Merge pull request #311 from ioos/main

update branch from main

.pre-commit-config.yaml

@@ -1,9 +1,9 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
-      # - id: trailing-whitespace
-      # - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
       - id: check-added-large-files
 
   - repo: https://github.com/codespell-project/codespell
@@ -17,6 +17,10 @@ repos:
         args:
           - --ignore-words-list=nd,ot
 
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.9.0.6
+    hooks:
+    - id: shellcheck
 
 ci:
     autofix_commit_msg: |

README.md

@@ -7,5 +7,4 @@ This is the main repository for the IOOS Glider DAC site, scripts, and tools.
 
 Detailed documentation on contact information, file format, user account registration, deployment registration and file submission can be found on the [IOOS National Glider DAC wiki](https://ioos.github.io/glider-dac/index.html).
 
-Inquires should be sent to glider **dot** dac **dot** support **at** noaa **dot** gov
-
+Inquires should be sent to [email protected]

config.yml

@@ -47,6 +47,8 @@ COMMON: &common
   REDIS_HOST: localhost
   REDIS_PORT: 6379
   REDIS_DB: 8
+  SESSION_PERMANENT: True
+  SESSION_TYPE: redis
 
   JSON_DIR: '/data/data/priv_erddap/'
   path2priv: '/data/data/priv_erddap/'
@@ -68,4 +70,3 @@ COMMON: &common
 DEVELOPMENT: &development
   <<: *common
   DEBUG: True
-

console

@@ -6,4 +6,3 @@ from bson import ObjectId
 
 with app.app_context():
     embed()
-

deploy/dap.supervisord.conf

@@ -46,4 +46,3 @@ directory=/home/glider
 autostart=true
 redirect_stderr=true
 stdout_logfile=logs/tunnel.log
-

deploy/env

@@ -20,4 +20,3 @@ export RSYNC_TO_PATH='{{ rsync_to_path }}'
 export MONGO_URI='{{ mongo_db }}'
 export ADMINS='{{ admins }}'
 export USER_DB_FILE='{{ user_db_file }}'
-

deploy/supervisord-perms-monitor.conf

@@ -27,4 +27,3 @@ stopsignal=TERM
 autostart=false
 redirect_stderr=true
 stdout_logfile=/root/perms-monitor.log
-

deploy/supervisord.conf

@@ -61,4 +61,3 @@ stopsignal=TERM
 autostart=true
 redirect_stderr=true
 stdout_logfile=logs/db-sync-monitor.log
-

dev_requirements.txt

@@ -1,2 +1,2 @@
 pytest
--r requirements.txt
+-r requirements.txt

docker-compose.yml

@@ -85,7 +85,7 @@ services:
   # TODO: THREDDS and ERDDAP will need volume configurations
   thredds:
     container_name: thredds
-    image: unidata/thredds-docker:5.3
+    image: unidata/thredds-docker:5.4
     ports:
       - 8082:8080
     volumes:
@@ -101,7 +101,7 @@ services:
 
   erddap:
     container_name: erddap
-    image: axiom/docker-erddap
+    image: axiom/docker-erddap:latest-jdk17-openjdk
     ports:
       - 8080:8080
     deploy:

glider_dac/__init__.py

@@ -3,7 +3,7 @@
 
 from flasgger import Swagger, LazyString, LazyJSONEncoder
 from flask import Flask, request
-from flask_kvsession import KVSessionExtension
+from flask_session import Session
 from flask_cors import CORS, cross_origin
 from flask_wtf import CSRFProtect
 from simplekv.memory.redisstore import RedisStore
@@ -47,16 +47,21 @@
 except KeyError:
     app.config.update(config_dict["DEVELOPMENT"])
 
+app.secret_key = app.config["SECRET_KEY"]
+app.config["SESSION_TYPE"] = "redis"
+app.config["SESSION_REDIS"] = redis.from_url(app.config["REDIS_URL"])
+Session(app)
+
 import redis
 redis_pool = redis.ConnectionPool(host=app.config.get('REDIS_HOST'),
                                   port=app.config.get('REDIS_PORT'),
                                   db=app.config.get('REDIS_DB'))
 redis_connection = redis.Redis(connection_pool=redis_pool)
 strict_redis = redis.StrictRedis(connection_pool=redis_pool)
 
+
 store = RedisStore(strict_redis)
 
-KVSessionExtension(store, app)
 
 from rq import Queue
 queue = Queue('default', connection=redis_connection)
@@ -192,4 +197,3 @@ def slugify(value):
 # Import everything
 import glider_dac.views
 import glider_dac.models
-

glider_dac/defaults.py

@@ -55,5 +55,3 @@
 MAIL_DEFAULT_SENDER = os.environ.get('MAIL_DEFAULT_SENDER')
 MAIL_DEFAULT_TO     = os.environ.get('MAIL_DEFAULT_TO')
 MAIL_DEFAULT_LIST   = os.environ.get('MAIL_DEFAULT_LIST', None)
-
-

glider_dac/development.py

@@ -1,3 +1,2 @@
 DEBUG = True
 LOG_FILE = True
-

glider_dac/glider_emails.py

@@ -23,6 +23,18 @@
 handler.setLevel(logging.INFO)
 root_logger.addHandler(handler)
 
+
+def send_email_wrapper(message):
+    """
+    Email sending function with exceptions to catch and log exceptions
+    """
+    try:
+        mail.send(message)
+    except:
+        app.logger.exception("Exception occurred while attempting to send "
+                             "email: ")
+
+
 def send_registration_email(username, deployment):
     if not app.config.get('MAIL_ENABLED', False): # Mail is disabled
         app.logger.info("Email is disabled")
@@ -43,7 +55,7 @@ def send_registration_email(username, deployment):
                         thredds_url=get_thredds_catalog_url(),
                         erddap_url=get_erddap_catalog_url())
 
-    mail.send(msg)
+    send_email_wrapper(msg)
 
 def send_deployment_cchecker_email(user, failing_deployments, attachment_msgs):
     if not app.config.get('MAIL_ENABLED', False): # Mail is disabled
@@ -67,7 +79,7 @@ def send_deployment_cchecker_email(user, failing_deployments, attachment_msgs):
         return
     msg.body       = message
 
-    mail.send(msg)
+    send_email_wrapper(msg)
 
 def get_thredds_catalog_url():
     args = {

glider_dac/models/institution.py

@@ -31,4 +31,3 @@ class Institution(Document):
             'unique': True,
         },
     ]
-

glider_dac/reverse_proxy.py

@@ -2,14 +2,14 @@
 '''
 glider_dac.reverse_proxy
 
-Ruthlessly stolen from: 
+Ruthlessly stolen from:
     http://flask.pocoo.org/snippets/35/
 '''
 
 class ReverseProxied(object):
-    '''Wrap the application in this middleware and configure the 
-    front-end server to add these headers, to let you quietly bind 
-    this to a URL other than / and to an HTTP scheme that is 
+    '''Wrap the application in this middleware and configure the
+    front-end server to add these headers, to let you quietly bind
+    this to a URL other than / and to an HTTP scheme that is
     different than what is used locally.
 
     In nginx:
@@ -38,4 +38,3 @@ def __call__(self, environ, start_response):
         if scheme:
             environ['wsgi.url_scheme'] = scheme
         return self.app(environ, start_response)
-

glider_dac/static/css/bootstrap-sortable.css

@@ -82,4 +82,3 @@ table.sortable thead th:hover:not([data-defaultsort=disabled]) {
 table.sortable thead th div.mozilla {
     position: relative;
 }
-

glider_dac/static/css/bootstrap-theme.css

@@ -381,4 +381,4 @@
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0);
   -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, 0.05), 0 1px 0 rgba(255, 255, 255, 0.1);
           box-shadow: inset 0 1px 3px rgba(0, 0, 0, 0.05), 0 1px 0 rgba(255, 255, 255, 0.1);
-}
+}