Refactor models into seperate directories
This commit is contained in:
Dan Funk
parent
cc33f686e5
commit
c4cbaeb64e
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@ -147,7 +147,7 @@ paths:
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operationId: crc.api.workflow.all_specifications
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summary: Provides a list of workflows specifications that can be added to a study manually. Please note that Protocol Builder will handle this most of the time.
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tags:
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- Workflow
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- Workflows and Tasks
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responses:
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'200':
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description: An array of workflow specifications
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@ -424,6 +424,11 @@ paths:
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components:
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schemas:
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DataModel:
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properties:
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id:
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type: string
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Study:
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properties:
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id:
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@ -7,7 +7,7 @@ from flask import send_file
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from crc import db
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from crc.api.common import ApiErrorSchema, ApiError
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from crc.models import FileSchema, FileModel, FileDataModel, FileType
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from crc.models.file import FileSchema, FileModel, FileDataModel, FileType
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def update_file_from_request(file_model):
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@ -1,14 +1,9 @@
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import os
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from datetime import datetime
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import connexion
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from connexion import NoContent
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from flask_marshmallow import Schema
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from crc import db, ma, connexion_app
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from crc import db
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from crc.api.common import ApiError, ApiErrorSchema
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from crc.models import WorkflowModel, WorkflowSchema, StudySchema, StudyModel, WorkflowSpecSchema, WorkflowSpecModel, \
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WorkflowStatus, Task, TaskSchema, FileSchema, FileModel, FileDataModel, FileType
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from crc.models.study import StudySchema, StudyModel
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from crc.models.workflow import WorkflowModel, WorkflowSchema, WorkflowSpecModel
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from crc.workflow_processor import WorkflowProcessor
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@ -1,5 +1,5 @@
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from crc import db
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from crc.models import WorkflowModel, WorkflowSchema, WorkflowSpecSchema, WorkflowSpecModel, \
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from crc.models.workflow import WorkflowModel, WorkflowSchema, WorkflowSpecSchema, WorkflowSpecModel, \
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Task, TaskSchema
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from crc.workflow_processor import WorkflowProcessor
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@ -36,7 +36,9 @@ def get_task(workflow_id, task_id):
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def update_task(workflow_id, task_id, body):
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global bpmn_workflow
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for field in body["task"]["form"]:
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print("Setting " + field["id"] + " to " + field["value"])
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workflow_spec_model = db.session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
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task = TaskSchema().load(body)
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if task.form:
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for field in task.form["fields"]:
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print("Setting " + field["id"] + " to " + field["value"])
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return body
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@ -0,0 +1,40 @@
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import enum
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from flask_marshmallow.sqla import ModelSchema
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from marshmallow_enum import EnumField
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from sqlalchemy import func
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from crc import db
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class FileType(enum.Enum):
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bpmn = "bpmm"
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svg = "svg"
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dmn = "dmn"
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class FileDataModel(db.Model):
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__tablename__ = 'file_data'
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id = db.Column(db.Integer, primary_key=True)
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data = db.Column(db.LargeBinary)
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file_model_id = db.Column(db.Integer, db.ForeignKey('file.id'))
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file_model = db.relationship("FileModel")
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class FileModel(db.Model):
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__tablename__ = 'file'
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id = db.Column(db.Integer, primary_key=True)
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name = db.Column(db.String)
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version = db.Column(db.Integer, default=0)
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last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
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type = db.Column(db.Enum(FileType))
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primary = db.Column(db.Boolean)
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content_type = db.Column(db.String)
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workflow_spec_id = db.Column(db.Integer, db.ForeignKey('workflow_spec.id'))
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class FileSchema(ModelSchema):
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class Meta:
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model = FileModel
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type = EnumField(FileType)
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@ -0,0 +1,32 @@
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import enum
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from marshmallow_enum import EnumField
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from marshmallow_sqlalchemy import ModelSchema
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from sqlalchemy import func
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from crc import db
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class ProtocolBuilderStatus(enum.Enum):
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out_of_date = "out_of_date"
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in_process = "in_process"
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complete = "complete"
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updating = "updating"
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class StudyModel(db.Model):
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__tablename__ = 'study'
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id = db.Column(db.Integer, primary_key=True)
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title = db.Column(db.String)
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last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
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protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
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primary_investigator_id = db.Column(db.String)
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sponsor = db.Column(db.String)
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ind_number = db.Column(db.String)
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class StudySchema(ModelSchema):
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class Meta:
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model = StudyModel
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protocol_builder_status = EnumField(ProtocolBuilderStatus)
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@ -1,39 +1,12 @@
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import enum
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from SpiffWorkflow import Task
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from flask_marshmallow.sqla import ModelSchema
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from marshmallow import post_load, fields
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import marshmallow
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from marshmallow_enum import EnumField
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from sqlalchemy import func
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from marshmallow_sqlalchemy import ModelSchema
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from crc import db, ma
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class ProtocolBuilderStatus(enum.Enum):
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out_of_date = "out_of_date"
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in_process = "in_process"
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complete = "complete"
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updating = "updating"
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class StudyModel(db.Model):
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__tablename__ = 'study'
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id = db.Column(db.Integer, primary_key=True)
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title = db.Column(db.String)
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last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
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protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus))
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primary_investigator_id = db.Column(db.String)
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sponsor = db.Column(db.String)
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ind_number = db.Column(db.String)
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class StudySchema(ModelSchema):
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class Meta:
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model = StudyModel
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protocol_builder_status = EnumField(ProtocolBuilderStatus)
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class WorkflowSpecModel(db.Model):
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__tablename__ = 'workflow_spec'
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id = db.Column(db.String, primary_key=True)
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@ -45,38 +18,6 @@ class WorkflowSpecSchema(ModelSchema):
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class Meta:
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model = WorkflowSpecModel
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class FileType(enum.Enum):
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bpmn = "bpmm"
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svg = "svg"
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dmn = "dmn"
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class FileDataModel(db.Model):
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__tablename__ = 'file_data'
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id = db.Column(db.Integer, primary_key=True)
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data = db.Column(db.LargeBinary)
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file_model_id = db.Column(db.Integer, db.ForeignKey('file.id'))
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file_model = db.relationship("FileModel")
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class FileModel(db.Model):
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__tablename__ = 'file'
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id = db.Column(db.Integer, primary_key=True)
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name = db.Column(db.String)
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version = db.Column(db.Integer, default=0)
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last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
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type = db.Column(db.Enum(FileType))
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primary = db.Column(db.Boolean)
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content_type = db.Column(db.String)
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workflow_spec_id = db.Column(db.Integer, db.ForeignKey('workflow_spec.id'))
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class FileSchema(ModelSchema):
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class Meta:
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model = FileModel
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type = EnumField(FileType)
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class WorkflowStatus(enum.Enum):
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new = "new"
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user_input_required = "user_input_required"
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@ -140,30 +81,28 @@ class PropertiesSchema(ma.Schema):
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fields = ["id", "value"]
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class FieldSchema(ma.Schema):
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class FormFieldSchema(ma.Schema):
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class Meta:
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fields = [
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"id", "type", "label", "defaultValue", "options", "validation", "properties"
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"id", "type", "label", "defaultValue", "options", "validation", "properties", "value"
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]
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options = fields.List(fields.Nested(OptionSchema))
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validation = fields.List(fields.Nested(ValidationSchema))
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properties = fields.List(fields.Nested(PropertiesSchema))
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options = marshmallow.fields.List(marshmallow.fields.Nested(OptionSchema))
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validation = marshmallow.fields.List(marshmallow.fields.Nested(ValidationSchema))
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properties = marshmallow.fields.List(marshmallow.fields.Nested(PropertiesSchema))
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class FormSchema(ma.Schema):
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class Meta:
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fields = ["key", "fields"]
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fields = fields.List(fields.Nested(FieldSchema))
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key = marshmallow.fields.String(required=True, allow_none=False)
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fields = marshmallow.fields.List(marshmallow.fields.Nested(FormFieldSchema))
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class TaskSchema(ma.Schema):
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class Meta:
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fields = ["id", "name", "title", "type", "state", "form", "documentation"]
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documentation = marshmallow.fields.String(required=False, allow_none=True)
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form = marshmallow.fields.Nested(FormSchema)
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form = fields.Nested(FormSchema)
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@post_load
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@marshmallow.post_load
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def make_task(self, data, **kwargs):
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return Task(**data)
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@ -95,7 +95,7 @@
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<dc:Bounds x="270" y="210" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
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<dc:Bounds x="480" y="210" width="100" height="80" />
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<dc:Bounds x="470" y="210" width="100" height="80" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNShape id="TextAnnotation_09fq7kh_di" bpmnElement="TextAnnotation_09fq7kh">
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<dc:Bounds x="330" y="116" width="99.99202297383536" height="68.28334396936822" />
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@ -108,19 +108,19 @@
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<dc:Bounds x="570" y="120" width="100" height="68" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="Association_1qirnyy_di" bpmnElement="Association_1qirnyy">
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<di:waypoint x="567" y="210" />
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<di:waypoint x="588" y="188" />
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<di:waypoint x="561" y="210" />
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<di:waypoint x="584" y="188" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNShape id="EndEvent_0u1cgrf_di" bpmnElement="EndEvent_0u1cgrf">
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<dc:Bounds x="692" y="232" width="36" height="36" />
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</bpmndi:BPMNShape>
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<bpmndi:BPMNEdge id="SequenceFlow_0am07in_di" bpmnElement="SequenceFlow_0am07in">
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<di:waypoint x="580" y="250" />
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<di:waypoint x="570" y="250" />
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<di:waypoint x="692" y="250" />
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</bpmndi:BPMNEdge>
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<bpmndi:BPMNEdge id="SequenceFlow_1291h6i_di" bpmnElement="SequenceFlow_1291h6i">
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<di:waypoint x="370" y="250" />
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<di:waypoint x="480" y="250" />
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<di:waypoint x="470" y="250" />
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</bpmndi:BPMNEdge>
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</bpmndi:BPMNPlane>
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</bpmndi:BPMNDiagram>
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@ -1,14 +1,14 @@
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import os
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import xml.etree.ElementTree as ElementTree
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from SpiffWorkflow.bpmn.BpmnScriptEngine import BpmnScriptEngine
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from SpiffWorkflow.bpmn.serializer.CompactWorkflowSerializer import CompactWorkflowSerializer
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from SpiffWorkflow.bpmn.workflow import BpmnWorkflow
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from SpiffWorkflow.camunda.parser.CamundaParser import CamundaParser
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from SpiffWorkflow.camunda.serializer.CamundaSerializer import CamundaSerializer
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from crc import app, db
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from crc.models import WorkflowStatus, WorkflowSpecModel, FileDataModel, FileModel
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import xml.etree.ElementTree as ElementTree
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from crc import db
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from crc.models.file import FileDataModel, FileModel
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from crc.models.workflow import WorkflowStatus
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class CustomBpmnScriptEngine(BpmnScriptEngine):
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"""This is a custom script processor that can be easily injected into Spiff Workflow.
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@ -2,7 +2,9 @@ import datetime
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import os
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from crc import db, app
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from crc.models import StudyModel, WorkflowSpecModel, FileType, FileModel, FileDataModel
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from crc.models.study import StudyModel
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from crc.models.workflow import WorkflowSpecModel
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from crc.models.file import FileType, FileModel, FileDataModel
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class ExampleDataLoader:
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@ -28,31 +30,33 @@ class ExampleDataLoader:
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),
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]
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workflow_specs = [WorkflowSpecModel(
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id="random_fact",
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display_name="Random Fact Generator",
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description='Displays a random fact about a topic of your choosing.',
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)]
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workflow_specifications = \
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self.create_spec(id="random_fact",
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display_name="Random Fact Generator",
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description='Displays a random fact about a topic of your choosing.')
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workflow_specifications += \
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self.create_spec(id="two_forms",
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display_name="Two dump questions on two seperate tasks",
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description='Displays a random fact about a topic of your choosing.')
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workflow_spec_files = [WorkflowSpecModel(
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id="random_fact",
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display_name="Random Fact Generator",
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description='Displays a random fact about a topic of your choosing.',
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)]
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workflow_spec_files = [FileModel(name="random_fact.bpmn",
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type=FileType.bpmn,
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version="1",
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last_updated=datetime.datetime.now(),
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primary=True,
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workflow_spec_id=workflow_specs[0].id)]
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filename = os.path.join(app.root_path, 'static', 'bpmn', 'random_fact', 'random_fact.bpmn')
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file = open(filename, "rb")
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workflow_data = [FileDataModel(data=file.read(), file_model=workflow_spec_files[0])]
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all_data = studies+workflow_specs+workflow_spec_files+workflow_data
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all_data = studies + workflow_specifications
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return all_data
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def create_spec(self, id, display_name, description):
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"""Assumes that a file exists in static/bpmn with the same name as the given id.
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returns an array of data models to be added to the database."""
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spec = WorkflowSpecModel(id=id,
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display_name=display_name,
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description=description)
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file_model = FileModel(name=id + ".bpmn", type=FileType.bpmn, version="1",
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last_updated=datetime.datetime.now(), primary=True,
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workflow_spec_id=id)
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filename = os.path.join(app.root_path, 'static', 'bpmn', id + ".bpmn")
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file = open(filename, "rb")
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workflow_data = FileDataModel(data=file.read(), file_model=file_model)
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file.close()
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return [spec, file_model, workflow_data]
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@staticmethod
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def clean_db():
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db.session.flush() # Clear out any transactions before deleting it all to avoid spurious errors.
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@ -1,12 +1,10 @@
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import json
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import unittest
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from sqlalchemy import func
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from crc import db
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from crc.models import StudyModel, StudySchema, WorkflowSpecModel, WorkflowSpecSchema, WorkflowModel, WorkflowStatus, \
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from crc.models.study import StudyModel, StudySchema
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from crc.models.workflow import WorkflowSpecModel, WorkflowSpecSchema, WorkflowModel, WorkflowStatus, \
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WorkflowSchema, TaskSchema
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from crc.workflow_processor import WorkflowProcessor
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from tests.base_test import BaseTest
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@ -81,7 +79,6 @@ class TestStudy(BaseTest, unittest.TestCase):
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self.assert_success(rv)
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self.assertEqual(0, db.session.query(WorkflowModel).count())
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def test_get_current_user_tasks(self):
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self.load_example_data()
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study = db.session.query(StudyModel).first()
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@ -93,4 +90,24 @@ class TestStudy(BaseTest, unittest.TestCase):
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json_data = json.loads(rv.get_data(as_text=True))
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tasks = TaskSchema(many=True).load(json_data)
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self.assertEqual("Task_User_Select_Type", tasks[0].name)
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self.assertEqual(3, len(tasks[0].form["fields"][0]["options"]))
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self.assertEqual(3, len(tasks[0].form["fields"][0]["options"]))
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def test_two_forms_task(self):
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self.load_example_data()
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study = db.session.query(StudyModel).first()
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spec = db.session.query(WorkflowSpecModel).filter_by(id='two_forms').first()
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rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
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data=json.dumps(WorkflowSpecSchema().dump(spec)))
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json_data = json.loads(rv.get_data(as_text=True))
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workflow = WorkflowSchema().load(json_data, session=db.session)
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rv = self.app.get('/v1.0/workflow/%i/tasks' % workflow.id, content_type="application/json")
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json_data = json.loads(rv.get_data(as_text=True))
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tasks = TaskSchema(many=True).load(json_data)
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self.assertEqual(1, len(tasks))
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self.assertIsNotNone(tasks[0].form)
|
||||
self.assertEqual(1, len(tasks[0].form['fields']))
|
||||
tasks[0].form['fields'][0]['value']="Blue"
|
||||
rv = self.app.put('/v1.0/workflow/%i/task/%s' % (workflow.id, tasks[0].id), content_type="application/json",
|
||||
data=json.dumps(TaskSchema().dump(tasks[0])))
|
||||
self.assert_success(rv)
|
||||
|
|
|
|||
|
|
@ -4,7 +4,8 @@ import unittest
|
|||
from datetime import datetime
|
||||
|
||||
from crc import db
|
||||
from crc.models import WorkflowSpecModel, FileModel, FileType, FileSchema, FileDataModel
|
||||
from crc.models.workflow import WorkflowSpecModel
|
||||
from crc.models.file import FileModel, FileType, FileSchema, FileDataModel
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
import unittest
|
||||
|
||||
from crc import db
|
||||
from crc.models import WorkflowSpecModel, WorkflowStatus
|
||||
from crc.models.workflow import WorkflowSpecModel, WorkflowStatus
|
||||
from crc.workflow_processor import WorkflowProcessor
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
|
|
@ -31,3 +31,13 @@ class TestWorkflowProcessor(BaseTest, unittest.TestCase):
|
|||
data = processor.get_data()
|
||||
self.assertIsNotNone(data)
|
||||
self.assertIn("details", data)
|
||||
|
||||
def test_two_forms(self):
|
||||
self.load_example_data()
|
||||
workflow_spec_model = db.session.query(WorkflowSpecModel).filter_by(id="two_forms").first()
|
||||
processor = WorkflowProcessor.create(workflow_spec_model.id)
|
||||
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
|
||||
next_user_tasks = processor.next_user_tasks()
|
||||
task = next_user_tasks[0]
|
||||
data = processor.get_data()
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue