feat: add full support for service info fields

pro_wes/api/additions.openapi.yaml

@@ -59,9 +59,101 @@ paths:
                 $ref: "#/components/schemas/ErrorResponse"
 components:
   schemas:
+    # `Service` and `ServiceType` schemas copied over from Service Info API specs
+    # workaround for Connexion problem preventing the resolving of nested references
+    # in `ServiceInfoRegister` in `POST request
+    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: "#/components/schemas/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:[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"
+    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"
     ServiceInfoRegister:
       title: ServiceInfoRegister
       allOf:
+        #        - $ref: "#/components/schemas/Service"
         - type: object
           properties:
             workflow_type_versions:

pro_wes/config.yaml

@@ -122,14 +122,33 @@ custom:
   list_runs:
     default_page_size: 5
   service_info:
-    auth_instructions_url: "https://www.elixir-europe.org/services/compute/aai"
+    auth_instructions_url: "https://example.org/auth_instructions"
+    default_workflow_engine_parameters: []
+    id: v1.wes.ga4gh.org.example
+    name: "proWES example deployment"
     supported_filesystem_protocols:
-      - http
+      - https
     supported_wes_versions:
-      - 1.0.0
+      - 1.0.1
+    tags:
+      key: "value"
+    type:
+      group: "org.ga4gh"
+      artifact: "wes"
+      version: "1.0.1"
+    workflow_engine_versions:
+      cwl-engine: "1.2.3"
     workflow_type_versions:
       CWL:
         workflow_type_version:
           - v1.0
-    tags:
-      service_repo: https://github.com/elixir-europe/proWES
+    description: "WES gateway service"
+    organization:
+      name: "Example organization"
+      url: "https://example.org"
+    contactUrl: "[email protected]"
+    documentationUrl: "https://example.org/docs"
+    createdAt: "2020-01-01T00:00:00Z"
+    updatedAt: "2022-12-31T00:00:00Z"
+    environment: "test"
+    version: "0.18.0"

pro_wes/config_models.py

@@ -1,15 +1,11 @@
 """Custom app config models."""
 
-from typing import Dict, List, Optional
+from typing import Optional
 from pathlib import Path
 
-from pydantic import AnyUrl, BaseModel  # pylint: disable=no-name-in-module
+from pydantic import BaseModel  # pylint: disable=no-name-in-module
 
-from pro_wes.ga4gh.wes.models import (
-    DefaultWorkflowEngineParameter,
-    ServiceInfoBase,
-    WorkflowTypeVersion,
-)
+from pro_wes.ga4gh.wes.models import ServiceInfoBase as ServiceInfo
 
 # pragma pylint: disable=too-few-public-methods
 
@@ -72,55 +68,6 @@ class ListRuns(BaseModel):
     default_page_size: int = 5
 
 
-class ServiceInfo(ServiceInfoBase):
-    """Model for initial service info configuration.
-
-    Args:
-        workflow_type_versions: Workflow types and versions supported by this
-            service.
-        supported_wes_versions: The version(s) of the WES schema supported by
-            this service.
-        supported_filesystem_protocols: The filesystem protocols supported by
-            this service.
-        workflow_engine_versions: Workflow engine versions supported by this
-            service.
-        default_workflow_engine_parameters: Default workflow engine parameters
-            set by this service.
-        auth_instructions_url: URL to web page with human-readable instructions
-            on how to get an authorization token for use with this service.
-        tags: Additional information about this service as key-value pairs.
-
-    Attributes:
-        workflow_type_versions: Workflow types and versions supported by this
-            service.
-        supported_wes_versions: The version(s) of the WES schema supported by
-            this service.
-        supported_filesystem_protocols: The filesystem protocols supported by
-            this service.
-        workflow_engine_versions: Workflow engine versions supported by this
-            service.
-        default_workflow_engine_parameters: Default workflow engine parameters
-            set by this service.
-        auth_instructions_url: URL to web page with human-readable instructions
-            on how to get an authorization token for use with this service.
-        tags: Additional information about this service as key-value pairs.
-    """
-
-    workflow_type_versions: Dict[str, WorkflowTypeVersion] = {
-        "CWL": WorkflowTypeVersion(workflow_type_version=["v1.0"]),
-    }
-    supported_wes_versions: List[str] = [
-        "1.0.0",
-    ]
-    supported_filesystem_protocols: List[str] = [
-        "http",
-    ]
-    workflow_engine_versions: Dict[str, str] = {}
-    default_workflow_engine_parameters: List[DefaultWorkflowEngineParameter] = []
-    auth_instructions_url: AnyUrl = "https://lifescience-ri.eu/ls-login/"
-    tags: Dict[str, str] = {"service_repo": "https://github.com/elixir-europe/proWES"}
-
-
 class CustomConfig(BaseModel):
     """Custom app configuration.
 
@@ -142,4 +89,4 @@ class CustomConfig(BaseModel):
     defaults: Defaults = Defaults()
     post_runs: PostRuns = PostRuns()
     list_runs: ListRuns = ListRuns()
-    service_info: ServiceInfo = ServiceInfo()
+    service_info: ServiceInfo

pro_wes/ga4gh/service_info/__init__.py

@@ -0,0 +1 @@
+"""GA4GH Service Info API subpackage."""

pro_wes/ga4gh/service_info/models.py

@@ -0,0 +1,86 @@
+"""proWES schema models."""
+
+from datetime import datetime
+from typing import Optional, Union
+
+from pydantic import AnyUrl, BaseModel, EmailStr  # pylint: disable=no-name-in-module
+
+
+# pragma pylint: disable=too-few-public-methods
+
+
+class Organization(BaseModel):
+    """Model for organization implementing GA4GH services.
+
+    Attributes:
+        name: Name of the organization responsible for the service.
+        url: URL of the website of the organization (RFC 3986 format).
+    """
+
+    name: str
+    url: AnyUrl
+
+
+class ServiceType(BaseModel):
+    """Model for GA4GH service type.
+
+    Attributes:
+        group: 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).
+        artifact: Name of the API or GA4GH specification implemented. Official GA4GH
+            types should be assigned as part of standards approval process. Custom
+            artifacts are supported.
+        version: Version of the API or specification. GA4GH specifications use
+            semantic versioning.
+    """
+
+    group: str
+    artifact: str
+    version: str
+
+
+class Service(BaseModel):
+    """Model for GA4GH service.
+
+    Attributes:
+        id: 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.
+        name: Name of this service. Should be human readable.
+        type: Type of this service.
+        description: Description of the service. Should be human readable and provide
+            information about the service.
+        organization: Organization providing the service.
+        contactUrl: 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).
+        documentationUrl: 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.
+        createdAt: Timestamp describing when the service was first deployed and
+            available (RFC 3339 format).
+        updatedAt: Timestamp describing when the service was last updated (RFC 3339
+            format).
+        environment: 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.
+        version: 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.
+    """
+
+    id: str
+    name: str
+    type: ServiceType
+    description: Optional[str]
+    organization: Organization
+    contactUrl: Optional[Union[AnyUrl, EmailStr]]
+    documentationUrl: Optional[AnyUrl]
+    createdAt: Optional[datetime]
+    updatedAt: Optional[datetime]
+    environment: Optional[str]
+    version: str

pro_wes/ga4gh/wes/__init__.py

@@ -0,0 +1 @@
+"""GA4GH WES API subpackage."""

pro_wes/ga4gh/wes/controllers.py

@@ -1,7 +1,7 @@
 """Controller for GA4GH WES API endpoints."""
 
 import logging
-from typing import Dict, Literal, Tuple
+from typing import Dict, Literal, Optional, Tuple
 
 from connexion import request
 from foca.utils.logging import log_traffic
@@ -29,7 +29,7 @@ def GetServiceInfo() -> Dict:
 
 
 @log_traffic
-def PostServiceInfo(**kwargs) -> Tuple[None, Literal["201"]]:
+def PostServiceInfo(**kwargs) -> Tuple[None, Literal["201"], Optional[dict[str, str]]]:
     """Set information about this service.
 
     Controller for `POST /service-info`.
@@ -42,7 +42,8 @@ def PostServiceInfo(**kwargs) -> Tuple[None, Literal["201"]]:
     """
     service_info = ServiceInfo()
     service_info.set_service_info(data=request.json)
-    return (None, "201")
+    headers = None
+    return (None, "201", headers)
 
 
 @log_traffic

pro_wes/ga4gh/wes/models.py

@@ -12,6 +12,7 @@
 )
 
 from pro_wes.exceptions import NoSuitableEngine
+from pro_wes.ga4gh.service_info.models import Service
 from pro_wes.ga4gh.wes.service_info import ServiceInfo as ServiceInfoController
 
 # pragma pylint: disable=too-few-public-methods
@@ -455,8 +456,8 @@ class DefaultWorkflowEngineParameter(BaseModel):
     default_value: Optional[str]
 
 
-class ServiceInfoBase(BaseModel):
-    """Base model for service info.
+class ServiceInfoWesBase(BaseModel):
+    """Base model for WES-specific service info fields.
 
     Args:
         workflow_type_versions: Workflow types and versions supported by this
@@ -498,6 +499,10 @@ class ServiceInfoBase(BaseModel):
     tags: Dict[str, str]
 
 
+class ServiceInfoBase(ServiceInfoWesBase, Service):
+    """Based model for service info."""
+
+
 class ServiceInfo(ServiceInfoBase):
     """Full model for service info.
 

requirements.txt

@@ -1,2 +1,4 @@
+connexion<3
+email-validator>=2.1.0,<3
 foca>=0.12.1
 gunicorn>=20.1.0,<21