def test_maximal_search(self):
"""
Test that the maximal search is finding different results.
"""
culled_results = self.ips.client_state_map[
self.doc_id]['search_results']
self.ips.cull_overlapping = Mock(side_effect=self.return_value)
self.ips.process_analyze_document([], [])
pa_results = json.loads(self.ips.send_response.call_args[0][2])
actions = pa_results['actions']
self.assertTrue(actions[0]['action'] == 'showProgressbar')
startTime = time.time()
while actions[0]['action'] != 'highlightText' and (
time.time() - startTime < 100):
self.ips.process_analyze_document([], [])
pa_results = json.loads(self.ips.send_response.call_args[0][2])
actions = pa_results['actions']
self.assertTrue(actions[0]['action'] == 'highlightText'
or actions[0]['action'] == 'updateProgress')
time.sleep(0.25)
self.assertTrue(actions[0]['action'] == 'highlightText')
self.assertTrue(actions[1]['action'] == 'showSidebar')
unculled_results = self.ips.client_state_map[
self.doc_id]['search_results']
self.assertFalse(
compare_search_results(unculled_results, culled_results))
def test_analyze_basic(self):
"""
Basic check, ensure that spellcheck runs and the results are as expected
"""
# Basic sanity checks
self.assertTrue(self.ips.client_state_map[self.doc_id]['document_id']
== self.doc_id)
self.assertTrue(
self.ips.client_state_map[self.doc_id]['search_result_index'] is 1)
self.assertTrue(
len(self.ips.client_state_map[self.doc_id]['search_results']) is
self.expected_search_size)
self.assertTrue(
compare_search_results(
self.search_gt,
self.ips.client_state_map[self.doc_id]['search_results']),
'Search result sets do not match!')
def setUp(self):
"""
Configure an instance of IntentParserServer for spellcheck testing.
"""
# Clear all link preferences
if os.path.exists(IntentParserServer.LINK_PREF_PATH):
for file in os.listdir(IntentParserServer.LINK_PREF_PATH):
os.remove(os.path.join(IntentParserServer.LINK_PREF_PATH,
file))
os.rmdir(IntentParserServer.LINK_PREF_PATH)
self.doc_content = None
with open(os.path.join(self.dataDir, self.spellcheckFile), 'r') as fin:
self.doc_content = json.loads(fin.read())
if self.doc_content is None:
self.fail('Failed to read in test document! Path: ' +
os.path.join(self.dataDir, self.spellcheckFile))
self.doc_id = '1xMqOx9zZ7h2BIxSdWp2Vwi672iZ30N_2oPs8rwGUoTA'
self.user = '******'
self.user_email = '*****@*****.**'
self.json_body = {
'documentId': self.doc_id,
'user': self.user,
'userEmail': self.user_email
}
self.google_accessor = GoogleAccessor.create()
self.template_spreadsheet_id = '1r3CIyv75vV7A7ghkB0od-TM_16qSYd-byAbQ1DhRgB0'
self.spreadsheet_id = self.google_accessor.copy_file(
file_id=self.template_spreadsheet_id,
new_title='Intent Parser Server Test Sheet')
self.sbh_collection_uri = 'https://hub-staging.sd2e.org/user/sd2e/src/intent_parser_collection/1'
curr_path = os.path.dirname(os.path.realpath(__file__))
with open(os.path.join(curr_path, 'sbh_creds.json'), 'r') as file:
creds = json.load(file)
self.sbh_username = creds['username']
self.sbh_password = creds['password']
self.ips = IntentParserServer(
bind_port=8081,
bind_ip='0.0.0.0',
sbh_collection_uri=self.sbh_collection_uri,
spreadsheet_id=self.spreadsheet_id,
sbh_username=self.sbh_username,
sbh_password=self.sbh_password)
self.ips.initialize_server()
self.ips.start(background=True)
self.ips.analyze_processing_map_lock = Mock()
self.ips.client_state_lock = Mock()
self.ips.client_state_map = {}
self.ips.google_accessor = Mock()
self.ips.google_accessor.get_document = Mock(
return_value=self.doc_content)
self.ips.send_response = Mock()
self.ips.get_json_body = Mock(return_value=self.json_body)
self.ips.analyze_processing_map = {}
self.ips.analyze_processing_lock = {}
self.ips.item_map_lock = Mock()
with open(os.path.join(self.dataDir, self.items_json), 'r') as fin:
self.ips.item_map = json.load(fin)
self.ips.process_analyze_document([], [])
pa_results = json.loads(self.ips.send_response.call_args[0][2])
actions = pa_results['actions']
self.assertTrue(actions[0]['action'] == 'showProgressbar')
startTime = time.time()
while actions[0]['action'] != 'highlightText' and (
time.time() - startTime < 100):
self.ips.process_analyze_document([], [])
pa_results = json.loads(self.ips.send_response.call_args[0][2])
actions = pa_results['actions']
self.assertTrue(actions[0]['action'] == 'highlightText'
or actions[0]['action'] == 'updateProgress')
time.sleep(0.25)
self.assertTrue(actions[0]['action'] == 'highlightText')
self.assertTrue(actions[1]['action'] == 'showSidebar')
# Code to generate GT search results, for when test doc is updated
#with open(os.path.join(self.dataDir, self.searchResults), 'wb') as fout:
# pickle.dump(self.ips.client_state_map[self.doc_id]['search_results'], fout)
self.search_gt = None
with open(os.path.join(self.dataDir, self.searchResults), 'rb') as fin:
self.search_gt = pickle.load(fin)
if self.search_gt is None:
self.fail('Failed to read in spelling results! Path: ' +
os.path.join(self.dataDir, self.spellcheckResults))
compare_search_results(
self.search_gt,
self.ips.client_state_map[self.doc_id]['search_results'])
def test_maximal_search_ordering(self):
"""
I found that with a certain order, some overlaps weren't being found.
The issue is that, lets say indices 1&2 and 2&3 overlap.
If 2 is the maximal, then it will get removed when it overlaps with 1, but then won't get considered as overlapping with 3, so 3 won't be removed.
This test case covers that sitaution
"""
# Hand-coded test case based on real data. I found that the order of the results mattered for culling.
unculled_input = [{
'paragraph_index': 5,
'offset': 24,
'end_offset': 25,
'term': 'M9',
'uri': 'https://hub.sd2e.org/user/sd2e/design/M9/1',
'link': None,
'text': 'M9'
}, {
'paragraph_index': 167,
'offset': 0,
'end_offset': 1,
'term': 'M9',
'uri': 'https://hub.sd2e.org/user/sd2e/design/M9/1',
'link': None,
'text': 'M9'
}, {
'paragraph_index': 168,
'offset': 0,
'end_offset': 1,
'term': 'M9',
'uri': 'https://hub.sd2e.org/user/sd2e/design/M9/1',
'link': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'text': 'M9'
}, {
'paragraph_index': 5,
'offset': 24,
'end_offset': 37,
'term': 'M9 Media Salts',
'uri': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'link': None,
'text': 'M9 media salts'
}, {
'paragraph_index': 168,
'offset': 0,
'end_offset': 13,
'term': 'M9 Media Salts',
'uri': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'link': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'text': 'M9 media salts'
}, {
'paragraph_index': 162,
'offset': 13,
'end_offset': 17,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'Media'
}, {
'paragraph_index': 166,
'offset': 14,
'end_offset': 18,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'Media'
}, {
'paragraph_index': 193,
'offset': 15,
'end_offset': 19,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'Media'
}, {
'paragraph_index': 32,
'offset': 146,
'end_offset': 155,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 198,
'offset': 57,
'end_offset': 66,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 203,
'offset': 19,
'end_offset': 28,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 203,
'offset': 73,
'end_offset': 82,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 203,
'offset': 89,
'end_offset': 98,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 205,
'offset': 59,
'end_offset': 68,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 229,
'offset': 27,
'end_offset': 36,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 273,
'offset': 17,
'end_offset': 26,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 280,
'offset': 9,
'end_offset': 18,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 7,
'offset': 69,
'end_offset': 78,
'term': 'engineered',
'uri': 'https://hub.sd2e.org/user/sd2e/src/engineered/1',
'link': None,
'text': 'engineered'
}, {
'paragraph_index': 12,
'offset': 0,
'end_offset': 9,
'term': 'engineered',
'uri': 'https://hub.sd2e.org/user/sd2e/src/engineered/1',
'link': None,
'text': 'engineered'
}, {
'paragraph_index': 218,
'offset': 0,
'end_offset': 9,
'term': 'engineered',
'uri': 'https://hub.sd2e.org/user/sd2e/src/engineered/1',
'link': None,
'text': 'engineered'
}, {
'paragraph_index': 5,
'offset': 27,
'end_offset': 31,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 163,
'offset': 34,
'end_offset': 38,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 164,
'offset': 31,
'end_offset': 35,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 168,
'offset': 3,
'end_offset': 7,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'text': 'media'
}, {
'paragraph_index': 185,
'offset': 71,
'end_offset': 75,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 186,
'offset': 37,
'end_offset': 41,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 212,
'offset': 172,
'end_offset': 176,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 5,
'offset': 39,
'end_offset': 45,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteom'
}, {
'paragraph_index': 25,
'offset': 31,
'end_offset': 39,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomic'
}, {
'paragraph_index': 8,
'offset': 138,
'end_offset': 147,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 25,
'offset': 41,
'end_offset': 50,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 27,
'offset': 196,
'end_offset': 205,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 30,
'offset': 98,
'end_offset': 107,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 32,
'offset': 9,
'end_offset': 18,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'text': 'proteomics'
}, {
'paragraph_index': 126,
'offset': 41,
'end_offset': 50,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 158,
'offset': 58,
'end_offset': 67,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 5,
'offset': 4,
'end_offset': 12,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'roteomics'
}]
culled_gt = [{
'paragraph_index': 5,
'offset': 4,
'end_offset': 12,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'roteomics'
}, {
'paragraph_index': 5,
'offset': 24,
'end_offset': 37,
'term': 'M9 Media Salts',
'uri': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'link': None,
'text': 'M9 media salts'
}, {
'paragraph_index': 5,
'offset': 39,
'end_offset': 45,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteom'
}, {
'paragraph_index': 7,
'offset': 69,
'end_offset': 78,
'term': 'engineered',
'uri': 'https://hub.sd2e.org/user/sd2e/src/engineered/1',
'link': None,
'text': 'engineered'
}, {
'paragraph_index': 8,
'offset': 138,
'end_offset': 147,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 12,
'offset': 0,
'end_offset': 9,
'term': 'engineered',
'uri': 'https://hub.sd2e.org/user/sd2e/src/engineered/1',
'link': None,
'text': 'engineered'
}, {
'paragraph_index': 25,
'offset': 31,
'end_offset': 39,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomic'
}, {
'paragraph_index': 25,
'offset': 41,
'end_offset': 50,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 27,
'offset': 196,
'end_offset': 205,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 30,
'offset': 98,
'end_offset': 107,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 32,
'offset': 9,
'end_offset': 18,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'text': 'proteomics'
}, {
'paragraph_index': 32,
'offset': 146,
'end_offset': 155,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 126,
'offset': 41,
'end_offset': 50,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 158,
'offset': 58,
'end_offset': 67,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'proteomics'
}, {
'paragraph_index': 162,
'offset': 13,
'end_offset': 17,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'Media'
}, {
'paragraph_index': 163,
'offset': 34,
'end_offset': 38,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 164,
'offset': 31,
'end_offset': 35,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 166,
'offset': 14,
'end_offset': 18,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'Media'
}, {
'paragraph_index': 167,
'offset': 0,
'end_offset': 1,
'term': 'M9',
'uri': 'https://hub.sd2e.org/user/sd2e/design/M9/1',
'link': None,
'text': 'M9'
}, {
'paragraph_index': 168,
'offset': 0,
'end_offset': 13,
'term': 'M9 Media Salts',
'uri': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'link': 'https://hub.sd2e.org/user/sd2e/design/teknova_M1902/1',
'text': 'M9 media salts'
}, {
'paragraph_index': 185,
'offset': 71,
'end_offset': 75,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 186,
'offset': 37,
'end_offset': 41,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 193,
'offset': 15,
'end_offset': 19,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'Media'
}, {
'paragraph_index': 198,
'offset': 57,
'end_offset': 66,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 203,
'offset': 19,
'end_offset': 28,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 203,
'offset': 73,
'end_offset': 82,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 203,
'offset': 89,
'end_offset': 98,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 205,
'offset': 59,
'end_offset': 68,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 212,
'offset': 172,
'end_offset': 176,
'term': 'Media',
'uri': 'https://hub.sd2e.org/user/sd2e/design/Media/1',
'link': None,
'text': 'media'
}, {
'paragraph_index': 218,
'offset': 0,
'end_offset': 9,
'term': 'engineered',
'uri': 'https://hub.sd2e.org/user/sd2e/src/engineered/1',
'link': None,
'text': 'engineered'
}, {
'paragraph_index': 229,
'offset': 27,
'end_offset': 36,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 273,
'offset': 17,
'end_offset': 26,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}, {
'paragraph_index': 280,
'offset': 9,
'end_offset': 18,
'term': 'proteomics',
'uri': 'https://hub.sd2e.org/user/sd2e/src/proteomics/1',
'link': None,
'text': 'Proteomics'
}]
culled_result = self.ips.cull_overlapping(unculled_input)
culled_result = sorted(culled_result,
key=itemgetter('paragraph_index', 'offset'))
self.assertTrue(compare_search_results(culled_result, culled_gt))