mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-22 12:48:25 +00:00
da7cae51b8
Improving the study_info script documentation to provide detailed examples of values returned based on arguments. Making the tests a little more targetted and less subject to breaking through better mocks. Allow all tests to pass even when ther protocol builder mock isn't running locally. Removing the duplication of reference files in tests and static, as this seems silly to me at the moment.
253 lines
10 KiB
Python
253 lines
10 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='From PB',
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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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WorkflowSpecCategoryModel(
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id=6,
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name='status',
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display_name='Status',
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display_order=6
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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="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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self.create_spec(id="documents_approvals",
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name="documents_approvals",
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display_name="Documents & Approvals",
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description="Status of all approvals and documents required from Protocol Builder",
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category_id=0,
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display_order=2)
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self.create_spec(id="ide_supplement",
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name="ide_supplement",
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display_name="IDE Supplement Info",
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description="Supplemental information for the IDE number entered in Protocol Builder",
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category_id=0,
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display_order=3)
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self.create_spec(id="ind_supplement",
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name="ind_supplement",
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display_name="IND Supplement Info",
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description="Supplement information for the Investigational New Drug(s) specified in Protocol Builder",
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category_id=0,
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display_order=4)
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# Core Info
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self.create_spec(id="protocol",
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name="protocol",
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display_name="Protocol",
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description="Upload the Study Protocol here.",
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category_id=1,
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display_order=0)
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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=1)
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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="Investigational Drug Service (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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self.create_spec(id="rsc_hire_submission",
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name="rsc_hire_submission",
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display_name="RSC/HIRE Submission",
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description="TBD",
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category_id=2,
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display_order=2)
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self.create_spec(id="rsc_hire_committee",
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name="rsc_hire_committee",
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display_name="RSC/HIRE Committee",
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description="TBD",
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category_id=2,
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display_order=3)
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# Data Security Plan
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self.create_spec(id="data_security_plan",
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name="data_security_plan",
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display_name="Data Security Plan",
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description="Create and generate Data Security Plan",
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category_id=3,
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display_order=0)
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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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# Status
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self.create_spec(id="enrollment_date",
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name="enrollment_date",
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display_name="Enrollment Date",
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description="Study enrollment date",
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category_id=6,
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display_order=0)
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self.create_spec(id="abandoned",
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name="abandoned",
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display_name="Abandoned",
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description="Place study into Abandoned status",
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category_id=6,
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display_order=1)
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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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file = None
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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.DOCUMENT_LIST,
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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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file_path = os.path.join(app.root_path, 'static', 'reference', 'investigators.xlsx')
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file = open(file_path, "rb")
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FileService.add_reference_file(FileService.INVESTIGATOR_LIST,
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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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