add ruff + ruff gha

.github/workflows/ruff.yml

@@ -0,0 +1,20 @@
+name: Ruff
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+      - run: ruff format --check
+      - run: ruff check . 

context.py

@@ -10,35 +10,34 @@
 from flask_authnz import FlaskAuthnz, MongoDBRoles, UserGroups
 
 from kafka import KafkaProducer
-from kafka.errors import KafkaError
 
 from dal.utils import JSONEncoder
 import jwt
 
 logger = logging.getLogger(__name__)
 
-__author__ = 'mshankar@slac.stanford.edu'
+__author__ = "mshankar@slac.stanford.edu"
 
 # Application context.
 app = None
 
-MONGODB_HOST=os.environ.get('MONGODB_HOST', "localhost")
-MONGODB_PORT=int(os.environ.get('MONGODB_PORT', 27017))
-MONGODB_HOSTS=os.environ.get("MONGODB_HOSTS", None)
+MONGODB_HOST = os.environ.get("MONGODB_HOST", "localhost")
+MONGODB_PORT = int(os.environ.get("MONGODB_PORT", 27017))
+MONGODB_HOSTS = os.environ.get("MONGODB_HOSTS", None)
 if not MONGODB_HOSTS:
     MONGODB_HOSTS = MONGODB_HOST + ":" + str(MONGODB_PORT)
-MONGODB_URL=os.environ.get("MONGODB_URL", None)
+MONGODB_URL = os.environ.get("MONGODB_URL", None)
 if not MONGODB_URL:
     MONGODB_URL = "mongodb://" + MONGODB_HOSTS + "/admin"
 
-MONGODB_USERNAME=os.environ['MONGODB_USERNAME']
-MONGODB_PASSWORD=os.environ['MONGODB_PASSWORD']
+MONGODB_USERNAME = os.environ["MONGODB_USERNAME"]
+MONGODB_PASSWORD = os.environ["MONGODB_PASSWORD"]
 
 
 # This identifies the current deployment site.
 # Functionality that depends on the deployment location is based off this variable.
 # For example, use LCLS for LCLS, Cryo for Cryo.
-LOGBOOK_SITE = os.environ.get('LOGBOOK_SITE', 'test')
+LOGBOOK_SITE = os.environ.get("LOGBOOK_SITE", "test")
 
 # Use this information to get proposal information from the questionnaire.
 # This is typically a ws-auth endpoint
@@ -48,35 +47,61 @@
 # Support for serving previews from the web server. Previews can get quite large and having python serve them is sometimes not practical.
 # Add run parms using ws/ext_preview. This preview_prefix will then be prepended to the path to serve the image.
 # A hash is added as part of the URL hashed with the PREVIEW_PREFIX_SHARED_SECRET
-PREVIEW_PREFIX = os.environ.get('PREVIEW_PREFIX', '../../..')
-PREVIEW_PREFIX_SHARED_SECRET = os.environ.get('PREVIEW_PREFIX_SHARED_SECRET', "SLACExpLgBk")
+PREVIEW_PREFIX = os.environ.get("PREVIEW_PREFIX", "../../..")
+PREVIEW_PREFIX_SHARED_SECRET = os.environ.get(
+    "PREVIEW_PREFIX_SHARED_SECRET", "SLACExpLgBk"
+)
 
 
 # Set up the security manager
-mongorolereaderclient = MongoClient(host=MONGODB_URL, username=MONGODB_USERNAME, password=MONGODB_PASSWORD, tz_aware=True, read_preference=ReadPreference.SECONDARY_PREFERRED)
+mongorolereaderclient = MongoClient(
+    host=MONGODB_URL,
+    username=MONGODB_USERNAME,
+    password=MONGODB_PASSWORD,
+    tz_aware=True,
+    read_preference=ReadPreference.SECONDARY_PREFERRED,
+)
 usergroups = UserGroups()
 roleslookup = MongoDBRoles(mongorolereaderclient, usergroups)
 security = FlaskAuthnz(roleslookup, "LogBook")
 
-logbookclient = MongoClient(host=MONGODB_URL, username=MONGODB_USERNAME, password=MONGODB_PASSWORD, tz_aware=True, read_preference=ReadPreference.PRIMARY_PREFERRED)
+logbookclient = MongoClient(
+    host=MONGODB_URL,
+    username=MONGODB_USERNAME,
+    password=MONGODB_PASSWORD,
+    tz_aware=True,
+    read_preference=ReadPreference.PRIMARY_PREFERRED,
+)
 
 local_kafka_events = Queue()
 
+
 class MyKafkaProducer(KafkaProducer):
     def __init__(self, *args, **kwargs):
         super(MyKafkaProducer, self).__init__(*args, **kwargs)
+
     def send(self, topic, value, *args, **kwargs):
-        local_kafka_events.put({"topic": topic, "value": JSONEncoder().encode(value).encode('utf-8')})
+        local_kafka_events.put(
+            {"topic": topic, "value": JSONEncoder().encode(value).encode("utf-8")}
+        )
         super(MyKafkaProducer, self).send(topic, value, *args, **kwargs)
 
+
 def __getKafkaProducer():
     misc_params = {}
     if os.environ.get("SKIP_KAFKA_CONNECTION", False):
         return None
     else:
         # if LOGBOOK_SITE=="CryoEM":
         #     misc_params["acks"] = 0
-        return MyKafkaProducer(bootstrap_servers=os.environ.get("KAFKA_BOOTSTRAP_SERVER", "localhost:9092").split(","), value_serializer=lambda m: JSONEncoder().encode(m).encode('utf-8'), **misc_params)
+        return MyKafkaProducer(
+            bootstrap_servers=os.environ.get(
+                "KAFKA_BOOTSTRAP_SERVER", "localhost:9092"
+            ).split(","),
+            value_serializer=lambda m: JSONEncoder().encode(m).encode("utf-8"),
+            **misc_params,
+        )
+
 
 kafka_producer = __getKafkaProducer()
 
@@ -92,36 +117,62 @@ def __getKafkaProducer():
 instrument_scientists_run_table_defintions = {}
 run_table_secions_json = os.environ.get("RUNTABLE_SECTIONS_JSON", None)
 
+
 def load_sections_json():
     if run_table_secions_json and os.path.exists(run_table_secions_json):
-        logger.info("Loading run table instrument scientist descriptions from %s", run_table_secions_json)
+        logger.info(
+            "Loading run table instrument scientist descriptions from %s",
+            run_table_secions_json,
+        )
         new_instrument_scientists_run_table_defintions = {}
+
         def reverse_mapping_for_section(section):
-            return { x["name"]: {"section" : section["SECTION"], "title": section["TITLE"], "pv": x["name"]} for x in section["PARAMS"] }
-        with open(run_table_secions_json, 'r') as f:
+            return {
+                x["name"]: {
+                    "section": section["SECTION"],
+                    "title": section["TITLE"],
+                    "pv": x["name"],
+                }
+                for x in section["PARAMS"]
+            }
+
+        with open(run_table_secions_json, "r") as f:
             isdefs = json.load(f)
             for instrument, sections in isdefs.items():
                 new_instrument_scientists_run_table_defintions[instrument] = {}
                 for section in sections:
-                    new_instrument_scientists_run_table_defintions[instrument].update(reverse_mapping_for_section(section))
+                    new_instrument_scientists_run_table_defintions[instrument].update(
+                        reverse_mapping_for_section(section)
+                    )
         global instrument_scientists_run_table_defintions
         instrument_scientists_run_table_defintions.clear()
-        instrument_scientists_run_table_defintions.update(new_instrument_scientists_run_table_defintions)
+        instrument_scientists_run_table_defintions.update(
+            new_instrument_scientists_run_table_defintions
+        )
+
 
 load_sections_json()
 
 # Cache some of the instrument definitions.
 instrument_definitions = {}
+
+
 def load_instrument_definitions():
     global instrument_definitions
     instrument_definitions.clear()
-    instrument_definitions.update({ x["_id"]: x for x in logbookclient["site"]["instruments"].find() })
+    instrument_definitions.update(
+        {x["_id"]: x for x in logbookclient["site"]["instruments"].find()}
+    )
+
 
 load_instrument_definitions()
 
+
 def reload_named_caches(cache_name):
     if cache_name == "instrument_scientists_run_table_defintions":
-        logger.info("Reloading the instrument_scientists_run_table_defintions named cache")
+        logger.info(
+            "Reloading the instrument_scientists_run_table_defintions named cache"
+        )
         load_sections_json()
     elif cache_name == "instrument_defintions":
         logger.info("Reloading the instrument_defintions named cache")
@@ -130,7 +181,20 @@ def reload_named_caches(cache_name):
 
 def generateArpToken(userid, experiment_name, token_duration_in_mins=10):
     if "WFLOW_TRIG_ARP_PRIVATE_KEY" not in os.environ:
-        raise Exception("Please specify the ARP private key in the environment variable WFLOW_TRIG_ARP_PRIVATE_KEY")
+        raise Exception(
+            "Please specify the ARP private key in the environment variable WFLOW_TRIG_ARP_PRIVATE_KEY"
+        )
     with open(os.environ["WFLOW_TRIG_ARP_PRIVATE_KEY"], "rb") as f:
         private_key = f.read()
-    return jwt.encode({"user": userid, "experiment_name": experiment_name, "expires": (datetime.datetime.now(tz=datetime.timezone.utc) + datetime.timedelta(minutes=token_duration_in_mins)).timestamp()}, private_key, algorithm="RS256")
+    return jwt.encode(
+        {
+            "user": userid,
+            "experiment_name": experiment_name,
+            "expires": (
+                datetime.datetime.now(tz=datetime.timezone.utc)
+                + datetime.timedelta(minutes=token_duration_in_mins)
+            ).timestamp(),
+        },
+        private_key,
+        algorithm="RS256",
+    )

dal/__init__.py

@@ -1 +1 @@
-__author__ = 'mshankar@slac.stanford.edu'
+__author__ = "mshankar@slac.stanford.edu"