Fixes belbio/bel_api#83

# Conflicts:
#	bel/utils.py

bel/lang/bel_specification.py

@@ -104,7 +104,6 @@ def get_specification(version: str) -> Mapping[str, Any]:
     """
 
     spec_dir = config['bel']['lang']['specifications']
-
     spec_dict = {}
 
     bel_versions = get_bel_versions()
@@ -196,7 +195,6 @@ def update_specifications():
 def github_belspec_files(spec_dir):
     """Get belspec files from Github repo
 
-        Repo:  https://github.com/belbio/bel_specifications/tree/master/specifications
 
     """
     repo_url = 'https://api.github.com/repos/belbio/bel_specifications/contents/specifications'

bel/lang/belobj.py

@@ -78,6 +78,7 @@ def __init__(self, version: str = None, api_url: str = None) -> None:
         # use importlib to import our parser (a .py file) and set the BELParse object as an instance variable
         try:
             parser_fn = self.spec['admin']['parser_fn']
+
             parser_name = os.path.basename(parser_fn).replace('.py', '')
             module_spec = importlib.util.spec_from_file_location(parser_name, parser_fn)
             imported_parser = importlib.util.module_from_spec(module_spec)

bel/lang/semantics.py

@@ -241,7 +241,6 @@ def validate_arg_values(ast, bo):
             request_url = bo.api_url + '/terms/{}'.format(url_path_param_quoting(term_id))
             log.info(f'Validate Arg Values url {request_url}')
             r = get_url(request_url)
-
             if r and r.status_code == 200:
                 result = r.json()
                 # function signature term value_types doesn't match up with API term entity_types
@@ -254,13 +253,8 @@ def validate_arg_values(ast, bo):
                 # Term is valid
                 else:
                     log.debug('Valid Term: {}'.format(term_id))
-            elif r and r.status_code == 404:
-                msg = r.json()
-                if msg.get('title', None) == 'No Term':
-                    log.debug(f"No term found for /terms/{term_id}")
-                    bo.validation_messages.append(('WARNING', f'Term: {term_id} not found'))
-                else:
-                    log.error(f'Status 404 - Bad URL: {request_url}')
+            elif r.status_code == 404:
+                bo.validation_messages.append(('WARNING', f'Term: {term_id} not found in namespace'))
             else:
                 log.error(f'Status {r.status_code} - Bad URL: {request_url}')
 

bel/utils.py

@@ -22,8 +22,8 @@
 from cachecontrol import CacheControl
 from cachecontrol.heuristics import ExpiresAfter
 
-import logging
-log = logging.getLogger(__name__)
+from structlog import get_logger
+log = get_logger()
 
 # Caches Requests Library GET requests -
 reqsess = CacheControl(requests.Session(), heuristic=ExpiresAfter(days=1))
@@ -43,6 +43,8 @@ def get_url(url: str, params: dict = None, timeout: float = 5.0, cache: bool = T
         Requests Result obj or None if timed out
     """
 
+    start = datetime.datetime.now()
+
     if cache:
         req_obj = reqsess
     else:
@@ -58,13 +60,25 @@ def get_url(url: str, params: dict = None, timeout: float = 5.0, cache: bool = T
         else:
             r = req_obj.get(url, timeout=timeout)
 
-        log.info('Successful get_url')
+        timespan = datetime.datetime.now() - start
+        timespan_ms = timespan.total_seconds() * 1000  # converted to milliseconds
+        # log.debug(f'GET url success', cache_allowed=cache, timespan_ms=timespan_ms, url=url, params=params)
 
         return r
 
     except requests.exceptions.Timeout:
-        log.info(f'Timed out getting url in get_url: {url}')
+        log.warn(f'Timed out getting url in get_url: {url}')
         return None
+    except Exception as e:
+        log.warn(f'Error getting url: {url}  error: {e}')
+
+
+def timespan(start_time):
+    """Return time in milliseconds from start_time"""
+
+    timespan = datetime.datetime.now() - start_time
+    timespan_ms = timespan.total_seconds() * 1000
+    return timespan_ms
 
 
 def download_file(url):
@@ -76,7 +90,7 @@ def download_file(url):
         if chunk:  # filter out keep-alive new chunks
             fp.write(chunk)
 
-    log.info(f'Download file - tmp file: {fp.name}  size: {fp.tell()}')
+    # log.info(f'Download file - tmp file: {fp.name}  size: {fp.tell()}')
     return fp