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cr-connect-workflow
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When you can't delete a file, mark it as archived. Don't include archived files in new approval requests.

This commit is contained in:
Dan Funk 2020-06-03 17:34:27 -04:00
parent c179c7781b
commit 217ecfc911
7 changed files with 73 additions and 22 deletions
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2
crc/api.yml
View File

@ -468,7 +468,7 @@ paths:
$ref: "#/components/schemas/File"
delete:
operationId: crc.api.file.delete_file
summary: Removes an existing file
summary: Removes an existing file. In the event the file can not be deleted, it is archived.
tags:
- Files
responses:

6
crc/api/approval.py
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@ -15,9 +15,9 @@ from crc.services.ldap_service import LdapService
def get_approvals(everything=False):
if everything:
approvals = ApprovalService.get_all_approvals(ignore_cancelled=True)
approvals = ApprovalService.get_all_approvals(include_cancelled=True)
else:
approvals = ApprovalService.get_approvals_per_user(g.user.uid, ignore_cancelled=True)
approvals = ApprovalService.get_approvals_per_user(g.user.uid, include_cancelled=False)
results = ApprovalSchema(many=True).dump(approvals)
return results
@ -33,7 +33,7 @@ def get_approvals_for_study(study_id=None):
def get_csv():
"""A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
man to do just about anything"""
approvals = ApprovalService.get_all_approvals(ignore_cancelled=True)
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
output = []
errors = []
ldapService = LdapService()

5
crc/models/file.py
View File

@ -82,7 +82,10 @@ class FileModel(db.Model):
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=True)
irb_doc_code = db.Column(db.String, nullable=True) # Code reference to the irb_documents.xlsx reference file.
# A request was made to delete the file, but we can't because there are
# active approvals or running workflows that depend on it. So we archive
# it instead, hide it in the interface.
archived = db.Column(db.Boolean, default=False)
class File(object):
@classmethod

21
crc/services/approval_service.py
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@ -15,7 +15,7 @@ class ApprovalService(object):
"""Provides common tools for working with an Approval"""
@staticmethod
def __one_approval_from_study(study, approver_uid = None, ignore_cancelled=False):
def __one_approval_from_study(study, approver_uid = None, include_cancelled=True):
"""Returns one approval, with all additional approvals as 'related_approvals',
the main approval can be pinned to an approver with an optional argument.
Will return null if no approvals exist on the study."""
@ -23,7 +23,7 @@ class ApprovalService(object):
related_approvals = []
query = db.session.query(ApprovalModel).\
filter(ApprovalModel.study_id == study.id)
if ignore_cancelled:
if not include_cancelled:
query=query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
approvals = query.all()
@ -40,35 +40,38 @@ class ApprovalService(object):
return main_approval
@staticmethod
def get_approvals_per_user(approver_uid, ignore_cancelled=False):
def get_approvals_per_user(approver_uid, include_cancelled=False):
"""Returns a list of approval objects (not db models) for the given
approver. """
studies = db.session.query(StudyModel).join(ApprovalModel).\
filter(ApprovalModel.approver_uid == approver_uid).all()
approvals = []
for study in studies:
approval = ApprovalService.__one_approval_from_study(study, approver_uid, ignore_cancelled)
approval = ApprovalService.__one_approval_from_study(study, approver_uid, include_cancelled)
if approval:
approvals.append(approval)
return approvals
@staticmethod
def get_all_approvals(ignore_cancelled=False):
def get_all_approvals(include_cancelled=True):
"""Returns a list of all approval objects (not db models), one record
per study, with any associated approvals grouped under the first approval."""
studies = db.session.query(StudyModel).all()
approvals = []
for study in studies:
approval = ApprovalService.__one_approval_from_study(study, ignore_cancelled=ignore_cancelled)
approval = ApprovalService.__one_approval_from_study(study, include_cancelled=include_cancelled)
if approval:
approvals.append(approval)
return approvals
@staticmethod
def get_approvals_for_study(study_id):
def get_approvals_for_study(study_id, include_cancelled=True):
"""Returns an array of Approval objects for the study, it does not
compute the related approvals."""
db_approvals = session.query(ApprovalModel).filter_by(study_id=study_id).all()
query = session.query(ApprovalModel).filter_by(study_id=study_id)
if not include_cancelled:
query = query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
db_approvals = query.all()
return [Approval.from_model(approval_model) for approval_model in db_approvals]
@ -101,7 +104,7 @@ class ApprovalService(object):
# Construct as hash of the latest files to see if things have changed since
# the last approval.
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
workflow_data_files = FileService.get_workflow_data_files(workflow_id)
workflow_data_files = FileService.get_workflow_data_files(workflow_id, include_archives=False)
current_data_file_ids = list(data_file.id for data_file in workflow_data_files)
if len(current_data_file_ids) == 0:

20
crc/services/file_service.py
View File

@ -195,7 +195,7 @@ class FileService(object):
@staticmethod
def get_files(workflow_spec_id=None, workflow_id=None,
name=None, is_reference=False, irb_doc_code=None):
name=None, is_reference=False, irb_doc_code=None, include_archives=True):
query = session.query(FileModel).filter_by(is_reference=is_reference)
if workflow_spec_id:
query = query.filter_by(workflow_spec_id=workflow_spec_id)
@ -208,6 +208,10 @@ class FileService(object):
if name:
query = query.filter_by(name=name)
if not include_archives:
query = query.filter(FileModel.archived == False)
query = query.order_by(FileModel.id)
results = query.all()
@ -238,11 +242,11 @@ class FileService(object):
return latest_data_files
@staticmethod
def get_workflow_data_files(workflow_id=None):
def get_workflow_data_files(workflow_id=None, include_archives=True):
"""Returns all the FileDataModels related to a running workflow -
So these are the latest data files that were uploaded or generated
that go along with this workflow. Not related to the spec in any way"""
file_models = FileService.get_files(workflow_id=workflow_id)
file_models = FileService.get_files(workflow_id=workflow_id, include_archives=include_archives)
latest_data_files = []
for file_model in file_models:
latest_data_files.append(FileService.get_file_data(file_model.id))
@ -316,6 +320,10 @@ class FileService(object):
session.query(FileModel).filter_by(id=file_id).delete()
session.commit()
except IntegrityError as ie:
app.logger.error("Failed to delete file: %i, due to %s" % (file_id, str(ie)))
raise ApiError('file_integrity_error', "You are attempting to delete a file that is "
"required by other records in the system.")
# We can't delete the file or file data, because it is referenced elsewhere,
# but we can at least mark it as deleted on the table.
session.rollback()
file_model = session.query(FileModel).filter_by(id=file_id).first()
file_model.archived = True
session.commit()
app.logger.error("Failed to delete file, so archiving it instead. %i, due to %s" % (file_id, str(ie)))

37
tests/test_files_api.py
View File

@ -9,6 +9,8 @@ from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
from example_data import ExampleDataLoader
from crc.services.approval_service import ApprovalService
from crc.models.approval import ApprovalModel, ApprovalStatus
class TestFilesApi(BaseTest):
@ -218,6 +220,41 @@ class TestFilesApi(BaseTest):
rv = self.app.get('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
self.assertEqual(404, rv.status_code)
def test_delete_file_after_approval(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anotother_anything.png", content_type="text",
binary_data=b'1234', irb_doc_code="Study_App_Doc")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
file = session.query(FileModel).\
filter(FileModel.workflow_id == workflow.id).\
filter(FileModel.name == "anything.png").first()
self.assertFalse(file.archived)
rv = self.app.get('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.delete('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
self.assert_success(rv)
session.refresh(file)
self.assertTrue(file.archived)
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
approvals = session.query(ApprovalModel)\
.filter(ApprovalModel.status == ApprovalStatus.PENDING.value)\
.filter(ApprovalModel.study_id == workflow.study_id).all()
self.assertEquals(1, len(approvals))
self.assertEquals(1, len(approvals[0].approval_files))
def test_change_primary_bpmn(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()

4
tests/test_workflow_spec_validation_api.py
View File

@ -71,7 +71,7 @@ class TestWorkflowSpecValidation(BaseTest):
self.load_example_data()
errors = self.validate_workflow("invalid_expression")
self.assertEqual(2, len(errors))
self.assertEqual("workflow_execution_exception", errors[0]['code'])
self.assertEqual("workflow_validation_exception", errors[0]['code'])
self.assertEqual("ExclusiveGateway_003amsm", errors[0]['task_id'])
self.assertEqual("Has Bananas Gateway", errors[0]['task_name'])
self.assertEqual("invalid_expression.bpmn", errors[0]['file_name'])
@ -92,7 +92,7 @@ class TestWorkflowSpecValidation(BaseTest):
self.load_example_data()
errors = self.validate_workflow("invalid_script")
self.assertEqual(2, len(errors))
self.assertEqual("workflow_execution_exception", errors[0]['code'])
self.assertEqual("workflow_validation_exception", errors[0]['code'])
self.assertTrue("NoSuchScript" in errors[0]['message'])
self.assertEqual("Invalid_Script_Task", errors[0]['task_id'])
self.assertEqual("An Invalid Script Reference", errors[0]['task_name'])