#6 added info output of env

improved logging config

cellxgene_gateway/env.py

@@ -8,6 +8,7 @@
 # the specific language governing permissions and limitations under the License.
 
 import os
+import logging
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
 cellxgene_data = os.environ.get("CELLXGENE_DATA")
@@ -26,6 +27,11 @@ env_vars = {
     "GATEWAY_IP": ip,
 }
 
+optional_env_vars = {
+    "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
+    "GATEWAY_TTL": ttl,
+    "GATEWAY_ENABLE_UPLOAD": enable_upload,
+}
 
 def validate():
     if not all(env_vars.values()):
@@ -46,3 +52,6 @@ def validate():
         export GATEWAY_IP=127.0.0.1
     """
         )
+    else:
+        logging.getLogger("cellxgene_gateway").info(f"Got required env: {env_vars}", )
+        logging.getLogger("cellxgene_gateway").info(f"Got optional env: {optional_env_vars}")

cellxgene_gateway/gateway.py

@@ -10,6 +10,7 @@
 # import BaseHTTPServer
 import datetime
 import os
+import logging
 from threading import Thread
 
 from flask import (
@@ -204,6 +205,7 @@ def do_relaunch(path):
 
 
 def main():
+    logging.basicConfig(level=logging.INFO, format='%(asctime)s:%(name)s:%(levelname)s:%(message)s')
     env.validate()
     pruner = PruneProcessCache(cache)
     background_thread = Thread(target=pruner)

cellxgene_gateway/prune_process_cache.py

@@ -29,11 +29,12 @@ class PruneProcessCache:
         cutoff = timestamp - self.expire_seconds
         processes_to_delete = [p for p in self.cache.entry_list if  p.timestamp < cutoff]
         processes_to_keep = [p for p in self.cache.entry_list if not p.timestamp < cutoff]
-        logging.getLogger("werkzeug").debug(f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}")
+        logger = logging.getLogger("cellxgene_gateway")
+        logger.debug(f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}")
         
         for process in processes_to_delete:
             try:
-                logging.getLogger("werkzeug").info(f"pruning process {process.pid} ({process.dataset})")
+                logger.info(f"pruning process {process.pid} ({process.dataset})")
                 self.cache.prune(process)
             except Exception:
-                logging.getLogger("werkzeug").exception("failed to prune process {process.pid} ({process.dataset})")
+                logger.exception("failed to prune process {process.pid} ({process.dataset})")

cellxgene_gateway/subprocess_backend.py

@@ -38,7 +38,7 @@ class SubprocessBackend:
         cmd = self.create_cmd(
             cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
         )
-        logging.getLogger("werkzeug").info(f"launching {cmd}")
+        logging.getLogger("cellxgene_gateway").info(f"launching {cmd}")
         process = subprocess.Popen(
             [cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
         )