[HOTFIX] Fix Affy docker image

foreman/data_refinery_foreman/foreman/main.py

@@ -84,7 +84,7 @@
 # How frequently we clean up the database.
 DBCLEAN_TIME = datetime.timedelta(hours=6)
 
-# Setting this to a recent date will prevent the Foreman from queuing/requeuing 
+# Setting this to a recent date will prevent the Foreman from queuing/requeuing
 # jobs created before this cutoff.
 JOB_CREATED_AT_CUTOFF = datetime.datetime(2019, 6, 5, tzinfo=timezone.utc)
 
@@ -578,7 +578,7 @@ def retry_lost_downloader_jobs() -> None:
     potentially_lost_jobs = DownloaderJob.objects.filter(
         success=None,
         retried=False,
-        no_retry=False,        
+        no_retry=False,
         created_at__gt=JOB_CREATED_AT_CUTOFF,
         start_time=None,
         end_time=None,
@@ -620,6 +620,8 @@ def retry_lost_downloader_jobs() -> None:
                 elif jobs_queued_from_this_page < queue_capacity:
                     # The job never got put in the Nomad queue, no
                     # need to recreate it, we just gotta queue it up!
+                    job.volume_index = get_emptiest_volume()
+                    job.save()
                     send_job(Downloaders[job.downloader_task], job=job, is_dispatch=True)
                     jobs_queued_from_this_page += 1
             except socket.timeout:

foreman/data_refinery_foreman/settings.py

@@ -145,6 +145,17 @@
 STATIC_URL = '/static/'
 
 
+# Caching
+# https://docs.djangoproject.com/en/2.2/topics/cache/
+
+CACHES = {
+    'default': {
+        'BACKEND': 'django.core.cache.backends.db.DatabaseCache',
+        'LOCATION': 'cache_table',
+    }
+}
+
+
 # Setting the RAVEN_CONFIG when RAVEN_DSN isn't set will cause the
 # following warning:
 # /usr/local/lib/python3.6/site-packages/raven/conf/remote.py:91:

infrastructure/deploy.sh

@@ -271,6 +271,14 @@ docker run \
        --env RUNNING_IN_CLOUD=False \
        $DOCKERHUB_REPO/$FOREMAN_DOCKER_IMAGE python3 manage.py migrate
 
+# Apply general migrations.
+docker run \
+       --env-file prod_env \
+       --env DATABASE_HOST=$RDS_HOST \
+       --env DATABASE_PORT=$DATABASE_HIDDEN_PORT \
+       --env RUNNING_IN_CLOUD=False \
+       $DOCKERHUB_REPO/$FOREMAN_DOCKER_IMAGE python3 manage.py createcachetable
+
 # Make sure to clear out any old nomad job specifications since we
 # will register everything in this directory.
 rm -r nomad-job-specs

workers/R_dependencies/affymetrix/dependencies.R

@@ -7,24 +7,24 @@ devtools::install_version('ff', version='2.2-13')
 devtools::install_version('XML', version='3.98-1.10')
 devtools::install_version('bitops', version='1.0-6')
 devtools::install_version('RCurl', version='1.95-4.10')
-devtools::install_version('bit64', version='0.9-7')
 devtools::install_version('pkgconfig', version='2.0.1')
 devtools::install_version('backports', version='1.1.4')
+devtools::install_version('rlang', version='0.4.0')
 devtools::install_version('zeallot', version='0.1.0')
 devtools::install_version('glue', version='1.3.1')
-devtools::install_version('rlang', version='0.4.0')
 devtools::install_version('digest', version='0.6.19')
 devtools::install_version('vctrs', version='0.1.0')
 devtools::install_version('magrittr', version='1.5')
 devtools::install_version('assertthat', version='0.2.1')
 devtools::install_version('prettyunits', version='1.0.2')
 devtools::install_version('blob', version='1.1.1')
 devtools::install_version('memoise', version='1.1.0')
-devtools::install_version('Rcpp', version='1.0.1')
 devtools::install_version('DBI', version='1.0.0')
+devtools::install_version('Rcpp', version='1.0.1')
+devtools::install_version('bit64', version='0.9-7')
 devtools::install_version('RSQLite', version='2.0')
-devtools::install_version('crayon', version='1.3.4')
 devtools::install_version('fansi', version='0.4.0')
+devtools::install_version('crayon', version='1.3.4')
 devtools::install_version('cli', version='1.1.0')
 devtools::install_version('utf8', version='1.1.4')
 devtools::install_version('pillar', version='1.4.2')
@@ -38,3 +38,14 @@ devtools::install_version('dplyr', version='0.7.8')
 devtools::install_version('dplyr', version='0.7.8')
 devtools::install_version('stringi', version='1.4.3')
 devtools::install_version('tidyr', version='0.8.2')
+devtools::install_version('sys', version='3.2')
+devtools::install_version('askpass', version='1.1')
+devtools::install_version('openssl', version='1.4')
+devtools::install_version('curl', version='3.3')
+devtools::install_version('mime', version='0.7')
+devtools::install_version('jsonlite', version='1.6')
+devtools::install_version('httr', version='1.4.0')
+devtools::install_version('hms', version='0.4.2')
+devtools::install_version('clipr', version='0.6.0')
+devtools::install_version('readr', version='1.3.1')
+devtools::install_version('xml2', version='1.2.0')

workers/R_dependencies/affymetrix/packages.txt

@@ -7,3 +7,7 @@ xtable
 pkgconfig
 dplyr
 tidyr
+httr
+readr
+xml2
+magrittr