Merge pull request #210 from ODM2/afterdjango2

Afterdjango2

.travis.yml

@@ -16,6 +16,14 @@ env:
 before_cache:
   - rm -rf $HOME/miniconda/envs/TEST
 
+services:
+  - postgresql
+addons:
+  postgresql: "9.5"
+  apt:
+    packages:
+      - postgresql-9.5-postgis-2.3
+
 matrix:
   fast_finish: true
   include:
@@ -29,6 +37,8 @@ matrix:
 
 
 before_install:
+  - psql -U postgres -c "create extension postgis"
+  - psql -c "CREATE DATABASE test;" -U postgres
   - |
     URL="http://bit.ly/miniconda"
     echo ""
@@ -44,14 +54,12 @@ before_install:
   - conda config --add channels conda-forge --force
   - conda create --name TEST python=$TRAVIS_PYTHON_VERSION libgdal --file requirements.txt --file requirements-dev.txt
   - source activate TEST
-  - pip install --upgrade http://github.com/miguelcleon/django-admin-shortcuts/zipball/master
+#   - pip install --upgrade http://github.com/miguelcleon/django-admin-shortcuts/zipball/master
+
 
 install:
   - python setup.py sdist && version=$(python setup.py --version) && pushd dist  && pip install odm2admin-${version}.tar.gz && popd
 
-before_script:
-- psql -c "CREATE DATABASE test;" -U postgres
-
 script:
   - if [[ $TEST_TARGET == 'default' ]]; then
       python $TRAVIS_BUILD_DIR/manage.py test tests/;

docker/docker-deploy/settings/base.py

@@ -58,6 +58,8 @@
             'django.template.context_processors.request',
             'django.contrib.auth.context_processors.auth',
             'django.contrib.messages.context_processors.messages',
+            'social_django.context_processors.backends',
+            'social_django.context_processors.login_redirect',
         ],
     },
 }]
@@ -103,36 +105,62 @@
 """ MEDIA CONFIGURATION """
 # Absolute filesystem path to the directory that will hold user-uploaded files.
 MEDIA_ROOT = '{}/{}/upfiles/'.format(BASE_DIR, APP_NAME)
-# URL that handles the media served from MEDIA_ROOT.
+#  URL that handles the media served from MEDIA_ROOT.
 MEDIA_URL = '/{}/{}/media/'.format(os.path.basename(BASE_DIR), APP_NAME)
 """ END MEDIA CONFIGURATION """
-
+# Absolute filesystem path to the directory that will hold database export and import files
+FIXTURE_DIR = '{}/{}/fixtures/'.format(BASE_DIR, APP_NAME)
 
 """ STATIC FILE CONFIGURATION """
 # 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.
-# STATIC_ROOT = '{}/{}/static'.format(BASE_DIR, APP_NAME)
-STATIC_DIR = '{}/{}/static'.format(BASE_DIR, APP_NAME)
-STATICFILES_DIRS = [STATIC_DIR]
+STATIC_ROOT = '{}/{}/static'.format(BASE_DIR, APP_NAME)
 # URL prefix for static files.
 STATIC_URL = '/static/'
 """ END STATIC FILE CONFIGURATION """
-
+""" END PATH CONFIGURATION """
 
 """ MIDDLEWARE CONFIGURATION """
-MIDDLEWARE_CLASSES = (
+MIDDLEWARE = (
     'django.contrib.sessions.middleware.SessionMiddleware',
     'django.middleware.common.CommonMiddleware',
     'django.middleware.csrf.CsrfViewMiddleware',
+    #'corsheaders.middleware.CorsMiddleware',
     'django.contrib.auth.middleware.AuthenticationMiddleware',
+    'social_django.middleware.SocialAuthExceptionMiddleware',
     # 'django.contrib.auth.middleware.SessionAuthenticationMiddleware', didn't work in production
     'django.contrib.messages.middleware.MessageMiddleware',
     'django.middleware.clickjacking.XFrameOptionsMiddleware',
     # 'admin_reorder.middleware.ModelAdminReorder',
 )
 """ END MIDDLEWARE CONFIGURATION """
 
+""" OAUTH SETTINGS """
+AUTHENTICATION_BACKENDS = (
+    'social_core.backends.open_id.OpenIdAuth',
+    'social_core.backends.google.GoogleOpenId',
+    'social_core.backends.google.GoogleOAuth2',
+    #'odm2admin.hydroshare_backend.HydroShareOAuth2',
+    'social_core.backends.google.GoogleOAuth',
+    'django.contrib.auth.backends.ModelBackend',
+)
+# Oauth CORS_ORIGIN_ALLOW_ALL = True
+
+SOCIAL_AUTH_URL_NAMESPACE = 'social'
+SOCIAL_AUTH_PIPELINE = (
+    'social_core.pipeline.social_auth.social_details',
+    'social_core.pipeline.social_auth.social_uid',
+    'social_core.pipeline.social_auth.social_user',
+    'social_core.pipeline.user.get_username',
+    'social_core.pipeline.user.create_user',
+    'social_core.pipeline.social_auth.associate_user',
+    'social_core.pipeline.social_auth.load_extra_data',
+    'social_core.pipeline.user.user_details',
+    'social_core.pipeline.social_auth.associate_by_email',
+)
+""" END OAUTH SETTINGS """
+
 """ URL AND WSGI CONFIGURATION """
 ROOT_URLCONF = 'templatesAndSettings.urls'
 
@@ -145,9 +173,11 @@
     'djangocms_admin_style',
     '{}'.format(APP_NAME),
     'import_export',
+    'social_django',
     'admin_shortcuts',
     'daterange_filter',
     'captcha',
+    'fixture_magic',
     # 'dal',
     # 'dal_select2',
     'ajax_select',
@@ -215,26 +245,6 @@
 """ END ADMIN SHORTCUTS CONFIGURATION """
 
 
-""" AJAX LOOKUPS CONFIGURATION """
-AJAX_LOOKUP_CHANNELS = dict(
-    cv_variable_name=('{}.lookups'.format(APP_NAME), 'CvVariableNameLookup'),
-    cv_variable_type=('{}.lookups'.format(APP_NAME), 'CvVariableTypeLookup'),
-    cv_unit_type=('{}.lookups'.format(APP_NAME), 'CvUnitTypeLookup'),
-    cv_speciation=('{}.lookups'.format(APP_NAME), 'CvVariableSpeciationLookup'),
-    featureaction_lookup=('{}.lookups'.format(APP_NAME), 'FeatureactionsLookup'),
-    result_lookup=('{}.lookups'.format(APP_NAME), 'ResultsLookup'),
-    profileresult_lookup=('{}.lookups'.format(APP_NAME), 'ProfileResultsLookup'),
-    measurementresult_lookup=('{}.lookups'.format(APP_NAME), 'MeasurementResultsLookup'),
-    timeseriesresult_lookup=('{}.lookups'.format(APP_NAME), 'TimeseriesResultsLookup'),
-    sampling_feature_lookup=('{}.lookups'.format(APP_NAME), 'SamplingFeatureLookup'),
-    cv_taxonomic_classifier_type=('{}.lookups'.format(APP_NAME), 'CvTaxonomicClassifierTypeLookup'),
-    cv_method_type=('{}.lookups'.format(APP_NAME), 'CvMethodTypeLookup'),
-    cv_site_type=('{}.lookups'.format(APP_NAME), 'CvSitetypeLookup'),
-    cv_action_type=('{}.lookups'.format(APP_NAME), 'CvActionTypeLookup'),
-    cv_sampling_feature_type=('{}.lookups'.format(APP_NAME), 'CvSamplingFeatureTypeLookup'),
-    cv_sampling_feature_geo_type=('{}.lookups'.format(APP_NAME), 'CvSamplingFeatureGeoTypeLookup'),
-    cv_elevation_datum=('{}.lookups'.format(APP_NAME), 'CvElevationDatumLookup'))
-""" END AJAX LOOKUPS CONFIGURATION """
 
 """ SAMPLING FEATURE TYPE LEGEND MAPPING """
 LEGEND_MAP = {
@@ -266,7 +276,7 @@
 CACHES = {
     "default": {
         "BACKEND": "django_redis.cache.RedisCache",
-        "LOCATION": "redis://redis:6379/0",
+        "LOCATION": "redis://127.0.0.1:6379/1",
         "OPTIONS": {
             "CLIENT_CLASS": "django_redis.client.DefaultClient"
         },
@@ -276,4 +286,4 @@
 
 # Cache time to live is 15 minutes.
 CACHE_TTL = 60 * 15
-""" END REDIS CACHING CONFIGURATION"""
+""" END REDIS CACHING CONFIGURATION"""

docker/docker-deploy/settings/development.py

@@ -2,13 +2,17 @@
 Development settings and globals.
 """
 
-from base import *
+from .base import *
 
 """ DEBUG CONFIGURATION """
 # Disable debugging by default.
 DEBUG = True
 """ END DEBUG CONFIGURATION """
 
+""" EXPORTDB FLAG CONFIGURATION - if set to true this will use Camel case table names for SQLite"""
+EXPORTDB = False
+""" EXPORTDB FLAG CONFIGURATION """
+
 """ ALLOWED HOSTS CONFIGURATION """
 ALLOWED_HOSTS = ['127.0.0.1',]
 """ END ALLOWED HOSTS CONFIGURATION """

docker/odm2admin/Dockerfile

@@ -18,14 +18,15 @@ RUN apt-get update --fix-missing && apt-get install --yes apt-utils postgresql-c
 
 EXPOSE 8000
 
-RUN git clone "https://github.com/miguelcleon/ODM2-Admin"
-RUN cd ODM2-Admin && latest=$(git describe --tags) && git checkout ${latest}
+# && latest=$(git describe --tags) && git checkout ${latest}
+RUN git clone -b django2 "https://github.com/ODM2/ODM2-Admin"
+RUN cd ODM2-Admin
 
 WORKDIR /ODM2-Admin
 
 VOLUME templatesAndSettings/settings/
 
-RUN conda create --yes -n odm2adminenv -c conda-forge python=2.7 pytz gdal --file requirements.txt
+RUN conda create --yes -n odm2adminenv -c conda-forge python=3.6 libgdal boost pytz gdal --file requirements.txt
 
 COPY odm2database/odm2adminDB.sql /odm2adminDB.sql
 COPY odm2database/cvload.py /cvload.py

docker/odm2admin/startup.sh

@@ -3,6 +3,7 @@
 echo "Activating environment..."
 source activate odm2adminenv
 conda install --yes -c conda-forge sqlalchemy
+# pip install git+git://github.com/miguelcleon/django-admin-shortcuts --upgrade
 
 #echo "Building database..."
 #su - postgres -c 'pg_restore -d odm2_db -1 -v "/ODM2-Admin/ODM2AdminDBBlank"'
@@ -17,4 +18,4 @@ wget https://raw.githubusercontent.com/ODM2/ODM2/master/src/load_cvs/cvload.py
 python cvload.py postgresql+psycopg2://postgres:test@db:5432/odm2
 
 echo "Running server..."
-python manage.py runserver 0.0.0.0:8000
+python manage.py runserver 0.0.0.0:8000

docker/odm2admin/wait-for-postgres.sh

@@ -12,7 +12,25 @@ until psql -h "$host" -U "postgres" -c '\l'; do
   sleep 1
 done
 
-psql -v ON_ERROR_STOP=1 --host "$host" --username "postgres" -c "CREATE DATABASE odm2;"
+
+
+# sql to check whether given database exist
+sql1="select count(1) from pg_catalog.pg_database where datname = 'odm2'"
+
+# depending on how PATH is set psql may require a fully qualified path
+cmd="psql -h \"$host\" -U \"postgres\" -t -c \"$sql1\""
+
+db_exists=`eval $cmd`
+
+if [ $db_exists -eq 0 ] ; then
+   # create the database, discard the output
+   >&2 echo " create odm2 db 1 time "
+   psql -v ON_ERROR_STOP=1 --host "$host" --username "postgres" -c "CREATE DATABASE odm2;"
+   eval $cmd
+fi
+
+
+# psql -v ON_ERROR_STOP=1 --host "$host" --username "postgres" -c "CREATE DATABASE odm2;"
 psql -v ON_ERROR_STOP=1 --host "$host" --username "postgres" --dbname "odm2" --file /odm2adminDB.sql
 
 >&2 echo "Postgres is up - executing command"

docs/source/DataQAQC.rst

@@ -47,4 +47,4 @@ points position in the set of points selected.
 :ref:`5) Data visualization and URL parameters <Data-Visualization>`
 
 * :ref:`ODM2 Admin docs home page<ODM2-Admin>`
-* :ref:`Search the docs <search>`
+* :ref:`Search the docs <search>`

docs/source/ODM2AdminDemo.rst

@@ -1,9 +1,9 @@
-OODM2 Admin Walkthrough
+ODM2 Admin Walkthrough
 ======================
 .. 2017 BiG-CZ / ODM2 Hands-On Workshop, November 15-16, 2017 at UC Riverside, CA.
 ..
 
-This walthough explains many of the features of ODM2 Admin. This tutorial was developed for the CUAHSI Tools
+Below is a tutorial which explains many of the features of ODM2 Admin. This tutorial was developed for the CUAHSI Tools
 and Services for Managing Research Data Workshop at the CUAHSI Biennial Colloquium on July 7-31-2018. It is meant as a
 demonstration of the capabilities of ODM2 Admin and as a use case for ODM2. Links contained here access a demonstartion
 version of ODM2 Admin populated with data from the `Luquillo Critical Zone Observatory <http://criticalzone.org/luquillo/>`_
@@ -49,10 +49,15 @@ The Authentication and Authorization link will allow you to create users and gro
 The ODM2 Admin Administration link will take you to a list of all 44 ODM2 entities that can be directly managed in
 ODM2 Admin. See the ODM2 Admin Forms for details about the ODM2 Admin Forms :ref:`ODM2-Administration`.
 
-Some entities described by the ODM2 data model do not have forms associated with them in ODM2 Admin and need to be
-managed with another tool such as with the ODM2PythonAPI. Django models exist for each ODM2 entity so it is also
-possible to write Python scripts using the Django Object relational mapper. See :ref:`Managing-ODM2-With-The-Django-ORM`
-for details on using the Django ORM with ODM2 databases.
+The recent actions section shows changes you have recently completed in ODM2 Admin such as adding or editing an item
+in the forms. In the example above we can see that a method, a data result and a variable were recently changed.
+
+The Authentication and Authorization link will allow you to create users and groups so others can login to the system.
+
+Additional entities exist within the ODM2 information model these need to be managed with another tool
+Such as with the ODM2PythonAPI. Django models exist for each ODM2 entity so it is also possible to write Python scripts
+using the Django Object relational mapper. See :ref:`Managing-ODM2-With-The-Django-ORM` for details on using the Django
+ORM with ODM2 databases.
 
 
 .. toctree::
@@ -69,4 +74,3 @@ for details on using the Django ORM with ODM2 databases.
 
 * :ref:`ODM2 Admin docs home page <ODM2-Admin>`
 * :ref:`Search the docs <search>`
-

manageexport.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+import os
+import sys
+
+if __name__ == "__main__":
+    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "templatesAndSettings.settings.exportdb")
+
+    from django.core.management import execute_from_command_line
+    print(sys.argv)
+    execute_from_command_line(sys.argv)