138 lines
6.0 KiB
Python
138 lines
6.0 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
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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
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from crc.services.workflow_processor import WorkflowProcessor
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from models.protocol_builder import ProtocolBuilderStatus
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class ExampleDataLoader:
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def make_data(self):
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users = [
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UserModel(
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uid='dhf8r',
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email_address='dhf8r@virginia.EDU',
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display_name='Daniel Harold Funk',
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affiliation='staff@virginia.edu;member@virginia.edu',
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eppn='dhf8r@virginia.edu',
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first_name='Daniel',
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last_name='Funk',
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title='SOFTWARE ENGINEER V'
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)
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]
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studies = [
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StudyModel(
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id=1,
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title='The impact of fried pickles on beer consumption in bipedal software developers.',
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last_updated=datetime.datetime.now(),
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protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS.name,
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primary_investigator_id='dhf8r',
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sponsor='Sartography Pharmaceuticals',
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ind_number='1234',
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user_uid='dhf8r'
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),
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StudyModel(
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id=2,
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title='Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
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last_updated=datetime.datetime.now(),
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protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS.name,
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primary_investigator_id='dhf8r',
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sponsor='Makerspace & Co.',
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ind_number='5678',
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user_uid='dhf8r'
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),
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]
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workflow_specifications = \
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self.create_spec(id="crc2_training_session_enter_core_info",
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name="crc2_training_session_enter_core_info",
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display_name="CR Connect2 - Training Session - Core Info",
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description='Part of Milestone 3 Deliverable')
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workflow_specifications += \
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self.create_spec(id="crc2_training_session_data_security_plan",
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name="crc2_training_session_data_security_plan",
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display_name="CR Connect2 - Training Session - Data Security Plan",
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description='Part of Milestone 3 Deliverable')
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workflow_specifications += \
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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 and/or Funding Source ",
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description='TBD')
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# workflow_specifications += \
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# self.create_spec(id="m2_demo",
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# name="m2_demo",
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# display_name="Milestone 2 Demo",
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# description='A simplified CR Connect workflow for demonstration purposes.')
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# workflow_specifications += \
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# self.create_spec(id="crc_study_workflow",
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# name="crc_study_workflow",
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# display_name="CR Connect Study Workflow",
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# description='Draft workflow for CR Connect studies.')
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all_data = users + studies + workflow_specifications
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return all_data
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def create_spec(self, id, name, display_name="", description="", filepath=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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models = []
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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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models.append(spec)
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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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if file_extension.lower() == '.bpmn':
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type = FileType.bpmn
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elif file_extension.lower() == '.dmn':
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type = FileType.dmn
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elif file_extension.lower() == '.svg':
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type = FileType.svg
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elif file_extension.lower() == '.docx':
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type = FileType.docx
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else:
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raise Exception("Unsupported file type:" + file_path)
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continue
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is_primary = filename.lower() == id + ".bpmn"
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file_model = FileModel(name=filename, type=type, content_type='text/xml', version="1",
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last_updated=datetime.datetime.now(), primary=is_primary,
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workflow_spec_id=id)
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models.append(file_model)
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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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if (is_primary):
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bpmn: ElementTree.Element = ElementTree.fromstring(data)
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spec.primary_process_id = WorkflowProcessor.get_process_id(bpmn)
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print("Locating Process Id for " + filename + " " + spec.primary_process_id)
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models.append(FileDataModel(data=data, file_model=file_model))
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finally:
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file.close()
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return models
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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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for data in self.make_data():
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session.add(data)
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session.commit()
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session.flush()
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