string) --
The job's service role ARN.
status (string) --
The job's status.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_reference_stores(**kwargs)¶Retrieves a list of reference stores.
See also: AWS API Documentation
Request Syntax
response = client.list_reference_stores(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string'
},
maxResults=123,
nextToken='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
The name to filter on.
dict
Response Syntax
{
'nextToken': 'string',
'referenceStores': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
referenceStores (list) --
A list of reference stores.
(dict) --
Details about a reference store.
arn (string) --
The store's ARN.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_references(**kwargs)¶Retrieves a list of references.
See also: AWS API Documentation
Request Syntax
response = client.list_references(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'md5': 'string',
'name': 'string'
},
maxResults=123,
nextToken='string',
referenceStoreId='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
An MD5 checksum to filter on.
A name to filter on.
[REQUIRED]
The references' reference store ID.
dict
Response Syntax
{
'nextToken': 'string',
'references': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'md5': 'string',
'name': 'string',
'referenceStoreId': 'string',
'status': 'ACTIVE'|'DELETING'|'DELETED',
'updateTime': datetime(2015, 1, 1)
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
references (list) --
A list of references.
(dict) --
A genome reference.
arn (string) --
The reference's ARN.
creationTime (datetime) --
When the reference was created.
description (string) --
The reference's description.
id (string) --
The reference's ID.
md5 (string) --
The reference's MD5 checksum.
name (string) --
The reference's name.
referenceStoreId (string) --
The reference's store ID.
status (string) --
The reference's status.
updateTime (datetime) --
When the reference was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_run_groups(**kwargs)¶Retrieves a list of run groups.
See also: AWS API Documentation
Request Syntax
response = client.list_run_groups(
maxResults=123,
name='string',
startingToken='string'
)
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'maxCpus': 123,
'maxDuration': 123,
'maxRuns': 123,
'name': 'string'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of groups.
(dict) --
A run group.
arn (string) --
The group's ARN.
creationTime (datetime) --
When the group was created.
id (string) --
The group's ID.
maxCpus (integer) --
The group's maximum CPU count setting.
maxDuration (integer) --
The group's maximum duration setting.
maxRuns (integer) --
The group's maximum concurrent run setting.
name (string) --
The group's name.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_run_tasks(**kwargs)¶Retrieves a list of tasks for a run.
See also: AWS API Documentation
Request Syntax
response = client.list_run_tasks(
id='string',
maxResults=123,
startingToken='string',
status='PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED'
)
[REQUIRED]
The run's ID.
dict
Response Syntax
{
'items': [
{
'cpus': 123,
'creationTime': datetime(2015, 1, 1),
'memory': 123,
'name': 'string',
'startTime': datetime(2015, 1, 1),
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
'stopTime': datetime(2015, 1, 1),
'taskId': 'string'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of tasks.
(dict) --
A workflow run task.
cpus (integer) --
The task's CPU count.
creationTime (datetime) --
When the task was created.
memory (integer) --
The task's memory.
name (string) --
The task's name.
startTime (datetime) --
When the task started.
status (string) --
The task's status.
stopTime (datetime) --
When the task stopped.
taskId (string) --
The task's ID.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_runs(**kwargs)¶Retrieves a list of runs.
See also: AWS API Documentation
Request Syntax
response = client.list_runs(
maxResults=123,
name='string',
runGroupId='string',
startingToken='string'
)
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'name': 'string',
'priority': 123,
'startTime': datetime(2015, 1, 1),
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'stopTime': datetime(2015, 1, 1),
'storageCapacity': 123,
'workflowId': 'string'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of runs.
(dict) --
A workflow run.
arn (string) --
The run's ARN.
creationTime (datetime) --
When the run was created.
id (string) --
The run's ID.
name (string) --
The run's name.
priority (integer) --
The run's priority.
startTime (datetime) --
When the run started.
status (string) --
The run's status.
stopTime (datetime) --
When the run stopped.
storageCapacity (integer) --
The run's storage capacity.
workflowId (string) --
The run's workflow ID.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_sequence_stores(**kwargs)¶Retrieves a list of sequence stores.
See also: AWS API Documentation
Request Syntax
response = client.list_sequence_stores(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string'
},
maxResults=123,
nextToken='string'
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A name to filter on.
dict
Response Syntax
{
'nextToken': 'string',
'sequenceStores': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
sequenceStores (list) --
A list of sequence stores.
(dict) --
Details about a sequence store.
arn (string) --
The store's ARN.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionRetrieves a list of tags for a resource.
See also: AWS API Documentation
Request Syntax
response = client.list_tags_for_resource(
resourceArn='string'
)
[REQUIRED]
The resource's ARN.
{
'tags': {
'string': 'string'
}
}
Response Structure
A list of tags.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionlist_variant_import_jobs(**kwargs)¶Retrieves a list of variant import jobs.
See also: AWS API Documentation
Request Syntax
response = client.list_variant_import_jobs(
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'storeName': 'string'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
A filter to apply to the list.
A status to filter on.
A store name to filter on.
A list of job IDs.
dict
Response Syntax
{
'nextToken': 'string',
'variantImportJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destinationName': 'string',
'id': 'string',
'roleArn': 'string',
'runLeftNormalization': True|False,
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'updateTime': datetime(2015, 1, 1)
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
variantImportJobs (list) --
A list of jobs.
(dict) --
A variant import job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destinationName (string) --
The job's destination variant store.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
runLeftNormalization (boolean) --
The job's left normalization setting.
status (string) --
The job's status.
updateTime (datetime) --
When the job was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionlist_variant_stores(**kwargs)¶Retrieves a list of variant stores.
See also: AWS API Documentation
Request Syntax
response = client.list_variant_stores(
filter={
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
A filter to apply to the list.
A status to filter on.
A list of store IDs.
dict
Response Syntax
{
'nextToken': 'string',
'variantStores': [
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'statusMessage': 'string',
'storeArn': 'string',
'storeSizeBytes': 123,
'updateTime': datetime(2015, 1, 1)
},
]
}
Response Structure
(dict) --
nextToken (string) --
A pagination token that's included if more results are available.
variantStores (list) --
A list of variant stores.
(dict) --
A variant store.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
status (string) --
The store's status.
statusMessage (string) --
The store's status message.
storeArn (string) --
The store's ARN.
storeSizeBytes (integer) --
The store's size in bytes.
updateTime (datetime) --
When the store was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionlist_workflows(**kwargs)¶Retrieves a list of workflows.
See also: AWS API Documentation
Request Syntax
response = client.list_workflows(
maxResults=123,
name='string',
startingToken='string',
type='PRIVATE'
)
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'digest': 'string',
'id': 'string',
'name': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED',
'type': 'PRIVATE'
},
],
'nextToken': 'string'
}
Response Structure
(dict) --
items (list) --
The workflows' items.
(dict) --
A workflow.
arn (string) --
The workflow's ARN.
creationTime (datetime) --
When the workflow was created.
digest (string) --
The workflow's digest.
id (string) --
The workflow's ID.
name (string) --
The workflow's name.
status (string) --
The workflow's status.
type (string) --
The workflow's type.
nextToken (string) --
A pagination token that's included if more results are available.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionstart_annotation_import_job(**kwargs)¶Starts an annotation import job.
See also: AWS API Documentation
Request Syntax
response = client.start_annotation_import_job(
destinationName='string',
formatOptions={
'tsvOptions': {
'readOptions': {
'comment': 'string',
'encoding': 'string',
'escape': 'string',
'escapeQuotes': True|False,
'header': True|False,
'lineSep': 'string',
'quote': 'string',
'quoteAll': True|False,
'sep': 'string'
}
},
'vcfOptions': {
'ignoreFilterField': True|False,
'ignoreQualField': True|False
}
},
items=[
{
'source': 'string'
},
],
roleArn='string',
runLeftNormalization=True|False
)
[REQUIRED]
A destination annotation store for the job.
Formatting options for the annotation file.
Note
This is a Tagged Union structure. Only one of the following top level keys can be set: tsvOptions, vcfOptions.
Options for a TSV file.
The file's read options.
The file's comment character.
The file's encoding.
A character for escaping quotes in the file.
Whether quotes need to be escaped in the file.
Whether the file has a header row.
A line separator for the file.
The file's quote character.
Whether all values need to be quoted, or just those that contain quotes.
The file's field separator.
Options for a VCF file.
The file's ignore filter field setting.
The file's ignore qual field setting.
[REQUIRED]
Items to import.
A source for an annotation import job.
The source file's location in Amazon S3.
[REQUIRED]
A service role for the job.
dict
Response Syntax
{
'jobId': 'string'
}
Response Structure
(dict) --
jobId (string) --
The job's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionstart_read_set_activation_job(**kwargs)¶Starts a read set activation job.
See also: AWS API Documentation
Request Syntax
response = client.start_read_set_activation_job(
clientToken='string',
sequenceStoreId='string',
sources=[
{
'readSetId': 'string'
},
]
)
[REQUIRED]
The read set's sequence store ID.
[REQUIRED]
The job's sources.
A source for a read set activation job.
The source's read set ID.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
}
Response Structure
(dict) --
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
sequenceStoreId (string) --
The read set's sequence store ID.
status (string) --
The job's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionstart_read_set_export_job(**kwargs)¶Starts a read set export job.
See also: AWS API Documentation
Request Syntax
response = client.start_read_set_export_job(
clientToken='string',
destination='string',
roleArn='string',
sequenceStoreId='string',
sources=[
{
'readSetId': 'string'
},
]
)
[REQUIRED]
A location for exported files in Amazon S3.
[REQUIRED]
A service role for the job.
[REQUIRED]
The read set's sequence store ID.
[REQUIRED]
Sources for the job.
A read set.
The set's ID.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'destination': 'string',
'id': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
}
Response Structure
(dict) --
creationTime (datetime) --
When the job was created.
destination (string) --
The job's output location.
id (string) --
The job's ID.
sequenceStoreId (string) --
The read set's sequence store ID.
status (string) --
The job's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionstart_read_set_import_job(**kwargs)¶Starts a read set import job.
See also: AWS API Documentation
Request Syntax
response = client.start_read_set_import_job(
clientToken='string',
roleArn='string',
sequenceStoreId='string',
sources=[
{
'description': 'string',
'generatedFrom': 'string',
'name': 'string',
'referenceArn': 'string',
'sampleId': 'string',
'sourceFileType': 'FASTQ'|'BAM'|'CRAM',
'sourceFiles': {
'source1': 'string',
'source2': 'string'
},
'subjectId': 'string',
'tags': {
'string': 'string'
}
},
]
)
[REQUIRED]
A service role for the job.
[REQUIRED]
The read set's sequence store ID.
[REQUIRED]
Source files to import.
A source for a read set import job.
The source's description.
Where the source originated.
The source's name.
The source's reference ARN.
The source's sample ID.
The source's file type.
The source files' location in Amazon S3.
The location of the first file in Amazon S3.
The location of the second file in Amazon S3.
The source's subject ID.
The source's tags.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'roleArn': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
}
Response Structure
(dict) --
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
sequenceStoreId (string) --
The read set's sequence store ID.
status (string) --
The job's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionstart_reference_import_job(**kwargs)¶Starts a reference import job.
See also: AWS API Documentation
Request Syntax
response = client.start_reference_import_job(
clientToken='string',
referenceStoreId='string',
roleArn='string',
sources=[
{
'description': 'string',
'name': 'string',
'sourceFile': 'string',
'tags': {
'string': 'string'
}
},
]
)
[REQUIRED]
The job's reference store ID.
[REQUIRED]
A service role for the job.
[REQUIRED]
Sources for the job.
A source for a reference import job.
The source's description.
The source's name.
The source file's location in Amazon S3.
The source's tags.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'referenceStoreId': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
}
Response Structure
(dict) --
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
referenceStoreId (string) --
The job's reference store ID.
roleArn (string) --
The job's service role ARN.
status (string) --
The job's status.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionstart_run(**kwargs)¶Starts a run.
See also: AWS API Documentation
Request Syntax
response = client.start_run(
logLevel='OFF'|'FATAL'|'ERROR'|'ALL',
name='string',
outputUri='string',
parameters={...}|[...]|123|123.4|'string'|True|None,
priority=123,
requestId='string',
roleArn='string',
runGroupId='string',
runId='string',
storageCapacity=123,
tags={
'string': 'string'
},
workflowId='string',
workflowType='PRIVATE'
)
[REQUIRED]
A request ID for the run.
This field is autopopulated if not provided.
[REQUIRED]
A service role for the run.
Tags for the run.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
arn (string) --
The run's ARN.
id (string) --
The run's ID.
status (string) --
The run's status.
tags (dict) --
The run's tags.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionstart_variant_import_job(**kwargs)¶Starts a variant import job.
See also: AWS API Documentation
Request Syntax
response = client.start_variant_import_job(
destinationName='string',
items=[
{
'source': 'string'
},
],
roleArn='string',
runLeftNormalization=True|False
)
[REQUIRED]
The destination variant store for the job.
[REQUIRED]
Items to import.
A imported variant item's source.
The source file's location in Amazon S3.
[REQUIRED]
A service role for the job.
dict
Response Syntax
{
'jobId': 'string'
}
Response Structure
(dict) --
jobId (string) --
The job's ID.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptiontag_resource(**kwargs)¶Tags a resource.
See also: AWS API Documentation
Request Syntax
response = client.tag_resource(
resourceArn='string',
tags={
'string': 'string'
}
)
[REQUIRED]
The resource's ARN.
[REQUIRED]
Tags for the resource.
dict
Response Syntax
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionuntag_resource(**kwargs)¶Removes tags from a resource.
See also: AWS API Documentation
Request Syntax
response = client.untag_resource(
resourceArn='string',
tagKeys=[
'string',
]
)
[REQUIRED]
The resource's ARN.
[REQUIRED]
Keys of tags to remove.
dict
Response Syntax
{}
Response Structure
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionupdate_annotation_store(**kwargs)¶Updates an annotation store.
See also: AWS API Documentation
Request Syntax
response = client.update_annotation_store(
description='string',
name='string'
)
[REQUIRED]
A name for the store.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'storeFormat': 'GFF'|'TSV'|'VCF',
'storeOptions': {
'tsvStoreOptions': {
'annotationType': 'GENERIC'|'CHR_POS'|'CHR_POS_REF_ALT'|'CHR_START_END_ONE_BASE'|'CHR_START_END_REF_ALT_ONE_BASE'|'CHR_START_END_ZERO_BASE'|'CHR_START_END_REF_ALT_ZERO_BASE',
'formatToHeader': {
'string': 'string'
},
'schema': [
{
'string': 'LONG'|'INT'|'STRING'|'FLOAT'|'DOUBLE'|'BOOLEAN'
},
]
}
},
'updateTime': datetime(2015, 1, 1)
}
Response Structure
(dict) --
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
status (string) --
The store's status.
storeFormat (string) --
The annotation file format of the store.
storeOptions (dict) --
Parsing options for the store.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: tsvStoreOptions. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
tsvStoreOptions (dict) --
File settings for a TSV store.
annotationType (string) --
The store's annotation type.
formatToHeader (dict) --
The store's header key to column name mapping.
schema (list) --
The store's schema.
updateTime (datetime) --
When the store was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionupdate_run_group(**kwargs)¶Updates a run group.
See also: AWS API Documentation
Request Syntax
response = client.update_run_group(
id='string',
maxCpus=123,
maxDuration=123,
maxRuns=123,
name='string'
)
[REQUIRED]
The group's ID.
None
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionupdate_variant_store(**kwargs)¶Updates a variant store.
See also: AWS API Documentation
Request Syntax
response = client.update_variant_store(
description='string',
name='string'
)
[REQUIRED]
A name for the store.
dict
Response Syntax
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'updateTime': datetime(2015, 1, 1)
}
Response Structure
(dict) --
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
status (string) --
The store's status.
updateTime (datetime) --
When the store was updated.
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionupdate_workflow(**kwargs)¶Updates a workflow.
See also: AWS API Documentation
Request Syntax
response = client.update_workflow(
description='string',
id='string',
name='string'
)
[REQUIRED]
The workflow's ID.
None
Exceptions
Omics.Client.exceptions.InternalServerExceptionOmics.Client.exceptions.ServiceQuotaExceededExceptionOmics.Client.exceptions.ThrottlingExceptionOmics.Client.exceptions.ValidationExceptionOmics.Client.exceptions.ConflictExceptionOmics.Client.exceptions.ResourceNotFoundExceptionOmics.Client.exceptions.AccessDeniedExceptionOmics.Client.exceptions.RequestTimeoutExceptionThe available paginators are:
Omics.Paginator.ListAnnotationImportJobsOmics.Paginator.ListAnnotationStoresOmics.Paginator.ListReadSetActivationJobsOmics.Paginator.ListReadSetExportJobsOmics.Paginator.ListReadSetImportJobsOmics.Paginator.ListReadSetsOmics.Paginator.ListReferenceImportJobsOmics.Paginator.ListReferenceStoresOmics.Paginator.ListReferencesOmics.Paginator.ListRunGroupsOmics.Paginator.ListRunTasksOmics.Paginator.ListRunsOmics.Paginator.ListSequenceStoresOmics.Paginator.ListVariantImportJobsOmics.Paginator.ListVariantStoresOmics.Paginator.ListWorkflowsOmics.Paginator.ListAnnotationImportJobs¶paginator = client.get_paginator('list_annotation_import_jobs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_annotation_import_jobs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'storeName': 'string'
},
ids=[
'string',
],
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
A status to filter on.
A store name to filter on.
IDs of annotation import jobs to retrieve.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'annotationImportJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destinationName': 'string',
'id': 'string',
'roleArn': 'string',
'runLeftNormalization': True|False,
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'updateTime': datetime(2015, 1, 1)
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
annotationImportJobs (list) --
A list of jobs.
(dict) --
An annotation import job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destinationName (string) --
The job's destination annotation store.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
runLeftNormalization (boolean) --
The job's left normalization setting.
status (string) --
The job's status.
updateTime (datetime) --
When the job was updated.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListAnnotationStores¶paginator = client.get_paginator('list_annotation_stores')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_annotation_stores().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
},
ids=[
'string',
],
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
A status to filter on.
IDs of stores to list.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'annotationStores': [
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'statusMessage': 'string',
'storeArn': 'string',
'storeFormat': 'GFF'|'TSV'|'VCF',
'storeSizeBytes': 123,
'updateTime': datetime(2015, 1, 1)
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
annotationStores (list) --
A list of stores.
(dict) --
An annotation store.
creationTime (datetime) --
The store's creation time.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
status (string) --
The store's status.
statusMessage (string) --
The store's status message.
storeArn (string) --
The store's ARN.
storeFormat (string) --
The store's file format.
storeSizeBytes (integer) --
The store's size in bytes.
updateTime (datetime) --
When the store was updated.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReadSetActivationJobs¶paginator = client.get_paginator('list_read_set_activation_jobs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_read_set_activation_jobs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
sequenceStoreId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
The filter's status.
[REQUIRED]
The read set's sequence store ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'activationJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
activationJobs (list) --
A list of jobs.
(dict) --
A read set activation job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReadSetExportJobs¶paginator = client.get_paginator('list_read_set_export_jobs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_read_set_export_jobs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
sequenceStoreId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A status to filter on.
[REQUIRED]
The jobs' sequence store ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'exportJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destination': 'string',
'id': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
exportJobs (list) --
A list of jobs.
(dict) --
Details about a read set export job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destination (string) --
The job's destination in Amazon S3.
id (string) --
The job's ID.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReadSetImportJobs¶paginator = client.get_paginator('list_read_set_import_jobs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_read_set_import_jobs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
sequenceStoreId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A status to filter on.
[REQUIRED]
The jobs' sequence store ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'importJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'roleArn': 'string',
'sequenceStoreId': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
importJobs (list) --
A list of jobs.
(dict) --
An import read set job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
sequenceStoreId (string) --
The job's sequence store ID.
status (string) --
The job's status.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReadSets¶paginator = client.get_paginator('list_read_sets')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_read_sets().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string',
'referenceArn': 'string',
'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'
},
sequenceStoreId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A name to filter on.
A genome reference ARN to filter on.
A status to filter on.
[REQUIRED]
The jobs' sequence store ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'readSets': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'fileType': 'FASTQ'|'BAM'|'CRAM',
'id': 'string',
'name': 'string',
'referenceArn': 'string',
'sampleId': 'string',
'sequenceInformation': {
'alignment': 'string',
'generatedFrom': 'string',
'totalBaseCount': 123,
'totalReadCount': 123
},
'sequenceStoreId': 'string',
'status': 'ARCHIVED'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED',
'subjectId': 'string'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
readSets (list) --
A list of read sets.
(dict) --
A read set.
arn (string) --
The read set's ARN.
creationTime (datetime) --
When the read set was created.
description (string) --
The read set's description.
fileType (string) --
The read set's file type.
id (string) --
The read set's ID.
name (string) --
The read set's name.
referenceArn (string) --
The read set's genome reference ARN.
sampleId (string) --
The read set's sample ID.
sequenceInformation (dict) --
Details about a sequence.
alignment (string) --
The sequence's alignment setting.
generatedFrom (string) --
Where the sequence originated.
totalBaseCount (integer) --
The sequence's total base count.
totalReadCount (integer) --
The sequence's total read count.
sequenceStoreId (string) --
The read set's sequence store ID.
status (string) --
The read set's status.
subjectId (string) --
The read set's subject ID.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReferenceImportJobs¶paginator = client.get_paginator('list_reference_import_jobs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_reference_import_jobs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
referenceStoreId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A status to filter on.
[REQUIRED]
The job's reference store ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'importJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'referenceStoreId': 'string',
'roleArn': 'string',
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLING'|'CANCELLED'|'FAILED'|'COMPLETED'|'COMPLETED_WITH_FAILURES'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
importJobs (list) --
A lis of jobs.
(dict) --
An import reference job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
id (string) --
The job's ID.
referenceStoreId (string) --
The job's reference store ID.
roleArn (string) --
The job's service role ARN.
status (string) --
The job's status.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReferenceStores¶paginator = client.get_paginator('list_reference_stores')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_reference_stores().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string'
},
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
The name to filter on.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'referenceStores': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
referenceStores (list) --
A list of reference stores.
(dict) --
Details about a reference store.
arn (string) --
The store's ARN.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListReferences¶paginator = client.get_paginator('list_references')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_references().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'md5': 'string',
'name': 'string'
},
referenceStoreId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
An MD5 checksum to filter on.
A name to filter on.
[REQUIRED]
The references' reference store ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'references': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'md5': 'string',
'name': 'string',
'referenceStoreId': 'string',
'status': 'ACTIVE'|'DELETING'|'DELETED',
'updateTime': datetime(2015, 1, 1)
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
references (list) --
A list of references.
(dict) --
A genome reference.
arn (string) --
The reference's ARN.
creationTime (datetime) --
When the reference was created.
description (string) --
The reference's description.
id (string) --
The reference's ID.
md5 (string) --
The reference's MD5 checksum.
name (string) --
The reference's name.
referenceStoreId (string) --
The reference's store ID.
status (string) --
The reference's status.
updateTime (datetime) --
When the reference was updated.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListRunGroups¶paginator = client.get_paginator('list_run_groups')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_run_groups().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
name='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'maxCpus': 123,
'maxDuration': 123,
'maxRuns': 123,
'name': 'string'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of groups.
(dict) --
A run group.
arn (string) --
The group's ARN.
creationTime (datetime) --
When the group was created.
id (string) --
The group's ID.
maxCpus (integer) --
The group's maximum CPU count setting.
maxDuration (integer) --
The group's maximum duration setting.
maxRuns (integer) --
The group's maximum concurrent run setting.
name (string) --
The group's name.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListRunTasks¶paginator = client.get_paginator('list_run_tasks')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_run_tasks().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
id='string',
status='PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
[REQUIRED]
The run's ID.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'items': [
{
'cpus': 123,
'creationTime': datetime(2015, 1, 1),
'memory': 123,
'name': 'string',
'startTime': datetime(2015, 1, 1),
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED',
'stopTime': datetime(2015, 1, 1),
'taskId': 'string'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of tasks.
(dict) --
A workflow run task.
cpus (integer) --
The task's CPU count.
creationTime (datetime) --
When the task was created.
memory (integer) --
The task's memory.
name (string) --
The task's name.
startTime (datetime) --
When the task started.
status (string) --
The task's status.
stopTime (datetime) --
When the task stopped.
taskId (string) --
The task's ID.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListRuns¶paginator = client.get_paginator('list_runs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_runs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
name='string',
runGroupId='string',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'name': 'string',
'priority': 123,
'startTime': datetime(2015, 1, 1),
'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED',
'stopTime': datetime(2015, 1, 1),
'storageCapacity': 123,
'workflowId': 'string'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
items (list) --
A list of runs.
(dict) --
A workflow run.
arn (string) --
The run's ARN.
creationTime (datetime) --
When the run was created.
id (string) --
The run's ID.
name (string) --
The run's name.
priority (integer) --
The run's priority.
startTime (datetime) --
When the run started.
status (string) --
The run's status.
stopTime (datetime) --
When the run stopped.
storageCapacity (integer) --
The run's storage capacity.
workflowId (string) --
The run's workflow ID.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListSequenceStores¶paginator = client.get_paginator('list_sequence_stores')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_sequence_stores().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string'
},
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
The filter's start date.
The filter's end date.
A name to filter on.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'sequenceStores': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
}
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
sequenceStores (list) --
A list of sequence stores.
(dict) --
Details about a sequence store.
arn (string) --
The store's ARN.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListVariantImportJobs¶paginator = client.get_paginator('list_variant_import_jobs')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_variant_import_jobs().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'storeName': 'string'
},
ids=[
'string',
],
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
A status to filter on.
A store name to filter on.
A list of job IDs.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'variantImportJobs': [
{
'completionTime': datetime(2015, 1, 1),
'creationTime': datetime(2015, 1, 1),
'destinationName': 'string',
'id': 'string',
'roleArn': 'string',
'runLeftNormalization': True|False,
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'updateTime': datetime(2015, 1, 1)
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
variantImportJobs (list) --
A list of jobs.
(dict) --
A variant import job.
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destinationName (string) --
The job's destination variant store.
id (string) --
The job's ID.
roleArn (string) --
The job's service role ARN.
runLeftNormalization (boolean) --
The job's left normalization setting.
status (string) --
The job's status.
updateTime (datetime) --
When the job was updated.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListVariantStores¶paginator = client.get_paginator('list_variant_stores')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_variant_stores().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
filter={
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
},
ids=[
'string',
],
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A filter to apply to the list.
A status to filter on.
A list of store IDs.
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'variantStores': [
{
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'id': 'string',
'name': 'string',
'reference': {
'referenceArn': 'string'
},
'sseConfig': {
'keyArn': 'string',
'type': 'KMS'
},
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
'statusMessage': 'string',
'storeArn': 'string',
'storeSizeBytes': 123,
'updateTime': datetime(2015, 1, 1)
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
variantStores (list) --
A list of variant stores.
(dict) --
A variant store.
creationTime (datetime) --
When the store was created.
description (string) --
The store's description.
id (string) --
The store's ID.
name (string) --
The store's name.
reference (dict) --
The store's genome reference.
Note
This is a Tagged Union structure. Only one of the following top level keys will be set: referenceArn. If a client receives an unknown member it will set SDK_UNKNOWN_MEMBER as the top level key, which maps to the name or tag of the unknown member. The structure of SDK_UNKNOWN_MEMBER is as follows:
'SDK_UNKNOWN_MEMBER': {'name': 'UnknownMemberName'}
referenceArn (string) --
The reference's ARN.
sseConfig (dict) --
The store's server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
status (string) --
The store's status.
statusMessage (string) --
The store's status message.
storeArn (string) --
The store's ARN.
storeSizeBytes (integer) --
The store's size in bytes.
updateTime (datetime) --
When the store was updated.
NextToken (string) --
A token to resume pagination.
Omics.Paginator.ListWorkflows¶paginator = client.get_paginator('list_workflows')
paginate(**kwargs)¶Creates an iterator that will paginate through responses from Omics.Client.list_workflows().
See also: AWS API Documentation
Request Syntax
response_iterator = paginator.paginate(
name='string',
type='PRIVATE',
PaginationConfig={
'MaxItems': 123,
'PageSize': 123,
'StartingToken': 'string'
}
)
A dictionary that provides parameters to control pagination.
The total number of items to return. If the total number of items available is more than the value specified in max-items then a NextToken will be provided in the output that you can use to resume pagination.
The size of each page.
A token to specify where to start paginating. This is the NextToken from a previous response.
dict
Response Syntax
{
'items': [
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'digest': 'string',
'id': 'string',
'name': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED',
'type': 'PRIVATE'
},
],
'NextToken': 'string'
}
Response Structure
(dict) --
items (list) --
The workflows' items.
(dict) --
A workflow.
arn (string) --
The workflow's ARN.
creationTime (datetime) --
When the workflow was created.
digest (string) --
The workflow's digest.
id (string) --
The workflow's ID.
name (string) --
The workflow's name.
status (string) --
The workflow's status.
type (string) --
The workflow's type.
NextToken (string) --
A token to resume pagination.
The available waiters are:
Omics.Waiter.AnnotationImportJobCreatedOmics.Waiter.AnnotationStoreCreatedOmics.Waiter.AnnotationStoreDeletedOmics.Waiter.ReadSetActivationJobCompletedOmics.Waiter.ReadSetExportJobCompletedOmics.Waiter.ReadSetImportJobCompletedOmics.Waiter.ReferenceImportJobCompletedOmics.Waiter.RunCompletedOmics.Waiter.RunRunningOmics.Waiter.TaskCompletedOmics.Waiter.TaskRunningOmics.Waiter.VariantImportJobCreatedOmics.Waiter.VariantStoreCreatedOmics.Waiter.VariantStoreDeletedOmics.Waiter.WorkflowActiveOmics.Waiter.AnnotationImportJobCreated¶waiter = client.get_waiter('annotation_import_job_created')
wait(**kwargs)¶Polls Omics.Client.get_annotation_import_job() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
jobId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The job's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.AnnotationStoreCreated¶waiter = client.get_waiter('annotation_store_created')
wait(**kwargs)¶Polls Omics.Client.get_annotation_store() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
name='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The store's name.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.AnnotationStoreDeleted¶waiter = client.get_waiter('annotation_store_deleted')
wait(**kwargs)¶Polls Omics.Client.get_annotation_store() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
name='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The store's name.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.ReadSetActivationJobCompleted¶waiter = client.get_waiter('read_set_activation_job_completed')
wait(**kwargs)¶Polls Omics.Client.get_read_set_activation_job() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
id='string',
sequenceStoreId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's sequence store ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.ReadSetExportJobCompleted¶waiter = client.get_waiter('read_set_export_job_completed')
wait(**kwargs)¶Polls Omics.Client.get_read_set_export_job() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
id='string',
sequenceStoreId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's sequence store ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.ReadSetImportJobCompleted¶waiter = client.get_waiter('read_set_import_job_completed')
wait(**kwargs)¶Polls Omics.Client.get_read_set_import_job() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
id='string',
sequenceStoreId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's sequence store ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.ReferenceImportJobCompleted¶waiter = client.get_waiter('reference_import_job_completed')
wait(**kwargs)¶Polls Omics.Client.get_reference_import_job() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
id='string',
referenceStoreId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The job's ID.
[REQUIRED]
The job's reference store ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.RunCompleted¶waiter = client.get_waiter('run_completed')
wait(**kwargs)¶Polls Omics.Client.get_run() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
export=[
'DEFINITION',
],
id='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
The run's export format.
[REQUIRED]
The run's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.RunRunning¶waiter = client.get_waiter('run_running')
wait(**kwargs)¶Polls Omics.Client.get_run() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
export=[
'DEFINITION',
],
id='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
The run's export format.
[REQUIRED]
The run's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.TaskCompleted¶waiter = client.get_waiter('task_completed')
wait(**kwargs)¶Polls Omics.Client.get_run_task() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
id='string',
taskId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The task's ID.
[REQUIRED]
The task's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.TaskRunning¶waiter = client.get_waiter('task_running')
wait(**kwargs)¶Polls Omics.Client.get_run_task() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
id='string',
taskId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The task's ID.
[REQUIRED]
The task's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.VariantImportJobCreated¶waiter = client.get_waiter('variant_import_job_created')
wait(**kwargs)¶Polls Omics.Client.get_variant_import_job() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
jobId='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The job's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.VariantStoreCreated¶waiter = client.get_waiter('variant_store_created')
wait(**kwargs)¶Polls Omics.Client.get_variant_store() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
name='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The store's name.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.VariantStoreDeleted¶waiter = client.get_waiter('variant_store_deleted')
wait(**kwargs)¶Polls Omics.Client.get_variant_store() every 30 seconds until a successful state is reached. An error is returned after 20 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
name='string',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
[REQUIRED]
The store's name.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 30
The maximum number of attempts to be made. Default: 20
None
Omics.Waiter.WorkflowActive¶waiter = client.get_waiter('workflow_active')
wait(**kwargs)¶Polls Omics.Client.get_workflow() every 3 seconds until a successful state is reached. An error is returned after 10 failed checks.
See also: AWS API Documentation
Request Syntax
waiter.wait(
export=[
'DEFINITION',
],
id='string',
type='PRIVATE',
WaiterConfig={
'Delay': 123,
'MaxAttempts': 123
}
)
The export format for the workflow.
[REQUIRED]
The workflow's ID.
A dictionary that provides parameters to control waiting behavior.
The amount of time in seconds to wait between attempts. Default: 3
The maximum number of attempts to be made. Default: 10
None