def create_test_file(self, compression=None):
"""Helper to generate a temporary file to save
Returns the filename, potenially pointing to a file containing
the content of self.text and compressed as requested.
NB File will need to be opened to use.
"""
# In case tests loop over file used - clean as we go
if hasattr(self, "tempfile"): # pragma: no cover
os.remove(self.tempfile.name)
del self.tempfile
# Generate a safe filename - deletion is tearDown's job
if compression is None:
self.tempfile = NamedTemporaryFile(prefix="unittest", delete=False)
self.tempfile.write(self.test_text)
self.tempfile.close()
elif compression == "gzip":
self.tempfile = NamedTemporaryFile(prefix="unittest", suffix=".gz", delete=False)
self.tempfile.close()
fh = gzip.open(self.tempfile.name, "wb")
fh.write(self.test_text)
fh.close()
elif compression == "zip":
self.tempfile = NamedTemporaryFile(prefix="unittest", suffix=".zip", delete=False)
self.tempfile.close()
os.remove(self.tempfile.name)
content = StringIO(self.test_text)
self.tempfile.name = zip_file(self.tempfile.name, content, compression)
else: # pragma: no cover
raise ValueError("Can't handle compression '%s'", compression)
return self.tempfile.name
def extract_content(self, compress_with):
content = self.content
if compress_with is not None and\
self.document.get('compression') is not None:
# Note, we're compressing on the fly, not persisting
content = zip_file(filename=self.document['filename'],
fileobj=content,
zip_protocol=compress_with)
return content
def create_test_file(self, compression=None):
"""Helper to generate a temporary file to save
Returns the filename, potenially pointing to a file containing
the content of self.text and compressed as requested.
NB File will need to be opened to use.
"""
# In case tests loop over file used - clean as we go
if hasattr(self, 'tempfile'): # pragma: no cover
os.remove(self.tempfile.name)
del self.tempfile
# Generate a safe filename - deletion is tearDown's job
if compression is None:
self.tempfile = NamedTemporaryFile(prefix='unittest', delete=False)
self.tempfile.write(self.test_text)
self.tempfile.close()
elif compression == 'gzip':
self.tempfile = NamedTemporaryFile(prefix='unittest',
suffix='.gz',
delete=False)
self.tempfile.close()
fh = gzip.open(self.tempfile.name, 'wb')
fh.write(self.test_text)
fh.close()
elif compression == 'zip':
self.tempfile = NamedTemporaryFile(prefix='unittest',
suffix='.zip',
delete=False)
self.tempfile.close()
os.remove(self.tempfile.name)
content = StringIO(self.test_text)
self.tempfile.name = zip_file(self.tempfile.name, content,
compression)
else: # pragma: no cover
raise ValueError("Can't handle compression '%s'", compression)
return self.tempfile.name
def upload_report(context, request):
"""View callable method for uploading reports
Persist the provided content in the database. If query args
include the following, take action:
:query param compress_with: Can be 'gzip' or 'zip' (or None)
to invoke compression before persisting.
:query param allow_duplicate_filename: Set true to override
default of not allowing duplicate filename inserts.
:query param metadata: Optional dictionary defining additional
metadata to store with the document. It is suggested to include
criteria used in report creation (i.e. 'reportable_region',
'patient_class', 'include_updates')
"""
if not hasattr(context, 'filename'):
raise HTTPBadRequest("Missing upload filename")
if not hasattr(context, 'file'):
context.file = request.params[context.filename].file
def content_type_lookup(compression):
content_type_map = {
None: 'text/plain',
'gzip': 'application/x-gzip',
'zip': 'application/zip'
}
return content_type_map[compression]
compression = request.params.get('compress_with', None)
content_type = content_type_lookup(compression)
if compression:
zipfile = zip_file(request.params[context.filename].filename,
request.params[context.filename].file, compression)
context.filename = os.path.basename(zipfile)
context.file = open(zipfile, 'rb')
allow_duplicate = request.params.get('allow_duplicate_filename', None)
if not allow_duplicate:
# Confirm a matching report wasn't already created.
criteria = {
'filename': context.filename,
'report_type': context.report_type
}
metadata = json.loads(request.params.get('metadata', "{}"))
for k in 'reportable_region', 'patient_class',\
'include_updates':
if k in metadata:
criteria[k] = metadata[k]
match = request.document_store.find_one(criteria)
if match:
err = "duplicate filename '%s' exists for '%s'" %\
(context.filename, context.report_type)
logging.error(err)
raise HTTPBadRequest(err)
# gridfs automatically includes uploadDate of utcnow()
# content_type is the Mime-type
kwargs = {
'filename': context.filename,
'report_type': context.report_type,
'compression': compression,
'content_type': content_type
}
for k, v in context.additional_save_attributes():
kwargs[k] = v
for k, v in json.loads(request.params.get('metadata', '{}')).items():
kwargs[k] = v
oid = request.fs.put(context.file, **kwargs)
context.file.close()
logging.info("New report uploaded: http://localhost:6543/%s/%s",
context.report_type, oid)
return {'document_id': str(oid)}
def test_gzip(self):
filename = self.create_test_file(compression=None)
result = zip_file(filename, open(filename, 'rb'), 'gzip')
f = gzip.GzipFile(mode='rb', fileobj=open(result, 'rb'))
self.assertEqual(f.read(), self.test_text)
def test_zip(self):
filename = self.create_test_file(compression=None)
result = zip_file(filename, open(filename, 'rb'), 'zip')
# hand verified the contents were zipped and matched...
self.assertTrue(os.path.exists(result))
def test_gzip(self):
filename = self.create_test_file(compression=None)
result = zip_file(filename, open(filename, "rb"), "gzip")
f = gzip.GzipFile(mode="rb", fileobj=open(result, "rb"))
self.assertEqual(f.read(), self.test_text)
self.assertEqual(filename + ".gz", result)
def test_zip(self):
filename = self.create_test_file(compression=None)
result = zip_file(filename, open(filename, "rb"), "zip")
# hand verified the contents were zipped and matched...
self.assertTrue(os.path.exists(result))
self.assertEqual(filename + ".zip", result)
def test_gzip(self):
filename = self.create_test_file(compression=None)
result = zip_file(filename, open(filename, 'rb'), 'gzip')
f = gzip.GzipFile(mode='rb', fileobj=open(result, 'rb'))
self.assertEqual(f.read(), self.test_text)
self.assertEqual(filename + '.gz', result)
def test_zip(self):
filename = self.create_test_file(compression=None)
result = zip_file(filename, open(filename, 'rb'), 'zip')
# hand verified the contents were zipped and matched...
self.assertTrue(os.path.exists(result))
self.assertEqual(filename + '.zip', result)
