Merge branch 'dev' into foca_change

drs_filer/api/20200131.11d2c12.service-info.yaml

@@ -0,0 +1,148 @@
+swagger: '2.0'
+basePath: '/ga4gh/drs/v1'
+info:
+  title: GA4GH service-info API specification
+  description: A way for a service to describe basic metadata concerning a service
+    alongside a set of capabilities and/or limitations of the service. More information
+    on [GitHub](https://github.com/ga4gh-discovery/ga4gh-service-info/).
+  version: 1.0.0
+  license:
+    name: Apache 2.0
+    url: https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/develop/LICENSE
+  contact:
+    name: GA4GH Discovery Networks Team
+    email: ga4gh-discovery-networks@ga4gh.org
+schemes:
+  - https
+  - http
+consumes:
+  - application/json
+produces:
+  - application/json
+paths:
+  "/service-info":
+    get:
+      summary: Show information about this service. It is assumed that removing this
+        endpoint from a URL will result in a valid URL to query against
+      operationId: getServiceInfo
+      tags:
+      - service-info
+      responses:
+        '200':
+          description: A successful operation to request the service information about
+            this running service.
+          schema:
+            "$ref": "#/definitions/Service"
+      parameters: []
+      produces:
+      - application/json
+      x-swagger-router-controller: ga4gh.drs.server
+definitions:
+  Service:
+    description: GA4GH service
+    type: object
+    required:
+    - id
+    - name
+    - type
+    - organization
+    - version
+    properties:
+      id:
+        type: string
+        description: Unique ID of this service. Reverse domain name notation is recommended,
+          though not required. The identifier should attempt to be globally unique
+          so it can be used in downstream aggregator services e.g. Service Registry.
+        example: org.ga4gh.myservice
+      name:
+        type: string
+        description: Name of this service. Should be human readable.
+        example: My project
+      type:
+        "$ref": "#/definitions/ServiceType"
+      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:support@example.com
+      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
+  ServiceType:
+    description: Type of a GA4GH service
+    type: object
+    required:
+    - group
+    - artifact
+    - version
+    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
+x-components: {}

drs_filer/api/additional.data_repository_service.swagger.yaml

@@ -1,4 +1,38 @@
 paths:
+  '/service-info':
+    post:
+      summary: Register service info.
+      description: Create or update the service info.
+      operationId: postServiceInfo
+      tags:
+        - DRS-Filer
+      parameters:
+        - in: body
+          required: true
+          name: Service info to add.
+          description: Data object metadata.
+          schema:
+            $ref: '#/definitions/ServiceRegister'     
+      responses:
+        '201':
+          description: The service info was successfully created.
+        '400':
+          description: The request is malformed.
+          schema:
+            $ref: '#/definitions/Error'
+        '401':
+          description: The request is unauthorized.
+          schema:
+            $ref: '#/definitions/Error'
+        '403':
+          description: The requester is not authorized to perform this action.
+          schema:
+            $ref: '#/definitions/Error'
+        '500':
+          description: An unexpected error occurred.
+          schema:
+            $ref: '#/definitions/Error'
+      x-swagger-router-controller: ga4gh.drs.server
   '/objects':
     post:
       summary: Create object.
@@ -158,6 +192,96 @@ paths:
         - DRS-Filer
       x-swagger-router-controller: ga4gh.drs.server    
 definitions:
+  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: '#/definitions/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:support@example.com'
+        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'
   DrsObjectRegister:
     type: object
     additionalProperties: false

drs_filer/app.py

@@ -1,12 +1,22 @@
+"""Main app module."""
+
 import logging
 
 from foca.foca import foca
 
+from drs_filer.ga4gh.drs.endpoints.service_info import RegisterServiceInfo
+
 logger = logging.getLogger(__name__)
 
 
 def main():
     app = foca("config.yaml")
+
+    # register service info
+    with app.app.app_context():
+        service_info = RegisterServiceInfo()
+        service_info.set_service_info_from_config()
+    # start app
     app.run(port=app.port)
 
 

drs_filer/config.yaml

@@ -19,10 +19,17 @@ db:
                               id: 1
                           options: 
                             'unique': True
+                service_info:
+                    indexes:
+                        - keys:
+                              id: 1
+                          options:
+                            'unique': True
 
 api:
     specs:
         - path:
+            - api/20200131.11d2c12.service-info.yaml
             - api/20200622.383121d.data_repository_service.swagger.yaml
             - api/additional.data_repository_service.swagger.yaml
           append: null
@@ -64,6 +71,23 @@ endpoints:
     access_methods:
         id_charset: 'string.ascii_letters + string.digits + ".-_~"'
         id_length: 6
+    service_info:
+        id: "TEMPID1"
+        name: "TEMP_STUB"
+        type:
+            group: "TEMP_GROUP"
+            artifact: "TEMP_ARTIFACT"
+            version: "v1"
+        description: "Description of service."
+        organization:
+            name: "Parent organization"
+            url: "parent/abc"
+        contactUrl: "contact/abc"
+        documentationUrl: "docs/abc"
+        createdAt: "2020-01-01"
+        updatedAt: "2020-01-01"
+        environment: "ENV"
+        version: "0.0.0"
     url_prefix: http
     external_host: 193.166.24.114
     external_port: 8080

drs_filer/errors/exceptions.py

@@ -28,6 +28,10 @@ class URLNotFound(NotFound):
     pass
 
 
+class ValidationError(Exception):
+    """Value or object is not compatible with required type or schema."""
+
+
 exceptions = {
     Exception: {
         "msg": "An unexpected error occurred.",