Merge pull request #23 from sartography/feature/workflow_spec_categories

Feature/workflow spec categories

crc/api.yml

@@ -299,6 +299,83 @@ paths:
       responses:
         '204':
           description: The workflow specification has been removed.
+  /workflow-specification-category:
+    get:
+      operationId: crc.api.workflow.list_workflow_spec_categories
+      summary: Provides a list of categories that can be added to a workflow spec.
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: An array of workflow specification categories
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/WorkflowSpecCategory"
+    post:
+      operationId: crc.api.workflow.add_workflow_spec_category
+      summary: Creates a new workflow spec category with the given parameters.
+      tags:
+        - Workflow Specifications
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/WorkflowSpecCategory'
+      responses:
+        '200':
+          description: Workflow spec category created successfully.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkflowSpecCategory"
+  /workflow-specification-category/{cat_id}:
+    parameters:
+      - name: cat_id
+        in: path
+        required: false
+        description: The unique id of an existing workflow spec category to modify.
+        schema:
+          type: string
+    get:
+      operationId: crc.api.workflow.get_workflow_spec_category
+      summary: Returns a single workflow spec category
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: Workflow spec category.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkflowSpecCategory"
+    put:
+      operationId: crc.api.workflow.update_workflow_spec_category
+      summary: Modifies an existing workflow spec category with the given parameters.
+      tags:
+        - Workflow Specifications
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/WorkflowSpecCategory'
+      responses:
+        '200':
+          description: Workflow spec category created successfully.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkflowSpecCategory"
+    delete:
+      operationId: crc.api.workflow.delete_workflow_spec_category
+      summary: Removes an existing workflow spec category
+      tags:
+        - Workflow Specifications
+      responses:
+        '204':
+          description: The workflow spec category has been removed.
   /file:
     parameters:
       - name: workflow_spec_id

crc/api/study.py

@@ -166,7 +166,9 @@ def get_study_workflows(study_id):
 
     # Get study status spec
     status_spec: WorkflowSpecModel = session.query(WorkflowSpecModel)\
-        .filter_by(is_status=True).first()
+        .filter_by(is_status=True)\
+        .filter_by(id=study.status_spec_id)\
+        .first()
 
     status_data = None
 

crc/api/workflow.py

@@ -6,7 +6,8 @@ from crc.api.common import ApiError, ApiErrorSchema
 from crc.api.file import delete_file
 from crc.models.api_models import Task, WorkflowApi, WorkflowApiSchema
 from crc.models.file import FileModel
-from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel
+from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
+    WorkflowSpecCategoryModelSchema
 from crc.services.workflow_processor import WorkflowProcessor
 
 
@@ -18,7 +19,6 @@ def all_specifications():
 @auth.login_required
 def add_workflow_specification(body):
     new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session)
-    new_spec.is_status = new_spec.id == 'status'
     session.add(new_spec)
     session.commit()
     return WorkflowSpecModelSchema().dump(new_spec)
@@ -41,11 +41,21 @@ def get_workflow_specification(spec_id):
 
 @auth.login_required
 def update_workflow_specification(spec_id, body):
-    spec = WorkflowSpecModelSchema().load(body, session=session)
-    spec.id = spec_id
+    if spec_id is None:
+        error = ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.')
+        return ApiErrorSchema.dump(error), 404
+
+    spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
+
+    if spec is None:
+        error = ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.')
+        return ApiErrorSchema.dump(error), 404
+
+    schema = WorkflowSpecModelSchema()
+    spec = schema.load(body, session=session, instance=spec, partial=True)
     session.add(spec)
     session.commit()
-    return WorkflowSpecModelSchema().dump(spec)
+    return schema.dump(spec)
 
 
 @auth.login_required
@@ -133,3 +143,49 @@ def update_task(workflow_id, task_id, body):
     update_workflow_stats(workflow_model, workflow_api_model)
     log_task_complete(workflow_model, task_id)
     return WorkflowApiSchema().dump(workflow_api_model)
+
+
+@auth.login_required
+def list_workflow_spec_categories():
+    schema = WorkflowSpecCategoryModelSchema(many=True)
+    return schema.dump(session.query(WorkflowSpecCategoryModel).all())
+
+
+@auth.login_required
+def get_workflow_spec_category(cat_id):
+    schema = WorkflowSpecCategoryModelSchema()
+    return schema.dump(session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first())
+
+
+@auth.login_required
+def add_workflow_spec_category(body):
+    schema = WorkflowSpecCategoryModelSchema()
+    new_cat: WorkflowSpecCategoryModel = schema.load(body, session=session)
+    session.add(new_cat)
+    session.commit()
+    return schema.dump(new_cat)
+
+
+@auth.login_required
+def update_workflow_spec_category(cat_id, body):
+    if cat_id is None:
+        error = ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.')
+        return ApiErrorSchema.dump(error), 404
+
+    category = session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first()
+
+    if category is None:
+        error = ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.')
+        return ApiErrorSchema.dump(error), 404
+
+    schema = WorkflowSpecCategoryModelSchema()
+    category = schema.load(body, session=session, instance=category, partial=True)
+    session.add(category)
+    session.commit()
+    return schema.dump(category)
+
+
+@auth.login_required
+def delete_workflow_spec_category(cat_id):
+    session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).delete()
+    session.commit()

crc/models/workflow.py

@@ -1,9 +1,12 @@
 import enum
 
+import marshmallow
+from marshmallow import EXCLUDE
 from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 
 from crc import db
 
+
 class WorkflowSpecCategoryModel(db.Model):
     __tablename__ = 'workflow_spec_category'
     id = db.Column(db.Integer, primary_key=True)
@@ -36,6 +39,9 @@ class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
         load_instance = True
         include_relationships = True
         include_fk = True  # Includes foreign keys
+        unknown = EXCLUDE
+
+    workflow_spec_category = marshmallow.fields.Nested(WorkflowSpecCategoryModelSchema, dump_only=True)
 
 
 class WorkflowStatus(enum.Enum):