396 lines
16 KiB
Python
396 lines
16 KiB
Python
import glob
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import glob
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import os
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from crc import app, db, session
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from crc.models.file import CONTENT_TYPES
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from crc.models.ldap import LdapModel
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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.document_service import DocumentService
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from crc.services.file_service import FileService
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from crc.services.study_service import StudyService
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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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engine = session.bind.engine
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connection = engine.connect()
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for table in reversed(db.metadata.sorted_tables):
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if engine.dialect.has_table(connection, table):
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session.execute(table.delete())
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session.commit()
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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.execute("select setval('workflow_spec_category_id_seq',7);")
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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_update",
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name="ind_update",
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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="non_uva_approval",
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name="non_uva",
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display_name="Non-UVA Institutional Approval",
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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",
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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=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="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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self.create_spec(id="department_chair_approval",
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name="department_chair_approval",
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display_name="Department Chair Approval",
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description="TBD",
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category_id=2,
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display_order=4)
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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 load_rrt(self):
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file_path = os.path.join(app.root_path, 'static', 'reference', 'rrt_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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category = WorkflowSpecCategoryModel(
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id=0,
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name='research_rampup_category',
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display_name='Research Ramp-up Category',
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display_order=0
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)
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db.session.add(category)
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db.session.commit()
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self.create_spec(id="rrt_top_level_workflow",
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name="rrt_top_level_workflow",
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display_name="Top Level Workflow",
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description="Does nothing, we don't use the master workflow here.",
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category_id=None,
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master_spec=True)
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self.create_spec(id="research_rampup",
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name="research_rampup",
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display_name="Research Ramp-up Toolkit",
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description="Process for creating a new research ramp-up request.",
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category_id=0,
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master_spec=False)
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def load_test_data(self):
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self.load_reference_documents()
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category = WorkflowSpecCategoryModel(
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id=0,
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name='test_category',
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display_name='Test Category',
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display_order=0
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)
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db.session.add(category)
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db.session.commit()
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self.create_spec(id="empty_workflow",
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name="empty_workflow",
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display_name="Top Level Workflow",
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description="Does nothing, we don't use the master workflow here.",
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category_id=None,
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master_spec=True,
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from_tests = True)
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self.create_spec(id="random_fact",
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name="random_fact",
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display_name="Random Fact",
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description="The workflow for a Random Fact.",
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category_id=0,
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master_spec=False,
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from_tests=True)
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def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False,
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category_id=None, display_order=None, from_tests=False, standalone=False, library=False):
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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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standalone=standalone,
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library=library)
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db.session.add(spec)
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db.session.commit()
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if not filepath and not from_tests:
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filepath = os.path.join(app.root_path, 'static', 'bpmn', id, "*.*")
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if not filepath and from_tests:
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filepath = os.path.join(app.root_path, '..', 'tests', 'data', id, "*.*")
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files = glob.glob(filepath)
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for file_path in files:
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if os.path.isdir(file_path):
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continue # Don't try to process sub directories
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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(DocumentService.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(StudyService.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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def load_default_user(self):
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user = UserModel(uid="dhf8r", email_address="dhf8r@virginia.edu", display_name="Development User")
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ldap_info = LdapModel(uid="dhf8r", email_address="dhf8r@virginia.edu", display_name="Development User")
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db.session.add(user)
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db.session.add(ldap_info)
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db.session.commit()
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def ldap(): return "x";
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def study_info(i): return {"x":"Y"};
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me = ldap()
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investigators = study_info('investigators')
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pi = investigators.get('PI', None)
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is_me_pi = False
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if pi is not None:
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hasPI = True
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if pi['uid'] == me['uid']:
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is_me_pi = True
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else:
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hasPI = False
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dc = investigators.get('DEPT_CH', None)
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pcs = {}
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is_me_pc = False
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for k in investigators.keys():
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if k in ['SC_I','SC_II','IRBC']:
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investigator = investigators.get(k)
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if investigator['uid'] != me['uid']:
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pcs[k] = investigator
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else:
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is_me_pc = True
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is_me_pc_role = investigator['label']
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del(investigator)
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cnt_pcs = len(pcs.keys())
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acs = {}
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is_me_ac = False
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for k in investigators.keys():
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if k == 'AS_C':
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investigator = investigators.get(k)
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if investigator['uid'] != me['uid']:
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acs[k] = investigator
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else:
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is_me_ac = True
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is_me_ac_role = investigator['label']
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del investigator
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cnt_acs = len(acs.keys())
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subs = {}
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is_me_subs = False
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for k in investigators.keys():
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if k[:2] == 'SI':
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investigator = investigators.get(k)
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if investigator['uid'] != me['uid']:
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subs[k] = investigator
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else:
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is_me_subs = True
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del investigator
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cnt_subs = len(subs.keys())
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del investigators |