feat(medcat-trainer): configurable remote model service timeout & prev suggestion from PR on context manager (#309)

Co-authored-by: Tom Searle <tom@cogstack.org>

Author: tomolopolis

medcat-trainer/envs/env

@@ -46,3 +46,6 @@ EMAIL_USER=example@cogstack.org
 EMAIL_PASS="to be changed"
 EMAIL_HOST=mail.cogstack.org
 EMAIL_PORT=465
+
+# Remote model service timeout in seconds
+REMOTE_MODEL_SERVICE_TIMEOUT=60

medcat-trainer/envs/env-prod

@@ -44,4 +44,7 @@ LOAD_NUM_DOC_PAGES=10
 EMAIL_USER=example@cogstack.org
 EMAIL_PASS="to be changed"
 EMAIL_HOST=mail.cogstack.org
-EMAIL_PORT=465
+EMAIL_PORT=465
+
+# Remote model service timeout in seconds
+REMOTE_MODEL_SERVICE_TIMEOUT=60

medcat-trainer/webapp/api/api/utils.py

@@ -64,8 +64,11 @@ def call_remote_model_service(service_url, text):
         "text": text
     }
 
+    # Get timeout from environment variable, default to 60 seconds
+    timeout = int(os.getenv('REMOTE_MODEL_SERVICE_TIMEOUT', '60'))
+
     try:
-        response = requests.post(api_url, json=payload, timeout=60)
+        response = requests.post(api_url, json=payload, timeout=timeout)
         response.raise_for_status()
         result = response.json()
 

medcat-trainer/webapp/api/api/views.py

@@ -19,6 +19,8 @@
 from rest_framework.response import Response
 from medcat.components.ner.trf.deid import DeIdModel
 from medcat.utils.cdb_utils import ch2pt_from_pt2ch, get_all_ch, snomed_ct_concept_path
+from medcat.utils.config_utils import temp_changed_config
+
 
 from .admin import download_projects_with_text, download_projects_without_text, \
     import_concepts_from_cdb
@@ -678,10 +680,8 @@ def annotate_text(request):
                 logger.warning(f'Failed to get children for CUI {parent_cui}: {e}')
         cuis_set = expanded_cuis
 
-    curr_cuis = cat.config.components.linking.filters
-    cat.config.components.linking.filters.cuis = cuis_set
-    spacy_doc = cat(message)
-    cat.config.components.linking.filters = curr_cuis
+    with temp_changed_config(cat.config.components.linking, 'filters', cuis_set):
+        spacy_doc = cat(message)
 
     ents = []
     anno_tkns = []