AWS API Changes

2023/08/14 - Amazon Omics - 10 new 5 updated api methods

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

GetShare (new)

Retrieves the metadata for a share.

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.

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.

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.
  Note
  
  This is a Tagged Union structure. Only one of the following top level keys will be set: tsvVersionOptions. 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'}
```
  - 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.

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.

Note

This is a Tagged Union structure. Only one of the following top level keys can be set: tsvVersionOptions.

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.
  Note
  
  This is a Tagged Union structure. Only one of the following top level keys will be set: tsvVersionOptions. 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'}
```
  - 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.

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.

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.

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.

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.

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.

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.

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.

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) --

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.
  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.
- 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) --
- 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.
  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.
      - 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.
  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.
- 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.
  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) --
- 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.

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.
  - 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.