From 33d3286e7448d7152ba75aed1f8ffd427ff26772 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 12:44:48 +0200
Subject: [PATCH 01/13] Change the tomcat roles so that we are now able to
 change the default temporary directory.

---
 tomcat-multiple-instances/tasks/main.yml              | 7 ++++++-
 tomcat-multiple-instances/templates/tomcat-default.j2 | 3 +++
 tomcat/tasks/tomcat-pkgs.yml                          | 6 ++++++
 tomcat/templates/tomcat-default.j2                    | 4 +++-
 4 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/tomcat-multiple-instances/tasks/main.yml b/tomcat-multiple-instances/tasks/main.yml
index ee42680..c49dec1 100644
--- a/tomcat-multiple-instances/tasks/main.yml
+++ b/tomcat-multiple-instances/tasks/main.yml
@@ -56,6 +56,12 @@
   register: tomcat_first_install
   tags: [ 'tomcat', 'tomcat_instances' ]
 
+- name: Create the tmp directory
+  file: dest={{ item.catalina_tmp_directory }} state=directory
+  with_items: '{{ tomcat_m_instances }}'
+  when: item.catalina_tmp_directory is defined
+  tags: [ 'tomcat', 'tomcat_instances' ]
+
 - name: Populate the instances conf directory
   copy: src={{ item[1] }} dest={{ item.0.instance_path }}/conf/{{ item[1] }} owner={{ item.0.user }} group={{ item.0.user }} mode=0640
   with_nested:
@@ -76,7 +82,6 @@
     - tomcat restart instances with changed configs 
   tags: [ 'tomcat', 'tomcat_instances', 'tomcat_catalina_properties' ]
 
-
 - name: Populate the instances conf/policy.d directory
   copy: src=policy.d/{{ item[1] }} dest={{ item.0.instance_path }}/conf/policy.d/{{ item[1] }} owner={{ item.0.user }} group={{ item.0.user }} mode=0640
   with_nested:
diff --git a/tomcat-multiple-instances/templates/tomcat-default.j2 b/tomcat-multiple-instances/templates/tomcat-default.j2
index 74ac914..8e165ad 100644
--- a/tomcat-multiple-instances/templates/tomcat-default.j2
+++ b/tomcat-multiple-instances/templates/tomcat-default.j2
@@ -50,6 +50,9 @@ JAVA_OPTS="${JAVA_OPTS} -Xdebug -Xrunjdwp:transport=dt_socket,address={{ item.re
 {% endif %}
 # WARNING: This directory will be destroyed and recreated at every startup !
 JVM_TMP={{ item.instance_path }}/tmp
+{% if item.catalina_tmp_directory is defined %}
+export CATALINA_TMPDIR={{ item.catalina_tmp_directory }}
+{% endif %}
 # Additional options not managed by the provisioning tools
 if [ -f /etc/default/tomcat-instance-{{ item.http_port }}.local ] ; then
     . /etc/default/tomcat-instance-{{ item.http_port }}.local
diff --git a/tomcat/tasks/tomcat-pkgs.yml b/tomcat/tasks/tomcat-pkgs.yml
index 184f8ad..e5487d9 100644
--- a/tomcat/tasks/tomcat-pkgs.yml
+++ b/tomcat/tasks/tomcat-pkgs.yml
@@ -9,6 +9,12 @@
   notify: tomcat restart
   tags: tomcat
   
+- name: Create the catalina temp directory, if different from the default
+  file: dest={{ catalina_tmp_directory }} state=directory owner={{ tomcat_user }} group={{ tomcat_user }}
+  when: catalina_tmp_directory is defined
+  notify: tomcat restart 
+  tags: tomcat
+  
 - name: Configure tomcat defaults
   template: src=tomcat-default.j2 dest=/etc/default/tomcat{{ tomcat_version }}
   when: tomcat_install_default_conf
diff --git a/tomcat/templates/tomcat-default.j2 b/tomcat/templates/tomcat-default.j2
index 02ad697..8d8862f 100644
--- a/tomcat/templates/tomcat-default.j2
+++ b/tomcat/templates/tomcat-default.j2
@@ -48,7 +48,9 @@ JAVA_OPTS="${JAVA_OPTS} -Xdebug -Xrunjdwp:transport=dt_socket,address={{ tomcat_
 # Location of the JVM temporary directory
 # WARNING: This directory will be destroyed and recreated at every startup !
 JVM_TMP={{ tomcat_tmp_dir }}
-
+{% if catalina_tmp_directory is defined %}
+export CATALINA_TMPDIR={{ catalina_tmp_directory }}
+{% endif %}
 {% if tomcat_load_additional_default_conf %}
 if [ -f /etc/default/tomcat.local ] ; then
     . /etc/default/tomcat.local

From ce4442395571fb7202c81b912681422043d3d4fd Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 12:52:03 +0200
Subject: [PATCH 02/13] library/roles/smartgears/smartgears/defaults/main.yml:
 add a default for the catalina (tomcat) tmp directory, so that we can change
 it when needed.

---
 smartgears/smartgears/defaults/main.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/smartgears/smartgears/defaults/main.yml b/smartgears/smartgears/defaults/main.yml
index a9fa8b4..65c069a 100644
--- a/smartgears/smartgears/defaults/main.yml
+++ b/smartgears/smartgears/defaults/main.yml
@@ -55,6 +55,7 @@ smartgears_log_max_history: 30
 smartgears_log_max_file_size: 10MB
 smartgears_log_total_file_cap: 2GB
 smartgears_log_dir: '{{ smartgears_user_home }}/tomcat/logs'
+smartgears_tomcat_tmp_dir: '{{ smartgears_user_home }}/tomcat/tmp'
 smartgears_logback_template: True
 
 smartgears_tomcat_contexts: [ '' ]
@@ -65,7 +66,7 @@ http_port: '{{ smartgears_http_port }}'
 
 tomcat_m_webapps_unpack: True
 tomcat_m_instances:
-  - {  http_enabled: True, http_port: '{{ smartgears_http_port }}', http_address: '{{ smartgears_tomcat_listen_address }}', ajp_enabled: False, ajp_port: '8109', ajp_address: '127.0.0.1', restart_timeout: '{{ tomcat_m_restart_timeout }}', shutdown_port: '-1', java_home: '{{ jdk_java_home }}', user: '{{ smartgears_user }}', user_home: '{{ smartgears_user_home }}', user_shell: '{{ tomcat_m_default_user_shell }}', instance_path: '{{ smartgears_instance_path }}', max_threads: '{{ tomcat_m_max_threads }}', autodeploy: '{{ tomcat_m_webapps_autodeploy }}', unpack: '{{ tomcat_m_webapps_unpack }}', default_conf: True, java_opts: '{{ tomcat_m_java_opts }}', java_gc_opts: '{{ tomcat_m_java_gc_opts }}', other_java_opts: '{{ tomcat_m_other_java_opts }}', jmx_enabled: '{{ tomcat_m_jmx_enabled }}', jmx_disable_additional_ports: '{{ tomcat_m_jmx_disable_additional_ports }}', jmx_port: '{{ tomcat_m_jmx_port }}', jmx_use_ssl: '{{ tomcat_m_jmx_use_ssl }}', jmx_auth_enabled: '{{ tomcat_m_jmx_auth_enabled }}', jmx_auth_dir: '{{ tomcat_m_instances_base_path }}/{{ smartgears_http_port }}/conf', jmx_monitorpass: '{{ tomcat_m_jmx_monitorpass | default(omit) }}', jmx_controlpass: '{{ tomcat_m_jmx_controlpass | default(omit) }}', remote_debugging: '{{ tomcat_m_enable_remote_debugging }}', remote_debugging_port: '{{ smartgears_debugging_port }}' , access_log_enabled: True, log_rotation_freq: daily, log_retain: 30, allowed_hosts: [ '0.0.0.0/0' ], app_contexts: '{{ smartgears_tomcat_contexts }}', skip_smartgears: False,smartgears_id: 1, servername: '{{ ansible_fqdn }}' }
+  - {  http_enabled: True, http_port: '{{ smartgears_http_port }}', http_address: '{{ smartgears_tomcat_listen_address }}', ajp_enabled: False, ajp_port: '8109', ajp_address: '127.0.0.1', restart_timeout: '{{ tomcat_m_restart_timeout }}', shutdown_port: '-1', java_home: '{{ jdk_java_home }}', user: '{{ smartgears_user }}', user_home: '{{ smartgears_user_home }}', user_shell: '{{ tomcat_m_default_user_shell }}', instance_path: '{{ smartgears_instance_path }}', max_threads: '{{ tomcat_m_max_threads }}', autodeploy: '{{ tomcat_m_webapps_autodeploy }}', unpack: '{{ tomcat_m_webapps_unpack }}', default_conf: True, java_opts: '{{ tomcat_m_java_opts }}', java_gc_opts: '{{ tomcat_m_java_gc_opts }}', other_java_opts: '{{ tomcat_m_other_java_opts }}', jmx_enabled: '{{ tomcat_m_jmx_enabled }}', jmx_disable_additional_ports: '{{ tomcat_m_jmx_disable_additional_ports }}', jmx_port: '{{ tomcat_m_jmx_port }}', jmx_use_ssl: '{{ tomcat_m_jmx_use_ssl }}', jmx_auth_enabled: '{{ tomcat_m_jmx_auth_enabled }}', jmx_auth_dir: '{{ tomcat_m_instances_base_path }}/{{ smartgears_http_port }}/conf', jmx_monitorpass: '{{ tomcat_m_jmx_monitorpass | default(omit) }}', jmx_controlpass: '{{ tomcat_m_jmx_controlpass | default(omit) }}', catalina_tmp_directory: '{{ smartgears_tomcat_tmp_dir }}' remote_debugging: '{{ tomcat_m_enable_remote_debugging }}', remote_debugging_port: '{{ smartgears_debugging_port }}', access_log_enabled: True, log_rotation_freq: daily, log_retain: 30, allowed_hosts: [ '0.0.0.0/0' ], app_contexts: '{{ smartgears_tomcat_contexts }}', skip_smartgears: False,smartgears_id: 1, servername: '{{ ansible_fqdn }}' }
 
 # To enable debugging:
 # - Set

From 6dfaef66d0b36ad79090ed60a7f8aa9064fb1dc0 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 12:57:05 +0200
Subject: [PATCH 03/13] nginx: create the directory defined by the variable
 nginx_client_body_temp_dir, when the variable has been defined.

---
 nginx/tasks/nginx-config.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/nginx/tasks/nginx-config.yml b/nginx/tasks/nginx-config.yml
index 6edd9d5..5e7c5ef 100644
--- a/nginx/tasks/nginx-config.yml
+++ b/nginx/tasks/nginx-config.yml
@@ -6,6 +6,10 @@
     - name: Create the pki directory
       file: dest={{ pki_dir }}/nginx state=directory
 
+    - name: Create the client body tmp directory, if needed
+      file: dest={{ nginx_client_body_temp_dir }}/nginx state=directory owner=www-data group=www-data mode=0700
+      when: nginx_client_body_temp_dir is defined
+
     - name: Create a dhparams file 2048 bits long
       shell: openssl dhparam -out {{ pki_dir }}/nginx/dhparams.pem 2048
       args:

From 25eebdf57f50161ce77f1aa5d8dfab7f896e4759 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 13:02:18 +0200
Subject: [PATCH 04/13] Fix a typo.

---
 smartgears/smartgears/defaults/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/smartgears/smartgears/defaults/main.yml b/smartgears/smartgears/defaults/main.yml
index 65c069a..27822ec 100644
--- a/smartgears/smartgears/defaults/main.yml
+++ b/smartgears/smartgears/defaults/main.yml
@@ -66,7 +66,7 @@ http_port: '{{ smartgears_http_port }}'
 
 tomcat_m_webapps_unpack: True
 tomcat_m_instances:
-  - {  http_enabled: True, http_port: '{{ smartgears_http_port }}', http_address: '{{ smartgears_tomcat_listen_address }}', ajp_enabled: False, ajp_port: '8109', ajp_address: '127.0.0.1', restart_timeout: '{{ tomcat_m_restart_timeout }}', shutdown_port: '-1', java_home: '{{ jdk_java_home }}', user: '{{ smartgears_user }}', user_home: '{{ smartgears_user_home }}', user_shell: '{{ tomcat_m_default_user_shell }}', instance_path: '{{ smartgears_instance_path }}', max_threads: '{{ tomcat_m_max_threads }}', autodeploy: '{{ tomcat_m_webapps_autodeploy }}', unpack: '{{ tomcat_m_webapps_unpack }}', default_conf: True, java_opts: '{{ tomcat_m_java_opts }}', java_gc_opts: '{{ tomcat_m_java_gc_opts }}', other_java_opts: '{{ tomcat_m_other_java_opts }}', jmx_enabled: '{{ tomcat_m_jmx_enabled }}', jmx_disable_additional_ports: '{{ tomcat_m_jmx_disable_additional_ports }}', jmx_port: '{{ tomcat_m_jmx_port }}', jmx_use_ssl: '{{ tomcat_m_jmx_use_ssl }}', jmx_auth_enabled: '{{ tomcat_m_jmx_auth_enabled }}', jmx_auth_dir: '{{ tomcat_m_instances_base_path }}/{{ smartgears_http_port }}/conf', jmx_monitorpass: '{{ tomcat_m_jmx_monitorpass | default(omit) }}', jmx_controlpass: '{{ tomcat_m_jmx_controlpass | default(omit) }}', catalina_tmp_directory: '{{ smartgears_tomcat_tmp_dir }}' remote_debugging: '{{ tomcat_m_enable_remote_debugging }}', remote_debugging_port: '{{ smartgears_debugging_port }}', access_log_enabled: True, log_rotation_freq: daily, log_retain: 30, allowed_hosts: [ '0.0.0.0/0' ], app_contexts: '{{ smartgears_tomcat_contexts }}', skip_smartgears: False,smartgears_id: 1, servername: '{{ ansible_fqdn }}' }
+  - {  http_enabled: True, http_port: '{{ smartgears_http_port }}', http_address: '{{ smartgears_tomcat_listen_address }}', ajp_enabled: False, ajp_port: '8109', ajp_address: '127.0.0.1', restart_timeout: '{{ tomcat_m_restart_timeout }}', shutdown_port: '-1', java_home: '{{ jdk_java_home }}', user: '{{ smartgears_user }}', user_home: '{{ smartgears_user_home }}', user_shell: '{{ tomcat_m_default_user_shell }}', instance_path: '{{ smartgears_instance_path }}', max_threads: '{{ tomcat_m_max_threads }}', autodeploy: '{{ tomcat_m_webapps_autodeploy }}', unpack: '{{ tomcat_m_webapps_unpack }}', default_conf: True, java_opts: '{{ tomcat_m_java_opts }}', java_gc_opts: '{{ tomcat_m_java_gc_opts }}', other_java_opts: '{{ tomcat_m_other_java_opts }}', jmx_enabled: '{{ tomcat_m_jmx_enabled }}', jmx_disable_additional_ports: '{{ tomcat_m_jmx_disable_additional_ports }}', jmx_port: '{{ tomcat_m_jmx_port }}', jmx_use_ssl: '{{ tomcat_m_jmx_use_ssl }}', jmx_auth_enabled: '{{ tomcat_m_jmx_auth_enabled }}', jmx_auth_dir: '{{ tomcat_m_instances_base_path }}/{{ smartgears_http_port }}/conf', jmx_monitorpass: '{{ tomcat_m_jmx_monitorpass | default(omit) }}', jmx_controlpass: '{{ tomcat_m_jmx_controlpass | default(omit) }}', catalina_tmp_directory: '{{ smartgears_tomcat_tmp_dir }}', remote_debugging: '{{ tomcat_m_enable_remote_debugging }}', remote_debugging_port: '{{ smartgears_debugging_port }}', access_log_enabled: True, log_rotation_freq: daily, log_retain: 30, allowed_hosts: [ '0.0.0.0/0' ], app_contexts: '{{ smartgears_tomcat_contexts }}', skip_smartgears: False,smartgears_id: 1, servername: '{{ ansible_fqdn }}' }
 
 # To enable debugging:
 # - Set

From 042c6a7767c1d38e5df703924b0a62bae5a50172 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 13:02:27 +0200
Subject: [PATCH 05/13] tomcat-multiple-instances: Create the tmp directory
 with the correct permissions and ownership.

---
 tomcat-multiple-instances/tasks/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tomcat-multiple-instances/tasks/main.yml b/tomcat-multiple-instances/tasks/main.yml
index c49dec1..114f785 100644
--- a/tomcat-multiple-instances/tasks/main.yml
+++ b/tomcat-multiple-instances/tasks/main.yml
@@ -56,8 +56,8 @@
   register: tomcat_first_install
   tags: [ 'tomcat', 'tomcat_instances' ]
 
-- name: Create the tmp directory
-  file: dest={{ item.catalina_tmp_directory }} state=directory
+- name: Create the catalina tmp directory
+  file: dest={{ item.catalina_tmp_directory }} state=directory owner={{ item.0.user }} group={{ item.0.user }} mode=0700
   with_items: '{{ tomcat_m_instances }}'
   when: item.catalina_tmp_directory is defined
   tags: [ 'tomcat', 'tomcat_instances' ]

From 9308f7cdf01c428bca89530abe68723bb26984d0 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 13:05:31 +0200
Subject: [PATCH 06/13] tomcat-multiple-instances: Fix the permissions of the
 temp directory, again.

---
 tomcat-multiple-instances/tasks/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tomcat-multiple-instances/tasks/main.yml b/tomcat-multiple-instances/tasks/main.yml
index 114f785..792556a 100644
--- a/tomcat-multiple-instances/tasks/main.yml
+++ b/tomcat-multiple-instances/tasks/main.yml
@@ -57,7 +57,7 @@
   tags: [ 'tomcat', 'tomcat_instances' ]
 
 - name: Create the catalina tmp directory
-  file: dest={{ item.catalina_tmp_directory }} state=directory owner={{ item.0.user }} group={{ item.0.user }} mode=0700
+  file: dest={{ item.catalina_tmp_directory }} state=directory owner={{ item.user }} group={{ item.user }} mode=0700
   with_items: '{{ tomcat_m_instances }}'
   when: item.catalina_tmp_directory is defined
   tags: [ 'tomcat', 'tomcat_instances' ]

From cb8cc3f3561b1869dee78351f17dc4bcccabf358 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 16:02:37 +0200
Subject: [PATCH 07/13] shiniproxy: Install version 1.0. Introduce a memory
 limit for the shiny apps.

---
 shinyproxy/defaults/main.yml                | 6 ++++--
 shinyproxy/templates/shinyproxy-conf.yml.j2 | 4 ++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/shinyproxy/defaults/main.yml b/shinyproxy/defaults/main.yml
index 8317353..4d0105f 100644
--- a/shinyproxy/defaults/main.yml
+++ b/shinyproxy/defaults/main.yml
@@ -1,6 +1,6 @@
 ---
 shinyproxy_install: False
-shinyproxy_version: 0.9.3
+shinyproxy_version: 1.0.0
 shinyproxy_file_name: 'shinyproxy-{{ shinyproxy_version }}.jar'
 shinyproxy_url: 'https://www.shinyproxy.io/downloads/{{ shinyproxy_file_name }}'
 shinyproxy_app_name: shinyproxy.jar
@@ -10,8 +10,10 @@ shinyproxy_http_port: 8080
 # For logrotate. In days
 shinyproxy_log_retention: 10
 shinyproxy_default_apps: True
-shinyproxy_docker_url: 'http://localhost:2375/'
+shinyproxy_docker_url: 'http://localhost:2375'
 shinyproxy_docker_port_range_start: 20000
+shinyproxy_container_wait_time: 60000
+shinyproxy_hide_navbar: 'false'
 
 shinyproxy_app_title: 'Open Analytics Shiny Proxy'
 shinyproxy_logo_url: 'http://www.openanalytics.eu/sites/www.openanalytics.eu/themes/oa/logo.png'
diff --git a/shinyproxy/templates/shinyproxy-conf.yml.j2 b/shinyproxy/templates/shinyproxy-conf.yml.j2
index b75b1c5..482c2fc 100644
--- a/shinyproxy/templates/shinyproxy-conf.yml.j2
+++ b/shinyproxy/templates/shinyproxy-conf.yml.j2
@@ -5,7 +5,9 @@ shiny:
     landing-page: /
     heartbeat-rate: 10000
     heartbeat-timeout: 60000
+    container-wait-time: {{ shinyproxy_container_wait_time }}
     port: {{ shinyproxy_http_port }}
+    hide-navbar: {{ shinyproxy_hide_navbar }}
     authentication: {{ shinyproxy_authentication }}
     admin-groups: {{ shinyproxy_admin_group }}
 {% if shinyproxy_ldap_enabled %}
@@ -49,9 +51,11 @@ shiny:
     description: {{ app.description }}
     docker-cmd: ["R", "-e {{ app.cmd }}"]
     docker-image: {{ app.docker_image }}
+    docker-memory: {{ app.docker_memory | default('2g') }}
     {% if app.groups is defined %}
     groups: {{ app.groups }}
     {% endif %}
+
 {% endfor %}
 {% endif %}
 

From cc74bb44f12097a4a713e2364e97b92f59915019 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 16:16:24 +0200
Subject: [PATCH 08/13] shinyproxy: add a task that pulls the new images.

---
 shinyproxy/tasks/main.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/shinyproxy/tasks/main.yml b/shinyproxy/tasks/main.yml
index 596ac19..574f13a 100644
--- a/shinyproxy/tasks/main.yml
+++ b/shinyproxy/tasks/main.yml
@@ -20,7 +20,7 @@
     - name: Install the shinyproxy configuration file
       template: src=shinyproxy-conf.yml.j2 dest={{ shinyproxy_install_dir }}/application.yml owner=root group={{ shinyproxy_user }} mode=0640
       notify: Restart shinyproxy
-      tags: [ 'shinyproxy', 'shinyproxy_conf' ]
+      tags: [ 'shinyproxy', 'shinyproxy_conf', 'shinyproxy_images' ]
 
     - name: Install the shinyproxy logrotate configuration
       template: src=shinyproxy-logrotate.j2 dest=/etc/logrotate.d/shinyproxy owner=root group=root mode=0444
@@ -29,6 +29,12 @@
     - name: Ensure that the shinyproxy service is enabled and running
       service: name=shinyproxy state=started enabled=yes
 
+    - name: Pull the Docker images of shiny apps
+      docker_image: name={{ item.docker_image }} pull=yes state=present
+      with_items: '{{ shinyproxy_apps }}'
+      when: shinyproxy_apps is defined
+      tags: [ 'shinyproxy', 'shinyproxy_images' ]
+
   when: shinyproxy_install
   tags: shinyproxy
 

From f2196b3cf9318b7e4e0c378705a1497c8753eacf Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 19:22:56 +0200
Subject: [PATCH 09/13] More fixes to the algorithms updater script.

---
 .../templates/algorithms-updater.j2           | 67 ++++++++++---------
 1 file changed, 34 insertions(+), 33 deletions(-)

diff --git a/smartgears/dataminer_app/templates/algorithms-updater.j2 b/smartgears/dataminer_app/templates/algorithms-updater.j2
index 879bae0..450c1b6 100644
--- a/smartgears/dataminer_app/templates/algorithms-updater.j2
+++ b/smartgears/dataminer_app/templates/algorithms-updater.j2
@@ -87,40 +87,13 @@ function algorithms_updater() {
         ALGO_NAME=$( echo "$algo" | awk -F \| '{ print $1 }' )
         ALGO_BODY=$( echo "$algo" | awk -F \| '{ print $2 }' )
         ALGO_DATE=$( echo "$algo" | awk -F \| '{ print $3 }' )
-        ALGO_TIMESTAMP=$( date +%s -d "$ALGO_DATE" )
+        ALGO_TIMESTAMP=$( date +%s -d "$ALGO_DATE" 2>/dev/null )
         if [ $? -ne 0 ] ; then
             echo "the date for algorithm $ALGO_NAME is wrong"
-        fi
-        ALGO_LINE=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE )
-        ALGO_PRESENT=$?
-        if [ $ALGO_PRESENT -ne 0 ] ; then
-            echo "logger 'algorithms-updater: running the add command of algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "logger 'algorithms-updater: the add command string is $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "RETVAL=" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo '-------------------------------------------'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo 'Adding algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo 'With command $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "$ALGO_BODY" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo 'RETVAL=$?' >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo 'Done.'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo 'if [ $RETVAL -ne 0 ] ; then' >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME failed'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "    echo '$ALGO_NAME | $ALGO_DATE' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_
-            echo "fi" >> $ALGORITHMS_TEMP_SCRIPT.body_
         else
-            ALGO_LOCAL_TIMESTAMP=0
-            ALGO_LOCAL_DATE=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE | awk -F \| '{ print $2 }' | grep -v \' )
-            ALGO_LOCAL_TIMESTAMP=$(  date +%s -d "$ALGO_LOCAL_DATE" )
-            if [ $? -ne 0 ] ; then
-                echo "the locally saved date for algorithm $ALGO_NAME is wrong"
-            fi            
-            if [ $ALGO_LOCAL_TIMESTAMP -ne $ALGO_TIMESTAMP ] ; then
+            ALGO_LINE=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE )
+            ALGO_PRESENT=$?
+            if [ $ALGO_PRESENT -ne 0 ] ; then
                 echo "logger 'algorithms-updater: running the add command of algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "logger 'algorithms-updater: the add command string is $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "RETVAL=" >> $ALGORITHMS_TEMP_SCRIPT.body_
@@ -137,11 +110,39 @@ function algorithms_updater() {
                 echo 'if [ $RETVAL -ne 0 ] ; then' >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME failed'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
-                echo "    echo 'grep -v $ALGO_NAME $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
+                echo "    echo 'egrep -v ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    echo 'mv ${ALGORITHMS_INSTALLED_FILE}_ $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
-                echo "    echo '$ALGO_NAME | $ALGO_DATE' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                echo "    echo '$ALGO_NAME | $ALGO_TIMESTAMP' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "fi" >> $ALGORITHMS_TEMP_SCRIPT.body_
+            else
+                ALGO_LOCAL_TIMESTAMP=0
+                # ALGO_LOCAL_DATE=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE | awk -F \| '{ print $2 }' | grep -v \' )
+                # ALGO_LOCAL_TIMESTAMP=$(  date +%s -d "$ALGO_LOCAL_DATE" 2>/dev/null )
+                ALGO_LOCAL_TIMESTAMP=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE | tail -1 | awk -F \| '{ print $2 }' | grep -v \' )
+                if [ $? -ne 0 ] || [ $ALGO_LOCAL_TIMESTAMP -ne $ALGO_TIMESTAMP ]; then
+                    echo "logger 'algorithms-updater: running the add command of algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "logger 'algorithms-updater: the add command string is $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "RETVAL=" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo '-------------------------------------------'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo 'Adding algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo 'With command $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "$ALGO_BODY" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo 'RETVAL=$?' >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo 'Done.'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "echo ''" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo 'if [ $RETVAL -ne 0 ] ; then' >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME failed'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    echo 'egrep -v ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    echo 'mv ${ALGORITHMS_INSTALLED_FILE}_ $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    echo '$ALGO_NAME | $ALGO_TIMESTAMP' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "fi" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                fi
             fi                
         fi
     done < ${ALGORITHMS_TEMP_SCRIPT}.algorithmslist

From daeda765a16a86b12c0d99f67b7b7adfc231e88f Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 19:25:06 +0200
Subject: [PATCH 10/13] Other fixes to
 library/roles/smartgears/dataminer_app/templates/algorithms-updater.j2.

---
 smartgears/dataminer_app/templates/algorithms-updater.j2 | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/smartgears/dataminer_app/templates/algorithms-updater.j2 b/smartgears/dataminer_app/templates/algorithms-updater.j2
index 450c1b6..19d2e91 100644
--- a/smartgears/dataminer_app/templates/algorithms-updater.j2
+++ b/smartgears/dataminer_app/templates/algorithms-updater.j2
@@ -112,14 +112,13 @@ function algorithms_updater() {
                 echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    echo 'egrep -v ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    echo 'mv ${ALGORITHMS_INSTALLED_FILE}_ $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
-                echo "    echo '$ALGO_NAME | $ALGO_TIMESTAMP' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                echo "    echo '$ALGO_NAME | $ALGO_DATE' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "fi" >> $ALGORITHMS_TEMP_SCRIPT.body_
             else
                 ALGO_LOCAL_TIMESTAMP=0
-                # ALGO_LOCAL_DATE=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE | awk -F \| '{ print $2 }' | grep -v \' )
-                # ALGO_LOCAL_TIMESTAMP=$(  date +%s -d "$ALGO_LOCAL_DATE" 2>/dev/null )
-                ALGO_LOCAL_TIMESTAMP=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE | tail -1 | awk -F \| '{ print $2 }' | grep -v \' )
+                ALGO_LOCAL_DATE=$( egrep ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE | tail -1 | awk -F \| '{ print $2 }' | grep -v \' )
+                ALGO_LOCAL_TIMESTAMP=$(  date +%s -d "$ALGO_LOCAL_DATE" 2>/dev/null )
                 if [ $? -ne 0 ] || [ $ALGO_LOCAL_TIMESTAMP -ne $ALGO_TIMESTAMP ]; then
                     echo "logger 'algorithms-updater: running the add command of algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "logger 'algorithms-updater: the add command string is $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
@@ -139,7 +138,7 @@ function algorithms_updater() {
                     echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    echo 'egrep -v ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    echo 'mv ${ALGORITHMS_INSTALLED_FILE}_ $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
-                    echo "    echo '$ALGO_NAME | $ALGO_TIMESTAMP' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    echo '$ALGO_NAME | $ALGO_DATE' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "fi" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 fi

From 56df697c0e9460849ffc3b4f125a5baa7aaced7c Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 19:25:58 +0200
Subject: [PATCH 11/13] Fix the ckan-connector-fixer.sh.j2 script.

---
 smartgears/ckan_connector/templates/ckan-connector-fixer.sh.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/smartgears/ckan_connector/templates/ckan-connector-fixer.sh.j2 b/smartgears/ckan_connector/templates/ckan-connector-fixer.sh.j2
index 992e2e8..028f791 100644
--- a/smartgears/ckan_connector/templates/ckan-connector-fixer.sh.j2
+++ b/smartgears/ckan_connector/templates/ckan-connector-fixer.sh.j2
@@ -47,8 +47,8 @@ cd /usr/lib/ckan/default/src/ckan
 if [ "$CKAN_CREATE_USER" == "True" ] ; then
 # Create the admin user
     paster sysadmin add $CK_ADMIN -c $CK_INI << EOF
-
 y
+
 $CK_ADMIN_PWD
 $CK_ADMIN_PWD
 

From b011d82213f9ca8308d463a4e3a9c8515c3aec21 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Fri, 15 Sep 2017 19:38:57 +0200
Subject: [PATCH 12/13] Correct another case of the algorithms-updater script.

---
 .../dataminer_app/templates/algorithms-updater.j2      | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/smartgears/dataminer_app/templates/algorithms-updater.j2 b/smartgears/dataminer_app/templates/algorithms-updater.j2
index 19d2e91..b82a145 100644
--- a/smartgears/dataminer_app/templates/algorithms-updater.j2
+++ b/smartgears/dataminer_app/templates/algorithms-updater.j2
@@ -91,7 +91,7 @@ function algorithms_updater() {
         if [ $? -ne 0 ] ; then
             echo "the date for algorithm $ALGO_NAME is wrong"
         else
-            ALGO_LINE=$( egrep ^"$ALGO_NAME" $ALGORITHMS_INSTALLED_FILE )
+            ALGO_LINE=$( egrep ^"$ALGO_NAME " $ALGORITHMS_INSTALLED_FILE )
             ALGO_PRESENT=$?
             if [ $ALGO_PRESENT -ne 0 ] ; then
                 echo "logger 'algorithms-updater: running the add command of algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
@@ -110,15 +110,15 @@ function algorithms_updater() {
                 echo 'if [ $RETVAL -ne 0 ] ; then' >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME failed'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
-                echo "    echo 'egrep -v ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
+                echo "    echo 'egrep -v ^"$ALGO_NAME "  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    echo 'mv ${ALGORITHMS_INSTALLED_FILE}_ $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    echo '$ALGO_NAME | $ALGO_DATE' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                 echo "fi" >> $ALGORITHMS_TEMP_SCRIPT.body_
             else
                 ALGO_LOCAL_TIMESTAMP=0
-                ALGO_LOCAL_DATE=$( egrep ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE | tail -1 | awk -F \| '{ print $2 }' | grep -v \' )
-                ALGO_LOCAL_TIMESTAMP=$(  date +%s -d "$ALGO_LOCAL_DATE" 2>/dev/null )
+                ALGO_LOCAL_DATE=$( egrep ^"$ALGO_NAME " $ALGORITHMS_INSTALLED_FILE | tail -1 | awk -F \| '{ print $2 }' | grep -v \' )
+                ALGO_LOCAL_TIMESTAMP=$( date +%s -d "$ALGO_LOCAL_DATE" 2>/dev/null )
                 if [ $? -ne 0 ] || [ $ALGO_LOCAL_TIMESTAMP -ne $ALGO_TIMESTAMP ]; then
                     echo "logger 'algorithms-updater: running the add command of algorithm $ALGO_NAME'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "logger 'algorithms-updater: the add command string is $ALGO_BODY'" >> $ALGORITHMS_TEMP_SCRIPT.body_
@@ -136,7 +136,7 @@ function algorithms_updater() {
                     echo 'if [ $RETVAL -ne 0 ] ; then' >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME failed'" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "else" >> $ALGORITHMS_TEMP_SCRIPT.body_
-                    echo "    echo 'egrep -v ^$ALGO_NAME\  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
+                    echo "    echo 'egrep -v "^$ALGO_NAME "  $ALGORITHMS_INSTALLED_FILE > ${ALGORITHMS_INSTALLED_FILE}_ " >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    echo 'mv ${ALGORITHMS_INSTALLED_FILE}_ $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    echo '$ALGO_NAME | $ALGO_DATE' >> $ALGORITHMS_INSTALLED_FILE" >> $ALGORITHMS_TEMP_SCRIPT.body_
                     echo "    logger 'algorithms-updater: the adding of algorithm $ALGO_NAME succeeded'" >> $ALGORITHMS_TEMP_SCRIPT.body_

From 4f79fdd574ec94d11617688a4e08c023aecf03d5 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <adellam@isti.cnr.it>
Date: Sun, 17 Sep 2017 16:27:28 +0200
Subject: [PATCH 13/13] shinyproxy: Force the pull of newer images.

---
 shinyproxy/tasks/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shinyproxy/tasks/main.yml b/shinyproxy/tasks/main.yml
index 574f13a..28e5ddd 100644
--- a/shinyproxy/tasks/main.yml
+++ b/shinyproxy/tasks/main.yml
@@ -30,7 +30,7 @@
       service: name=shinyproxy state=started enabled=yes
 
     - name: Pull the Docker images of shiny apps
-      docker_image: name={{ item.docker_image }} pull=yes state=present
+      docker_image: name={{ item.docker_image }} pull=yes state={{ item.image_state | default('present') }} force=yes
       with_items: '{{ shinyproxy_apps }}'
       when: shinyproxy_apps is defined
       tags: [ 'shinyproxy', 'shinyproxy_images' ]