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