rubi-za/jms

A workflow management system and web-based cluster front-end for high performance computing

jms's Issues

Missing Table "column_stats"

Hello,

when running "python manage.py migrate" I get an error due to a missing table:
_mysql_exceptions.Warning: Table 'mysql.column_stats' doesn't exist

Connection refused

I get the server running (after fixes discrebed before) but can't login as the admin user I created:

System check identified 1 issue (0 silenced).
November 04, 2017 - 10:52:53
Django version 1.7.1, using settings 'JMS.settings'
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.
[04/Nov/2017 10:53:01] "GET / HTTP/1.1" 302 0
[04/Nov/2017 10:53:01] "GET /account/login?next=/ HTTP/1.1" 200 2809
Internal Server Error: /account/login
Traceback (most recent call last):
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/django/core/handlers/base.py", line 111, in get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/srv/JMS/src/interface/views.py", line 65, in sign_in
    user = authenticate(username=username, password=password)
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/django/contrib/auth/__init__.py", line 59, in authenticate
    user = backend.authenticate(**credentials)
  File "/srv/JMS/src/filemanager/backends.py", line 33, in authenticate
    if self.linux_auth(encoded):
  File "/srv/JMS/src/filemanager/backends.py", line 46, in linux_auth
    r = requests.post(self.imp_url, data=data)
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/requests/api.py", line 94, in post
    return request('post', url, data=data, json=json, **kwargs)
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/requests/api.py", line 49, in request
    return session.request(method=method, url=url, **kwargs)
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/requests/sessions.py", line 457, in request
    resp = self.send(prep, **send_kwargs)
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/requests/sessions.py", line 569, in send
    r = adapter.send(request, **kwargs)
  File "/srv/JMS/src/venv/lib/python2.7/site-packages/requests/adapters.py", line 407, in send
    raise ConnectionError(err, request=request)
ConnectionError: ('Connection aborted.', error(111, 'Connection refused'))

Demo site user/password not working

When tying to connect to the demonstration sever referred in your Plos One Paper:

URL: https://jms.rubi.ru.ac.za/account/login?next=/
U: demo
P: demo

I get the following error.

Login attempt failed. Incorrect username or password.

always encountered with "job not found"!

in JMS installation I always encountered with "job not found"!
after installing Torque, NFS, and MySQL
in ubuntu I have found in pip install -r requirements.txt these packages should be installed:

apt-get install libmysqlclient-dev
apt-get install libxml2-dev libxslt1-dev
apt-get install libmemcached-dev

also after successfully downloading all dependencies, I have my settings.py as following:

# Django settings for JMS project.
import os

DEBUG = True
TEMPLATE_DEBUG = DEBUG

ADMINS = (
    # ('Your Name', '[email protected]'),
)

MANAGERS = ADMINS

DATABASES = {
    'default': {
        'ENGINE': 'django.db.backends.mysql', # Add 'postgresql_psycopg2', 'mysql', 'sqlite3' or 'oracle'.
        'NAME': 'JMS',                      # Or path to database file if using sqlite3.
        # The following settings are not used with sqlite3:
        'USER': 'jms',
        'PASSWORD': 'my_password',
        'HOST': 'localhost',      
        'PORT': '',                      # Set to empty string for default.
    }
}

# Hosts/domain names that are valid for this site; required if DEBUG is False
# See https://docs.djangoproject.com/en/1.5/ref/settings/#allowed-hosts
#ALLOWED_HOSTS = ['*']

# Local time zone for this installation. Choices can be found here:
# http://en.wikipedia.org/wiki/List_of_tz_zones_by_name
# although not all choices may be available on all operating systems.
# In a Windows environment this must be set to your system time zone.
TIME_ZONE = 'Asia/Tehran'

# Language code for this installation. All choices can be found here:
# http://www.i18nguy.com/unicode/language-identifiers.html
LANGUAGE_CODE = 'en-us'

SITE_ID = 1

# If you set this to False, Django will make some optimizations so as not
# to load the internationalization machinery.
USE_I18N = True

# If you set this to False, Django will not format dates, numbers and
# calendars according to the current locale.
USE_L10N = True

# If you set this to False, Django will not use timezone-aware datetimes.
USE_TZ = False

# Absolute filesystem path to the directory that will hold user-uploaded files.
# Example: "/var/www/example.com/media/"
MEDIA_ROOT = '/srv/JMS/media'

# URL that handles the media served from MEDIA_ROOT. Make sure to use a
# trailing slash.
# Examples: "http://example.com/media/", "http://media.example.com/"
MEDIA_URL = '/media/'

# Absolute path to the directory static files should be collected to.
# Don't put anything in this directory yourself; store your static files
# in apps' "static/" subdirectories and in STATICFILES_DIRS.
# Example: "/var/www/example.com/static/"
STATIC_ROOT = '/static/'

# URL prefix for static files.
# Example: "http://example.com/static/", "http://static.example.com/"
STATIC_URL = '/assets/'

BASE = '/srv/JMS/'
# Additional locations of static files
STATICFILES_DIRS = (
    os.path.join(BASE, "static"),  
)

# List of finder classes that know how to find static files in
# various locations.
STATICFILES_FINDERS = (
    'django.contrib.staticfiles.finders.FileSystemFinder',
    'django.contrib.staticfiles.finders.AppDirectoriesFinder',
#    'django.contrib.staticfiles.finders.DefaultStorageFinder',
)

# Make this unique, and don't share it with anybody.
SECRET_KEY = '4ibn4o6g2r(9y8)tk52uc3-$g26a_jf2vc)gzqb)l^kaz&p8&g'

# List of callables that know how to import templates from various sources.
TEMPLATE_LOADERS = (
    'django.template.loaders.filesystem.Loader',
    'django.template.loaders.app_directories.Loader',
#     'django.template.loaders.eggs.Loader',
)

MIDDLEWARE_CLASSES = (
    'django.middleware.common.CommonMiddleware',
    'django.contrib.sessions.middleware.SessionMiddleware',
    'django.middleware.csrf.CsrfViewMiddleware',
    'django.contrib.auth.middleware.AuthenticationMiddleware',
    'django.contrib.messages.middleware.MessageMiddleware',
    # Uncomment the next line for simple clickjacking protection:
    # 'django.middleware.clickjacking.XFrameOptionsMiddleware',
)

ROOT_URLCONF = 'JMS.urls'
#APPEND_SLASH = True

# Python dotted path to the WSGI application used by Django's runserver.
WSGI_APPLICATION = 'JMS.wsgi.application'

TEMPLATE_DIRS = ('/srv/JMS/templates',
    # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
    # Always use forward slashes, even on Windows.
    # Don't forget to use absolute paths, not relative paths.
)

INSTALLED_APPS = (
    'django.contrib.auth',
    'django.contrib.contenttypes',
    'django.contrib.sessions',
    'django.contrib.sites',
    'django.contrib.messages',
    'django.contrib.staticfiles',
    'django.contrib.admin',
    #REST framework apps
    'rest_framework',
    #'rest_framework_swagger',
    #my apps
    'users',
    'interface',
    'job',
    # Uncomment the next line to enable admin documentation:
    # 'django.contrib.admindocs',
)

SESSION_SERIALIZER = 'django.contrib.sessions.serializers.JSONSerializer'

# A sample logging configuration. The only tangible logging
# performed by this configuration is to send an email to
# the site admins on every HTTP 500 error when DEBUG=False.
# See http://docs.djangoproject.com/en/dev/topics/logging for
# more details on how to customize your logging configuration.
LOGGING = {
    'version': 1,
    'disable_existing_loggers': False,
    'filters': {
        'require_debug_false': {
            '()': 'django.utils.log.RequireDebugFalse'
        }
    },
    'handlers': {
        'mail_admins': {
            'level': 'ERROR',
            'filters': ['require_debug_false'],
            'class': 'django.utils.log.AdminEmailHandler'
        }
    },
    'loggers': {
        'django.request': {
            'handlers': ['mail_admins'],
            'level': 'ERROR',
            'propagate': True,
        },
    }
}

REST_FRAMEWORK = {
    'DEFAULT_AUTHENTICATION_CLASSES': (
    'rest_framework.authentication.SessionAuthentication',
    ),
    'DEFAULT_RENDERER_CLASSES': (
    'rest_framework.renderers.JSONRenderer',
    )
}

SWAGGER_SETTINGS = {
    "exclude_namespaces": ['internal_urls'],
}

AUTHENTICATION_BACKENDS = (
    "users.backends.LinuxBackend",
)

AUTH_PROFILE_MODULE = 'users.UserProfile'

JMS_SETTINGS = {
    "JMS_shared_directory": "/NFS/JMS/",
    "resource_manager": {
        "name": "torque",
        "log_file": os.path.join(BASE, "logs/torque.log")
    }
}

BASE_DIR = '/srv/JMS/src' 
IMPERSONATOR_SETTINGS = {
    "key": os.path.join(BASE_DIR, "impersonator/pub.key"),
    "url": "127.0.0.1:8123"
}

after all when I try python manage.py migrate these errors stop everything:

Traceback (most recent call last):
  File "manage.py", line 10, in <module>
    execute_from_command_line(sys.argv)
  File "/srv/JMS/src/venv/local/lib/python2.7/site-packages/django/core/management/__init__.py", line 385, in execute_from_command_line
    utility.execute()
  File "/srv/JMS/src/venv/local/lib/python2.7/site-packages/django/core/management/__init__.py", line 354, in execute
    django.setup()
  File "/srv/JMS/src/venv/local/lib/python2.7/site-packages/django/__init__.py", line 21, in setup
    apps.populate(settings.INSTALLED_APPS)
  File "/srv/JMS/src/venv/local/lib/python2.7/site-packages/django/apps/registry.py", line 85, in populate
    app_config = AppConfig.create(entry)
  File "/srv/JMS/src/venv/local/lib/python2.7/site-packages/django/apps/config.py", line 87, in create
    module = import_module(entry)
  File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named job

I have tried in Ubuntu 14.0.4 and CentOS 7 many times, but always I have this problem,
may you tell me where is my mistake?
Thanks for your help.