Update Main from Dev

main.py

@@ -545,6 +545,7 @@ def main(sessionName, trialName, trial_id, cameras_to_use=['all'],
                 maxThreshold = 0.015
                 increment = 0.001
                 success = False
+                lastException = None
                 while thresholdPosition <= maxThreshold and not success:
                     try:
                         timeRange4Scaling = getScaleTimeRange(
@@ -553,8 +554,14 @@ def main(sessionName, trialName, trial_id, cameras_to_use=['all'],
                             thresholdTime=0.1, removeRoot=True)
                         success = True
                     except Exception as e:
-                        logging.info(f"Attempt identifying scaling time range with thresholdPosition {thresholdPosition} failed: {e}")
-                        thresholdPosition += increment  # Increase the threshold for the next iteration
+                        lastException = e
+                        logging.debug(f"Attempt identifying scaling time range with thresholdPosition {thresholdPosition} failed: {e}")
+
+                    if not success:
+                        thresholdPosition += increment
+
+                if not success:
+                    raise lastException
 
                 # Run scale tool.
                 logging.info('Running Scaling')

tests/test_api.py

@@ -2,33 +2,39 @@
 import os
 import sys
 import pytest
-from unittest.mock import patch, Mock
+from unittest.mock import patch, Mock, mock_open
 from http.client import HTTPMessage
 
 thisDir = os.path.dirname(os.path.realpath(__file__))
 repoDir = os.path.abspath(os.path.join(thisDir,'../'))
 sys.path.append(repoDir)
-from utils import makeRequestWithRetry
+from utils import (
+    DEFAULT_REQUEST_TIMEOUT,
+    UPLOAD_REQUEST_TIMEOUT,
+    makeRequestWithRetry,
+    uploadFileToS3,
+)
 
 logging.getLogger('urllib3').setLevel(logging.DEBUG)
 
 @patch("requests.Session.request")
-def test_get(mock_response):
+def test_get(mock_request):
     status_code = 200
-    mock_response.return_value.status_code = status_code
+    mock_request.return_value.status_code = status_code
 
     response = makeRequestWithRetry('GET', 'https://test.com', retries=2)
     assert response.status_code == status_code
-    mock_response.assert_called_once_with('GET', 'https://test.com',
-                                          headers=None,
-                                          data=None,
-                                          params=None,
-                                          files=None)
+    mock_request.assert_called_once_with('GET', 'https://test.com',
+                                         headers=None,
+                                         data=None,
+                                         params=None,
+                                         files=None,
+                                         timeout=DEFAULT_REQUEST_TIMEOUT)
 
 @patch("requests.Session.request")
-def test_put(mock_response):
+def test_put(mock_request):
     status_code = 201
-    mock_response.return_value.status_code = status_code
+    mock_request.return_value.status_code = status_code
 
     data = {
         "key1": "value1",
@@ -47,20 +53,44 @@ def test_put(mock_response):
                                     retries=2)
 
     assert response.status_code == status_code
-    mock_response.assert_called_once_with('POST',
+    mock_request.assert_called_once_with('POST',
                                          'https://test.com',
                                          data=data,
                                          headers={"Authorization": "my_token"},
                                          params=params,
-                                         files=None)
+                                         files=None,
+                                         timeout=DEFAULT_REQUEST_TIMEOUT)
+
+@patch("builtins.open", new_callable=mock_open, read_data=b"file-data")
+@patch("utils.makeRequestWithRetry")
+def test_upload_timeout(mock_request, mock_file):
+    mock_request.return_value.json.return_value = {
+        'url': 'https://upload.test.com',
+        'fields': {'key': 'uploaded-file'},
+    }
+
+    key = uploadFileToS3('/tmp/upload.mov')
+
+    assert key == 'uploaded-file'
+    mock_request.assert_any_call('POST',
+                                 'https://upload.test.com',
+                                 data={'key': 'uploaded-file'},
+                                 files={'file': mock_file.return_value},
+                                 timeout=UPLOAD_REQUEST_TIMEOUT)
 
 @patch("urllib3.connectionpool.HTTPConnectionPool._get_conn")
-def test_success_after_retries(mock_response):
-    mock_response.return_value.getresponse.side_effect = [
-        Mock(status=500, msg=HTTPMessage()),
-        Mock(status=502, msg=HTTPMessage()),
-        Mock(status=200, msg=HTTPMessage()),
-        Mock(status=429, msg=HTTPMessage()),
+def test_success_after_retries(mock_get_conn):
+    def make_response(status):
+        response = Mock(status=status, msg=HTTPMessage(), headers={})
+        response.stream.return_value = []
+        response._original_response = None
+        return response
+
+    mock_get_conn.return_value.getresponse.side_effect = [
+        make_response(500),
+        make_response(502),
+        make_response(200),
+        make_response(429),
     ]
 
     response = makeRequestWithRetry('GET',
@@ -69,11 +99,11 @@ def test_success_after_retries(mock_response):
                                     backoff_factor=0.1)
 
     assert response.status_code == 200
-    assert mock_response.call_count == 3
+    assert mock_get_conn.call_count == 3
 
 # The httpbin test remains commented out for stability reasons
 # def test_httpbin():
 #     response = makeRequestWithRetry('GET',
 #                                     'https://httpbin.org/status/500',
 #                                     retries=4,
-#                                     backoff_factor=0.1)
+#                                     backoff_factor=0.1)

tests/test_utils.py

@@ -0,0 +1,91 @@
+import os
+import sys
+
+import pytest
+from unittest.mock import Mock, patch
+
+
+thisDir = os.path.dirname(os.path.realpath(__file__))
+repoDir = os.path.abspath(os.path.join(thisDir,'../'))
+sys.path.append(repoDir)
+
+from utils import getCalibration, getNeutralTrialID, changeSessionMetadata
+
+
+@patch('utils.getSessionJson')
+def test_get_neutral_trial_id_from_session_trial(mock_get_session):
+    mock_get_session.return_value = {
+        'trials': [
+            {'id': 'dynamic-id', 'name': 'squats'},
+            {'id': 'neutral-id', 'name': 'neutral'},
+        ],
+        'meta': {},
+    }
+
+    assert getNeutralTrialID('session-id') == 'neutral-id'
+
+
+@patch('utils.getSessionJson')
+def test_get_neutral_trial_id_from_metadata_fallback(mock_get_session):
+    mock_get_session.return_value = {
+        'trials': [
+            {'id': 'dynamic-id', 'name': 'squats'},
+        ],
+        'meta': {
+            'neutral_trial': {'id': 'metadata-neutral-id'},
+        },
+    }
+
+    assert getNeutralTrialID('session-id') == 'metadata-neutral-id'
+
+
+@patch('utils.getSessionJson')
+def test_get_neutral_trial_id_raises_clear_error_without_neutral_trial(mock_get_session):
+    mock_get_session.return_value = {
+        'trials': [
+            {'id': 'dynamic-id', 'name': 'squats'},
+        ],
+        'meta': {},
+    }
+
+    with pytest.raises(Exception, match='No neutral trial in session'):
+        getNeutralTrialID('session-id')
+
+
+@patch('utils.getTrialJson')
+@patch('utils.getCalibrationTrialID')
+def test_get_calibration_raises_clear_error_without_camera_mapping(
+        mock_get_calibration_trial_id, mock_get_trial):
+    mock_get_calibration_trial_id.return_value = 'calibration-id'
+    mock_get_trial.return_value = {
+        'results': [
+            {'tag': 'calibration_parameters', 'media': 'calibration-url'},
+        ],
+    }
+
+    with pytest.raises(Exception, match='Redo calibration before processing dynamic trials'):
+        getCalibration('session-id', '/tmp/session')
+
+@patch('utils.getTrialJson')
+@patch('utils.getNeutralTrialID')
+@patch('utils.makeRequestWithRetry')
+@patch('utils.getSessionJson')
+def test_change_session_metadata_uses_settings_framerate_for_filterfrequency(
+        mock_get_session, mock_make_request, mock_get_neutral, mock_get_trial):
+    mock_get_session.return_value = {
+        'meta': {
+            'settings': {
+                'framerate': 240,
+            },
+        },
+    }
+    mock_make_request.return_value = Mock(status_code=200)
+    mock_get_neutral.return_value = 'neutral-id'
+    mock_get_trial.return_value = {
+        'results': [],
+    }
+
+    changeSessionMetadata(['session-id'], {'filterfrequency': 100})
+
+    patched_meta = mock_make_request.call_args.kwargs['data']['meta']
+    assert '"filterfrequency": "100"' in patched_meta

utils.py

@@ -28,6 +28,8 @@
 
 API_URL = getAPIURL()
 API_TOKEN = getToken()
+DEFAULT_REQUEST_TIMEOUT = (10, 10)
+UPLOAD_REQUEST_TIMEOUT = (10, 300)
 DEPTH_DB_LEVEL = 10
 DEPTH_DB_TRANSFORM = "vertical_delta_shuffle16"
 DEPTH_CONTAINER_MAGIC = b"OCDEPTHDB1\n"
@@ -121,7 +123,8 @@ def uploadFileToS3(filePath):
         makeRequestWithRetry('POST',
                              r['url'],
                              data=r['fields'],
-                             files=files)
+                             files=files,
+                             timeout=UPLOAD_REQUEST_TIMEOUT)
 
     return r['fields']['key']
 
@@ -854,10 +857,11 @@ def getNeutralTrialID(session_id):
 
     if len(neutral_ids)>0:
         neutralID = neutral_ids[-1]
-    elif session['meta']['neutral_trial']:
-        neutralID = session['meta']['neutral_trial']['id']
     else:
-        raise Exception('No neutral trial in session.')
+        neutral_trial = (session.get('meta') or {}).get('neutral_trial')
+        if not neutral_trial:
+            raise Exception('No neutral trial in session.')
+        neutralID = neutral_trial['id']
 
     return neutralID       
 
@@ -892,6 +896,8 @@ def getCalibration(session_id,session_path,trial_type='dynamic',getCalibrationOp
     # download the mapping
     videoFolder = os.path.join(session_path,'Videos')
     os.makedirs(videoFolder, exist_ok=True)
+    if 'camera_mapping' not in calibResultTags:
+        raise Exception('Calibration is missing camera mapping results. Redo calibration before processing dynamic trials.')
     mapURL = trial['results'][calibResultTags.index('camera_mapping')]['media']
     mapLocalPath = os.path.join(videoFolder,'mappingCamDevice.pickle')
     download_file(mapURL,mapLocalPath)
@@ -979,10 +985,8 @@ def changeSessionMetadata(session_ids,newMetaDict):
         existingMeta = session['meta']
 
         # Check if framerate is in metadata. If not, set to 60
-        if 'framerate' not in existingMeta:
-            framerate = 60
-        else:
-            framerate = existingMeta['framerate']
+        framerate = existingMeta.get('settings', {}).get(
+            'framerate', existingMeta.get('framerate', 60))
         if 'filterfrequency' in newMetaDict:
             if newMetaDict['filterfrequency'] != 'default':
                 if float(newMetaDict['filterfrequency']) > framerate/2:
@@ -2081,7 +2085,8 @@ def postProcessedDuration(trial_url, duration):
 # utils for common HTTP requests
 def makeRequestWithRetry(method, url,
                          headers=None, data=None, params=None, files=None,
-                         retries=5, backoff_factor=1):
+                         retries=5, backoff_factor=1,
+                         timeout=DEFAULT_REQUEST_TIMEOUT):
     """
     Makes an HTTP request with retry logic and returns the Response object.
 
@@ -2094,6 +2099,8 @@ def makeRequestWithRetry(method, url,
         params (dict): URL query parameters.
         retries (int): Number of retry attempts.
         backoff_factor (float): Backoff factor for exponential delays.
+        timeout (float or tuple): Seconds to wait for connection/response
+            activity, as accepted by requests.Session().request().
 
     Returns:
         requests.Response: The response object for further processing.
@@ -2113,6 +2120,7 @@ def makeRequestWithRetry(method, url,
                                     headers=headers,
                                     data=data,
                                     params=params,
-                                    files=files)
+                                    files=files,
+                                    timeout=timeout)
     response.raise_for_status()
     return response