def testDuplicate(self):
"Use client API to store near duplicates and find"
doc_id = document_store(document=self.tempfile.name,
document_type='longitudinal')
duplicate_id = document_store(document=self.tempfile.name,
document_type='longitudinal',
allow_duplicate_filename=True)
self.doc_list.append(doc_id)
self.doc_list.append(duplicate_id)
criteria = {'filename': os.path.basename(self.tempfile.name)}
results = document_find(criteria)
self.assertEquals(len(results), 2)
self.assertNotEquals(results[0]['_id'], results[1]['_id'])
def testLimit(self):
"Use client API to store and limit search results"
doc_id = document_store(document=self.tempfile.name,
document_type='longitudinal')
duplicate_id = document_store(document=self.tempfile.name,
document_type='longitudinal',
allow_duplicate_filename=True)
self.doc_list.append(doc_id)
self.doc_list.append(duplicate_id)
criteria = {'filename': os.path.basename(self.tempfile.name)}
results = document_find(criteria)
self.assertEquals(len(results), 2)
result = document_find(criteria, limit=1)
# single result returns doc contents
self.assertEquals(result, self.test_text)
def testDocumentArchiveAPI(self):
"Use client API to store, fetch and delete a document"
doc_id = document_store(self.tempfile.name, 'longitudinal')
self.doc_list.append(doc_id)
self.assertTrue(doc_id)
# Pull from the store and see if metadata stuck
metadata = document_fetch_metadata(doc_id)
self.assertEqual(metadata.get('report_type', None),
'longitudinal')
def testFindOne(self):
"Use client API to find a single doc after storing"
doc_id = document_store(document=self.tempfile.name,
document_type='longitudinal')
self.doc_list.append(doc_id)
# Pull from the store and see if compressed
filename = os.path.basename(self.tempfile.name)
criteria = {'filename': filename}
document = document_find(criteria)
self.assertEquals(document, self.test_text)
def testUnZippedUpload(self):
"Can we upload an unzipped copy"
tmpfile = tempfile.NamedTemporaryFile('w')
tmpfile.write(lorem_ipsum)
tmpfile.seek(0)
doc_id = document_store(tmpfile.name,
document_type='essence',
compress_with=None)
self.assertTrue(doc_id)
agent = PHINMS_client(zip_first=False)
self.assertFalse(agent.transfer_file(doc_id))
def testUnZippedUpload(self):
"Can we upload an unzipped copy"
tmpfile = tempfile.NamedTemporaryFile('w')
tmpfile.write(lorem_ipsum)
tmpfile.seek(0)
metadata = {'reportable_region': 'wasc', }
doc_id = document_store(tmpfile.name,
document_type='essence',
**metadata)
self.assertTrue(doc_id)
agent = Distribute_client(zip_first=False)
self.assertFalse(agent.transfer_file(doc_id))
def testZipCompression(self):
"Use client API to compress and store a doc"
doc_id = document_store(document=self.tempfile.name,
document_type='longitudinal',
compress_with='zip')
self.doc_list.append(doc_id)
# Pull from the store and see if compressed
metadata = document_fetch_metadata(doc_id)
self.assertEqual(metadata.get('compression', None),
'zip')
filename = os.path.basename(self.tempfile.name) + '.zip'
self.assertEqual(self.test_text,
document_find({'filename': filename}))
def testDocumentArchiveMetaData(self):
"Persist and test additional metadata with a document"
now = datetime.now()
metadata = {'include_updates': True, 'jon': 'bon',
'report_type': 'foo', 'time_of_day': now}
doc_id = document_store(self.tempfile.name, 'longitudinal',
**metadata)
self.doc_list.append(doc_id)
self.assertTrue(doc_id)
# Pull from the store and see if metadata stuck
metadata = document_fetch_metadata(doc_id)
self.assertEqual(metadata['include_updates'], True)
self.assertEqual(metadata['jon'], 'bon')
self.assertEqual(metadata['time_of_day'], now.isoformat())
def _write_report(self, save_report=False):
""" Write out and potentially store the results.
Generate results via database queries and write the results to
self.output.
:param save_report: If set, persist the document and related
metadata to the mbds archive.
returns the document ID, the mbds archive key, if saved
"""
out = self.output
print >> out, self._header()
self._build_join_tables()
self._select_diagnosis()
self._select_vitals()
cursor = self.access.raw_query(self._select_from_essence_view())
for row in cursor.fetchall():
# Each row is the colums up to the diagnosis + the
# comma separated diagnosis + the rest of the columns
# and finally with vitals if configured for such
visit_pk = row[self.diagnosis_column_index] # yuck, but true
print >> out,\
'|'.join([strSansNone(column) for column in
row[:self.diagnosis_column_index]] +
self._diagnosis(visit_pk) +
[strSansNone(column) for column in
row[self.diagnosis_column_index + 1:]] +
self._vitals_for_visit(visit_pk))
# Close the file and persist to the document archive if
# requested
self.output.close()
if save_report:
metadata = {
k: v
for k, v in self.criteria._crit.items() if v is not None
}
# At this point, all documents are of 'essence' type
return document_store(document=self.output.name,
allow_duplicate_filename=True,
document_type='essence',
**metadata)
def _write_report(self, save_report=False):
""" Write out and potentially store the results.
Generate results via database queries and write the results to
self.output.
:param save_report: If set, persist the document and related
metadata to the mbds archive.
returns the document ID, the mbds archive key, if saved
"""
out = self.output
print >> out, self._header()
self._build_join_tables()
self._select_diagnosis()
self._select_vitals()
cursor = self.access.raw_query(self._select_from_essence_view())
for row in cursor.fetchall():
# Each row is the colums up to the diagnosis + the
# comma separated diagnosis + the rest of the columns
# and finally with vitals if configured for such
visit_pk = row[self.diagnosis_column_index] # yuck, but true
print >> out,\
'|'.join([strSansNone(column) for column in
row[:self.diagnosis_column_index]] +
self._diagnosis(visit_pk) +
[strSansNone(column) for column in
row[self.diagnosis_column_index + 1:]] +
self._vitals_for_visit(visit_pk))
# Close the file and persist to the document archive if
# requested
self.output.close()
if save_report:
metadata = {k: v for k, v in self.criteria._crit.items() if v
is not None}
# At this point, all documents are of 'essence' type
return document_store(document=self.output.name,
allow_duplicate_filename=True,
document_type='essence', **metadata)
