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additions.openapi.yaml
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additions.openapi.yaml
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paths:
/service-info:
post:
summary: Register service info.
description: Create or update the service info.
operationId: postServiceInfo
tags:
- TRS-Filer
requestBody:
description: Service info to add.
required: true
content:
application/json:
schema:
x-body-name: service_info
$ref: '#/components/schemas/ServiceRegister'
responses:
'201':
description: The service info was successfully created.
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
/tools:
post:
summary: Add a tool.
description: Create a tool object with a randomly generated unique ID.
operationId: postTool
tags:
- TRS-Filer
requestBody:
description: Tool (meta)data to add.
required: true
content:
application/json:
schema:
x-body-name: tool
$ref: '#/components/schemas/ToolRegister'
responses:
'200':
description: The tool was successfully created.
content:
application/json:
schema:
description: Tool identifier.
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
"/tools/{id}":
put:
summary: Add or update a tool.
description: Create a tool object with a predefined ID. Overwrites any
existing tool object with the same ID.
operationId: putTool
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool, scoped to this
registry, for example `123456`.
schema:
type: string
requestBody:
description: Tool (meta)data to add.
required: true
content:
application/json:
schema:
x-body-name: tool
$ref: '#/components/schemas/ToolRegister'
responses:
'200':
description: The tool was successfully created/updated.
content:
application/json:
schema:
description: Tool identifier.
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
delete:
summary: Delete a tool.
description: Delete an existing tool object.
operationId: deleteTool
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool, scoped to this
registry, for example `123456`.
schema:
type: string
responses:
'200':
description: The tool was successfully deleted.
content:
application/json:
schema:
type: string
description: Identifier of deleted tool.
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'404':
description: The requested tool was not found.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
"/tools/{id}/versions":
post:
summary: Add a tool version.
description: Create a tool version object.
operationId: postToolVersion
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool, scoped to this
registry, for example `123456`.
schema:
type: string
requestBody:
description: Tool version (meta)data to add.
required: true
content:
application/json:
schema:
x-body-name: tool_version
$ref: '#/components/schemas/ToolVersionRegister'
responses:
'200':
description: The tool version was successfully created.
content:
application/json:
schema:
description: Tool version identifier.
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
"/tools/{id}/versions/{version_id}":
delete:
summary: Delete a tool version.
description: Delete an existing tool version object.
operationId: deleteToolVersion
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool, scoped to this
registry, for example `123456`.
schema:
type: string
- name: version_id
in: path
required: true
description: An identifier of the tool version for this particular
tool registry, for example `v1`.
schema:
type: string
responses:
'200':
description: The tool version was successfully deleted.
content:
application/json:
schema:
description: Identifier of deleted tool version.
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'404':
description: The requested tool was not found.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
put:
summary: Add or update a tool version.
description: Create a tool version object with a predefined ID.
Overwrites any existing tool version object with the same ID.
operationId: putToolVersion
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool, scoped to this
registry, for example `123456`.
schema:
type: string
- name: version_id
in: path
required: true
description: A unique identifier of the tool version, scoped to this
registry, for example `123456`.
schema:
type: string
requestBody:
description: Tool version (meta)data to add.
required: true
content:
application/json:
schema:
x-body-name: tool_version
$ref: '#/components/schemas/ToolVersionRegister'
responses:
'200':
description: The tool version was successfully created/updated.
content:
application/json:
schema:
description: Tool identifier.
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
/toolClasses:
post:
summary: Create a tool class.
description: Create a tool class with a randomly generated unique ID.
operationId: postToolClass
tags:
- TRS-Filer
requestBody:
description: Tool class (meta)data to add.
required: true
content:
application/json:
schema:
x-body-name: tool_class
$ref: '#/components/schemas/ToolClassRegister'
responses:
'200':
description: The tool class was successfully created.
content:
application/json:
schema:
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
"/toolClasses/{id}":
delete:
summary: Delete a tool class.
description: Delete an existing tool object.
operationId: deleteToolClass
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool class, scoped to this
registry, for example `123456`.
schema:
type: string
responses:
'200':
description: The tool class was successfully deleted.
content:
application/json:
schema:
description: Identifier of deleted tool version.
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'404':
description: The requested tool was not found.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
put:
summary: Create or update a tool class.
description: Create a tool class with a predefined unique ID. Overwrites
any existing tool object with the same ID.
operationId: putToolClass
tags:
- TRS-Filer
parameters:
- name: id
in: path
required: true
description: A unique identifier of the tool class, scoped to this
registry, for example `123456`.
schema:
type: string
requestBody:
description: Tool class (meta)data to add.
required: true
content:
application/json:
schema:
x-body-name: tool_class
$ref: '#/components/schemas/ToolClassRegister'
responses:
'200':
description: The tool class was successfully created/updated.
content:
application/json:
schema:
type: string
'400':
description: The request is malformed.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'401':
description: The request is unauthorized.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'403':
description: The requester is not authorized to perform this action.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
'500':
description: An unexpected error occurred.
content:
application/json:
schema:
$ref: '#/components/schemas/Error'
components:
schemas:
ChecksumRegister:
type: object
required:
- checksum
- type
additionalProperties: false
properties:
checksum:
type: string
description: "The hex-string encoded checksum for the data. "
type:
type: string
description: >-
The digest method used to create the checksum.
The value (e.g. `sha-256`) SHOULD be listed as `Hash Name String` in the https://github.com/ga4gh-discovery/ga4gh-checksum/blob/master/hash-alg.csv[GA4GH Checksum Hash Algorithm Registry].
Other values MAY be used, as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920].
GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future.
TypeRegister:
type: string
description: Type of file. For descriptor files (`PRIMARY_DESCRIPTOR`
and `SECONDARY_DESCRIPTOR`), test files (`TEST_FILE`) and other files
(`OTHER`), the allowed file types are enumerated in the
`DescriptorType` schema. For container recipe files (`CONTAINERFILE`),
the allowed file types are enumerated in the
`ImageType` schema.
anyOf:
- $ref: '#/components/schemas/DescriptorType'
- $ref: '#/components/schemas/ImageType'
example: CWL
FilesRegister:
type: object
description: Properties and (a pointer to the) contents of a file.
required:
- tool_file
- file_wrapper
- type
additionalProperties: false
properties:
tool_file:
$ref: '#/components/schemas/ToolFileRegister'
file_wrapper:
$ref: '#/components/schemas/FileWrapperRegister'
type:
$ref: '#/components/schemas/TypeRegister'
FileWrapperRegister:
type: object
description: >
A file provides content for one of
- A tool descriptor is a metadata document that describes one or more tools.
- A tool document that describes how to test with one or more sample test
JSON.
- A containerfile is a document that describes how to build a particular
container image. Examples include Dockerfiles for creating Docker images
and Singularity recipes for Singularity images
additionalProperties: false
properties:
content:
type: string
description: The content of the file itself. One of url or content is required.
checksum:
type: array
items:
$ref: "#/components/schemas/ChecksumRegister"
description: "A production (immutable) tool version is required to have a
hashcode. Not required otherwise, but might be useful to detect
changes. "
example:
- checksum: ea2a5db69bd20a42976838790bc29294df3af02b
type: sha1
url:
type: string
description: Optional url to the underlying content, should include version
information, and can include a git hash. Note that this URL should
resolve to the raw unwrapped content that would otherwise be
available in content. One of url or content is required.
ImageDataRegister:
type: object
description: Describes one container image.
additionalProperties: false
properties:
registry_host:
type: string
description: A docker registry or a URL to a Singularity registry. Used along
with image_name to locate a specific image.
image_name:
type: string
description: Used in conjunction with a registry_url if provided to locate images.
size:
type: integer
description: Size of the container in bytes.
updated:
type: string
description: Last time the container was updated.
checksum:
type: array
items:
$ref: "#/components/schemas/ChecksumRegister"
description: A production (immutable) tool version is required to have a
hashcode. Not required otherwise, but might be useful to detect
changes. This exposes the hashcode for specific image versions to
verify that the container version pulled is actually the version
that was indexed by the registry.
example:
- checksum: 77af4d6b9913e693e8d0b4b294fa62ade6054e6b2f1ffb617ac955dd63fb0182
type: sha256
image_type:
$ref: "#/components/schemas/ImageType"
ServiceRegister:
description: 'GA4GH service'
type: object
required:
- id
- name
- type
- organization
- version
additionalProperties: false
properties:
id:
type: string
description: 'Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.'
example: 'org.ga4gh.myservice'
name:
type: string
description: 'Name of this service. Should be human readable.'
example: 'My project'
type:
$ref: '#/components/schemas/ServiceTypeRegister'
description:
type: string
description: 'Description of the service. Should be human readable and provide information about the service.'
example: 'This service provides...'
organization:
type: object
description: 'Organization providing the service'
required:
- name
- url
properties:
name:
type: string
description: 'Name of the organization responsible for the service'
example: 'My organization'
url:
type: string
format: uri
description: 'URL of the website of the organization (RFC 3986 format)'
example: 'https://example.com'
contactUrl:
type: string
format: uri
description: 'URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).'
example: 'mailto:[email protected]'
documentationUrl:
type: string
format: uri
description: 'URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.'
example: 'https://docs.myservice.example.com'
createdAt:
type: string
format: date-time
description: 'Timestamp describing when the service was first deployed and available (RFC 3339 format)'
example: '2019-06-04T12:58:19Z'
updatedAt:
type: string
format: date-time
description: 'Timestamp describing when the service was last updated (RFC 3339 format)'
example: '2019-06-04T12:58:19Z'
environment:
type: string
description: 'Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.'
example: 'test'
version:
type: string
description: 'Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.'
example: '1.0.0'
ServiceTypeRegister:
description: 'Type of a GA4GH service'
type: object
required:
- group
- artifact
- version
additionalProperties: false
properties:
group:
type: string
description: 'Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization''s reverse domain name).'
example: 'org.ga4gh'
artifact:
type: string
description: 'Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.'
example: 'beacon'
version:
type: string
description: 'Version of the API or specification. GA4GH specifications use semantic versioning.'
example: '1.0.0'
ToolClassRegister:
type: object
description: Describes a class (type) of tool allowing us to categorize
workflows, tasks, and maybe even other entities (such as services)
separately.
additionalProperties: false
properties:
name:
type: string
description: A short friendly name for the class.
description:
type: string
description: A longer explanation of what this class is and what it can
accomplish.
ToolClassRegisterId:
type: object
description: Describes a class (type) of tool allowing us to categorize
workflows, tasks, and maybe even other entities (such as services)
separately.
additionalProperties: false
properties:
id:
type: string
description: The unique identifier for the class.
name:
type: string
description: A short friendly name for the class.
description:
type: string
description: A longer explanation of what this class is and what it can
accomplish.
ToolFileRegister:
type: object
additionalProperties: false
required:
- path
- file_type
properties:
path:
type: string
description: Relative path of the file. A descriptor's path can be used with
the GA4GH .../{type}/descriptor/{relative_path} endpoint.
file_type:
type: string
enum:
- TEST_FILE
- PRIMARY_DESCRIPTOR
- SECONDARY_DESCRIPTOR
- CONTAINERFILE
- OTHER
example: OTHER
ToolRegister:
type: object
description: A tool (or described tool) is defined as a tuple of a
descriptor file (which potentially consists of multiple files), a set
of container images, and a set of instructions for creating those
images.
required:
- organization
- toolclass
- versions
additionalProperties: false
properties:
aliases:
type: array
items:
type: string
example:
- 630d31c3-381e-488d-b639-ce5d047a0142
- dockstore.org:630d31c3-381e-488d-b639-ce5d047a0142
- bio.tools:630d31c3-381e-488d-b639-ce5d047a0142
description: >-
Support for this parameter is optional for tool registries that
support aliases. A list of strings that can be used to identify
this tool which could be straight up URLs. This can be used to
expose alternative ids (such as GUIDs) for a tool for registries.
Can be used to match tools across registries.
organization:
type: string
description: The organization that published the image.
name:
type: string
description: The name of the tool.
toolclass:
$ref: "#/components/schemas/ToolClassRegisterId"
description:
type: string
description: The description of the tool.
has_checker:
type: boolean
description: Whether this tool has a checker tool associated with it.
checker_url:
type: string
description: Optional url to the checker tool that will exit
successfully if this tool produced the expected result given test
data.
versions:
description: A list of versions for this tool.
type: array
items:
anyOf:
- $ref: "#/components/schemas/ToolVersionRegister"
- $ref: "#/components/schemas/ToolVersionRegisterId"
ToolVersionRegister:
type: object
description: A tool version describes a particular iteration of a tool as
described by a reference to a specific image and/or documents.
additionalProperties: false
properties:
author:
type: array
items:
type: string
description: Contact information for the author of this version of
the tool in the registry. (More complex authorship information is
handled by the descriptor).
name:
type: string
description: The name of the version.
is_production:
type: boolean
description: This version of a tool is guaranteed to not change over
time (for example, a tool built from a tag in git as opposed to a
branch). A production quality tool is required to have a checksum.
images:
description: All known docker images (and versions/hashes) used by
this tool. If the tool has to evaluate any of the docker images
strings at runtime, those ones cannot be reported here.
type: array
items:
$ref: "#/components/schemas/ImageDataRegister"
descriptor_type:
type: array
description: The type (or types) of descriptors available.
items:
$ref: "#/components/schemas/DescriptorType"
verified:
type: boolean
description: Reports whether this tool has been verified by a
specific organization or individual.
verified_source:
type: array
items:
type: string
description: Source of metadata that can support a verified tool,
such as an email or URL.
signed:
type: boolean
description: Reports whether this version of the tool has been
signed.
included_apps:
description: An array of IDs for the applications that are stored
inside this tool.
example:
- https://bio.tools/tool/mytum.de/SNAP2/1
- https://bio.tools/bioexcel_seqqc
type: array
items:
type: string
files:
description: Properties and (pointers to) contents of files
associated with a tool.
type: array
items:
$ref: "#/components/schemas/FilesRegister"
ToolVersionRegisterId:
type: object
description: A tool version describes a particular iteration of a tool as
described by a reference to a specific image and/or documents.
required:
- id
additionalProperties: false
properties:
author:
type: array
items:
type: string
description: Contact information for the author of this version of
the tool in the registry. (More complex authorship information is
handled by the descriptor).
name:
type: string
description: The name of the version.
is_production:
type: boolean
description: This version of a tool is guaranteed to not change over
time (for example, a tool built from a tag in git as opposed to a
branch). A production quality tool is required to have a checksum.
images:
description: All known docker images (and versions/hashes) used by
this tool. If the tool has to evaluate any of the docker images
strings at runtime, those ones cannot be reported here.
type: array
items:
$ref: "#/components/schemas/ImageDataRegister"
descriptor_type:
type: array
description: The type (or types) of descriptors available.
items:
$ref: "#/components/schemas/DescriptorType"
verified:
type: boolean
description: Reports whether this tool has been verified by a
specific organization or individual.
verified_source:
type: array
items:
type: string
description: Source of metadata that can support a verified tool,
such as an email or URL.
signed:
type: boolean
description: Reports whether this version of the tool has been
signed.
included_apps:
description: An array of IDs for the applications that are stored
inside this tool.
example:
- https://bio.tools/tool/mytum.de/SNAP2/1
- https://bio.tools/bioexcel_seqqc
type: array
items:
type: string
files:
description: Properties and (pointers to) contents of files
associated with a tool.
type: array
items:
$ref: "#/components/schemas/FilesRegister"
id:
type: string
description: A unique identifier of the version of this tool for this
particular tool registry. If not provided, will be auto-generated
by the implementation. Note that a `BadRequest` will be returned if
multiple versions with the same `id` properties are provided.
example: v1