diff --git a/crc/__init__.py b/crc/__init__.py
index cab9ccde..11c0c4d6 100644
--- a/crc/__init__.py
+++ b/crc/__init__.py
@@ -15,6 +15,7 @@ connexion_app = connexion.FlaskApp(__name__)
app = connexion_app.app
app.config.from_object('config.default')
+app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = False
auth = HTTPTokenAuth('Bearer')
if "TESTING" in os.environ and os.environ["TESTING"] == "true":
diff --git a/crc/api.yml b/crc/api.yml
index 5d120aaa..1b8a7c98 100644
--- a/crc/api.yml
+++ b/crc/api.yml
@@ -443,11 +443,14 @@ paths:
content:
multipart/form-data:
schema:
+ x-body-name: file
type: object
properties:
file:
type: string
format: binary
+ required:
+ - file
responses:
'200':
description: Returns the actual file
@@ -716,10 +719,31 @@ components:
properties:
id:
type: string
+ name:
+ type: string
display_name:
type: string
description:
type: string
+ primary_process_id:
+ type: string
+ nullable: true
+ workflow_spec_category_id:
+ type: integer
+ nullable: true
+ workflow_spec_category:
+ $ref: "#/components/schemas/WorkflowSpecCategory"
+ is_status:
+ type: boolean
+ nullable: true
+ WorkflowSpecCategory:
+ properties:
+ id:
+ type: integer
+ name:
+ type: string
+ display_name:
+ type: string
File:
properties:
id:
diff --git a/crc/api/study.py b/crc/api/study.py
index 9a77c36d..fbdc96c1 100644
--- a/crc/api/study.py
+++ b/crc/api/study.py
@@ -23,16 +23,46 @@ def all_studies():
@auth.login_required
def add_study(body):
- study = StudyModelSchema().load(body, session=session)
+ study: StudyModel = StudyModelSchema().load(body, session=session)
+ status_spec = __get_status_spec(study.status_spec_id)
+
+ # Get latest status spec version
+ if status_spec is not None:
+ study.status_spec_id = status_spec.id
+ study.status_spec_version = WorkflowProcessor.get_latest_version_string(status_spec.id)
+
session.add(study)
session.commit()
- # FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all.
- for spec in session.query(WorkflowSpecModel).all():
- WorkflowProcessor.create(study.id, spec.id)
+ __add_study_workflows_from_status(study.id, status_spec)
return StudyModelSchema().dump(study)
+def __get_status_spec(status_spec_id):
+ if status_spec_id is None:
+ return session.query(WorkflowSpecModel).filter_by(is_status=True).first()
+ else:
+ return session.query(WorkflowSpecModel).filter_by(id=status_spec_id).first()
+
+
+def __add_study_workflows_from_status(study_id, status_spec):
+ all_specs = session.query(WorkflowSpecModel).all()
+ if status_spec is not None:
+ # Run status spec to get list of workflow specs applicable to this study
+ status_processor = WorkflowProcessor.create(study_id, status_spec)
+ status_processor.do_engine_steps()
+ status_data = status_processor.next_task().data
+
+ # Only add workflow specs listed in status spec
+ for spec in all_specs:
+ if spec.id in status_data and status_data[spec.id]:
+ WorkflowProcessor.create(study_id, spec.id)
+ else:
+ # No status spec. Just add all workflows.
+ for spec in all_specs:
+ WorkflowProcessor.create(study_id, spec.id)
+
+
@auth.login_required
def update_study(study_id, body):
if study_id is None:
@@ -130,23 +160,63 @@ def post_update_study_from_protocol_builder(study_id):
@auth.login_required
def get_study_workflows(study_id):
- workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all()
+
+ # Get study
+ study: StudyModel = session.query(StudyModel).filter_by(id=study_id).first()
+
+ # Get study status spec
+ status_spec: WorkflowSpecModel = session.query(WorkflowSpecModel)\
+ .filter_by(is_status=True).first()
+
+ status_data = None
+
+ if status_spec is not None:
+ # Run status spec
+ status_workflow_model: WorkflowModel = session.query(WorkflowModel)\
+ .filter_by(study_id=study.id)\
+ .filter_by(workflow_spec_id=status_spec.id)\
+ .first()
+ status_processor = WorkflowProcessor(status_workflow_model)
+
+ # Get list of active workflow specs for study
+ status_processor.do_engine_steps()
+ status_data = status_processor.bpmn_workflow.last_task.data
+
+ # Get study workflows
+ workflow_models = session.query(WorkflowModel)\
+ .filter_by(study_id=study_id)\
+ .filter(WorkflowModel.workflow_spec_id != status_spec.id)\
+ .all()
+ else:
+ # Get study workflows
+ workflow_models = session.query(WorkflowModel)\
+ .filter_by(study_id=study_id)\
+ .all()
api_models = []
for workflow_model in workflow_models:
processor = WorkflowProcessor(workflow_model,
workflow_model.bpmn_workflow_json)
- api_models.append(__get_workflow_api_model(processor))
+ api_models.append(__get_workflow_api_model(processor, status_data))
schema = WorkflowApiSchema(many=True)
return schema.dump(api_models)
@auth.login_required
def add_workflow_to_study(study_id, body):
- workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
+ workflow_spec_model: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
if workflow_spec_model is None:
error = ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.')
return ApiErrorSchema.dump(error), 404
processor = WorkflowProcessor.create(study_id, workflow_spec_model.id)
+
+ # If workflow spec is a status spec, update the study status spec
+ if workflow_spec_model.is_status:
+ study = session.query(StudyModel).filter_by(id=study_id).first()
+ study.status_spec_id = workflow_spec_model.id
+ study.status_spec_version = processor.get_spec_version()
+ session.add(study)
+ session.commit()
+
return WorkflowApiSchema().dump(__get_workflow_api_model(processor))
@@ -193,3 +263,4 @@ def map_pb_study_to_study(pb_study):
study_info['inactive'] = False
return study_info
+
diff --git a/crc/api/workflow.py b/crc/api/workflow.py
index 49990bec..25536423 100644
--- a/crc/api/workflow.py
+++ b/crc/api/workflow.py
@@ -17,7 +17,8 @@ def all_specifications():
@auth.login_required
def add_workflow_specification(body):
- new_spec = WorkflowSpecModelSchema().load(body, session=session)
+ 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)
@@ -69,9 +70,14 @@ def delete_workflow_specification(spec_id):
session.commit()
-def __get_workflow_api_model(processor: WorkflowProcessor):
+def __get_workflow_api_model(processor: WorkflowProcessor, status_data=None):
spiff_tasks = processor.get_all_user_tasks()
user_tasks = list(map(Task.from_spiff, spiff_tasks))
+ is_active = True
+
+ if status_data is not None and processor.workflow_spec_id in status_data:
+ is_active = status_data[processor.workflow_spec_id]
+
workflow_api = WorkflowApi(
id=processor.get_workflow_id(),
status=processor.get_status(),
@@ -80,7 +86,8 @@ def __get_workflow_api_model(processor: WorkflowProcessor):
user_tasks=user_tasks,
workflow_spec_id=processor.workflow_spec_id,
spec_version=processor.get_spec_version(),
- is_latest_spec=processor.get_spec_version() == processor.get_latest_version_string(processor.workflow_spec_id)
+ is_latest_spec=processor.get_spec_version() == processor.get_latest_version_string(processor.workflow_spec_id),
+ is_active=is_active
)
if processor.next_task():
workflow_api.next_task = Task.from_spiff(processor.next_task())
@@ -89,9 +96,8 @@ def __get_workflow_api_model(processor: WorkflowProcessor):
@auth.login_required
def get_workflow(workflow_id, soft_reset=False, hard_reset=False):
- workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
+ workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first()
processor = WorkflowProcessor(workflow_model, soft_reset=soft_reset, hard_reset=hard_reset)
-
workflow_api_model = __get_workflow_api_model(processor)
update_workflow_stats(workflow_model, workflow_api_model)
return WorkflowApiSchema().dump(workflow_api_model)
diff --git a/crc/models/api_models.py b/crc/models/api_models.py
index 0e325f9d..6c4c7b2d 100644
--- a/crc/models/api_models.py
+++ b/crc/models/api_models.py
@@ -95,7 +95,8 @@ class TaskSchema(ma.Schema):
class WorkflowApi(object):
- def __init__(self, id, status, user_tasks, last_task, next_task, workflow_spec_id, spec_version, is_latest_spec):
+ def __init__(self, id, status, user_tasks, last_task, next_task, workflow_spec_id, spec_version,
+ is_latest_spec, is_active):
self.id = id
self.status = status
self.user_tasks = user_tasks
@@ -104,13 +105,13 @@ class WorkflowApi(object):
self.workflow_spec_id = workflow_spec_id
self.spec_version = spec_version
self.is_latest_spec = is_latest_spec
+ self.is_active = is_active
class WorkflowApiSchema(ma.Schema):
class Meta:
model = WorkflowApi
fields = ["id", "status", "user_tasks", "last_task", "next_task",
- "workflow_spec_id", "spec_version", "is_latest_spec",
- "num_tasks_total", "num_tasks_complete", "num_tasks_incomplete"]
+ "workflow_spec_id", "spec_version", "is_latest_spec", "is_active"]
unknown = INCLUDE
status = EnumField(WorkflowStatus)
@@ -120,15 +121,7 @@ class WorkflowApiSchema(ma.Schema):
@marshmallow.post_load
def make_workflow(self, data, **kwargs):
- keys = [
- 'id',
- 'status',
- 'user_tasks',
- 'last_task',
- 'next_task',
- 'workflow_spec_id',
- 'spec_version',
- 'is_latest_spec'
- ]
+ keys = ['id', 'status', 'user_tasks', 'last_task', 'next_task',
+ 'workflow_spec_id', 'spec_version', 'is_latest_spec', "is_active"]
filtered_fields = {key: data[key] for key in keys}
return WorkflowApi(**filtered_fields)
diff --git a/crc/models/file.py b/crc/models/file.py
index ce7c8a34..a98ca68e 100644
--- a/crc/models/file.py
+++ b/crc/models/file.py
@@ -1,7 +1,7 @@
import enum
from marshmallow_enum import EnumField
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from sqlalchemy import func
from sqlalchemy.dialects.postgresql import UUID
@@ -71,6 +71,7 @@ class FileModel(db.Model):
name = db.Column(db.String)
type = db.Column(db.Enum(FileType))
primary = db.Column(db.Boolean)
+ is_status = db.Column(db.Boolean)
content_type = db.Column(db.String)
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=True)
@@ -80,8 +81,10 @@ class FileModel(db.Model):
latest_version = db.Column(db.Integer, default=0)
-class FileModelSchema(ModelSchema):
+class FileModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = FileModel
+ load_instance = True
+ include_relationships = True
include_fk = True # Includes foreign keys
type = EnumField(FileType)
diff --git a/crc/models/stats.py b/crc/models/stats.py
index 70132b22..1bc1935d 100644
--- a/crc/models/stats.py
+++ b/crc/models/stats.py
@@ -1,4 +1,4 @@
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from crc import db
@@ -16,9 +16,11 @@ class WorkflowStatsModel(db.Model):
last_updated = db.Column(db.DateTime)
-class WorkflowStatsModelSchema(ModelSchema):
+class WorkflowStatsModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = WorkflowStatsModel
+ load_instance = True
+ include_relationships = True
include_fk = True # Includes foreign keys
@@ -35,7 +37,9 @@ class TaskEventModel(db.Model):
date = db.Column(db.DateTime)
-class TaskEventModelSchema(ModelSchema):
+class TaskEventModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = TaskEventModel
+ load_instance = True
+ include_relationships = True
include_fk = True # Includes foreign keys
diff --git a/crc/models/study.py b/crc/models/study.py
index ac7d708d..7e0d6dda 100644
--- a/crc/models/study.py
+++ b/crc/models/study.py
@@ -1,5 +1,5 @@
from marshmallow_enum import EnumField
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from sqlalchemy import func
from crc import db
@@ -20,11 +20,15 @@ class StudyModel(db.Model):
investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
inactive = db.Column(db.Boolean, default=False)
requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
+ status_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))
+ status_spec_version = db.Column(db.String)
-class StudyModelSchema(ModelSchema):
+class StudyModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = StudyModel
+ load_instance = True
+ include_relationships = True
include_fk = True # Includes foreign keys
protocol_builder_status = EnumField(ProtocolBuilderStatus)
diff --git a/crc/models/user.py b/crc/models/user.py
index 16a528c8..65b46de4 100644
--- a/crc/models/user.py
+++ b/crc/models/user.py
@@ -1,7 +1,7 @@
import datetime
import jwt
-from marshmallow_sqlalchemy import ModelSchema
+from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from crc import db, app
from crc.api.common import ApiError
@@ -52,7 +52,9 @@ class UserModel(db.Model):
raise ApiError('token_invalid', 'The Authentication token you provided. You need a new token. ')
-class UserModelSchema(ModelSchema):
+class UserModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = UserModel
+ load_instance = True
+ include_relationships = True
diff --git a/crc/models/workflow.py b/crc/models/workflow.py
index 92e74137..438daab7 100644
--- a/crc/models/workflow.py
+++ b/crc/models/workflow.py
@@ -1,9 +1,22 @@
import enum
-from marshmallow_sqlalchemy import ModelSchema
+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)
+ name = db.Column(db.String)
+ display_name = db.Column(db.String)
+
+
+class WorkflowSpecCategoryModelSchema(SQLAlchemyAutoSchema):
+ class Meta:
+ model = WorkflowSpecCategoryModel
+ load_instance = True
+ include_relationships = True
+
class WorkflowSpecModel(db.Model):
__tablename__ = 'workflow_spec'
@@ -12,11 +25,17 @@ class WorkflowSpecModel(db.Model):
display_name = db.Column(db.String)
description = db.Column(db.Text)
primary_process_id = db.Column(db.String)
+ workflow_spec_category_id = db.Column(db.Integer, db.ForeignKey('workflow_spec_category.id'), nullable=True)
+ workflow_spec_category = db.relationship("WorkflowSpecCategoryModel")
+ is_status = db.Column(db.Boolean, default=False)
-class WorkflowSpecModelSchema(ModelSchema):
+class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = WorkflowSpecModel
+ load_instance = True
+ include_relationships = True
+ include_fk = True # Includes foreign keys
class WorkflowStatus(enum.Enum):
@@ -34,4 +53,3 @@ class WorkflowModel(db.Model):
study_id = db.Column(db.Integer, db.ForeignKey('study.id'))
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))
spec_version = db.Column(db.String)
-
diff --git a/crc/scripts/complete_template.py b/crc/scripts/complete_template.py
index ee25d48f..8b190038 100644
--- a/crc/scripts/complete_template.py
+++ b/crc/scripts/complete_template.py
@@ -28,6 +28,11 @@ class CompleteTemplate(Script):
"the name of the docx template to use.")
file_name = args[0]
workflow_spec_model = self.find_spec_model_in_db(task.workflow)
+ task_study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
+
+ if task_study_id != study_id:
+ raise ApiError(code="invalid_argument",
+ message="The given task does not match the given study.")
if workflow_spec_model is None:
raise ApiError(code="workflow_model_error",
@@ -44,7 +49,6 @@ class CompleteTemplate(Script):
"within workflow specification '%s'") % (args[0], workflow_spec_model.id)
final_document_stream = self.make_template(BytesIO(file_data_model.data), task.data)
- study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
FileService.add_task_file(study_id=study_id, workflow_id=workflow_id, task_id=task.id,
name=file_name,
diff --git a/crc/services/file_service.py b/crc/services/file_service.py
index 0163ab11..aa0182d1 100644
--- a/crc/services/file_service.py
+++ b/crc/services/file_service.py
@@ -16,12 +16,13 @@ class FileService(object):
@staticmethod
def add_workflow_spec_file(workflow_spec: WorkflowSpecModel,
- name, content_type, binary_data, primary=False):
+ name, content_type, binary_data, primary=False, is_status=False):
"""Create a new file and associate it with a workflow spec."""
file_model = FileModel(
workflow_spec_id=workflow_spec.id,
name=name,
- primary=primary
+ primary=primary,
+ is_status=is_status
)
if primary:
bpmn: ElementTree.Element = ElementTree.fromstring(binary_data)
diff --git a/example_data.py b/example_data.py
index ddbcd9b0..dc1d1869 100644
--- a/example_data.py
+++ b/example_data.py
@@ -82,11 +82,11 @@ class ExampleDataLoader:
returns an array of data models to be added to the database."""
global file
file_service = FileService()
-
spec = WorkflowSpecModel(id=id,
name=name,
display_name=display_name,
- description=description)
+ description=description,
+ is_status=id == 'status')
db.session.add(spec)
db.session.commit()
if not filepath:
@@ -95,13 +95,15 @@ class ExampleDataLoader:
for file_path in files:
noise, file_extension = os.path.splitext(file_path)
filename = os.path.basename(file_path)
- is_primary = filename.lower() == id + ".bpmn"
+
+ is_status = filename.lower() == 'status.bpmn'
+ is_primary = filename.lower() == id + '.bpmn'
try:
- file = open(file_path, "rb")
+ file = open(file_path, 'rb')
data = file.read()
content_type = CONTENT_TYPES[file_extension[1:]]
file_service.add_workflow_spec_file(workflow_spec=spec, name=filename, content_type=content_type,
- binary_data=data, primary=is_primary)
+ binary_data=data, primary=is_primary, is_status=is_status)
except IsADirectoryError as de:
# Ignore sub directories
pass
diff --git a/migrations/versions/5f06108116ae_.py b/migrations/versions/5f06108116ae_.py
new file mode 100644
index 00000000..9b651a70
--- /dev/null
+++ b/migrations/versions/5f06108116ae_.py
@@ -0,0 +1,41 @@
+"""empty message
+
+Revision ID: 5f06108116ae
+Revises: 90dd63672e0a
+Create Date: 2020-03-13 14:55:32.214380
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '5f06108116ae'
+down_revision = '90dd63672e0a'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+ # ### commands auto generated by Alembic - please adjust! ###
+ op.create_table('workflow_spec_category',
+ sa.Column('id', sa.Integer(), nullable=False),
+ sa.Column('name', sa.String(), nullable=True),
+ sa.Column('display_name', sa.String(), nullable=True),
+ sa.PrimaryKeyConstraint('id')
+ )
+ op.add_column('file', sa.Column('is_status', sa.Boolean(), nullable=True))
+ op.add_column('workflow_spec', sa.Column('is_status', sa.Boolean(), nullable=True))
+ op.add_column('workflow_spec', sa.Column('workflow_spec_category_id', sa.Integer(), nullable=True))
+ op.create_foreign_key(None, 'workflow_spec', 'workflow_spec_category', ['workflow_spec_category_id'], ['id'])
+ # ### end Alembic commands ###
+
+
+def downgrade():
+ # ### commands auto generated by Alembic - please adjust! ###
+ op.drop_constraint(None, 'workflow_spec', type_='foreignkey')
+ op.drop_column('workflow_spec', 'workflow_spec_category_id')
+ op.drop_column('workflow_spec', 'is_status')
+ op.drop_column('file', 'is_status')
+ op.drop_table('workflow_spec_category')
+ # ### end Alembic commands ###
diff --git a/migrations/versions/65f3fce6031a_.py b/migrations/versions/65f3fce6031a_.py
new file mode 100644
index 00000000..5fa2ce0b
--- /dev/null
+++ b/migrations/versions/65f3fce6031a_.py
@@ -0,0 +1,32 @@
+"""empty message
+
+Revision ID: 65f3fce6031a
+Revises: 5f06108116ae
+Create Date: 2020-03-15 12:40:42.314190
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '65f3fce6031a'
+down_revision = '5f06108116ae'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+ # ### commands auto generated by Alembic - please adjust! ###
+ op.add_column('study', sa.Column('status_spec_id', sa.String(), nullable=True))
+ op.add_column('study', sa.Column('status_spec_version', sa.String(), nullable=True))
+ op.create_foreign_key(None, 'study', 'workflow_spec', ['status_spec_id'], ['id'])
+ # ### end Alembic commands ###
+
+
+def downgrade():
+ # ### commands auto generated by Alembic - please adjust! ###
+ op.drop_constraint(None, 'study', type_='foreignkey')
+ op.drop_column('study', 'status_spec_version')
+ op.drop_column('study', 'status_spec_id')
+ # ### end Alembic commands ###
diff --git a/tests/data/status/crc2_training_session_data_security_plan.dmn b/tests/data/status/crc2_training_session_data_security_plan.dmn
new file mode 100644
index 00000000..4acadb96
--- /dev/null
+++ b/tests/data/status/crc2_training_session_data_security_plan.dmn
@@ -0,0 +1,41 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ false
+
+
+
+
+
+ false
+
+
+
+
+ true
+
+
+
+
+
+ true
+
+
+
+
+
diff --git a/tests/data/status/crc2_training_session_enter_core_info.dmn b/tests/data/status/crc2_training_session_enter_core_info.dmn
new file mode 100644
index 00000000..2fbdd5ce
--- /dev/null
+++ b/tests/data/status/crc2_training_session_enter_core_info.dmn
@@ -0,0 +1,32 @@
+
+
+
+
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+
+
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+
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+ false
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+ false
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+ true
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+ true
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+
diff --git a/tests/data/status/crc2_training_session_sponsor_funding_source.dmn b/tests/data/status/crc2_training_session_sponsor_funding_source.dmn
new file mode 100644
index 00000000..e5020439
--- /dev/null
+++ b/tests/data/status/crc2_training_session_sponsor_funding_source.dmn
@@ -0,0 +1,30 @@
+
+
+
+
diff --git a/tests/data/status/status.bpmn b/tests/data/status/status.bpmn
new file mode 100644
index 00000000..13f144ed
--- /dev/null
+++ b/tests/data/status/status.bpmn
@@ -0,0 +1,121 @@
+
+
+
+
+ SequenceFlow_1ees8ka
+
+
+
+ Flow_1nimppb
+ Flow_1txrak2
+
+
+ Flow_1m8285h
+ Flow_1sggkit
+
+
+ Flow_18pl92p
+ Flow_0x9580l
+
+
+ Flow_024q2cw
+ Flow_1m8285h
+ Flow_1nimppb
+ Flow_18pl92p
+
+
+
+
+
+ Flow_1txrak2
+ Flow_1sggkit
+ Flow_0x9580l
+ Flow_0pwtiqm
+
+
+ Flow_0pwtiqm
+
+
+
+
+
+
+
+
+
+
+
+
+ SequenceFlow_1ees8ka
+ Flow_024q2cw
+
+
+
+
+
+
+
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+
+
+
+
+
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+
+
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diff --git a/tests/test_study_api.py b/tests/test_study_api.py
index 0b49f100..1988c43b 100644
--- a/tests/test_study_api.py
+++ b/tests/test_study_api.py
@@ -3,7 +3,7 @@ from datetime import datetime, timezone
from unittest.mock import patch, Mock
from crc import session
-from crc.models.api_models import WorkflowApiSchema
+from crc.models.api_models import WorkflowApiSchema, WorkflowApi
from crc.models.study import StudyModel, StudyModelSchema
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudyDetailsSchema, \
ProtocolBuilderStudySchema
@@ -160,9 +160,6 @@ class TestStudyApi(BaseTest):
rv = self.app.delete('/v1.0/study/%i' % study.id)
self.assert_failure(rv, error_code="study_integrity_error")
-
-
-
def test_delete_workflow(self):
self.load_example_data()
study = session.query(StudyModel).first()
@@ -207,3 +204,79 @@ class TestStudyApi(BaseTest):
json_data_after = json.loads(response_after.get_data(as_text=True))
workflows_after = WorkflowApiSchema(many=True).load(json_data_after)
self.assertEqual(1, len(workflows_after))
+
+ """
+ Workflow Specs that have been made available (or not) to a particular study via the status.bpmn should be flagged
+ as available (or not) when the list of a study's workflows is retrieved.
+ """
+ def test_workflow_spec_status(self):
+ self.load_example_data()
+ study = session.query(StudyModel).first()
+ study_id = study.id
+
+ # Add status workflow
+ self.load_test_spec('status')
+
+ # Add status workflow to the study
+ status_spec = session.query(WorkflowSpecModel).filter_by(is_status=True).first()
+ add_status_response = self.app.post('/v1.0/study/%i/workflows' % study.id,
+ content_type="application/json",
+ headers=self.logged_in_headers(),
+ data=json.dumps(WorkflowSpecModelSchema().dump(status_spec)))
+ self.assert_success(add_status_response)
+ json_data_status = json.loads(add_status_response.get_data(as_text=True))
+ status_workflow: WorkflowApi = WorkflowApiSchema().load(json_data_status)
+ self.assertIsNotNone(status_workflow)
+ self.assertIsNotNone(status_workflow.workflow_spec_id)
+ self.assertIsNotNone(status_workflow.spec_version)
+ self.assertIsNotNone(status_workflow.next_task)
+ self.assertIsNotNone(status_workflow.next_task['id'])
+ status_task_id = status_workflow.next_task['id']
+
+ # Verify that the study status spec is populated
+ updated_study: StudyModel = session.query(StudyModel).filter_by(id=study_id).first()
+ self.assertIsNotNone(updated_study)
+ self.assertIsNotNone(updated_study.status_spec_id)
+ self.assertIsNotNone(updated_study.status_spec_version)
+ self.assertEqual(updated_study.status_spec_id, status_workflow.workflow_spec_id)
+ self.assertEqual(updated_study.status_spec_version, status_workflow.spec_version)
+
+ # Add all available non-status workflows to the study
+ specs = session.query(WorkflowSpecModel).filter_by(is_status=False).all()
+ for spec in specs:
+ add_response = self.app.post('/v1.0/study/%i/workflows' % study.id,
+ content_type="application/json",
+ headers=self.logged_in_headers(),
+ data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
+ self.assert_success(add_response)
+
+ for is_active in [False, True]:
+ # Set all workflow specs to inactive|active
+ update_status_response = self.app.put('/v1.0/workflow/%i/task/%s/data' % (status_workflow.id, status_task_id),
+ headers=self.logged_in_headers(),
+ content_type="application/json",
+ data=json.dumps({'some_input': is_active}))
+ self.assert_success(update_status_response)
+ json_workflow_api = json.loads(update_status_response.get_data(as_text=True))
+ updated_workflow_api: WorkflowApi = WorkflowApiSchema().load(json_workflow_api)
+ self.assertIsNotNone(updated_workflow_api)
+ self.assertEqual(updated_workflow_api.status, WorkflowStatus.complete)
+ self.assertIsNotNone(updated_workflow_api.last_task)
+ self.assertIsNotNone(updated_workflow_api.last_task['data'])
+ self.assertIsNotNone(updated_workflow_api.last_task['data']['some_input'])
+ self.assertEqual(updated_workflow_api.last_task['data']['some_input'], is_active)
+
+ # List workflows for study
+ response_after = self.app.get('/v1.0/study/%i/workflows' % study.id,
+ content_type="application/json",
+ headers=self.logged_in_headers())
+ self.assert_success(response_after)
+
+ json_data_after = json.loads(response_after.get_data(as_text=True))
+ workflows_after = WorkflowApiSchema(many=True).load(json_data_after)
+ self.assertEqual(len(specs), len(workflows_after))
+
+ # All workflows should be inactive|active
+ for workflow in workflows_after:
+ self.assertEqual(workflow.is_active, is_active)
+
diff --git a/tests/test_tasks_api.py b/tests/test_tasks_api.py
index db2b33f0..75af55c5 100644
--- a/tests/test_tasks_api.py
+++ b/tests/test_tasks_api.py
@@ -159,7 +159,7 @@ class TestTasksApi(BaseTest):
}
workflow_api = self.complete_form(workflow, tasks[0], data)
self.assertIsNotNone(workflow_api.next_task)
- self.assertEquals("EndEvent_0evb22x", workflow_api.next_task['name'])
+ self.assertEqual("EndEvent_0evb22x", workflow_api.next_task['name'])
self.assertTrue(workflow_api.status == WorkflowStatus.complete)
rv = self.app.get('/v1.0/file?workflow_id=%i' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
diff --git a/tests/test_workflow_processor.py b/tests/test_workflow_processor.py
index c4ff3f21..02aa0300 100644
--- a/tests/test_workflow_processor.py
+++ b/tests/test_workflow_processor.py
@@ -165,7 +165,7 @@ class TestWorkflowProcessor(BaseTest):
study = session.query(StudyModel).first()
with self.assertRaises(ApiError) as context:
WorkflowProcessor.create(study.id, workflow_spec_model.id)
- self.assertEquals("workflow_validation_error", context.exception.code)
+ self.assertEqual("workflow_validation_error", context.exception.code)
self.assertTrue("bpmn:startEvent" in context.exception.message)
def test_workflow_spec_key_error(self):
@@ -311,14 +311,14 @@ class TestWorkflowProcessor(BaseTest):
# Setting up another processor should not error out, but doesn't pick up the update.
workflow_model.bpmn_workflow_json = processor.serialize()
processor2 = WorkflowProcessor(workflow_model)
- self.assertEquals("Step 1", processor2.bpmn_workflow.last_task.task_spec.description)
- self.assertNotEquals("# This is some documentation I wanted to add.",
+ self.assertEqual("Step 1", processor2.bpmn_workflow.last_task.task_spec.description)
+ self.assertNotEqual("# This is some documentation I wanted to add.",
processor2.bpmn_workflow.last_task.task_spec.documentation)
# You can do a soft update and get the right response.
processor3 = WorkflowProcessor(workflow_model, soft_reset=True)
- self.assertEquals("Step 1", processor3.bpmn_workflow.last_task.task_spec.description)
- self.assertEquals("# This is some documentation I wanted to add.",
+ self.assertEqual("Step 1", processor3.bpmn_workflow.last_task.task_spec.description)
+ self.assertEqual("# This is some documentation I wanted to add.",
processor3.bpmn_workflow.last_task.task_spec.documentation)
@@ -336,7 +336,7 @@ class TestWorkflowProcessor(BaseTest):
task.data = {"color": "blue"}
processor.complete_task(task)
next_task = processor.next_task()
- self.assertEquals("Step 2", next_task.task_spec.description)
+ self.assertEqual("Step 2", next_task.task_spec.description)
# Modify the specification, with a major change that alters the flow and can't be serialized effectively.
file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'two_forms', 'mods', 'two_forms_struc_mod.bpmn')
@@ -349,13 +349,40 @@ class TestWorkflowProcessor(BaseTest):
# Do a hard reset, which should bring us back to the beginning, but retain the data.
processor3 = WorkflowProcessor(workflow_model, hard_reset=True)
- self.assertEquals("Step 1", processor3.next_task().task_spec.description)
- self.assertEquals({"color": "blue"}, processor3.next_task().data)
+ self.assertEqual("Step 1", processor3.next_task().task_spec.description)
+ self.assertEqual({"color": "blue"}, processor3.next_task().data)
processor3.complete_task(processor3.next_task())
- self.assertEquals("New Step", processor3.next_task().task_spec.description)
- self.assertEquals({"color": "blue"}, processor3.next_task().data)
+ self.assertEqual("New Step", processor3.next_task().task_spec.description)
+ self.assertEqual({"color": "blue"}, processor3.next_task().data)
def test_get_latest_spec_version(self):
workflow_spec_model = self.load_test_spec("two_forms")
version = WorkflowProcessor.get_latest_version_string("two_forms")
self.assertTrue(version.startswith("v1 "))
+
+ def test_status_bpmn(self):
+ self.load_example_data()
+
+ specs = session.query(WorkflowSpecModel).all()
+
+ study = session.query(StudyModel).first()
+ workflow_spec_model = self.load_test_spec("status")
+
+ for enabled in [True, False]:
+ processor = WorkflowProcessor.create(study.id, workflow_spec_model.id)
+ task = processor.next_task()
+
+ # Turn all specs on or off
+ task.data = {"some_input": enabled}
+ processor.complete_task(task)
+
+ # Finish out rest of workflow
+ while processor.get_status() == WorkflowStatus.waiting:
+ task = processor.next_task()
+ processor.complete_task(task)
+
+ self.assertEqual(processor.get_status(), WorkflowStatus.complete)
+
+ # Enabled status of all specs should match the value set in the first task
+ for spec in specs:
+ self.assertEqual(task.data[spec.id], enabled)
diff --git a/tests/test_workflow_spec_api.py b/tests/test_workflow_spec_api.py
index 08faf16f..b5553247 100644
--- a/tests/test_workflow_spec_api.py
+++ b/tests/test_workflow_spec_api.py
@@ -2,7 +2,7 @@ import json
from crc import session
from crc.models.file import FileModel
-from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
+from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
from tests.base_test import BaseTest
@@ -25,7 +25,7 @@ class TestWorkflowSpec(BaseTest):
def test_add_new_workflow_specification(self):
self.load_example_data();
num_before = session.query(WorkflowSpecModel).count()
- spec = WorkflowSpecModel(id='make_cookies', display_name='Cooooookies',
+ spec = WorkflowSpecModel(id='make_cookies', name='make_cookies', display_name='Cooooookies',
description='Om nom nom delicious cookies')
rv = self.app.post('/v1.0/workflow-specification',
headers=self.logged_in_headers(),
@@ -46,6 +46,32 @@ class TestWorkflowSpec(BaseTest):
api_spec = WorkflowSpecModelSchema().load(json_data, session=session)
self.assertEqual(db_spec, api_spec)
+ def test_update_workflow_specification(self):
+ self.load_example_data()
+
+ category = WorkflowSpecCategoryModel(id=0, name='trap', display_name="It's a trap!")
+ session.add(category)
+ session.commit()
+
+ db_spec_before: WorkflowSpecModel = session.query(WorkflowSpecModel).first()
+ spec_id = db_spec_before.id
+ self.assertIsNone(db_spec_before.workflow_spec_category_id)
+
+ db_spec_before.workflow_spec_category_id = 0
+ rv = self.app.put('/v1.0/workflow-specification/%s' % spec_id,
+ content_type="application/json",
+ headers=self.logged_in_headers(),
+ data=json.dumps(WorkflowSpecModelSchema().dump(db_spec_before)))
+ self.assert_success(rv)
+ json_data = json.loads(rv.get_data(as_text=True))
+ api_spec = WorkflowSpecModelSchema().load(json_data, session=session)
+ self.assertEqual(db_spec_before, api_spec)
+
+ db_spec_after: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
+ self.assertIsNotNone(db_spec_after.workflow_spec_category_id)
+ self.assertIsNotNone(db_spec_after.workflow_spec_category)
+ self.assertEqual(db_spec_after.workflow_spec_category.display_name, category.display_name)
+
def test_delete_workflow_specification(self):
self.load_example_data()
spec_id = 'random_fact'