Amazon Omics

2023/08/14 - Amazon Omics - 10 new5 updated api methods

Changes  This release provides support for annotation store versioning and cross account sharing for Omics Analytics

GetShare (new) Link ¶

Retrieves the metadata for a share.

See also: AWS API Documentation

Request Syntax

client.get_share(
    shareId='string'
)
type shareId:

string

param shareId:

[REQUIRED]

The generated ID for a share.

rtype:

dict

returns:

Response Syntax

{
    'share': {
        'shareId': 'string',
        'resourceArn': 'string',
        'principalSubscriber': 'string',
        'ownerId': 'string',
        'status': 'PENDING'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'FAILED',
        'statusMessage': 'string',
        'shareName': 'string',
        'creationTime': datetime(2015, 1, 1),
        'updateTime': datetime(2015, 1, 1)
    }
}

Response Structure

  • (dict) --

    • share (dict) --

      An analytic store share details object. contains status, resourceArn, ownerId, etc.

      • shareId (string) --

        The ID for a share offer for an analytics store .

      • resourceArn (string) --

        The resource Arn of the analytics store being shared.

      • principalSubscriber (string) --

        The principal subscriber is the account the analytics store data is being shared with.

      • ownerId (string) --

        The account ID for the data owner. The owner creates the share offer.

      • status (string) --

        The status of a share.

      • statusMessage (string) --

        The status message for a share. It provides more details on the status of the share.

      • shareName (string) --

        The name of the share.

      • creationTime (datetime) --

        The timestamp for when the share was created.

      • updateTime (datetime) --

        The timestamp of the share update.

DeleteShare (new) Link ¶

Deletes a share of an analytics store.

See also: AWS API Documentation

Request Syntax

client.delete_share(
    shareId='string'
)
type shareId:

string

param shareId:

[REQUIRED]

The ID for the share request to be deleted.

rtype:

dict

returns:

Response Syntax

{
    'status': 'PENDING'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'FAILED'
}

Response Structure

  • (dict) --

    • status (string) --

      The status of the share being deleted.

ListAnnotationStoreVersions (new) Link ¶

Lists the versions of an annotation store.

See also: AWS API Documentation

Request Syntax

client.list_annotation_store_versions(
    name='string',
    maxResults=123,
    nextToken='string',
    filter={
        'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED'
    }
)
type name:

string

param name:

[REQUIRED]

The name of an annotation store.

type maxResults:

integer

param maxResults:

The maximum number of annotation store versions to return in one page of results.

type nextToken:

string

param nextToken:

Specifies the pagination token from a previous request to retrieve the next page of results.

type filter:

dict

param filter:

A filter to apply to the list of annotation store versions.

  • status (string) --

    The status of an annotation store version.

rtype:

dict

returns:

Response Syntax

{
    'annotationStoreVersions': [
        {
            'storeId': 'string',
            'id': 'string',
            'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
            'versionArn': 'string',
            'name': 'string',
            'versionName': 'string',
            'description': 'string',
            'creationTime': datetime(2015, 1, 1),
            'updateTime': datetime(2015, 1, 1),
            'statusMessage': 'string',
            'versionSizeBytes': 123
        },
    ],
    'nextToken': 'string'
}

Response Structure

  • (dict) --

    • annotationStoreVersions (list) --

      Lists all versions of an annotation store.

      • (dict) --

        Annotation store versions.

        • storeId (string) --

          The store ID for an annotation store version.

        • id (string) --

          The annotation store version ID.

        • status (string) --

          The status of an annotation store version.

        • versionArn (string) --

          The Arn for an annotation store version.

        • name (string) --

          A name given to an annotation store version to distinguish it from others.

        • versionName (string) --

          The name of an annotation store version.

        • description (string) --

          The description of an annotation store version.

        • creationTime (datetime) --

          The time stamp for when an annotation store version was created.

        • updateTime (datetime) --

          The time stamp for when an annotation store version was updated.

        • statusMessage (string) --

          The status of an annotation store version.

        • versionSizeBytes (integer) --

          The size of an annotation store version in Bytes.

    • nextToken (string) --

      Specifies the pagination token from a previous request to retrieve the next page of results.

GetAnnotationStoreVersion (new) Link ¶

Retrieves the metadata for an annotation store version.

See also: AWS API Documentation

Request Syntax

client.get_annotation_store_version(
    name='string',
    versionName='string'
)
type name:

string

param name:

[REQUIRED]

The name given to an annotation store version to distinguish it from others.

type versionName:

string

param versionName:

[REQUIRED]

The name given to an annotation store version to distinguish it from others.

rtype:

dict

returns:

Response Syntax

{
    'storeId': 'string',
    'id': 'string',
    'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
    'versionArn': 'string',
    'name': 'string',
    'versionName': 'string',
    'description': 'string',
    'creationTime': datetime(2015, 1, 1),
    'updateTime': datetime(2015, 1, 1),
    'tags': {
        'string': 'string'
    },
    'versionOptions': {
        'tsvVersionOptions': {
            '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'
                },
            ]
        }
    },
    'statusMessage': 'string',
    'versionSizeBytes': 123
}

Response Structure

  • (dict) --

    • storeId (string) --

      The store ID for annotation store version.

    • id (string) --

      The annotation store version ID.

    • status (string) --

      The status of an annotation store version.

    • versionArn (string) --

      The Arn for the annotation store.

    • name (string) --

      The name of the annotation store.

    • versionName (string) --

      The name given to an annotation store version to distinguish it from others.

    • description (string) --

      The description for an annotation store version.

    • creationTime (datetime) --

      The time stamp for when an annotation store version was created.

    • updateTime (datetime) --

      The time stamp for when an annotation store version was updated.

    • tags (dict) --

      Any tags associated with an annotation store version.

      • (string) --

        • (string) --

    • versionOptions (dict) --

      The options for an annotation store version.

      • tsvVersionOptions (dict) --

        File settings for a version of a TSV store.

        • annotationType (string) --

          The store version's annotation type.

        • formatToHeader (dict) --

          The annotation store version's header key to column name mapping.

          • (string) --

            • (string) --

        • schema (list) --

          The TSV schema for an annotation store version.

          • (dict) --

            • (string) --

              • (string) --

    • statusMessage (string) --

      The status of an annotation store version.

    • versionSizeBytes (integer) --

      The size of the annotation store version in Bytes.

UpdateAnnotationStoreVersion (new) Link ¶

Updates the description of an annotation store version.

See also: AWS API Documentation

Request Syntax

client.update_annotation_store_version(
    name='string',
    versionName='string',
    description='string'
)
type name:

string

param name:

[REQUIRED]

The name of an annotation store.

type versionName:

string

param versionName:

[REQUIRED]

The name of an annotation store version.

type description:

string

param description:

The description of an annotation store.

rtype:

dict

returns:

Response Syntax

{
    'storeId': 'string',
    'id': 'string',
    'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
    'name': 'string',
    'versionName': 'string',
    'description': 'string',
    'creationTime': datetime(2015, 1, 1),
    'updateTime': datetime(2015, 1, 1)
}

Response Structure

  • (dict) --

    • storeId (string) --

      The annotation store ID.

    • id (string) --

      The annotation store version ID.

    • status (string) --

      The status of an annotation store version.

    • name (string) --

      The name of an annotation store.

    • versionName (string) --

      The name of an annotation store version.

    • description (string) --

      The description of an annotation store version.

    • creationTime (datetime) --

      The time stamp for when an annotation store version was created.

    • updateTime (datetime) --

      The time stamp for when an annotation store version was updated.

CreateAnnotationStoreVersion (new) Link ¶

Creates a new version of an annotation store.

See also: AWS API Documentation

Request Syntax

client.create_annotation_store_version(
    name='string',
    versionName='string',
    description='string',
    versionOptions={
        'tsvVersionOptions': {
            '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'
    }
)
type name:

string

param name:

[REQUIRED]

The name of an annotation store version from which versions are being created.

type versionName:

string

param versionName:

[REQUIRED]

The name given to an annotation store version to distinguish it from other versions.

type description:

string

param description:

The description of an annotation store version.

type versionOptions:

dict

param versionOptions:

The options for an annotation store version.

  • tsvVersionOptions (dict) --

    File settings for a version of a TSV store.

    • annotationType (string) --

      The store version's annotation type.

    • formatToHeader (dict) --

      The annotation store version's header key to column name mapping.

      • (string) --

        • (string) --

    • schema (list) --

      The TSV schema for an annotation store version.

      • (dict) --

        • (string) --

          • (string) --

type tags:

dict

param tags:

Any tags added to annotation store version.

  • (string) --

    • (string) --

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'versionName': 'string',
    'storeId': 'string',
    'versionOptions': {
        'tsvVersionOptions': {
            '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'
                },
            ]
        }
    },
    'name': 'string',
    'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
    'creationTime': datetime(2015, 1, 1)
}

Response Structure

  • (dict) --

    • id (string) --

      A generated ID for the annotation store

    • versionName (string) --

      The name given to an annotation store version to distinguish it from other versions.

    • storeId (string) --

      The ID for the annotation store from which new versions are being created.

    • versionOptions (dict) --

      The options for an annotation store version.

      • tsvVersionOptions (dict) --

        File settings for a version of a TSV store.

        • annotationType (string) --

          The store version's annotation type.

        • formatToHeader (dict) --

          The annotation store version's header key to column name mapping.

          • (string) --

            • (string) --

        • schema (list) --

          The TSV schema for an annotation store version.

          • (dict) --

            • (string) --

              • (string) --

    • name (string) --

      The name given to an annotation store version to distinguish it from other versions.

    • status (string) --

      The status of a annotation store version.

    • creationTime (datetime) --

      The time stamp for the creation of an annotation store version.

ListShares (new) Link ¶

Lists all shares associated with an account.

See also: AWS API Documentation

Request Syntax

client.list_shares(
    resourceOwner='SELF'|'OTHER',
    filter={
        'resourceArns': [
            'string',
        ],
        'status': [
            'PENDING'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'FAILED',
        ]
    },
    nextToken='string',
    maxResults=123
)
type resourceOwner:

string

param resourceOwner:

[REQUIRED]

The account that owns the analytics store shared.

type filter:

dict

param filter:

Attributes used to filter for a specific subset of shares.

  • resourceArns (list) --

    The Amazon Resource Number (Arn) for an analytics store.

    • (string) --

  • status (list) --

    The status of an annotation store version.

    • (string) --

type nextToken:

string

param nextToken:

Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.

type maxResults:

integer

param maxResults:

The maximum number of shares to return in one page of results.

rtype:

dict

returns:

Response Syntax

{
    'shares': [
        {
            'shareId': 'string',
            'resourceArn': 'string',
            'principalSubscriber': 'string',
            'ownerId': 'string',
            'status': 'PENDING'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'FAILED',
            'statusMessage': 'string',
            'shareName': 'string',
            'creationTime': datetime(2015, 1, 1),
            'updateTime': datetime(2015, 1, 1)
        },
    ],
    'nextToken': 'string'
}

Response Structure

  • (dict) --

    • shares (list) --

      The shares available and their meta details.

      • (dict) --

        The details of a share.

        • shareId (string) --

          The ID for a share offer for an analytics store .

        • resourceArn (string) --

          The resource Arn of the analytics store being shared.

        • principalSubscriber (string) --

          The principal subscriber is the account the analytics store data is being shared with.

        • ownerId (string) --

          The account ID for the data owner. The owner creates the share offer.

        • status (string) --

          The status of a share.

        • statusMessage (string) --

          The status message for a share. It provides more details on the status of the share.

        • shareName (string) --

          The name of the share.

        • creationTime (datetime) --

          The timestamp for when the share was created.

        • updateTime (datetime) --

          The timestamp of the share update.

    • nextToken (string) --

      Next token returned in the response of a previous ListSharesResponse call. Used to get the next page of results.

DeleteAnnotationStoreVersions (new) Link ¶

Deletes one or multiple versions of an annotation store.

See also: AWS API Documentation

Request Syntax

client.delete_annotation_store_versions(
    name='string',
    versions=[
        'string',
    ],
    force=True|False
)
type name:

string

param name:

[REQUIRED]

The name of the annotation store from which versions are being deleted.

type versions:

list

param versions:

[REQUIRED]

The versions of an annotation store to be deleted.

  • (string) --

type force:

boolean

param force:

Forces the deletion of an annotation store version when imports are in-progress..

rtype:

dict

returns:

Response Syntax

{
    'errors': [
        {
            'versionName': 'string',
            'message': 'string'
        },
    ]
}

Response Structure

  • (dict) --

    • errors (list) --

      Any errors that occur when attempting to delete an annotation store version.

      • (dict) --

        The error preventing deletion of the annotation store version.

        • versionName (string) --

          The name given to an annotation store version.

        • message (string) --

          The message explaining the error in annotation store deletion.

CreateShare (new) Link ¶

Creates a share offer that can be accepted outside the account by a subscriber. The share is created by the owner and accepted by the principal subscriber.

See also: AWS API Documentation

Request Syntax

client.create_share(
    resourceArn='string',
    principalSubscriber='string',
    shareName='string'
)
type resourceArn:

string

param resourceArn:

[REQUIRED]

The resource ARN for the analytics store to be shared.

type principalSubscriber:

string

param principalSubscriber:

[REQUIRED]

The principal subscriber is the account being given access to the analytics store data through the share offer.

type shareName:

string

param shareName:

A name given to the share.

rtype:

dict

returns:

Response Syntax

{
    'shareId': 'string',
    'status': 'PENDING'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'FAILED',
    'shareName': 'string'
}

Response Structure

  • (dict) --

    • shareId (string) --

      An ID generated for the share.

    • status (string) --

      The status of a share.

    • shareName (string) --

      A name given to the share.

AcceptShare (new) Link ¶

Accepts a share for an analytics store.

See also: AWS API Documentation

Request Syntax

client.accept_share(
    shareId='string'
)
type shareId:

string

param shareId:

[REQUIRED]

The ID for a share offer for analytics store data.

rtype:

dict

returns:

Response Syntax

{
    'status': 'PENDING'|'ACTIVATING'|'ACTIVE'|'DELETING'|'DELETED'|'FAILED'
}

Response Structure

  • (dict) --

    • status (string) --

      The status of an analytics store share.

CreateAnnotationStore (updated) Link ¶
Changes (both) 
{'versionName': 'string'}

Creates an annotation store.

See also: AWS API Documentation

Request Syntax

client.create_annotation_store(
    reference={
        'referenceArn': 'string'
    },
    name='string',
    description='string',
    tags={
        'string': 'string'
    },
    versionName='string',
    sseConfig={
        'type': 'KMS',
        'keyArn': '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'
                },
            ]
        }
    }
)
type reference:

dict

param reference:

The genome reference for the store's annotations.

  • referenceArn (string) --

    The reference's ARN.

type name:

string

param name:

A name for the store.

type description:

string

param description:

A description for the store.

type tags:

dict

param tags:

Tags for the store.

  • (string) --

    • (string) --

type versionName:

string

param versionName:

The name given to an annotation store version to distinguish it from other versions.

type sseConfig:

dict

param sseConfig:

Server-side encryption (SSE) settings for the store.

  • type (string) -- [REQUIRED]

    The encryption type.

  • keyArn (string) --

    An encryption key ARN.

type storeFormat:

string

param storeFormat:

[REQUIRED]

The annotation file format of the store.

type storeOptions:

dict

param storeOptions:

File parsing options for the annotation store.

  • 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) --

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'reference': {
        'referenceArn': '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'
                },
            ]
        }
    },
    'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
    'name': 'string',
    'versionName': 'string',
    'creationTime': datetime(2015, 1, 1)
}

Response Structure

  • (dict) --

    • id (string) --

      The store's ID.

    • reference (dict) --

      The store's genome reference. Required for all stores except TSV format with generic annotations.

      • referenceArn (string) --

        The reference's ARN.

    • storeFormat (string) --

      The annotation file format of the store.

    • storeOptions (dict) --

      The store's file parsing options.

      • 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) --

    • status (string) --

      The store's status.

    • name (string) --

      The store's name.

    • versionName (string) --

      The name given to an annotation store version to distinguish it from other versions.

    • creationTime (datetime) --

      When the store was created.

GetAnnotationImportJob (updated) Link ¶
Changes (response) 
{'versionName': 'string'}

Gets information about an annotation import job.

See also: AWS API Documentation

Request Syntax

client.get_annotation_import_job(
    jobId='string'
)
type jobId:

string

param jobId:

[REQUIRED]

The job's ID.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'destinationName': 'string',
    'versionName': 'string',
    'roleArn': 'string',
    'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
    'statusMessage': 'string',
    'creationTime': datetime(2015, 1, 1),
    'updateTime': datetime(2015, 1, 1),
    'completionTime': datetime(2015, 1, 1),
    'items': [
        {
            'source': 'string',
            'jobStatus': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES'
        },
    ],
    'runLeftNormalization': True|False,
    'formatOptions': {
        'tsvOptions': {
            'readOptions': {
                'sep': 'string',
                'encoding': 'string',
                'quote': 'string',
                'quoteAll': True|False,
                'escape': 'string',
                'escapeQuotes': True|False,
                'comment': 'string',
                'header': True|False,
                'lineSep': 'string'
            }
        },
        'vcfOptions': {
            'ignoreQualField': True|False,
            'ignoreFilterField': True|False
        }
    },
    'annotationFields': {
        'string': 'string'
    }
}

Response Structure

  • (dict) --

    • id (string) --

      The job's ID.

    • destinationName (string) --

      The job's destination annotation store.

    • versionName (string) --

      The name of the annotation store version.

    • roleArn (string) --

      The job's service role ARN.

    • status (string) --

      The job's status.

    • statusMessage (string) --

      The job's status message.

    • creationTime (datetime) --

      When the job was created.

    • updateTime (datetime) --

      When the job was updated.

    • completionTime (datetime) --

      When the job completed.

    • items (list) --

      The job's imported items.

      • (dict) --

        Details about an imported annotation item.

        • source (string) --

          The source file's location in Amazon S3.

        • jobStatus (string) --

          The item's job status.

    • runLeftNormalization (boolean) --

      The job's left normalization setting.

    • formatOptions (dict) --

      Formatting options for a file.

      • tsvOptions (dict) --

        Options for a TSV file.

        • readOptions (dict) --

          The file's read options.

          • sep (string) --

            The file's field separator.

          • encoding (string) --

            The file's encoding.

          • quote (string) --

            The file's quote character.

          • quoteAll (boolean) --

            Whether all values need to be quoted, or just those that contain quotes.

          • escape (string) --

            A character for escaping quotes in the file.

          • escapeQuotes (boolean) --

            Whether quotes need to be escaped in the file.

          • comment (string) --

            The file's comment character.

          • header (boolean) --

            Whether the file has a header row.

          • lineSep (string) --

            A line separator for the file.

      • vcfOptions (dict) --

        Options for a VCF file.

        • ignoreQualField (boolean) --

          The file's ignore qual field setting.

        • ignoreFilterField (boolean) --

          The file's ignore filter field setting.

    • annotationFields (dict) --

      The annotation schema generated by the parsed annotation data.

      • (string) --

        • (string) --

GetAnnotationStore (updated) Link ¶
Changes (response) 
{'numVersions': 'integer'}

Gets information about an annotation store.

See also: AWS API Documentation

Request Syntax

client.get_annotation_store(
    name='string'
)
type name:

string

param name:

[REQUIRED]

The store's name.

rtype:

dict

returns:

Response Syntax

{
    'id': 'string',
    'reference': {
        'referenceArn': 'string'
    },
    'status': 'CREATING'|'UPDATING'|'DELETING'|'ACTIVE'|'FAILED',
    'storeArn': 'string',
    'name': 'string',
    'description': 'string',
    'sseConfig': {
        'type': 'KMS',
        'keyArn': 'string'
    },
    'creationTime': datetime(2015, 1, 1),
    'updateTime': datetime(2015, 1, 1),
    'tags': {
        'string': 'string'
    },
    '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'
                },
            ]
        }
    },
    'storeFormat': 'GFF'|'TSV'|'VCF',
    'statusMessage': 'string',
    'storeSizeBytes': 123,
    'numVersions': 123
}

Response Structure

  • (dict) --

    • id (string) --

      The store's ID.

    • reference (dict) --

      The store's genome reference.

      • referenceArn (string) --

        The reference's ARN.

    • status (string) --

      The store's status.

    • storeArn (string) --

      The store's ARN.

    • name (string) --

      The store's name.

    • description (string) --

      The store's description.

    • sseConfig (dict) --

      The store's server-side encryption (SSE) settings.

      • type (string) --

        The encryption type.

      • keyArn (string) --

        An encryption key ARN.

    • creationTime (datetime) --

      When the store was created.

    • updateTime (datetime) --

      When the store was updated.

    • tags (dict) --

      The store's tags.

      • (string) --

        • (string) --

    • storeOptions (dict) --

      The store's parsing options.

      • 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) --

    • storeFormat (string) --

      The store's annotation file format.

    • statusMessage (string) --

      A status message.

    • storeSizeBytes (integer) --

      The store's size in bytes.

    • numVersions (integer) --

      An integer indicating how many versions of an annotation store exist.

ListAnnotationImportJobs (updated) Link ¶
Changes (response) 
{'annotationImportJobs': {'versionName': 'string'}}

Retrieves a list of annotation import jobs.

See also: AWS API Documentation

Request Syntax

client.list_annotation_import_jobs(
    maxResults=123,
    ids=[
        'string',
    ],
    nextToken='string',
    filter={
        'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
        'storeName': 'string'
    }
)
type maxResults:

integer

param maxResults:

The maximum number of jobs to return in one page of results.

type ids:

list

param ids:

IDs of annotation import jobs to retrieve.

  • (string) --

type nextToken:

string

param nextToken:

Specifies the pagination token from a previous request to retrieve the next page of results.

type filter:

dict

param filter:

A filter to apply to the list.

  • status (string) --

    A status to filter on.

  • storeName (string) --

    A store name to filter on.

rtype:

dict

returns:

Response Syntax

{
    'annotationImportJobs': [
        {
            'id': 'string',
            'destinationName': 'string',
            'versionName': 'string',
            'roleArn': 'string',
            'status': 'SUBMITTED'|'IN_PROGRESS'|'CANCELLED'|'COMPLETED'|'FAILED'|'COMPLETED_WITH_FAILURES',
            'creationTime': datetime(2015, 1, 1),
            'updateTime': datetime(2015, 1, 1),
            'completionTime': datetime(2015, 1, 1),
            'runLeftNormalization': True|False,
            'annotationFields': {
                'string': 'string'
            }
        },
    ],
    'nextToken': 'string'
}

Response Structure

  • (dict) --

    • annotationImportJobs (list) --

      A list of jobs.

      • (dict) --

        An annotation import job.

        • id (string) --

          The job's ID.

        • destinationName (string) --

          The job's destination annotation store.

        • versionName (string) --

          The name of the annotation store version.

        • roleArn (string) --

          The job's service role ARN.

        • status (string) --

          The job's status.

        • creationTime (datetime) --

          When the job was created.

        • updateTime (datetime) --

          When the job was updated.

        • completionTime (datetime) --

          When the job completed.

        • runLeftNormalization (boolean) --

          The job's left normalization setting.

        • annotationFields (dict) --

          The annotation schema generated by the parsed annotation data.

          • (string) --

            • (string) --

    • nextToken (string) --

      Specifies the pagination token from a previous request to retrieve the next page of results.

StartAnnotationImportJob (updated) Link ¶
Changes (request) 
{'versionName': 'string'}

Starts an annotation import job.

See also: AWS API Documentation

Request Syntax

client.start_annotation_import_job(
    destinationName='string',
    roleArn='string',
    items=[
        {
            'source': 'string'
        },
    ],
    versionName='string',
    formatOptions={
        'tsvOptions': {
            'readOptions': {
                'sep': 'string',
                'encoding': 'string',
                'quote': 'string',
                'quoteAll': True|False,
                'escape': 'string',
                'escapeQuotes': True|False,
                'comment': 'string',
                'header': True|False,
                'lineSep': 'string'
            }
        },
        'vcfOptions': {
            'ignoreQualField': True|False,
            'ignoreFilterField': True|False
        }
    },
    runLeftNormalization=True|False,
    annotationFields={
        'string': 'string'
    }
)
type destinationName:

string

param destinationName:

[REQUIRED]

A destination annotation store for the job.

type roleArn:

string

param roleArn:

[REQUIRED]

A service role for the job.

type items:

list

param items:

[REQUIRED]

Items to import.

  • (dict) --

    A source for an annotation import job.

    • source (string) -- [REQUIRED]

      The source file's location in Amazon S3.

type versionName:

string

param versionName:

The name of the annotation store version.

type formatOptions:

dict

param formatOptions:

Formatting options for the annotation file.

  • tsvOptions (dict) --

    Options for a TSV file.

    • readOptions (dict) --

      The file's read options.

      • sep (string) --

        The file's field separator.

      • encoding (string) --

        The file's encoding.

      • quote (string) --

        The file's quote character.

      • quoteAll (boolean) --

        Whether all values need to be quoted, or just those that contain quotes.

      • escape (string) --

        A character for escaping quotes in the file.

      • escapeQuotes (boolean) --

        Whether quotes need to be escaped in the file.

      • comment (string) --

        The file's comment character.

      • header (boolean) --

        Whether the file has a header row.

      • lineSep (string) --

        A line separator for the file.

  • vcfOptions (dict) --

    Options for a VCF file.

    • ignoreQualField (boolean) --

      The file's ignore qual field setting.

    • ignoreFilterField (boolean) --

      The file's ignore filter field setting.

type runLeftNormalization:

boolean

param runLeftNormalization:

The job's left normalization setting.

type annotationFields:

dict

param annotationFields:

The annotation schema generated by the parsed annotation data.

  • (string) --

    • (string) --

rtype:

dict

returns:

Response Syntax

{
    'jobId': 'string'
}

Response Structure

  • (dict) --

    • jobId (string) --

      The job's ID.