110 lines
4.5 KiB
Python
110 lines
4.5 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
|
|
from crc.services.file_service import FileService
|
|
from crc.services.workflow_processor import WorkflowProcessor
|
|
|
|
|
|
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):
|
|
users = [
|
|
UserModel(
|
|
uid='dhf8r',
|
|
email_address='dhf8r@virginia.EDU',
|
|
display_name='Daniel Harold Funk',
|
|
affiliation='staff@virginia.edu;member@virginia.edu',
|
|
eppn='dhf8r@virginia.edu',
|
|
first_name='Daniel',
|
|
last_name='Funk',
|
|
title='SOFTWARE ENGINEER V'
|
|
)
|
|
]
|
|
db.session.add_all(users)
|
|
db.session.commit()
|
|
|
|
studies = [
|
|
StudyModel(
|
|
id=1,
|
|
title='The impact of fried pickles on beer consumption in bipedal software developers.',
|
|
last_updated=datetime.datetime.now(),
|
|
protocol_builder_status='in_process',
|
|
primary_investigator_id='dhf8r',
|
|
sponsor='Sartography Pharmaceuticals',
|
|
ind_number='1234',
|
|
user_uid='dhf8r'
|
|
),
|
|
StudyModel(
|
|
id=2,
|
|
title='Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
|
|
last_updated=datetime.datetime.now(),
|
|
protocol_builder_status='in_process',
|
|
primary_investigator_id='dhf8r',
|
|
sponsor='Makerspace & Co.',
|
|
ind_number='5678',
|
|
user_uid='dhf8r'
|
|
),
|
|
]
|
|
db.session.add_all(studies)
|
|
db.session.commit()
|
|
|
|
self.create_spec(id="crc2_training_session_enter_core_info",
|
|
name="crc2_training_session_enter_core_info",
|
|
display_name="CR Connect2 - Training Session - Core Info",
|
|
description='Part of Milestone 3 Deliverable')
|
|
self.create_spec(id="crc2_training_session_data_security_plan",
|
|
name="crc2_training_session_data_security_plan",
|
|
display_name="CR Connect2 - Training Session - Data Security Plan",
|
|
description='Part of Milestone 3 Deliverable')
|
|
self.create_spec(id="sponsor_funding_source",
|
|
name="sponsor_funding_source",
|
|
display_name="Sponsor and/or Funding Source ",
|
|
description='TBD')
|
|
|
|
def create_spec(self, id, name, display_name="", description="", filepath=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)
|
|
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_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)
|
|
except IsADirectoryError as de:
|
|
# Ignore sub directories
|
|
pass
|
|
finally:
|
|
if file:
|
|
file.close()
|
|
return spec
|