got library side working - still need to have parent working

Pipfile

@@ -10,7 +10,6 @@ coverage = "*"
 
 [packages]
 alembic = "*"
-connexion = {extras = ["swagger-ui"],version = "*"}
 coverage = "*"
 docxtpl = "*"
 flask = "*"
@@ -36,11 +35,8 @@ pyjwt = "*"
 python-dateutil = "*"
 recommonmark = "*"
 requests = "*"
-sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
 sphinx = "*"
 swagger-ui-bundle = "*"
-spiffworkflow = {git = "https://github.com/sartography/SpiffWorkflow.git"}
-# spiffworkflow = {editable = true, path = "./../SpiffWorkflow"}
 webtest = "*"
 werkzeug = "*"
 xlrd = "*"
@@ -50,4 +46,15 @@ python-levenshtein = "*"
 apscheduler = "*"
 
 [requires]
-python_version = "3.8"
+python_version = "3.9"
+
+[packages.connexion]
+extras = [ "swagger-ui",]
+version = "*"
+
+[packages.sentry-sdk]
+extras = [ "flask",]
+version = "==0.14.4"
+
+[packages.spiffworkflow]
+git = "https://github.com/sartography/SpiffWorkflow.git"

crc/api.yml

@@ -426,6 +426,70 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/WorkflowSpec"
+
+  /workflow-specification/{spec_id}/libraries:
+    parameters:
+      - name: spec_id
+        in: path
+        required: true
+        description: The unique id of an existing workflow specification.
+        schema:
+          type: string
+    get:
+      operationId: crc.api.workflow.get_workflow_specification_libraries
+      summary: Returns all libraries that are enabled for a workflow spec
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: Workflow specification.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkflowSpec"
+
+  /workflow-specification/{spec_id}/library/{library_id}:
+    parameters:
+      - name: spec_id
+        in: path
+        required: true
+        description: The unique id of an existing workflow specification.
+        schema:
+          type: string
+      - name: library_id
+        in: path
+        required: true
+        description: The unique id of an existing library specification.
+        schema:
+          type: string
+
+
+    post:
+      operationId: crc.api.workflow.add_workflow_spec_library
+      summary: Adds a library to a workflow spec
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: Workflow specification.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkflowSpec"
+    delete:
+      operationId: crc.api.workflow.drop_workflow_spec_library
+      summary: Delete a library from a workflow
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: Workflow specification.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/WorkflowSpec"
+
+
   /workflow-specification/{spec_id}:
     parameters:
       - name: spec_id
@@ -502,6 +566,21 @@ paths:
                 type: array
                 items:
                   $ref: "#/components/schemas/WorkflowSpec"
+  /workflow-specification/libraries:
+    get:
+      operationId: crc.api.workflow.library_workflow_specs
+      summary: Provides a list of workflow specifications that are considered libraries.
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: A list of workflow specifications
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/WorkflowSpec"
   /workflow-specification/{spec_id}/validate:
     parameters:
       - name: spec_id

crc/api/workflow.py

@@ -10,7 +10,7 @@ from crc.models.study import StudyModel, WorkflowMetadata, StudyStatus
 from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema
 from crc.models.user import UserModelSchema
 from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
-    WorkflowSpecCategoryModelSchema
+    WorkflowSpecCategoryModelSchema, WorkflowLibraryModel, WorkflowLibraryModelSchema
 from crc.services.error_service import ValidationErrorService
 from crc.services.file_service import FileService
 from crc.services.lookup_service import LookupService
@@ -22,7 +22,8 @@ from crc.services.workflow_service import WorkflowService
 
 def all_specifications():
     schema = WorkflowSpecModelSchema(many=True)
-    return schema.dump(session.query(WorkflowSpecModel).all())
+    return schema.dump(session.query(WorkflowSpecModel).filter((WorkflowSpecModel.library==False)|(
+            WorkflowSpecModel.library==None)).all())
 
 
 def add_workflow_specification(body):
@@ -45,6 +46,50 @@ def get_workflow_specification(spec_id):
 
     return WorkflowSpecModelSchema().dump(spec)
 
+def get_workflow_specification_libraries(spec_id):
+    if spec_id is None:
+        raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
+    spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
+    libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
+    if spec is None:
+        raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
+    return WorkflowLibraryModelSchema(many=True).dump(libraries)
+
+def validate_spec_and_library(spec_id,library_id):
+    if spec_id is None:
+        raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
+    if library_id is None:
+        raise ApiError('unknown_spec', 'Please provide a valid Library Specification ID.')
+    spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
+    library: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=library_id).first()
+    if spec is None:
+        raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
+    if library is None:
+        raise ApiError('unknown_spec', 'The Library Specification "' + library_id + '" is not recognized.')
+    if not library.library:
+        raise ApiError('unknown_spec', 'Linked workflow spec is not a library.')
+
+
+def add_workflow_spec_library(spec_id,library_id):
+    validate_spec_and_library(spec_id, library_id)
+    libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
+    libraryids = [x.library_spec_id for x in libraries]
+    if library_id in libraryids:
+        raise ApiError('unknown_spec', 'The Library Specification "' + spec_id + '" is already attached.')
+    newlib = WorkflowLibraryModel()
+    newlib.workflow_spec_id = spec_id
+    newlib.library_spec_id = library_id
+    session.add(newlib)
+    session.commit()
+    libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
+    return WorkflowLibraryModelSchema(many=True).dump(libraries)
+
+def drop_workflow_spec_library(spec_id,library_id):
+    validate_spec_and_library(spec_id, library_id)
+    session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id,library_spec_id=library_id).delete()
+    session.commit()
+    libraries: WorkflowLibraryModel = session.query(WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
+    return WorkflowLibraryModelSchema(many=True).dump(libraries)
 
 def validate_workflow_specification(spec_id, validate_study_id=None, test_until=None):
     errors = {}
@@ -118,6 +163,10 @@ def standalone_workflow_specs():
     specs = WorkflowService.get_standalone_workflow_specs()
     return schema.dump(specs)
 
+def library_workflow_specs():
+    schema = WorkflowSpecModelSchema(many=True)
+    specs = WorkflowService.get_library_workflow_specs()
+    return schema.dump(specs)
 
 def get_workflow(workflow_id, do_engine_steps=True):
     """Retrieve workflow based on workflow_id, and return it in the last saved State.

crc/api/workflow_sync.py

@@ -159,7 +159,6 @@ def create_or_update_local_spec(remote,workflow_spec_id):
             localcategory.name = specdict['category']['name']
             localcategory.display_name = specdict['category']['display_name']
             localcategory.display_order = specdict['category']['display_order']
-            localcategory.library = False
             session.add(localcategory)
         localspec.category = localcategory
 

crc/models/workflow.py

@@ -1,7 +1,7 @@
 import enum
 
 import marshmallow
-from marshmallow import EXCLUDE
+from marshmallow import EXCLUDE,fields
 from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
 from sqlalchemy import func
 
@@ -15,7 +15,6 @@ class WorkflowSpecCategoryModel(db.Model):
     name = db.Column(db.String)
     display_name = db.Column(db.String)
     display_order = db.Column(db.Integer)
-    library = db.Column(db.Boolean)
 
 
 class WorkflowSpecCategoryModelSchema(SQLAlchemyAutoSchema):
@@ -25,6 +24,7 @@ class WorkflowSpecCategoryModelSchema(SQLAlchemyAutoSchema):
         include_relationships = True
 
 
+
 class WorkflowSpecModel(db.Model):
     __tablename__ = 'workflow_spec'
     id = db.Column(db.String, primary_key=True)
@@ -36,6 +36,19 @@ class WorkflowSpecModel(db.Model):
     category = db.relationship("WorkflowSpecCategoryModel")
     is_master_spec = db.Column(db.Boolean, default=False)
     standalone = db.Column(db.Boolean, default=False)
+    library = db.Column(db.Boolean, default=False)
+
+
+class WorkflowLibraryModel(db.Model):
+   __tablename__ = 'workflow_library'
+   id = db.Column(db.Integer, primary_key=True)
+   workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
+   library_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
+   workflow_side = db.relationship(WorkflowSpecModel,
+                                   primaryjoin=workflow_spec_id==WorkflowSpecModel.id,
+                                  backref='libraries')
+   library = db.relationship(WorkflowSpecModel,primaryjoin=library_spec_id==WorkflowSpecModel.id,
+                                  backref='referred_by')
 
 
 class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
@@ -47,7 +60,10 @@ class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
         unknown = EXCLUDE
 
     category = marshmallow.fields.Nested(WorkflowSpecCategoryModelSchema, dump_only=True)
-
+    libraries = marshmallow.fields.Function(lambda obj: [{'id':x.library.id,
+                                                          'name':x.library.name,
+                                                          'display_name':x.library.display_name} for x in
+                                                             obj.libraries] )
 
 class WorkflowState(enum.Enum):
     hidden = "hidden"
@@ -79,6 +95,15 @@ class WorkflowSpecDependencyFile(db.Model):
     file_data = db.relationship(FileDataModel)
 
 
+
+class WorkflowLibraryModelSchema(SQLAlchemyAutoSchema):
+    class Meta:
+        model = WorkflowLibraryModel
+        load_instance = True
+        include_relationships = True
+
+    library = marshmallow.fields.Nested('WorkflowSpecModelSchema')
+
 class WorkflowModel(db.Model):
     __tablename__ = 'workflow'
     id = db.Column(db.Integer, primary_key=True)

crc/services/study_service.py

@@ -242,8 +242,7 @@ class StudyService(object):
     def get_categories():
         """Returns a list of category objects, in the correct order."""
         cat_models = db.session.query(WorkflowSpecCategoryModel) \
-            .order_by(WorkflowSpecCategoryModel.display_order) \
-            .filter((WorkflowSpecCategoryModel.library == None)|(WorkflowSpecCategoryModel.library ==False)).all()
+            .order_by(WorkflowSpecCategoryModel.display_order).all()
         categories = []
         for cat_model in cat_models:
             categories.append(Category(cat_model))

crc/services/workflow_service.py

@@ -886,6 +886,11 @@ class WorkflowService(object):
         specs = db.session.query(WorkflowSpecModel).filter_by(standalone=True).all()
         return specs
 
+    @staticmethod
+    def get_library_workflow_specs():
+        specs = db.session.query(WorkflowSpecModel).filter_by(library=True).all()
+        return specs
+
     @staticmethod
     def get_primary_workflow(workflow_spec_id):
         # Returns the FileModel of the primary workflow for a workflow_spec

migrations/versions/a931e2b7b070_.py

@@ -0,0 +1,35 @@
+"""empty message
+
+Revision ID: a931e2b7b070
+Revises: 47b10b171d7c
+Create Date: 2021-07-12 08:46:08.814577
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'a931e2b7b070'
+down_revision = 'bbf064082623'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('workflow_library',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('workflow_spec_id', sa.String(), nullable=True),
+    sa.Column('library_spec_id', sa.String(), nullable=True),
+    sa.ForeignKeyConstraint(['library_spec_id'], ['workflow_spec.id'], ),
+    sa.ForeignKeyConstraint(['workflow_spec_id'], ['workflow_spec.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('workflow_library')
+    # ### end Alembic commands ###

migrations/versions/b0f38c78db40_.py

@@ -0,0 +1,28 @@
+"""empty message
+
+Revision ID: b0f38c78db40
+Revises: a931e2b7b070
+Create Date: 2021-07-14 09:30:42.562825
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'b0f38c78db40'
+down_revision = 'a931e2b7b070'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('workflow_spec', sa.Column('library', sa.Boolean(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('workflow_spec', 'library')
+    # ### end Alembic commands ###