2022/11/29 - Amazon Omics - 66 new api methods
Changes Amazon Omics is a new, purpose-built service that can be used by healthcare and life science organizations to store, query, and analyze omics data. The insights from that data can be used to accelerate scientific discoveries and improve healthcare.
Retrieves a list of read set import jobs.
See also: AWS API Documentation
Request Syntax
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'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
status (string) --
A status to filter on.
integer
The maximum number of jobs to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
[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.
Cancels a run.
See also: AWS API Documentation
Request Syntax
client.cancel_run(
id='string'
)
string
[REQUIRED]
The run's ID.
None
Retrieves a list of references.
See also: AWS API Documentation
Request Syntax
client.list_references(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'md5': 'string',
'name': 'string'
},
maxResults=123,
nextToken='string',
referenceStoreId='string'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
md5 (string) --
An MD5 checksum to filter on.
name (string) --
A name to filter on.
integer
The maximum number of references to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
[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.
Creates a reference store.
See also: AWS API Documentation
Request Syntax
client.create_reference_store(
clientToken='string',
description='string',
name='string',
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
tags={
'string': 'string'
}
)
string
To ensure that requests don't run multiple times, specify a unique token for each request.
string
A description for the store.
string
[REQUIRED]
A name for the store.
dict
Server-side encryption (SSE) settings for the store.
keyArn (string) --
An encryption key ARN.
type (string) -- [REQUIRED]
The encryption type.
dict
Tags for the store.
(string) --
(string) --
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.
Retrieves a list of variant stores.
See also: AWS API Documentation
Request Syntax
client.list_variant_stores(
filter={
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
dict
A filter to apply to the list.
status (string) --
A status to filter on.
list
A list of store IDs.
(string) --
integer
The maximum number of stores to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Retrieves a list of run groups.
See also: AWS API Documentation
Request Syntax
client.list_run_groups(
maxResults=123,
name='string',
startingToken='string'
)
integer
The maximum number of run groups to return in one page of results.
string
The run groups' name.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Gets a reference file.
See also: AWS API Documentation
Request Syntax
client.get_reference(
file='SOURCE'|'INDEX',
id='string',
partNumber=123,
range='string',
referenceStoreId='string'
)
string
The file to retrieve.
string
[REQUIRED]
The reference's ID.
integer
[REQUIRED]
The part number to retrieve.
string
The range to retrieve.
string
[REQUIRED]
The reference's store ID.
dict
Response Syntax
{
'payload': StreamingBody()
}
Response Structure
(dict) --
payload (:class:`.StreamingBody`) --
The reference file payload.
Gets a file from a read set.
See also: AWS API Documentation
Request Syntax
client.get_read_set(
file='SOURCE1'|'SOURCE2'|'INDEX',
id='string',
partNumber=123,
sequenceStoreId='string'
)
string
The file to retrieve.
string
[REQUIRED]
The read set's ID.
integer
[REQUIRED]
The part number to retrieve.
string
[REQUIRED]
The read set's sequence store ID.
dict
Response Syntax
{
'payload': StreamingBody()
}
Response Structure
(dict) --
payload (:class:`.StreamingBody`) --
The read set file payload.
Gets information about a workflow run group.
See also: AWS API Documentation
Request Syntax
client.get_run_group(
id='string'
)
string
[REQUIRED]
The group's ID.
dict
Response Syntax
{
'arn': 'string',
'creationTime': datetime(2015, 1, 1),
'id': 'string',
'maxCpus': 123,
'maxDuration': 123,
'maxRuns': 123,
'name': 'string',
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
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 number of CPUs to use.
maxDuration (integer) --
The group's maximum run duration.
maxRuns (integer) --
The maximum number of concurrent runs for the group.
name (string) --
The group's name.
tags (dict) --
The group's tags.
(string) --
(string) --
Gets information about a sequence store.
See also: AWS API Documentation
Request Syntax
client.get_sequence_store(
id='string'
)
string
[REQUIRED]
The store's ID.
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 server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
Gets information about a read set import job.
See also: AWS API Documentation
Request Syntax
client.get_read_set_import_job(
id='string',
sequenceStoreId='string'
)
string
[REQUIRED]
The job's ID.
string
[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.
(string) --
(string) --
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
Deletes an annotation store.
See also: AWS API Documentation
Request Syntax
client.delete_annotation_store(
force=True|False,
name='string'
)
boolean
Whether to force deletion.
string
[REQUIRED]
The store's name.
dict
Response Syntax
{
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
}
Response Structure
(dict) --
status (string) --
The store's status.
Gets information about a workflow run task.
See also: AWS API Documentation
Request Syntax
client.get_run_task(
id='string',
taskId='string'
)
string
[REQUIRED]
The task's ID.
string
[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.
Starts a read set export job.
See also: AWS API Documentation
Request Syntax
client.start_read_set_export_job(
clientToken='string',
destination='string',
roleArn='string',
sequenceStoreId='string',
sources=[
{
'readSetId': 'string'
},
]
)
string
To ensure that jobs don't run multiple times, specify a unique token for each job.
string
[REQUIRED]
A location for exported files in Amazon S3.
string
[REQUIRED]
A service role for the job.
string
[REQUIRED]
The read set's sequence store ID.
list
[REQUIRED]
Sources for the job.
(dict) --
A read set.
readSetId (string) -- [REQUIRED]
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.
Deletes a variant store.
See also: AWS API Documentation
Request Syntax
client.delete_variant_store(
force=True|False,
name='string'
)
boolean
Whether to force deletion.
string
[REQUIRED]
The store's name.
dict
Response Syntax
{
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
}
Response Structure
(dict) --
status (string) --
The store's status.
Gets information about a read set activation job.
See also: AWS API Documentation
Request Syntax
client.get_read_set_activation_job(
id='string',
sequenceStoreId='string'
)
string
[REQUIRED]
The job's ID.
string
[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.
Creates a workflow.
See also: AWS API Documentation
Request Syntax
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'
}
)
string
The URI of a definition for the workflow.
bytes
A ZIP archive for the workflow.
string
A description for the workflow.
string
An engine for the workflow.
string
The path of the main definition file for the workflow.
string
A name for the workflow.
dict
A parameter template for the workflow.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
string
[REQUIRED]
A request ID for the workflow.
This field is autopopulated if not provided.
integer
A storage capacity for the workflow.
dict
Tags for the workflow.
(string) --
(string) --
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.
(string) --
(string) --
Gets information about a variant store.
See also: AWS API Documentation
Request Syntax
client.get_variant_store(
name='string'
)
string
[REQUIRED]
The store's name.
dict
Response Syntax
{
'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
(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.
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.
tags (dict) --
The store's tags.
(string) --
(string) --
updateTime (datetime) --
When the store was updated.
Deletes a workflow run group.
See also: AWS API Documentation
Request Syntax
client.delete_run_group(
id='string'
)
string
[REQUIRED]
The run group's ID.
None
Retrieves a list of reference import jobs.
See also: AWS API Documentation
Request Syntax
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'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
status (string) --
A status to filter on.
integer
The maximum number of jobs to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
[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.
Removes tags from a resource.
See also: AWS API Documentation
Request Syntax
client.untag_resource(
resourceArn='string',
tagKeys=[
'string',
]
)
string
[REQUIRED]
The resource's ARN.
list
[REQUIRED]
Keys of tags to remove.
(string) --
dict
Response Syntax
{}
Response Structure
(dict) --
Updates an annotation store.
See also: AWS API Documentation
Request Syntax
client.update_annotation_store(
description='string',
name='string'
)
string
A description for the store.
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.
(string) --
(string) --
schema (list) --
The store's schema.
(dict) --
(string) --
(string) --
updateTime (datetime) --
When the store was updated.
Gets information about a workflow.
See also: AWS API Documentation
Request Syntax
client.get_workflow(
export=[
'DEFINITION',
],
id='string',
type='PRIVATE'
)
list
The export format for the workflow.
(string) --
string
[REQUIRED]
The workflow's ID.
string
The workflow's type.
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.
(string) --
(string) --
type (string) --
The workflow's type.
Retrieves a list of reference stores.
See also: AWS API Documentation
Request Syntax
client.list_reference_stores(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string'
},
maxResults=123,
nextToken='string'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
name (string) --
The name to filter on.
integer
The maximum number of stores to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Deletes a genome reference.
See also: AWS API Documentation
Request Syntax
client.delete_reference(
id='string',
referenceStoreId='string'
)
string
[REQUIRED]
The reference's ID.
string
[REQUIRED]
The reference's store ID.
dict
Response Syntax
{}
Response Structure
(dict) --
Gets information about a variant import job.
See also: AWS API Documentation
Request Syntax
client.get_variant_import_job(
jobId='string'
)
string
[REQUIRED]
The job's ID.
dict
Response Syntax
{
'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
(dict) --
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.
items (list) --
The job's items.
(dict) --
Details about an imported variant item.
jobStatus (string) --
The item's job status.
source (string) --
The source file's location in Amazon S3.
roleArn (string) --
The job's service role ARN.
runLeftNormalization (boolean) --
The job's left normalization setting.
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
updateTime (datetime) --
When the job was updated.
Deletes a workflow run.
See also: AWS API Documentation
Request Syntax
client.delete_run(
id='string'
)
string
[REQUIRED]
The run's ID.
None
Creates a run group.
See also: AWS API Documentation
Request Syntax
client.create_run_group(
maxCpus=123,
maxDuration=123,
maxRuns=123,
name='string',
requestId='string',
tags={
'string': 'string'
}
)
integer
The maximum number of CPUs to use in the group.
integer
A max duration for the group.
integer
The maximum number of concurrent runs for the group.
string
A name for the group.
string
[REQUIRED]
A request ID for the group.
This field is autopopulated if not provided.
dict
Tags for the group.
(string) --
(string) --
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.
(string) --
(string) --
Starts a read set import job.
See also: AWS API Documentation
Request Syntax
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'
}
},
]
)
string
To ensure that jobs don't run multiple times, specify a unique token for each job.
string
[REQUIRED]
A service role for the job.
string
[REQUIRED]
The read set's sequence store ID.
list
[REQUIRED]
Source files to import.
(dict) --
A source for a read set import job.
description (string) --
The source's description.
generatedFrom (string) --
Where the source originated.
name (string) --
The source's name.
referenceArn (string) -- [REQUIRED]
The source's reference ARN.
sampleId (string) -- [REQUIRED]
The source's sample ID.
sourceFileType (string) -- [REQUIRED]
The source's file type.
sourceFiles (dict) -- [REQUIRED]
The source files' location in Amazon S3.
source1 (string) -- [REQUIRED]
The location of the first file in Amazon S3.
source2 (string) --
The location of the second file in Amazon S3.
subjectId (string) -- [REQUIRED]
The source's subject ID.
tags (dict) --
The source's tags.
(string) --
(string) --
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.
Starts a run.
See also: AWS API Documentation
Request Syntax
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'
)
string
A log level for the run.
string
A name for the run.
string
An output URI for the run.
Parameters for the run.
integer
A priority for the run.
string
[REQUIRED]
A request ID for the run.
This field is autopopulated if not provided.
string
[REQUIRED]
A service role for the run.
string
The run's group ID.
string
The run's ID.
integer
A storage capacity for the run.
dict
Tags for the run.
(string) --
(string) --
string
The run's workflow ID.
string
The run's workflows type.
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.
(string) --
(string) --
Retrieves a list of annotation stores.
See also: AWS API Documentation
Request Syntax
client.list_annotation_stores(
filter={
'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
dict
A filter to apply to the list.
status (string) --
A status to filter on.
list
IDs of stores to list.
(string) --
integer
The maximum number of stores to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Retrieves a list of variant import jobs.
See also: AWS API Documentation
Request Syntax
client.list_variant_import_jobs(
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'storeName': 'string'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
dict
A filter to apply to the list.
status (string) --
A status to filter on.
storeName (string) --
A store name to filter on.
list
A list of job IDs.
(string) --
integer
The maximum number of import jobs to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Retrieves a list of workflows.
See also: AWS API Documentation
Request Syntax
client.list_workflows(
maxResults=123,
name='string',
startingToken='string',
type='PRIVATE'
)
integer
The maximum number of workflows to return in one page of results.
string
The workflows' name.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
The workflows' type.
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.
Retrieves a list of read sets.
See also: AWS API Documentation
Request Syntax
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'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
name (string) --
A name to filter on.
referenceArn (string) --
A genome reference ARN to filter on.
status (string) --
A status to filter on.
integer
The maximum number of read sets to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
[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.
Gets information about a read set export job.
See also: AWS API Documentation
Request Syntax
client.get_read_set_export_job(
id='string',
sequenceStoreId='string'
)
string
[REQUIRED]
The job's ID.
string
[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.
Updates a workflow.
See also: AWS API Documentation
Request Syntax
client.update_workflow(
description='string',
id='string',
name='string'
)
string
A description for the workflow.
string
[REQUIRED]
The workflow's ID.
string
A name for the workflow.
None
Gets information about a reference store.
See also: AWS API Documentation
Request Syntax
client.get_reference_store(
id='string'
)
string
[REQUIRED]
The store's ID.
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 server-side encryption (SSE) settings.
keyArn (string) --
An encryption key ARN.
type (string) --
The encryption type.
Updates a variant store.
See also: AWS API Documentation
Request Syntax
client.update_variant_store(
description='string',
name='string'
)
string
A description for the store.
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.
Gets information about an annotation import job.
See also: AWS API Documentation
Request Syntax
client.get_annotation_import_job(
jobId='string'
)
string
[REQUIRED]
The job's ID.
dict
Response Syntax
{
'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
(dict) --
completionTime (datetime) --
When the job completed.
creationTime (datetime) --
When the job was created.
destinationName (string) --
The job's destination annotation store.
formatOptions (dict) --
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'}
tsvOptions (dict) --
Options for a TSV file.
readOptions (dict) --
The file's read options.
comment (string) --
The file's comment character.
encoding (string) --
The file's encoding.
escape (string) --
A character for escaping quotes in the file.
escapeQuotes (boolean) --
Whether quotes need to be escaped in the file.
header (boolean) --
Whether the file has a header row.
lineSep (string) --
A line separator for the file.
quote (string) --
The file's quote character.
quoteAll (boolean) --
Whether all values need to be quoted, or just those that contain quotes.
sep (string) --
The file's field separator.
vcfOptions (dict) --
Options for a VCF file.
ignoreFilterField (boolean) --
The file's ignore filter field setting.
ignoreQualField (boolean) --
The file's ignore qual field setting.
id (string) --
The job's ID.
items (list) --
The job's imported items.
(dict) --
Details about an imported annotation item.
jobStatus (string) --
The item's job status.
source (string) --
The source file's location in Amazon S3.
roleArn (string) --
The job's service role ARN.
runLeftNormalization (boolean) --
The job's left normalization setting.
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
updateTime (datetime) --
When the job was updated.
Creates a variant store.
See also: AWS API Documentation
Request Syntax
client.create_variant_store(
description='string',
name='string',
reference={
'referenceArn': 'string'
},
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
tags={
'string': 'string'
}
)
string
A description for the store.
string
A name for the store.
dict
[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.
referenceArn (string) --
The reference's ARN.
dict
Server-side encryption (SSE) settings for the store.
keyArn (string) --
An encryption key ARN.
type (string) -- [REQUIRED]
The encryption type.
dict
Tags for the store.
(string) --
(string) --
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.
Creates a sequence store.
See also: AWS API Documentation
Request Syntax
client.create_sequence_store(
clientToken='string',
description='string',
name='string',
sseConfig={
'keyArn': 'string',
'type': 'KMS'
},
tags={
'string': 'string'
}
)
string
To ensure that requests don't run multiple times, specify a unique token for each request.
string
A description for the store.
string
[REQUIRED]
A name for the store.
dict
Server-side encryption (SSE) settings for the store.
keyArn (string) --
An encryption key ARN.
type (string) -- [REQUIRED]
The encryption type.
dict
Tags for the store.
(string) --
(string) --
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.
Retrieves a list of tasks for a run.
See also: AWS API Documentation
Request Syntax
client.list_run_tasks(
id='string',
maxResults=123,
startingToken='string',
status='PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'CANCELLED'|'FAILED'
)
string
[REQUIRED]
The run's ID.
integer
The maximum number of run tasks to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
Filter the list by status.
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.
Retrieves a list of sequence stores.
See also: AWS API Documentation
Request Syntax
client.list_sequence_stores(
filter={
'createdAfter': datetime(2015, 1, 1),
'createdBefore': datetime(2015, 1, 1),
'name': 'string'
},
maxResults=123,
nextToken='string'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
name (string) --
A name to filter on.
integer
The maximum number of stores to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Deletes a workflow.
See also: AWS API Documentation
Request Syntax
client.delete_workflow(
id='string'
)
string
[REQUIRED]
The workflow's ID.
None
Gets information about a workflow run.
See also: AWS API Documentation
Request Syntax
client.get_run(
export=[
'DEFINITION',
],
id='string'
)
list
The run's export format.
(string) --
string
[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 (:ref:`document<document>`) --
The run's parameters.
priority (integer) --
The run's priority.
resourceDigests (dict) --
The run's resource digests.
(string) --
(string) --
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.
(string) --
(string) --
workflowId (string) --
The run's workflow ID.
workflowType (string) --
The run's workflow type.
Retrieves a list of runs.
See also: AWS API Documentation
Request Syntax
client.list_runs(
maxResults=123,
name='string',
runGroupId='string',
startingToken='string'
)
integer
The maximum number of runs to return in one page of results.
string
Filter the list by run name.
string
Filter the list by run group ID.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Starts an annotation import job.
See also: AWS API Documentation
Request Syntax
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
)
string
[REQUIRED]
A destination annotation store for the job.
dict
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.
tsvOptions (dict) --
Options for a TSV file.
readOptions (dict) --
The file's read options.
comment (string) --
The file's comment character.
encoding (string) --
The file's encoding.
escape (string) --
A character for escaping quotes in the file.
escapeQuotes (boolean) --
Whether quotes need to be escaped in the file.
header (boolean) --
Whether the file has a header row.
lineSep (string) --
A line separator for the file.
quote (string) --
The file's quote character.
quoteAll (boolean) --
Whether all values need to be quoted, or just those that contain quotes.
sep (string) --
The file's field separator.
vcfOptions (dict) --
Options for a VCF file.
ignoreFilterField (boolean) --
The file's ignore filter field setting.
ignoreQualField (boolean) --
The file's ignore qual field setting.
list
[REQUIRED]
Items to import.
(dict) --
A source for an annotation import job.
source (string) -- [REQUIRED]
The source file's location in Amazon S3.
string
[REQUIRED]
A service role for the job.
boolean
The job's left normalization setting.
dict
Response Syntax
{
'jobId': 'string'
}
Response Structure
(dict) --
jobId (string) --
The job's ID.
Deletes a sequence store.
See also: AWS API Documentation
Request Syntax
client.delete_sequence_store(
id='string'
)
string
[REQUIRED]
The sequence store's ID.
dict
Response Syntax
{}
Response Structure
(dict) --
Deletes a genome reference store.
See also: AWS API Documentation
Request Syntax
client.delete_reference_store(
id='string'
)
string
[REQUIRED]
The store's ID.
dict
Response Syntax
{}
Response Structure
(dict) --
Retrieves a list of read set activation jobs.
See also: AWS API Documentation
Request Syntax
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'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
status (string) --
The filter's status.
integer
The maximum number of read set activation jobs to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
[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.
Creates an annotation store.
See also: AWS API Documentation
Request Syntax
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'
}
)
string
A description for the store.
string
A name for the store.
dict
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.
referenceArn (string) --
The reference's ARN.
dict
Server-side encryption (SSE) settings for the store.
keyArn (string) --
An encryption key ARN.
type (string) -- [REQUIRED]
The encryption type.
string
[REQUIRED]
The annotation file format of the store.
dict
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.
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.
(string) --
(string) --
schema (list) --
The store's schema.
(dict) --
(string) --
(string) --
dict
Tags for the store.
(string) --
(string) --
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.
(string) --
(string) --
schema (list) --
The store's schema.
(dict) --
(string) --
(string) --
Starts a read set activation job.
See also: AWS API Documentation
Request Syntax
client.start_read_set_activation_job(
clientToken='string',
sequenceStoreId='string',
sources=[
{
'readSetId': 'string'
},
]
)
string
To ensure that jobs don't run multiple times, specify a unique token for each job.
string
[REQUIRED]
The read set's sequence store ID.
list
[REQUIRED]
The job's sources.
(dict) --
A source for a read set activation job.
readSetId (string) -- [REQUIRED]
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.
Retrieves a list of read set export jobs.
See also: AWS API Documentation
Request Syntax
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'
)
dict
A filter to apply to the list.
createdAfter (datetime) --
The filter's start date.
createdBefore (datetime) --
The filter's end date.
status (string) --
A status to filter on.
integer
The maximum number of jobs to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
string
[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.
Gets information about an annotation store.
See also: AWS API Documentation
Request Syntax
client.get_annotation_store(
name='string'
)
string
[REQUIRED]
The store's name.
dict
Response Syntax
{
'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
(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.
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) --
A status message.
storeArn (string) --
The store's ARN.
storeFormat (string) --
The store's annotation file format.
storeOptions (dict) --
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'}
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.
(string) --
(string) --
schema (list) --
The store's schema.
(dict) --
(string) --
(string) --
storeSizeBytes (integer) --
The store's size in bytes.
tags (dict) --
The store's tags.
(string) --
(string) --
updateTime (datetime) --
When the store was updated.
Cancels an annotation import job.
See also: AWS API Documentation
Request Syntax
client.cancel_annotation_import_job(
jobId='string'
)
string
[REQUIRED]
The job's ID.
dict
Response Syntax
{}
Response Structure
(dict) --
Starts a reference import job.
See also: AWS API Documentation
Request Syntax
client.start_reference_import_job(
clientToken='string',
referenceStoreId='string',
roleArn='string',
sources=[
{
'description': 'string',
'name': 'string',
'sourceFile': 'string',
'tags': {
'string': 'string'
}
},
]
)
string
To ensure that jobs don't run multiple times, specify a unique token for each job.
string
[REQUIRED]
The job's reference store ID.
string
[REQUIRED]
A service role for the job.
list
[REQUIRED]
Sources for the job.
(dict) --
A source for a reference import job.
description (string) --
The source's description.
name (string) -- [REQUIRED]
The source's name.
sourceFile (string) -- [REQUIRED]
The source file's location in Amazon S3.
tags (dict) --
The source's tags.
(string) --
(string) --
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.
Starts a variant import job.
See also: AWS API Documentation
Request Syntax
client.start_variant_import_job(
destinationName='string',
items=[
{
'source': 'string'
},
],
roleArn='string',
runLeftNormalization=True|False
)
string
[REQUIRED]
The destination variant store for the job.
list
[REQUIRED]
Items to import.
(dict) --
A imported variant item's source.
source (string) -- [REQUIRED]
The source file's location in Amazon S3.
string
[REQUIRED]
A service role for the job.
boolean
The job's left normalization setting.
dict
Response Syntax
{
'jobId': 'string'
}
Response Structure
(dict) --
jobId (string) --
The job's ID.
Retrieves a list of annotation import jobs.
See also: AWS API Documentation
Request Syntax
client.list_annotation_import_jobs(
filter={
'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED',
'storeName': 'string'
},
ids=[
'string',
],
maxResults=123,
nextToken='string'
)
dict
A filter to apply to the list.
status (string) --
A status to filter on.
storeName (string) --
A store name to filter on.
list
IDs of annotation import jobs to retrieve.
(string) --
integer
The maximum number of jobs to return in one page of results.
string
Specify the pagination token from a previous request to retrieve the next page of results.
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.
Gets information about a genome reference's metadata.
See also: AWS API Documentation
Request Syntax
client.get_reference_metadata(
id='string',
referenceStoreId='string'
)
string
[REQUIRED]
The reference's ID.
string
[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.
Tags a resource.
See also: AWS API Documentation
Request Syntax
client.tag_resource(
resourceArn='string',
tags={
'string': 'string'
}
)
string
[REQUIRED]
The resource's ARN.
dict
[REQUIRED]
Tags for the resource.
(string) --
(string) --
dict
Response Syntax
{}
Response Structure
(dict) --
Gets information about a reference import job.
See also: AWS API Documentation
Request Syntax
client.get_reference_import_job(
id='string',
referenceStoreId='string'
)
string
[REQUIRED]
The job's ID.
string
[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.
(string) --
(string) --
status (string) --
The job's status.
statusMessage (string) --
The job's status message.
Cancels a variant import job.
See also: AWS API Documentation
Request Syntax
client.cancel_variant_import_job(
jobId='string'
)
string
[REQUIRED]
The job's ID.
dict
Response Syntax
{}
Response Structure
(dict) --
Gets details about a read set.
See also: AWS API Documentation
Request Syntax
client.get_read_set_metadata(
id='string',
sequenceStoreId='string'
)
string
[REQUIRED]
The read set's ID.
string
[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.
Retrieves a list of tags for a resource.
See also: AWS API Documentation
Request Syntax
client.list_tags_for_resource(
resourceArn='string'
)
string
[REQUIRED]
The resource's ARN.
dict
Response Syntax
{
'tags': {
'string': 'string'
}
}
Response Structure
(dict) --
tags (dict) --
A list of tags.
(string) --
(string) --
Updates a run group.
See also: AWS API Documentation
Request Syntax
client.update_run_group(
id='string',
maxCpus=123,
maxDuration=123,
maxRuns=123,
name='string'
)
string
[REQUIRED]
The group's ID.
integer
The maximum number of CPUs to use.
integer
The maximum amount of time to run.
integer
The maximum number of concurrent runs for the group.
string
A name for the group.
None
Deletes one or more read sets.
See also: AWS API Documentation
Request Syntax
client.batch_delete_read_set(
ids=[
'string',
],
sequenceStoreId='string'
)
list
[REQUIRED]
The read sets' IDs.
(string) --
string
[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.