161 lines
6.5 KiB
Python
161 lines
6.5 KiB
Python
import datetime
|
|
import glob
|
|
import os
|
|
import xml.etree.ElementTree as ElementTree
|
|
|
|
from crc import app, db, session
|
|
from crc.models.file import FileType, FileModel, FileDataModel, CONTENT_TYPES
|
|
from crc.models.study import StudyModel
|
|
from crc.models.user import UserModel
|
|
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel
|
|
from crc.services.file_service import FileService
|
|
from crc.services.workflow_processor import WorkflowProcessor
|
|
from crc.models.protocol_builder import ProtocolBuilderStatus
|
|
|
|
|
|
class ExampleDataLoader:
|
|
@staticmethod
|
|
def clean_db():
|
|
session.flush() # Clear out any transactions before deleting it all to avoid spurious errors.
|
|
for table in reversed(db.metadata.sorted_tables):
|
|
session.execute(table.delete())
|
|
session.flush()
|
|
|
|
def load_all(self):
|
|
|
|
self.load_reference_documents()
|
|
|
|
categories = [
|
|
WorkflowSpecCategoryModel(
|
|
id=0,
|
|
name='irb_review',
|
|
display_name='Pass IRB Review',
|
|
display_order=0
|
|
),
|
|
WorkflowSpecCategoryModel(
|
|
id=1,
|
|
name='core_info',
|
|
display_name='Enter Core Info',
|
|
display_order=1
|
|
),
|
|
WorkflowSpecCategoryModel(
|
|
id=2,
|
|
name='approvals',
|
|
display_name='Obtain Approvals',
|
|
display_order=2
|
|
),
|
|
WorkflowSpecCategoryModel(
|
|
id=3,
|
|
name='data_security_plan',
|
|
display_name='Enter Data Security Plan',
|
|
display_order=3
|
|
),
|
|
WorkflowSpecCategoryModel(
|
|
id=4,
|
|
name='finance',
|
|
display_name='Enter Finance Data',
|
|
display_order=4
|
|
),
|
|
WorkflowSpecCategoryModel(
|
|
id=5,
|
|
name='notifications',
|
|
display_name='View and Send Notifications',
|
|
display_order=5
|
|
),
|
|
]
|
|
db.session.add_all(categories)
|
|
db.session.commit()
|
|
self.create_spec(id="top_level_workflow",
|
|
name="top_level_workflow",
|
|
display_name="Top Level Workflow",
|
|
description="Determines the status of other workflows in a study",
|
|
category_id=0,
|
|
master_spec=True
|
|
)
|
|
self.create_spec(id="irb_api_details",
|
|
name="irb_api_details",
|
|
display_name="IRB API Details",
|
|
description="TBD",
|
|
category_id=0)
|
|
self.create_spec(id="irb_api_personnel",
|
|
name="irb_api_personnel",
|
|
display_name="IRB API Personnel",
|
|
description="TBD",
|
|
category_id=0)
|
|
# self.create_spec(id="irb_api_required_docs",
|
|
# name="irb_api_required_docs",
|
|
# display_name="IRB API Required Documents",
|
|
# description="TBD",
|
|
# category_id=0)
|
|
self.create_spec(id="core_info",
|
|
name="core_info",
|
|
display_name="Core Data",
|
|
description="TBD",
|
|
category_id=1)
|
|
self.create_spec(id="ids",
|
|
name="ids",
|
|
display_name="Investigative Drug Services (IDS)",
|
|
description="TBD",
|
|
category_id=2)
|
|
self.create_spec(id="data_security_plan",
|
|
name="data_security_plan",
|
|
display_name="Data Security Plan",
|
|
description="TBD",
|
|
category_id=3)
|
|
self.create_spec(id="sponsor_funding_source",
|
|
name="sponsor_funding_source",
|
|
display_name="Sponsor Funding Source",
|
|
description="TBD",
|
|
category_id=4)
|
|
self.create_spec(id="finance",
|
|
name="finance",
|
|
display_name="Finance",
|
|
description="TBD",
|
|
category_id=4)
|
|
|
|
|
|
def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False, category_id=None):
|
|
"""Assumes that a directory exists in static/bpmn with the same name as the given id.
|
|
further assumes that the [id].bpmn is the primary file for the workflow.
|
|
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,
|
|
is_master_spec=master_spec,
|
|
category_id=category_id)
|
|
db.session.add(spec)
|
|
db.session.commit()
|
|
if not filepath:
|
|
filepath = os.path.join(app.root_path, 'static', 'bpmn', id, "*")
|
|
files = glob.glob(filepath)
|
|
for file_path in files:
|
|
noise, file_extension = os.path.splitext(file_path)
|
|
filename = os.path.basename(file_path)
|
|
|
|
is_status = filename.lower() == 'status.bpmn'
|
|
is_primary = filename.lower() == id + '.bpmn'
|
|
try:
|
|
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, is_status=is_status)
|
|
except IsADirectoryError as de:
|
|
# Ignore sub directories
|
|
pass
|
|
finally:
|
|
if file:
|
|
file.close()
|
|
return spec
|
|
|
|
def load_reference_documents(self):
|
|
file_path = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
|
|
file = open(file_path, "rb")
|
|
FileService.add_reference_file(FileService.IRB_PRO_CATEGORIES_FILE,
|
|
binary_data=file.read(),
|
|
content_type=CONTENT_TYPES['xls'])
|
|
file.close()
|