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openapi.yaml
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components:
schemas:
AliasObjInput:
description: "Alias object\n\naliases (list, optional): unique names to allow\
\ using in place of whatever GUID\n specified"
properties:
aliases:
items: {}
title: Aliases
type: array
title: AliasObjInput
type: object
CreateObjForIdInput:
description: "Create object.\n\nfile_name (str): Name for the file being uploaded\n\
aliases (list, optional): unique name to allow using in place of whatever\
\ GUID gets\n created for this upload\nmetadata (dict, optional): any additional\
\ metadata to attach to the upload"
properties:
aliases:
items: {}
title: Aliases
type: array
file_name:
title: File Name
type: string
metadata:
title: Metadata
type: object
required:
- file_name
title: CreateObjForIdInput
type: object
CreateObjInput:
description: "Create object.\n\nfile_name (str): Name for the file being uploaded\n\
authz (dict): authorization block with requirements for what's being uploaded\n\
aliases (list, optional): unique name to allow using in place of whatever\
\ GUID gets\n created for this upload\nmetadata (dict, optional): any additional\
\ metadata to attach to the upload"
properties:
aliases:
items: {}
title: Aliases
type: array
authz:
title: Authz
type: object
file_name:
title: File Name
type: string
metadata:
title: Metadata
type: object
required:
- file_name
- authz
title: CreateObjInput
type: object
HTTPValidationError:
properties:
detail:
items:
$ref: '#/components/schemas/ValidationError'
title: Detail
type: array
title: HTTPValidationError
type: object
ValidationError:
properties:
loc:
items:
type: string
title: Location
type: array
msg:
title: Message
type: string
type:
title: Error Type
type: string
required:
- loc
- msg
- type
title: ValidationError
type: object
securitySchemes:
HTTPBasic:
scheme: basic
type: http
HTTPBearer:
scheme: bearer
type: http
info:
title: Framework Services Object Management Service
version: 2.0.1
openapi: 3.0.2
paths:
/_status:
get:
description: "Returns the status of the MDS:\n * error: if there was no error\
\ this will be \"none\"\n * last_update: timestamp of the last data pull from\
\ the commons\n * count: number of entries"
operationId: get_status__status_get
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
summary: Get Status
/aggregate/commons:
get:
description: "Returns a list of all commons with data in the aggregate metadata-service\n\
\nExample:\n\n { commons: [\"commonsA\", \"commonsB\" ] }"
operationId: get_commons_aggregate_commons_get
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
summary: Get Commons
tags:
- Aggregate
/aggregate/info/{what}:
get:
description: "Returns status and configuration information about aggregate metadata\
\ service.\n\nReturn configuration information. Currently supports only 1\
\ information type:\n**schema**\n\nExample:\n\n {\n schema: {\n \
\ ...\n ...\n }\n }"
operationId: get_commons_info_aggregate_info__what__get
parameters:
- in: path
name: what
required: true
schema:
title: What
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Commons Info
tags:
- Aggregate
/aggregate/metadata:
get:
description: "Returns metadata records\n\nReturns medata records namespaced\
\ by commons as a JSON object.\nExample without pagination:\n\n {\n \
\ \"commonA\" : {\n ... Metadata\n },\n \"commonB\"\
\ : {\n ... Metadata\n }\n ...\n }\n\nThe pagination\
\ option adds a pagination object to the response:\n\n {\n results:\
\ {\n \"commonA\" : {\n ... Metadata\n },\n\
\ \"commonB\" : {\n ... Metadata\n }\n \
\ ...\n },\n \"pagination\": {\n \"hits\":\
\ 64,\n \"offset\": 0,\n \"pageSize\": 20,\n \
\ \"pages\": 4\n }\n }\n\nThe flatten option removes the commons'\
\ namespace so all results are a child or results:\n\n results: {\n \
\ ... Metadata from commons A\n ... Metadata from commons B\n\
\ }\n ...\n },\n\n\nThe counts options when applied to an array\
\ or dictionary will replace\nthe field value with its length. If the field\
\ values is None it will replace it with 0.\nAll other types will be unchanged."
operationId: get_aggregate_metadata_aggregate_metadata_get
parameters:
- description: 'Maximum number of records returned. (e.g. max: 2000)'
in: query
name: limit
required: false
schema:
default: 20
description: 'Maximum number of records returned. (e.g. max: 2000)'
title: Limit
type: integer
- description: Return results at this given offset.
in: query
name: offset
required: false
schema:
default: 0
description: Return results at this given offset.
title: Offset
type: integer
- description: 'Return count of a field instead of the value if field is an
array otherwise field is unchanged. If field is **null** will
set field to **0**. Multiple fields can be compressed by comma
separating the field names: **files,authors**'
in: query
name: counts
required: false
schema:
default: ''
description: 'Return count of a field instead of the value if field is an
array otherwise field is unchanged. If field is **null** will
set field to **0**. Multiple fields can be compressed by comma
separating the field names: **files,authors**'
title: Counts
type: string
- description: Return the results without grouping items by commons.
in: query
name: flatten
required: false
schema:
default: false
description: Return the results without grouping items by commons.
title: Flatten
type: boolean
- description: If true will return a pagination object in the response
in: query
name: pagination
required: false
schema:
default: false
description: If true will return a pagination object in the response
title: Pagination
type: boolean
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Aggregate Metadata
tags:
- Aggregate
/aggregate/metadata/guid/{guid}:
get:
description: "Returns a metadata record by GUID\n\nExample:\n\n { id2: {\
\ name: \"bear\" } }"
operationId: get_aggregate_metadata_guid_aggregate_metadata_guid__guid__get
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Aggregate Metadata Guid
tags:
- Aggregate
/aggregate/metadata/{name}:
get:
description: "et all metadata records from a commons by name\n\nReturns an array\
\ containing all the metadata entries for a single commons.\nThere are no\
\ limit/offset parameters.\n\nExample:\n\n [ { id2: { name: \"bear\" }\
\ } , { id3: { name: \"cat\" } }]"
operationId: get_aggregate_metadata_for_commons_aggregate_metadata__name__get
parameters:
- in: path
name: name
required: true
schema:
title: Name
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Aggregate Metadata For Commons
tags:
- Aggregate
/aggregate/metadata/{name}/info:
get:
description: "Returns information from the named commons.\n\nExample:\n\n \
\ { commons_url: \"gen3.datacommons.io\" }"
operationId: get_aggregate_metadata_commons_info_aggregate_metadata__name__info_get
parameters:
- in: path
name: name
required: true
schema:
title: Name
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Aggregate Metadata Commons Info
tags:
- Aggregate
/aggregate/tags:
get:
description: "Returns aggregate category, name and counts across all commons\n\
\nExample:\n\n {\n \"Data Type\": {\n \"total\"\
: 275,\n \"names\": [\n {\n \"Genotype\"\
: 103,\n \"Clinical Phenotype\": 100,\n \"DCC\
\ Harmonized\": 24,\n \"WGS\": 20,\n \"SNP/CNV\
\ Genotypes (NGS)\": 6,\n \"RNA-Seq\": 5,\n \
\ \"WXS\": 5,\n \"Targeted-Capture\": 3,\n \"\
miRNA-Seq\": 3,\n \"CNV Genotypes\": 2\n }\n \
\ ]\n }\n }"
operationId: get_aggregate_tags_aggregate_tags_get
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
summary: Get Aggregate Tags
tags:
- Aggregate
/metadata:
get:
description: "Search the metadata.\n\nWithout filters, this will return all\
\ data. Add filters as query strings like this:\n\n GET /metadata?a=1&b=2\n\
\nThis will match all records that have metadata containing all of:\n\n \
\ {\"a\": 1, \"b\": 2}\n\nThe values are always treated as strings for filtering.\
\ Nesting is supported:\n\n GET /metadata?a.b.c=3\n\nMatching records containing:\n\
\n {\"a\": {\"b\": {\"c\": 3}}}\n\nProviding the same key with more than\
\ one value filters records whose value of the\ngiven key matches any of the\
\ given values. But values of different keys must all\nmatch. For example:\n\
\n GET /metadata?a.b.c=3&a.b.c=33&a.b.d=4\n\nMatches these:\n\n {\"\
a\": {\"b\": {\"c\": 3, \"d\": 4}}}\n {\"a\": {\"b\": {\"c\": 33, \"d\"\
: 4}}}\n {\"a\": {\"b\": {\"c\": \"3\", \"d\": 4, \"e\": 5}}}\n\nBut won't\
\ match these:\n\n {\"a\": {\"b\": {\"c\": 3}}}\n {\"a\": {\"b\": {\"\
c\": 3, \"d\": 5}}}\n {\"a\": {\"b\": {\"d\": 5}}}\n {\"a\": {\"b\"\
: {\"c\": \"333\", \"d\": 4}}}\n\nTo query all rows with a given key, regardless\
\ of value, use the \"*\" wildcard. For example:\n\n GET /metadata?a=*\
\ or GET /metadata?a.b=*\n\nNote that only a single asterisk is supported,\
\ not true wildcarding. For\nexample: `?a=1.*` will only match the exact string\
\ `\"1.*\"`.\n\nTo query rows with a value of `\"*\"` exactly, escape the\
\ asterisk. For example: `?a=\\*`."
operationId: search_metadata_metadata_get
parameters:
- description: Switch to returning a list of GUIDs (false), or GUIDs mapping
to their metadata (true).
in: query
name: data
required: false
schema:
default: false
description: Switch to returning a list of GUIDs (false), or GUIDs mapping
to their metadata (true).
title: Data
type: boolean
- description: 'Maximum number of records returned. (max: 2000)'
in: query
name: limit
required: false
schema:
default: 10
description: 'Maximum number of records returned. (max: 2000)'
title: Limit
type: integer
- description: Return results at this given offset.
in: query
name: offset
required: false
schema:
default: 0
description: Return results at this given offset.
title: Offset
type: integer
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Search Metadata
tags:
- Query
post:
description: Create metadata in batch.
operationId: batch_create_metadata_metadata_post
parameters:
- in: query
name: overwrite
required: false
schema:
default: true
title: Overwrite
type: boolean
requestBody:
content:
application/json:
schema:
items: {}
title: Data List
type: array
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Batch Create Metadata
tags:
- Maintain
/metadata/{guid}:
delete:
description: Delete the metadata of the GUID.
operationId: delete_metadata_metadata__guid__delete
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Delete Metadata
tags:
- Maintain
get:
description: Get the metadata of the GUID.
operationId: get_metadata_metadata__guid__get
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Metadata
tags:
- Query
post:
description: Create metadata for the GUID.
operationId: create_metadata_metadata__guid__post
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
- in: query
name: overwrite
required: false
schema:
default: false
title: Overwrite
type: boolean
requestBody:
content:
application/json:
schema:
title: Data
type: object
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Create Metadata
tags:
- Maintain
put:
description: 'Update the metadata of the GUID.
If `merge` is True, then any top-level keys that are not in the new data will
be
kept, and those that also exist in the new data will be replaced completely.
This
is also known as the shallow merge. The metadata service currently doesn''t
support
deep merge.'
operationId: update_metadata_metadata__guid__put
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
- in: query
name: merge
required: false
schema:
default: false
title: Merge
type: boolean
requestBody:
content:
application/json:
schema:
title: Data
type: object
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Update Metadata
tags:
- Maintain
/metadata/{guid}/aliases:
delete:
description: Delete all metadata_aliases of the GUID.
operationId: delete_all_metadata_aliases_metadata__guid__aliases_delete
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Delete All Metadata Aliases
tags:
- Aliases
get:
description: Get the aliases for the provided GUID
operationId: get_metadata_aliases_metadata__guid__aliases_get
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Metadata Aliases
tags:
- Query
post:
description: Create metadata aliases for the GUID.
operationId: create_metadata_aliases_metadata__guid__aliases_post
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/AliasObjInput'
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Create Metadata Aliases
tags:
- Aliases
put:
description: 'Update the metadata aliases of the GUID.
If `merge` is True, then any aliases that are not in the new data will be
kept.'
operationId: update_metadata_alias_metadata__guid__aliases_put
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
- in: query
name: merge
required: false
schema:
default: false
title: Merge
type: boolean
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/AliasObjInput'
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Update Metadata Alias
tags:
- Aliases
/metadata/{guid}/aliases/{alias}:
delete:
description: Delete the specified metadata_alias of the GUID.
operationId: delete_metadata_alias_metadata__guid__aliases__alias__delete
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
- in: path
name: alias
required: true
schema:
title: Alias
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Delete Metadata Alias
tags:
- Aliases
/metadata_index:
get:
description: List all the metadata key paths indexed in the database.
operationId: list_metadata_indexes_metadata_index_get
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
security:
- HTTPBasic: []
- HTTPBearer: []
summary: List Metadata Indexes
tags:
- Index
/metadata_index/{path}:
delete:
description: Drop the database index on the given metadata key path.
operationId: drop_metadata_indexes_metadata_index__path__delete
parameters:
- in: path
name: path
required: true
schema:
title: Path
responses:
'204':
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Drop Metadata Indexes
tags:
- Index
post:
description: Create a database index on the given metadata key path.
operationId: create_metadata_indexes_metadata_index__path__post
parameters:
- in: path
name: path
required: true
schema:
title: Path
responses:
'201':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBasic: []
- HTTPBearer: []
summary: Create Metadata Indexes
tags:
- Index
/objects/upload:
post:
description: Create object placeholder and attach metadata, return Upload url
to the user.
operationId: create_object_objects_upload_post
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/CreateObjInput'
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBearer: []
summary: Create Object
tags:
- Object
/objects/{guid}:
delete:
description: 'Delete the metadata for the specified object and also delete the
record from indexd.
[Optional] Remove the object from existing bucket location(s) by proxying
to
fence DELETE /data/file_id by using an additional query parameter `delete_file_locations`.
Uses the response status code from fence/indexd to determine whether user
has
permission to delete metadata.'
operationId: delete_object_objects__guid__delete
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBearer: []
summary: Delete Object
tags:
- Object
get:
description: 'Get the metadata associated with the provided key. If the key
is an
indexd GUID or alias, also returns the indexd record.'
operationId: get_object_objects__guid__get
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Object
tags:
- Object
post:
description: 'Create object placeholder and attach metadata, return Upload url
to the
user. A new GUID (new version of the provided GUID) will be created for
this object. The new record will have the same authz as the original one.'
operationId: create_object_for_id_objects__guid__post
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/CreateObjForIdInput'
required: true
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
security:
- HTTPBearer: []
summary: Create Object For Id
tags:
- Object
/objects/{guid}/download:
get:
description: 'Send a GET request to the data access service to generate a signed
download
url for the given GUID or alias. Returns the generated signed download url
to the user.'
operationId: get_object_signed_download_url_objects__guid__download_get
parameters:
- in: path
name: guid
required: true
schema:
title: Guid
type: string
responses:
'200':
content:
application/json:
schema: {}
description: Successful Response
'422':
content:
application/json:
schema:
$ref: '#/components/schemas/HTTPValidationError'
description: Validation Error
summary: Get Object Signed Download Url
tags:
- Object
/objects/{guid}/latest:
get:
description: 'Attempt to fetch the latest version of the provided guid/key from
indexd.
If the provided guid/key is found in indexd, return the indexd record and