DATABASES/madrigal Commit - r9:2e29893b10f5

Update configs

jespinoza -

r9:2e29893b10f5

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r9:2e29893b10f5

.gitignore +1 -1

             # general
             .env
             .DS_store
             *.pyc
             *.sqlite
             # config
             madrigal.cfg
             # metadata
             siteTab.txt
             expTab.txt
             expTabAll.txt
             fileTab.txt
             fileTabAll.txt
             instData.txt
             instDataPriv.txt
             instParmLastUpdate.txt
             instTab.txt
             instType.txt
             siteTab.txt
             typeTab.txt
             instKindatTab.txt
             instParmTab.txt
             parmCodes.txt
-            # experiments
             experiments/
+            static_files/
  No newline at end of file

Dockerfile +1 -1

             FROM python:3.7-slim
             RUN mkdir /madrigal
             WORKDIR /madrigal
             ADD required_modules.txt ./required_modules.txt
             RUN apt clean && apt update && apt install -y --no-install-recommends \
-            	gcc gfortran build-essential automake autotools-dev autoconf m4 libtool hdf5-tools\
+            	gcc gfortran build-essential automake autotools-dev autoconf m4 libtool hdf5-tools libhdf5-dev libnetcdf-dev pkg-config\
             	&& rm -rf /var/lib/apt/lists/*\
                 && pip install -r required_modules.txt && pip install django-bootstrap3
             COPY . ./
             RUN ln -s /usr/local/bin/python3.7 /madrigal/bin/python && bash installMadrigal

docker-compose.yml +2 -6

             version: '3'
             services:
               web:
                 container_name: 'madrigal'
                 build: .
                 restart: always
                 image: madrigal
                 working_dir: /madrigal/source/madpy/djangoMad
                 command: gunicorn djangoMad.wsgi --bind 0.0.0.0:8000
-                # command: python manage.py runserver 0.0.0.0:8888
                 env_file: .env
-                # ports:
-                #   - 8888:8888
                 volumes:
                   - '${EXP_DIR}:/madrigal/experiments'
-                  # - '/usr/local/madrigal/metadata:/madrigal/metadata'
+                  - './source/madpy/djangoMad:/madrigal/source/madpy/djangoMad'
-                  - '/home/jespinoza/workspace/madrigal/source/madpy/djangoMad:/madrigal/source/madpy/djangoMad'
               nginx:
                 container_name: 'madrigal-nginx'
                 image: nginx:1.15-alpine
                 volumes:
-                    - ./source/madpy/djangoMad/madweb/static:/static
+                    - ./source/madpy/djangoMad/static_files:/static
                     - ./nginx:/etc/nginx/conf.d
                 ports:
                     - "${MAD_PORT}:8080"
                 depends_on:
                     - web
                 command: "/bin/sh -c 'while :; do sleep 6h & wait $${!}; nginx -s reload; done & nginx -g \"daemon off;\"'"

installMadrigal +1 -1

             #!/bin/sh
             #
             #   This script installs the entire Madrigal database.
             #   Use -c to skip conversion from Madrigal 2->3 files
             #
             # See the latest documentation at http://madrigal.haystack.mit.edu/madrigal/admin.html
             #   for the latest installation instructions
             #
             # $Id: installMadrigal 7342 2021-03-29 13:53:30Z brideout $
             function timer()
             {
                 if [[ $# -eq 0 ]]; then
                     echo $(date '+%s')
                 else
                     local  stime=$1
                     etime=$(date '+%s')
                     if [[ -z "$stime" ]]; then stime=$etime; fi
                     dt=$((etime - stime))
                     ds=$((dt % 60))
                     dm=$(((dt / 60) % 60))
                     dh=$((dt / 3600))
                     printf '%d:%02d:%02d' $dh $dm $ds
                 fi
             }
             tmr=$(timer)
             # verify we are indeed in the right pwd
             if [ ! -f installMadrigal ]
             then
                echo "You must run this script from the MADROOT directory"
                exit -1
             fi
             # if MADROOT is set, be sure it matches PWD
             if [ "$MADROOT" != "" ]
             then
                if [ $MADROOT != $PWD ]
                then
                   echo "Environmental variable MADROOT = $MADROOT does not match PWD = $PWD"
                   exit -1
                fi
             else
                export MADROOT=$PWD
             fi
             # test that h5repack installed
             path_to_executable=$(which h5repack)
              if [ -x "$path_to_executable" ] ; then
                 echo "h5repack installed"
              else
                 echo "h5repack needs to be installed"
                 exit -1
              fi
             # check whether test experiments have been installed
             if [[ (! -f experiments/1998/mlh/20jan98/mil980120g.002 ) && ( ! -f experiments/1998/mlh/20jan98/mil980120g.002.hdf5)  && ( ! -f experiments/1998/mlh/20jan98/mlh980120g.002.hdf5) ]]
             then
                echo "The standard test data must be installed before installing Madrigal"
                echo "See install instructions at http://madrigal.haystack.mit.edu/madrigal/ad_install.html"
                echo "Standard test experiments can be found at http://madrigal.haystack.mit.edu/madrigal/madDownload.html"
                exit -1
             fi
             # check if should convert to Madrigal3
             convert=1
             if [ $# -gt 0 ]
             then
                for arg in $@
                do
                   if [ $arg = "-c" ]
                   then
                      convert=0
                   fi
                done
             fi
             echo "Testing that all required python modules are already installed in the default python 3"
             $MADROOT/bin/python testRequirements.py
             if [ $? -ne 0 ]
             then
               exit -1
             fi
             echo "Installing Madrigal in $MADROOT"
             # verify correctness of madrigal.cfg
             if [ ! -f madrigal.cfg ]
             then
                echo
                echo "madrigal.cfg must be created first by copying madrigal.cfg.template and editing as needed"
                exit -1
             else
                $MADROOT/bin/python checkConfig.py
                if [ $? -ne 0 ]
                then
                    exit -1
                fi
             fi
             # Set all file permissions to owner and group write
             echo "********** setPermissions **********"
             $MADROOT/bin/python setPermissions.py
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** configureSource **********"
             $MADROOT/bin/python configureSource.py
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             # Compile the Libraries and Programs
             # ----------------------------------
             cd source
             echo "********** rebuilding dist with autotools **********"
             aclocal
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             autoconf
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             libtoolize
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             autoheader
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             automake --add-missing
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** ./configure **********"
-            ./configure --prefix=$MADROOT
+            ./configure --prefix=$MADROOT FFLAGS=-std=legacy
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** make clean **********"
             make clean
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** make **********"
             make
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** make check **********"
             make check
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** make install **********"
             make install
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             cd ..
             echo "********** configureScripts **********"
             $MADROOT/bin/python configureScripts.py
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** Installing bootstrap calendar **********"
             cd source/madpy/djangoMad/bootstrap_calendar/dist
             rm -rf django-bootstrap-calendar-0.1.0
             tar -xzf django-bootstrap-calendar-0.1.0.tar.gz
             cd django-bootstrap-calendar-0.1.0
             $MADROOT/bin/python setup.py install
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             cd ../../../../../..
             echo "********** Installing madrigal python library **********"
             cd source/madpy
             rm -f -r build
             $MADROOT/bin/python setup.py install
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             rm -f -r build
             echo "********** Installing madrigalWeb python library **********"
             cd madrigalWeb
             rm -f -r build
             $MADROOT/bin/python setup.py install
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             cd ../../..
             echo "********** Verifying this site is set to at least 3 in siteTab.txt **********"
             $MADROOT/bin/python source/madpy/scripts/bin/checkSiteIs3.py
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             # Install Experiments
             # -------------------
             echo "********** configureExperiments **********"
             chmod +x configureExperiments
             ./configureExperiments
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             # Update metadata
             # -------------------
             echo "********** Updating metadata tables **********"
             chmod +x -R bin/
             bin/updateMaster
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "********** The following script will create all the summary and hdf5 files needed **********"
             bin/rebuildInstParmTab.py
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             if [ $convert = 1 ]
             then
                 bin/convertToMadrigal3.py --numCPU=2
                 if [ $? -ne 0 ]
                 then
                     exit -1
                 fi
             fi
             # Test the Libraries and Programs
             echo "********** Testing installation **********"
             # ------------------------------
             bin/testGeolib
             if [ $? -ne 0 ]
             then
                 exit -1
             fi
             echo "--diff testGeolib.out source/madf/geolib/testGeolib.out.rock"
             diff testGeolib.out source/madf/geolib/testGeolib.out.rock
             echo "running test on Madrigal web services..."
             bin/python source/madpy/madrigalWeb/madrigalWeb/examples/testMadrigalWebServices.py
             echo "checking whether the web server needs extra configuration"
             bin/python source/madpy/scripts/bin/testWebConfig.py
             # Install complete
             # ---------------------
             echo ""
             printf 'Elapsed time: %s\n' $(timer $tmr)
             echo "Madrigal installation complete"

source/madpy/djangoMad/djangoMad/settings.py +1 0

             """
             Django settings for djangoMad project.
             For more information on this file, see
             https://docs.djangoproject.com/en/1.7/topics/settings/
             For the full list of settings and their values, see
             https://docs.djangoproject.com/en/1.7/ref/settings/
             """
             # Build paths inside the project like this: os.path.join(BASE_DIR, ...)
             import os
             BASE_DIR = os.path.dirname(os.path.dirname(__file__))
             # Quick-start development settings - unsuitable for production
             # See https://docs.djangoproject.com/en/1.7/howto/deployment/checklist/
             # SECURITY WARNING: keep the secret key used in production secret!
             SECRET_KEY = '^c1l3d35+q28^66d2pc1qlu(k$wmw^*gg3rfitz^s)t=9eu1ui'
             # SECURITY WARNING: don't run with debug turned on in production!
             DEBUG = True
             ALLOWED_HOSTS = ['localhost:8000', '127.0.0.1', 'localhost', '10.10.120.60']
             ADMINS = (('Bill Rideout', 'brideout@haystack.mit.edu'),)
             EMAIL_HOST = 'hyperion.haystack.mit.edu'
             SEND_BROKEN_LINK_EMAILS = True
             MANAGERS = (('Bill Rideout', 'brideout@haystack.mit.edu'),)
             # Application definition
             INSTALLED_APPS = (
                 'django.contrib.admin',
                 'django.contrib.auth',
                 'django.contrib.contenttypes',
                 'django.contrib.sessions',
                 'django.contrib.messages',
                 'django.contrib.staticfiles',
                 'madweb',
                 'django_bootstrap_calendar',
                 'bootstrap3',
                 'apps.login',
                 'apps.updata',
             )
             MIDDLEWARE = [
                 'django.middleware.security.SecurityMiddleware',
                 'django.contrib.sessions.middleware.SessionMiddleware',
                 'django.middleware.common.CommonMiddleware',
                 'django.middleware.csrf.CsrfViewMiddleware',
                 'django.contrib.auth.middleware.AuthenticationMiddleware',
                 'django.contrib.messages.middleware.MessageMiddleware',
                 'django.middleware.clickjacking.XFrameOptionsMiddleware',
             ]
             ROOT_URLCONF = 'djangoMad.urls'
             WSGI_APPLICATION = 'djangoMad.wsgi.application'
             TEMPLATES = [
                 {
                     'BACKEND': 'django.template.backends.django.DjangoTemplates',
                     'DIRS': [
                         os.path.join(BASE_DIR, "templates"),
                     ],
                     'APP_DIRS': True,
                     'OPTIONS': {
                         'context_processors': [
                             'django.contrib.auth.context_processors.auth',
                             'django.template.context_processors.debug',
                             'django.template.context_processors.i18n',
                             'django.template.context_processors.media',
                             'django.template.context_processors.static',
                             'django.template.context_processors.tz',
                             'django.contrib.messages.context_processors.messages',
                             'django.template.context_processors.request',
                         ],
                     },
                 },
             ]
             # Database
             # https://docs.djangoproject.com/en/1.7/ref/settings/#databases
             DATABASES = {
                 'default': {
                     'ENGINE': 'django.db.backends.sqlite3',
                     'NAME': 'madrigal.sqlite',
                 }
             }
             # Internationalization
             # https://docs.djangoproject.com/en/1.7/topics/i18n/
             LANGUAGE_CODE = 'en-us'
             TIME_ZONE = 'UTC'
             USE_I18N = True
             USE_L10N = True
             USE_TZ = True
             # Absolute filesystem path to the directory that will hold user-uploaded files.
             # Example: "/home/media/media.lawrence.com/media/"
             MEDIA_ROOT = os.path.join(BASE_DIR, 'media')
             # URL that handles the media served from MEDIA_ROOT. Make sure to use a
             # trailing slash.
             # Examples: "http://media.lawrence.com/media/", "http://example.com/media/"
             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: "/home/media/media.lawrence.com/static/"
             # STATIC_ROOT = os.path.join(BASE_DIR, 'static')
             # URL prefix for static files.
             # Example: "http://media.lawrence.com/static/"
             STATIC_URL = '/madrigal/static/'
+            STATIC_ROOT = '/madrigal/source/madpy/djangoMad/static_files/'
             BOOTSTRAP3 = {
                 # Include jQuery with Bootstrap JavaScript (affects django-bootstrap3 template tags)
                 'jquery_url': '/madrigal/static/jquery.min.js',
                 'include_jquery': True,
             }

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