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cr-connect-workflow
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Some additional cleanup - when a file is "archived" it is no longer returned for any endpoints about files, but it 

is directly accessible via id, in the event some request is made for it at a later date.
This commit is contained in:
Dan Funk 2020-06-04 09:49:42 -04:00
parent 217ecfc911
commit 1324533865
7 changed files with 80 additions and 13 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. In the event the file can not be deleted, it is archived.
summary: Removes an existing file. In the event the file can not be deleted, it is marked as "archived" in the database and is no longer returned unless specifically requested by id.
tags:
- Files
responses:

2
crc/api/approval.py
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@ -31,7 +31,7 @@ def get_approvals_for_study(study_id=None):
# ----- Being decent into madness ---- #
def get_csv():
"""A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
"""A damn lie, it's a json file. 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(include_cancelled=False)
output = []

2
crc/services/approval_service.py
View File

@ -104,7 +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, include_archives=False)
workflow_data_files = FileService.get_workflow_data_files(workflow_id)
current_data_file_ids = list(data_file.id for data_file in workflow_data_files)
if len(current_data_file_ids) == 0:

17
crc/services/file_service.py
View File

@ -96,6 +96,7 @@ class FileService(object):
def get_workflow_files(workflow_id):
"""Returns all the file models associated with a running workflow."""
return session.query(FileModel).filter(FileModel.workflow_id == workflow_id).\
filter(FileModel.archived == False).\
order_by(FileModel.id).all()
@staticmethod
@ -139,6 +140,7 @@ class FileService(object):
else:
file_model.type = FileType[file_extension]
file_model.content_type = content_type
file_model.archived = False # Unarchive the file if it is archived.
if latest_data_model is None:
version = 1
@ -188,14 +190,15 @@ class FileService(object):
def get_files_for_study(study_id, irb_doc_code=None):
query = session.query(FileModel).\
join(WorkflowModel).\
filter(WorkflowModel.study_id == study_id)
filter(WorkflowModel.study_id == study_id).\
filter(FileModel.archived == False)
if irb_doc_code:
query = query.filter(FileModel.irb_doc_code == irb_doc_code)
return query.all()
@staticmethod
def get_files(workflow_spec_id=None, workflow_id=None,
name=None, is_reference=False, irb_doc_code=None, include_archives=True):
name=None, is_reference=False, irb_doc_code=None):
query = session.query(FileModel).filter_by(is_reference=is_reference)
if workflow_spec_id:
query = query.filter_by(workflow_spec_id=workflow_spec_id)
@ -209,8 +212,7 @@ class FileService(object):
if name:
query = query.filter_by(name=name)
if not include_archives:
query = query.filter(FileModel.archived == False)
query = query.filter(FileModel.archived == False)
query = query.order_by(FileModel.id)
@ -242,11 +244,11 @@ class FileService(object):
return latest_data_files
@staticmethod
def get_workflow_data_files(workflow_id=None, include_archives=True):
def get_workflow_data_files(workflow_id=None):
"""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, include_archives=include_archives)
file_models = FileService.get_files(workflow_id=workflow_id)
latest_data_files = []
for file_model in file_models:
latest_data_files.append(FileService.get_file_data(file_model.id))
@ -274,7 +276,8 @@ class FileService(object):
@staticmethod
def get_workflow_file_data(workflow, file_name):
"""Given a SPIFF Workflow Model, tracks down a file with the given name in the database and returns its data"""
"""This method should be deleted, find where it is used, and remove this method.
Given a SPIFF Workflow Model, tracks down a file with the given name in the database and returns its data"""
workflow_spec_model = FileService.find_spec_model_in_db(workflow)
if workflow_spec_model is None:

33
tests/test_file_service.py
View File

@ -1,8 +1,9 @@
from tests.base_test import BaseTest
from crc import db
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
class TestFileService(BaseTest):
"""Largely tested via the test_file_api, and time is tight, but adding new tests here."""
@ -46,12 +47,42 @@ class TestFileService(BaseTest):
name="anything.png", content_type="text",
binary_data=b'5678')
def test_replace_archive_file_unarchives_the_file_and_updates(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
# Archive the file
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
file_model = file_models[0]
file_model.archived = True
db.session.add(file_model)
# Assure that the file no longer comes back.
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(0, len(file_models))
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_data))
self.assertEquals(2, file_data[0].version)
self.assertEquals(b'5678', file_data[0].data)
def test_add_file_from_form_allows_multiple_files_with_different_names(self):
self.load_example_data()

36
tests/test_files_api.py
View File

@ -3,7 +3,7 @@ import json
from tests.base_test import BaseTest
from crc import session
from crc import session, db
from crc.models.file import FileModel, FileType, FileSchema, FileModelSchema
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
@ -48,6 +48,7 @@ class TestFilesApi(BaseTest):
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(2, len(json_data))
def test_create_file(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()
@ -91,6 +92,39 @@ class TestFilesApi(BaseTest):
self.assert_success(rv)
def test_archive_file_no_longer_shows_up(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
correct_name = task.task_spec.form.fields[0].id
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
rv = self.app.post('/v1.0/file?study_id=%i&workflow_id=%s&task_id=%i&form_field_key=%s' %
(workflow.study_id, workflow.id, task.id, correct_name), data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEquals(1, len(json.loads(rv.get_data(as_text=True))))
file_model = db.session.query(FileModel).filter(FileModel.workflow_id == workflow.id).all()
self.assertEquals(1, len(file_model))
file_model[0].archived = True
db.session.commit()
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEquals(0, len(json.loads(rv.get_data(as_text=True))))
def test_set_reference_file(self):
file_name = "irb_document_types.xls"
data = {'file': (io.BytesIO(b"abcdef"), "does_not_matter.xls")}

1
tests/test_tasks_api.py
View File

@ -208,7 +208,6 @@ class TestTasksApi(BaseTest):
self.assert_success(rv)
def test_get_documentation_populated_in_end(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')