def test_gunzip_file_to_file(self):
compressed = self.create_test_file(compression='gzip')
expanded = expand_file(filename=compressed,
zip_protocol='gzip',
output='file')
with open(expanded, 'rb') as result:
self.assertEqual(result.read(), self.test_text)
def search(self, criteria, limit=0):
"""Search for documents matching criteria
:param criteria: dictionary defining search terms
:param limit: curtail lenght of result set
Returns empty string on no match, document contents on
a perfect match or with limit=1, and a list of document
meta-data on multiple matches.
"""
cursor = self.request.document_store.find(criteria).limit(limit)
count = cursor.count(with_limit_and_skip=True)
if count == 0:
return ''
elif count == 1:
# with a single document, return contents
document = cursor.next()
content = self.request.fs.get(document.get('_id'))
compression = document.get('compression')
if compression:
content = expand_file(fileobj=content,
zip_protocol=compression)
return content.read()
return [doc for doc in cursor]
def display_reports(context, request):
"""View callable method for displaying one or more reports
If the request included a filename or object id, display the
contents of the file. This is picked up in the traversal process,
set to context.filename. NB - it may define either the filename
used when persisting a report, or the document (Object) ID.
Otherwise, display table of metadata about persisted reports. If
the context is a subclass of BaseReport, the list will be limited
to those reports of like type.
"""
# If traversal included a filename, display file contents
if hasattr(context, 'filename'):
try:
# Attempt to access 'filename' as the document ID
try:
oid = ObjectId(context.filename)
except InvalidId:
raise NoFile
content = request.fs.get(oid)
document = request.document_store.find_one(oid)
compression = document.get('compression')
except NoFile:
# If the oid was not found, query filename of this type,
# if the context provided adequate data
try:
document = request.document_store.\
find_one({'filename': context.filename,
'report_type': context.report_type})
except AttributeError:
document = None
if not document:
raise NotFound
content = request.fs.get(document['_id'])
compression = document.get('compression')
if compression:
content = expand_file(fileobj=content, zip_protocol=compression)
return {'document': content.read()}
# Otherwise, query for all reports of this type
documents = ({
'filename': doc['filename'],
'uploadDate': doc['uploadDate'],
'length': doc['length'],
'id': doc['_id']
} for doc in request.document_store.find({
'report_type': context.report_type
}) if 'filename' in doc)
return {'documents': documents, 'report_type': context.report_type}
def upload(self, filename, filedate=None):
"""Upload the file to the PHEME_http_receiver channel
:param filename: batch filename to upload
:param filedate: needs to be defined for files that have been
archived, as the date is necessary to locate the archived
file.
"""
src = os.path.join(self.phinms_receiving_dir, filename)
if os.path.exists(src):
# Common case, the file is available in the receiving_dir
# as it hasn't yet been archived
self._feed(src, filename)
else:
# See if we can find the archived version. If so, it
# needs to be expanded before adding to the
# channelPath
try:
archive_dir = archive_by_date(self.phinms_archive_dir,
filedate)
src = os.path.join(archive_dir, filename + '.gz')
if os.path.exists(src):
expanded_file = expand_file(filename=src,
zip_protocol='gzip',
output='file')
self._feed(expanded_file, filename)
# remove the expanded_file, providing the source
# is still intact
if os.path.exists(src):
os.remove(expanded_file)
else:
raise RuntimeError("Archived batch file gone "
"after expansion")
else:
logging.error("Couldn't locate hl7 batch file "
"'%s' using date %s", filename,
str(filedate))
except:
logging.error("failed to locate hl7 batch file "
"'%s'", filename)
def upload(self, filename, filedate=None):
"""Upload the file to the PHEME_http_receiver channel
:param filename: batch filename to upload
:param filedate: needs to be defined for files that have been
archived, as the date is necessary to locate the archived
file.
"""
src = os.path.join(self.phinms_receiving_dir, filename)
if os.path.exists(src):
# Common case, the file is available in the receiving_dir
# as it hasn't yet been archived
self._feed(src, filename)
else:
# See if we can find the archived version. If so, it
# needs to be expanded before adding to the
# channelPath
try:
archive_dir = archive_by_date(self.phinms_archive_dir,
filedate)
src = os.path.join(archive_dir, filename + '.gz')
if os.path.exists(src):
expanded_file = expand_file(filename=src,
zip_protocol='gzip',
output='file')
self._feed(expanded_file, filename)
# remove the expanded_file, providing the source
# is still intact
if os.path.exists(src):
os.remove(expanded_file)
else:
raise RuntimeError("Archived batch file gone "
"after expansion")
else:
logging.error(
"Couldn't locate hl7 batch file "
"'%s' using date %s", filename, str(filedate))
except:
logging.error("failed to locate hl7 batch file "
"'%s'", filename)
def test_unzip_file(self):
compressed = self.create_test_file(compression='zip')
expanded = expand_file(filename=compressed,
zip_protocol='zip')
self.assertEqual(expanded.read(), self.test_text)
def test_unzip_stream(self):
compressed = self.create_test_file(compression='zip')
expanded = expand_file(fileobj=open(compressed, 'rb'),
zip_protocol='zip')
self.assertEqual(expanded.read(), self.test_text)
def test_gunzip_file_to_file(self):
compressed = self.create_test_file(compression="gzip")
expanded = expand_file(filename=compressed, zip_protocol="gzip", output="file")
with open(expanded, "rb") as result:
self.assertEqual(result.read(), self.test_text)
def test_gunzip_stream(self):
compressed = self.create_test_file(compression="gzip")
expanded = expand_file(fileobj=open(compressed, "rb"), zip_protocol="gzip")
self.assertEqual(expanded.read(), self.test_text)
def test_gunzip_file(self):
compressed = self.create_test_file(compression='gzip')
expanded = expand_file(filename=compressed, zip_protocol='gzip')
self.assertEqual(expanded.read(), self.test_text)
def test_gunzip_stream(self):
compressed = self.create_test_file(compression='gzip')
expanded = expand_file(fileobj=open(compressed, 'rb'),
zip_protocol='gzip')
self.assertEqual(expanded.read(), self.test_text)
