Feature/registry index

lifemonitor/api/controllers.py

@@ -64,6 +64,35 @@ def workflow_registries_get_by_uuid(registry_uuid):
     return serializers.WorkflowRegistrySchema().dump(registry)
 
 
+@authorized
+@cached(timeout=Timeout.REQUEST)
+def registry_index(registry_uuid):
+    if not current_user:
+        return lm_exceptions.report_problem(401, "Unauthorized")
+    registry = lm.get_workflow_registry_by_uuid(registry_uuid)
+    if not registry:
+        return lm_exceptions.report_problem(404, "Not Found",
+                                            detail=messages.no_registry_found.format(registry_uuid))
+    workflows = registry.get_index(current_user)
+    return serializers.ListOfRegistryIndexItemsSchema().dump(workflows)
+
+
+@authorized
+@cached(timeout=Timeout.REQUEST)
+def registry_index_workflow(registry_uuid, registry_workflow_identifier):
+    if not current_user:
+        return lm_exceptions.report_problem(401, "Unauthorized")
+    registry = lm.get_workflow_registry_by_uuid(registry_uuid)
+    if not registry:
+        return lm_exceptions.report_problem(404, "Not Found",
+                                            detail=messages.no_registry_found.format(registry_uuid))
+    workflow = registry.get_index_workflow(current_user, registry_workflow_identifier)
+    if not workflow:
+        return lm_exceptions.report_problem(404, "Not Found",
+                                            detail=messages.workflow_not_found.format(registry_workflow_identifier, 'latest'))
+    return serializers.RegistryIndexItemSchema().dump(workflow)
+
+
 @authorized
 @cached(timeout=Timeout.REQUEST)
 def workflow_registries_get_current():

lifemonitor/api/models/__init__.py

@@ -30,7 +30,7 @@
 from .status import Status, AggregateTestStatus, WorkflowStatus, SuiteStatus
 
 # 'registries' package
-from .registries import WorkflowRegistry, WorkflowRegistryClient
+from .registries import RegistryWorkflow, WorkflowRegistry, WorkflowRegistryClient
 
 # 'workflows' package
 from .workflows import Workflow, WorkflowVersion
@@ -72,6 +72,7 @@
     "WorkflowRegistryClient",
     "WorkflowStatus",
     "WorkflowVersion",
+    "RegistryWorkflow"
 ]
 
 # set module level logger

lifemonitor/api/models/registries/__init__.py

@@ -21,9 +21,9 @@
 from __future__ import annotations
 
 from lifemonitor.utils import ClassManager
-from .registry import WorkflowRegistry, WorkflowRegistryClient
+from .registry import RegistryWorkflow, WorkflowRegistry, WorkflowRegistryClient
 
 
-__all__ = [WorkflowRegistry, WorkflowRegistryClient] + \
+__all__ = [RegistryWorkflow, WorkflowRegistry, WorkflowRegistryClient] + \
     ClassManager('lifemonitor.api.models.registries',
                  class_suffix="WorkflowRegistry", skip=["registry"], lazy=False).get_classes()

lifemonitor/api/models/registries/registry.py

@@ -41,6 +41,51 @@
 logger = logging.getLogger(__name__)
 
 
+class RegistryWorkflow(object):
+    _registry: WorkflowRegistry
+    _identifier: str
+    _name: str
+    _latest_version: str
+    _versions: List[str] = None
+
+    def __init__(self,
+                 registry: WorkflowRegistry,
+                 identifier: str,
+                 name: str,
+                 latest_version: str = None,
+                 versions: List[str] = None) -> None:
+        self._registry = registry
+        self._identifier = identifier
+        self._name = name
+        self._latest_version = latest_version
+        if versions:
+            self._versions = versions.copy()
+
+    @property
+    def registry(self) -> WorkflowRegistry:
+        return self._registry
+
+    @property
+    def identifier(self) -> str:
+        return self._identifier
+
+    @property
+    def name(self) -> str:
+        return self._name
+
+    @property
+    def latest_version(self) -> str:
+        return self._latest_version
+
+    @property
+    def versions(self) -> List[str]:
+        return self._versions.copy()
+
+    @property
+    def external_link(self) -> str:
+        return self._registry.get_external_link(self._identifier, self._latest_version)
+
+
 class WorkflowRegistryClient(ABC):
 
     client_types = ClassManager('lifemonitor.api.models.registries', class_suffix="WorkflowRegistryClient", skip=["registry"])
@@ -78,6 +123,12 @@ def _get(self, user, *args, **kwargs):
         response.raise_for_status()
         return response
 
+    def get_index(self, user: auth_models.User) -> List[RegistryWorkflow]:
+        pass
+
+    def get_index_workflow(self, user: auth_models.User, workflow_identifier: str) -> RegistryWorkflow:
+        pass
+
     def download_url(self, url, user, target_path=None):
         return download_url(url, target_path,
                             authorization=f'Bearer {self._get_access_token(user.id)["access_token"]}')
@@ -240,6 +291,12 @@ def get_user_workflows(self, user: auth_models.User) -> List[models.Workflow]:
     def get_user_workflow_versions(self, user: auth_models.User) -> List[models.WorkflowVersion]:
         return self.client.filter_by_user(self.registered_workflow_versions, user)
 
+    def get_index(self, user: auth_models.User) -> List[RegistryWorkflow]:
+        return self.client.get_index(user)
+
+    def get_index_workflow(self, user: auth_models.User, workflow_identifier: str) -> RegistryWorkflow:
+        return self.client.get_index_workflow(user, workflow_identifier)
+
     @classmethod
     def all(cls) -> List[WorkflowRegistry]:
         return cls.query.all()

lifemonitor/api/models/registries/seek.py

@@ -21,13 +21,16 @@
 from __future__ import annotations
 
 import logging
-from typing import Union
+from typing import List, Union
 
+import requests
 from lifemonitor.api import models
 from lifemonitor.auth.models import User
-from lifemonitor.exceptions import EntityNotFoundException
+from lifemonitor.exceptions import (EntityNotFoundException,
+                                    LifeMonitorException)
 
-from .registry import WorkflowRegistry, WorkflowRegistryClient
+from .registry import (RegistryWorkflow, WorkflowRegistry,
+                       WorkflowRegistryClient)
 
 # set module level logger
 logger = logging.getLogger(__name__)
@@ -63,8 +66,26 @@ def get_workflow_metadata(self, user, w: Union[models.WorkflowVersion, str]):
             raise RuntimeError(f"ERROR: unable to get workflow (status code: {r.status_code})")
         return r.json()['data']
 
+    def get_index(self, user: User) -> List[RegistryWorkflow]:
+        result = []
+        for w in self.get_workflows_metadata(user):
+            result.append(RegistryWorkflow(self.registry, w['id'], w['attributes']['title']))
+        return result
+
+    def get_index_workflow(self, user: User, workflow_identifier: str) -> RegistryWorkflow:
+        try:
+            w = self.get_workflow_metadata(user, workflow_identifier)
+            return RegistryWorkflow(self.registry, w['id'], w['attributes']['title'],
+                                    latest_version=w['attributes']['version'],
+                                    versions=[_['version'] for _ in w['attributes']['versions']]) if w else None
+        except requests.exceptions.HTTPError as e:
+            if e.response.status_code == 404:
+                raise EntityNotFoundException(WorkflowRegistry, entity_id=workflow_identifier)
+            raise LifeMonitorException(original_error=e)
+
     def get_external_link(self, external_id: str, version: str) -> str:
-        return f"{self.registry.uri}/workflows/{external_id}?version={version}"
+        version_param = '' if not version or version == 'latest' else f"?version={version}"
+        return f"{self.registry.uri}/workflows/{external_id}{version_param}"
 
     def get_rocrate_external_link(self, external_id: str, version: str) -> str:
         return f'{self.registry.uri}/workflows/{external_id}/ro_crate?version={version}'

lifemonitor/api/serializers.py

@@ -59,6 +59,41 @@ class ListOfWorkflowRegistriesSchema(ListOfItems):
     __item_scheme__ = WorkflowRegistrySchema
 
 
+class RegistryIndexItemSchema(ResourceMetadataSchema):
+    __envelope__ = {"single": None, "many": "items"}
+    __model__ = models.RegistryWorkflow
+
+    class Meta:
+        model = models.RegistryWorkflow
+
+    identifier = fields.String(attribute="identifier")
+    name = fields.String(attribute="name")
+    latest_version = fields.String(attribute="latest_version")
+    versions = fields.List(fields.String, attribute="versions")
+    registry = ma.Nested(WorkflowRegistrySchema(exclude=('meta', 'links')), attribute="registry")
+    links = fields.Method('get_links')
+
+    def get_links(self, obj):
+        links = ResourceMetadataSchema.get_links(self, obj)
+        if links is not None:
+            links['origin'] = obj.external_link
+            return links
+        return {
+            'origin': obj.external_link
+        }
+
+    @post_dump
+    def remove_skip_values(self, data, **kwargs):
+        return {
+            key: value for key, value in data.items()
+            if value is not None
+        }
+
+
+class ListOfRegistryIndexItemsSchema(ListOfItems):
+    __item_scheme__ = RegistryIndexItemSchema
+
+
 class WorkflowSchema(ResourceMetadataSchema):
     __envelope__ = {"single": None, "many": "items"}
     __model__ = models.WorkflowVersion
@@ -273,7 +308,7 @@ def format_availability_issues(status: models.WorkflowStatus):
     issues = status.availability_issues
     logger.info(issues)
     if 'not_available' == status.aggregated_status and len(issues) > 0:
-        return ', '.join([f"{i['issue']}: Unable to get resource '{i['resource']}' from service '{i['service']}'" if 'service' in i else i['issue'] for i in issues])
+        return ', '.join([f"{i['issue']}: Unable to get resource '{i['resource']}' from service '{i['service']}'" if 'service' in i and 'resource' in i else i['issue'] for i in issues])
     return None
 
 

specs/api.yaml

@@ -83,6 +83,65 @@ paths:
         "404":
           $ref: "#/components/responses/NotFound"
 
+  /registries/{registry_uuid}/index:
+    get:
+      tags: ["Registries"]
+      x-openapi-router-controller: lifemonitor.api.controllers
+      operationId: "registry_index"
+      summary: "Get registry index"
+      description: "Get the index of workflows available on the registry"
+      security:
+        - apiKey: ["user.workflow.read"]
+        - RegistryCodeFlow: ["user.workflow.read"]
+        - AuthorizationCodeFlow: ["user.workflow.read"]
+      parameters:
+        - $ref: "#/components/parameters/registry_uuid"
+      responses:
+        "200":
+          description: List of workflows on the registry
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/ListOfRegistryWorkflows"
+        "400":
+          $ref: "#/components/responses/BadRequest"
+        "401":
+          $ref: "#/components/responses/Unauthorized"
+        "403":
+          $ref: "#/components/responses/Forbidden"
+        "404":
+          $ref: "#/components/responses/NotFound"
+
+  /registries/{registry_uuid}/index/{registry_workflow_identifier}:
+    get:
+      tags: ["Registries"]
+      x-openapi-router-controller: lifemonitor.api.controllers
+      operationId: "registry_index_workflow"
+      summary: "Get registry index workflow"
+      description: "Get information about the specified workflow of the registry index"
+      security:
+        - apiKey: ["user.workflow.read"]
+        - RegistryCodeFlow: ["user.workflow.read"]
+        - AuthorizationCodeFlow: ["user.workflow.read"]
+      parameters:
+        - $ref: "#/components/parameters/registry_uuid"
+        - $ref: "#/components/parameters/registry_workflow_identifier"
+      responses:
+        "200":
+          description: List of workflows on the registry
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/RegistryWorkflow"
+        "400":
+          $ref: "#/components/responses/BadRequest"
+        "401":
+          $ref: "#/components/responses/Unauthorized"
+        "403":
+          $ref: "#/components/responses/Forbidden"
+        "404":
+          $ref: "#/components/responses/NotFound"
+
   /users/current:
     get:
       tags: ["Users"]
@@ -1118,6 +1177,14 @@ components:
         type: string
       required: true
       example: aa16c6a9-571f-4a62-976f-60ea514ad2c1
+    registry_workflow_identifier:
+      name: "registry_workflow_identifier"
+      description: "Identifier of the workflow on the registry"
+      in: path
+      schema:
+        type: string
+      required: true
+      example: 123e4567-e89b-12d3-a456-426614174000
     user_id:
       name: "user_id"
       description: "Registry user's identifier"
@@ -1547,6 +1614,48 @@ components:
         #     (e.g., `authorization: "ApiKey 1234567890"`).
         #   example: "Bearer xxx__ZRBhqf9eeRasjqMw90pgEeMpTZ7__"
 
+    RegistryWorkflowBase:
+      allOf:
+        - $ref: "#/components/schemas/WorkflowBase"
+        - type: object
+          description: Registry workflow
+          properties:
+            identifier:
+              type: string
+              description: |
+                The identifier of the workflow on the registry
+              example: 148
+            registry:
+              description:
+              $ref: "#/components/schemas/Registry"
+
+    RegistryWorkflow:
+      allOf:
+        - $ref: "#/components/schemas/RegistryWorkflowBase"
+        - type: object
+          description: Registry workflow
+          properties:
+            latest_version:
+              type: string
+              description: The workflow identifier on the registry
+              example: '1.0'
+            versions:
+              description: The list of workflow versions
+              type: array
+              items:
+                type: string
+              example: ['1.0', "1.0-dev"]
+
+    ListOfRegistryWorkflows:
+      type: object
+      properties:
+        items:
+          type: array
+          items:
+            $ref: "#/components/schemas/RegistryWorkflowBase"
+      required:
+        - items
+
     WorkflowVersionBase:
       allOf:
         - $ref: "#/components/schemas/WorkflowBase"