From 9592c22577194ac173e13487b9c802decd91a4f9 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Sun, 20 May 2018 00:46:39 +0100
Subject: [PATCH 01/16] Change version of Java as versions after JDK8 u151
 cause problems in Grizzly/Glassfish 5

---
 centos74-openmq-glassfish/playbook.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/centos74-openmq-glassfish/playbook.yml b/centos74-openmq-glassfish/playbook.yml
index b763196..9ae7e2f 100644
--- a/centos74-openmq-glassfish/playbook.yml
+++ b/centos74-openmq-glassfish/playbook.yml
@@ -16,9 +16,9 @@
       home: /opt/glassfish
       shell: /bin/nologin
 
-  - name: Install OpenJDK 8
+  - name: Install OpenJDK 8 (versions after u151 cause problems in Grizzly/Glassfish 5 that affect Jersey OAuth1 client)
     yum:
-      name: 'java-1.8.0-openjdk'
+      name: 'java-1.8.0-openjdk-1.8.0.151-5.b12.el7_4.x86_64'
       state: present
         
   - name: Install unzip

From 8362e04a93a29ee52e1bc10c6a606d8cfcc0a9ed Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Mon, 16 Jul 2018 16:44:55 +0100
Subject: [PATCH 02/16] Update to Flu Detector 2.0

---
 .../conf/supervisor.ini.j2                    |  7 ++-
 centos74-matlab-fludetector/playbook.yml      | 44 +++++++++++--------
 2 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/centos74-matlab-fludetector/conf/supervisor.ini.j2 b/centos74-matlab-fludetector/conf/supervisor.ini.j2
index 9f52897..f0f64f9 100644
--- a/centos74-matlab-fludetector/conf/supervisor.ini.j2
+++ b/centos74-matlab-fludetector/conf/supervisor.ini.j2
@@ -1,4 +1,9 @@
 [program:fludetector]
 command = /opt/fludetector/scripts/serve.sh
 directory = /opt/fludetector
-user = {{fludetector_user}}
\ No newline at end of file
+user = {{fludetector_user}}
+
+[program:fludetector-google]
+command = /opt/fludetector/scripts/run.sh runmodelscheduler {{model_id}} '30 14 * * *'
+directory = /opt/fludetector
+user = {{fludetector_user}}
diff --git a/centos74-matlab-fludetector/playbook.yml b/centos74-matlab-fludetector/playbook.yml
index 211d20d..097e9bb 100644
--- a/centos74-matlab-fludetector/playbook.yml
+++ b/centos74-matlab-fludetector/playbook.yml
@@ -11,6 +11,8 @@
     fludetector_user: root
     installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
     license_file: license.txt
+    fludetector_version: v2.0
+    model_id: 1
   tasks:
     - name: Install EPEL repository
       yum: name=epel-release state=present
@@ -40,22 +42,11 @@
       file: path=/opt/fludetector/logs state=directory
 
     - name: Deploy fludetector Flask app
-      unarchive: src=https://github.com/UCL/fludetector-flask/archive/v1.1.tar.gz dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
+      unarchive: src="https://github.com/UCL/fludetector-flask/archive/{{fludetector_version}}.tar.gz" dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
 
     - name: Copy env file
       copy: src=conf/env dest=/opt/fludetector/.env
 
-    - name: Configure fludetector Flask app
-      command: /opt/fludetector/scripts/init.sh chdir=/opt/fludetector
-
-    - name: Upload seed data
-      copy: src=conf/seed.sql dest=/opt/fludetector/seed.sql
-
-    - name: Import seed data
-      shell: sqlite3 data.db < seed.sql
-      args:
-        chdir: /opt/fludetector
-
     - name: Install Supervisor
       yum: name=supervisor state=present
 
@@ -71,12 +62,6 @@
     - name: Enable nginx port in firewall
       command: firewall-cmd --zone=public --permanent --add-service={{listen_as}}
 
-    - name: Start nginx
-      systemd: name=nginx state=started enabled=yes
-
-    - name: Start supervisord
-      systemd: name=supervisord state=started enabled=yes
-
     - name: Restart firewalld
       systemd: name=firewalld state=restarted
 
@@ -127,6 +112,11 @@
         - /root/Downloads/MathWorks/R2017a
         - /mnt
 
+    - name: Install Matlab engine for Python
+      command: python setup.py install --prefix {{virtualenv_dir}}
+      args:
+        chdir: /opt/MATLAB/extern/engines/python
+
     - name: Create directory for GPML package
       file:
         path: "/opt/fludetector/matlab/gpml"
@@ -147,3 +137,21 @@
         - infer_ILI_rate_google_2018_04.m
         - logit.m
         - gp_model_all_data_logity1.mat
+
+    - name: Configure fludetector Flask app
+      command: /opt/fludetector/scripts/init.sh chdir=/opt/fludetector
+
+    - name: Upload seed data
+      copy: src=conf/seed.sql dest=/opt/fludetector/seed.sql
+
+    - name: Import seed data
+      shell: sqlite3 data.db < seed.sql
+      args:
+        chdir: /opt/fludetector
+
+    - name: Start nginx
+      systemd: name=nginx state=started enabled=yes
+
+    - name: Start supervisord
+      systemd: name=supervisord state=started enabled=yes
+

From 6abf9d07fc20b361c42ff84f791b8c58377e63a2 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Mon, 16 Jul 2018 16:50:37 +0100
Subject: [PATCH 03/16] Delete scientificlinux69-matlab-flask

---
 scientificlinux69-matlab-flask/.gitignore   |   6 --
 scientificlinux69-matlab-flask/README.md    |   1 -
 scientificlinux69-matlab-flask/Vagrantfile  |  24 -----
 scientificlinux69-matlab-flask/playbook.yml | 113 --------------------
 4 files changed, 144 deletions(-)
 delete mode 100644 scientificlinux69-matlab-flask/.gitignore
 delete mode 100644 scientificlinux69-matlab-flask/README.md
 delete mode 100644 scientificlinux69-matlab-flask/Vagrantfile
 delete mode 100644 scientificlinux69-matlab-flask/playbook.yml

diff --git a/scientificlinux69-matlab-flask/.gitignore b/scientificlinux69-matlab-flask/.gitignore
deleted file mode 100644
index 713be26..0000000
--- a/scientificlinux69-matlab-flask/.gitignore
+++ /dev/null
@@ -1,6 +0,0 @@
-installationKey.txt
-license.txt
-*.iso
-*.m
-*.mat
-
diff --git a/scientificlinux69-matlab-flask/README.md b/scientificlinux69-matlab-flask/README.md
deleted file mode 100644
index 5073dee..0000000
--- a/scientificlinux69-matlab-flask/README.md
+++ /dev/null
@@ -1 +0,0 @@
-# scientificlinux69-matlab-flask
diff --git a/scientificlinux69-matlab-flask/Vagrantfile b/scientificlinux69-matlab-flask/Vagrantfile
deleted file mode 100644
index beaf13f..0000000
--- a/scientificlinux69-matlab-flask/Vagrantfile
+++ /dev/null
@@ -1,24 +0,0 @@
-# -*- mode: ruby -*-
-# vi: set ft=ruby :
-
-Vagrant.configure("2") do |config|
-
-  config.vm.box = "scientificlinux-6.9"
-
-  config.vm.provision "ansible" do |ansible|
-    ansible.playbook = "playbook.yml"
-    ansible.compatibility_mode = "2.0"
-  end
-  
-  # Create a forwarded port mapping which allows access to a specific port
-  # within the machine from a port on the host machine. In the example below,
-  # accessing "localhost:8080" will access port 80 on the guest machine.
-  # NOTE: This will enable public access to the opened port
-  # config.vm.network "forwarded_port", guest: 80, host: 8080
-
-  # Create a forwarded port mapping which allows access to a specific port
-  # within the machine from a port on the host machine and only allow access
-  # via 127.0.0.1 to disable public access
-  # config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
-
-end
diff --git a/scientificlinux69-matlab-flask/playbook.yml b/scientificlinux69-matlab-flask/playbook.yml
deleted file mode 100644
index 9d39b15..0000000
--- a/scientificlinux69-matlab-flask/playbook.yml
+++ /dev/null
@@ -1,113 +0,0 @@
----
-- hosts: localhost
-  user: vagrant
-
-- hosts: all
-  become: True
-  become_method: sudo
-  vars:
-    flask_dir: /opt/matlab-flask
-    virtualenv_dir: /opt/matlab-flask/venv
-    installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
-    license_file: license.txt
-  tasks:
-    - name: Install requirements
-      yum:
-        name: "{{item}}"
-        state: present
-      with_items:
-        - gcc
-        - openssl-devel
-        - readline-devel
-        - sqlite-devel
-        - libX11
-        - libXext
-        - libXt
-
-    - name: Download Python 2.7
-      unarchive:
-        src: https://www.python.org/ftp/python/2.7.15/Python-2.7.15.tgz
-        dest: /usr/src
-        remote_src: yes
-
-    - name: Configure Python
-      command: ./configure --with-ensurepip=install
-      args:
-        chdir: /usr/src/Python-2.7.15
-
-    - name: Build Python
-      make:
-        chdir: /usr/src/Python-2.7.15
-        target: altinstall
-
-    - name: Update pip and virtualenv
-      pip:
-        name: "{{item}}"
-        state: latest
-        executable: /usr/local/bin/pip2.7
-      with_items:
-        - pip
-        - virtualenv
-      
-    - name: Setup a Python 2.7 environment
-      command: /usr/local/bin/virtualenv -p /usr/local/bin/python2.7 {{virtualenv_dir}}
-
-    - name: Mount Matlab DVD 1
-      mount:
-        path: /mnt
-        src: /vagrant/R2017a_glnxa64_dvd1.iso
-        fstype: auto
-        opts: loop
-        state: mounted
-
-    - name: Create directory for Matlab archives install
-      file:
-        path: /root/Downloads/MathWorks/R2017a
-        state: directory
-
-    - name: Mount Matlab DVD 2
-      mount:
-        path: /root/Downloads/MathWorks/R2017a
-        src: /vagrant/R2017a_glnxa64_dvd2.iso
-        fstype: auto
-        opts: loop
-        state: mounted
-
-    - name: Install Matlab
-      command: /mnt/install -mode silent -agreeToLicense yes -destinationFolder /opt/MATLAB -fileInstallationKey {{installation_key_file}} -licensePath /vagrant/{{license_file}} -product.MATLAB
-
-    - name: Create symlink to Matlab executable
-      file:
-        path: /usr/local/bin/matlab
-        src: /opt/MATLAB/bin/matlab
-        state: link
-
-    - name: Unmount DVDs
-      mount:
-        path: "{{item}}"
-        state: unmounted
-      with_items:
-        - /root/Downloads/MathWorks/R2017a
-        - /mnt
-
-    - name: Create directory for GPML package
-      file:
-        path: "{{flask_dir}}/gpml"
-        state: directory
-
-    - name: Download GPML package
-      unarchive:
-        src: http://gaussianprocess.org/gpml/code/matlab/release/gpml-matlab-v4.1-2017-10-19.tar.gz
-        dest: "{{flask_dir}}/gpml"
-        remote_src: yes
-        extra_opts: "--strip-components=1"
-
-    - name: Upload Matlab artifacts
-      copy:
-        src: "{{item}}"
-        dest: "{{flask_dir}}"
-      with_items:
-        - infer_ILI_rate_google_2018_04.m
-        - logit.m
-        - gp_model_all_data_logity1.mat
-

From 1f2d2e1260caa28e985c394d8eeab8ef42ba07c0 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 18 Jul 2018 13:13:02 +0100
Subject: [PATCH 04/16] Package model artifacts in a tar.gz archive

---
 centos74-matlab-fludetector/README.adoc  |  7 +++++
 centos74-matlab-fludetector/README.md    |  1 -
 centos74-matlab-fludetector/playbook.yml | 33 +++++++++++++++---------
 3 files changed, 28 insertions(+), 13 deletions(-)
 create mode 100644 centos74-matlab-fludetector/README.adoc
 delete mode 100644 centos74-matlab-fludetector/README.md

diff --git a/centos74-matlab-fludetector/README.adoc b/centos74-matlab-fludetector/README.adoc
new file mode 100644
index 0000000..d8f5b02
--- /dev/null
+++ b/centos74-matlab-fludetector/README.adoc
@@ -0,0 +1,7 @@
+= centos74-matlab-fludetector
+
+== Requirements
+
+- Vagrant
+- Ansible
+- Matlab
\ No newline at end of file
diff --git a/centos74-matlab-fludetector/README.md b/centos74-matlab-fludetector/README.md
deleted file mode 100644
index 582a7b5..0000000
--- a/centos74-matlab-fludetector/README.md
+++ /dev/null
@@ -1 +0,0 @@
-# centos74-matlab-fludetector
diff --git a/centos74-matlab-fludetector/playbook.yml b/centos74-matlab-fludetector/playbook.yml
index 097e9bb..164b5a1 100644
--- a/centos74-matlab-fludetector/playbook.yml
+++ b/centos74-matlab-fludetector/playbook.yml
@@ -9,6 +9,8 @@
     virtualenv_dir: /opt/fludetector/venv
     listen_as: http
     fludetector_user: root
+    fludetector_model: FluDetectorModel-Google201804.tar.gz
+    fludetector_sql: model_data_google_2018_04.sql
     installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
     license_file: license.txt
     fludetector_version: v2.0
@@ -104,10 +106,10 @@
         src: /opt/MATLAB/bin/matlab
         state: link
 
-    - name: Unmount DVDs
+    - name: Unmount DVDs and remove from fstab
       mount:
         path: "{{item}}"
-        state: unmounted
+        state: absent
       with_items:
         - /root/Downloads/MathWorks/R2017a
         - /mnt
@@ -124,25 +126,32 @@
 
     - name: Download GPML package
       unarchive:
-        src: http://gaussianprocess.org/gpml/code/matlab/release/gpml-matlab-v4.1-2017-10-19.tar.gz
+        src: http://gaussianprocess.org/gpml/code/matlab/release/gpml-matlab-v4.2-2018-06-11.tar.gz
         dest: "/opt/fludetector/matlab/gpml"
         remote_src: yes
         extra_opts: "--strip-components=1"
 
-    - name: Upload Matlab artifacts
+    - name: Upload FluDetector artifacts
       copy:
-        src: "{{item}}"
-        dest: "/opt/fludetector/matlab"
-      with_items:
-        - infer_ILI_rate_google_2018_04.m
-        - logit.m
-        - gp_model_all_data_logity1.mat
+        src: "{{fludetector_model}}"
+        dest: /tmp
+
+    - name: Deploy Matlab artifacts
+      unarchive:
+        src: "/tmp/{{fludetector_model}}"
+        exclude: "{{fludetector_sql}}"
+        dest: /opt/fludetector/matlab
+        remote_src: yes
 
     - name: Configure fludetector Flask app
-      command: /opt/fludetector/scripts/init.sh chdir=/opt/fludetector
+      command: /opt/fludetector/scripts/init.sh
+      args:
+        chdir: /opt/fludetector
 
     - name: Upload seed data
-      copy: src=conf/seed.sql dest=/opt/fludetector/seed.sql
+      copy:
+        src: conf/seed.sql
+        dest: /opt/fludetector/seed.sql
 
     - name: Import seed data
       shell: sqlite3 data.db < seed.sql

From d88d4ee6391c6f6f9fdd8e4419ed8c32adc50be5 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 18 Jul 2018 16:08:05 +0100
Subject: [PATCH 05/16] Update README

---
 centos74-matlab-fludetector/README.adoc | 44 +++++++++++++++++++++++--
 centos74-matlab-fludetector/hosts.ini   |  4 +--
 2 files changed, 43 insertions(+), 5 deletions(-)

diff --git a/centos74-matlab-fludetector/README.adoc b/centos74-matlab-fludetector/README.adoc
index d8f5b02..16ced9f 100644
--- a/centos74-matlab-fludetector/README.adoc
+++ b/centos74-matlab-fludetector/README.adoc
@@ -2,6 +2,44 @@
 
 == Requirements
 
-- Vagrant
-- Ansible
-- Matlab
\ No newline at end of file
+- Ansible (version 2.4.2) - https://www.ansible.com/
+- Matlab (version R2017a) - https://uk.mathworks.com/products/matlab.html
+- FluDetector model artifacts (version 2018.04) - tarball archive available by request
+
+== Installation
+
+Save the FluDetector model tarball archive in this directory
+
+== Testing
+
+A Vagrant (https://www.vagrantup.com/) file is provided for local testing
+
+....
+vagrant up
+....
+
+The web interface is available on http://localhost:10080/
+
+== Configuration of FluDetector model
+
+=== Install model data in SQLite instance
+
+An SQL script with all the parameters required to run the model is provided in the tarball archive.
+....
+cd /opt/fludetector
+tar xfO /tmp/FluDetectorModel-Google201804.tar.gz --wildcards '*.sql' | sudo sqlite3 data.db
+....
+
+=== Calculate model scores 
+
+....
+cd /opt/fludetector
+sudo sed -i 's/^\(GOOGLE_API_KEY=\).*/\1APIKEY/' .env
+sudo ./scripts/run.sh runmodel 1 --start [yyyy-mm-dd] --end [yyyy-mm-dd]
+....
+
+=== Start scheduler for calculation of model scores
+
+....
+sudo supervisorctl restart fludetector fludetector-google
+....
\ No newline at end of file
diff --git a/centos74-matlab-fludetector/hosts.ini b/centos74-matlab-fludetector/hosts.ini
index 1f5f51a..78f4ece 100644
--- a/centos74-matlab-fludetector/hosts.ini
+++ b/centos74-matlab-fludetector/hosts.ini
@@ -1,6 +1,6 @@
 [vagrant]
-127.0.0.1 ansible_connection=local
-localhost ansible_connection=local
+127.0.0.1:2222 ansible_connection=local
+localhost:2222 ansible_connection=local
 
 [production]
 fmdetect.cs.ucl.ac.uk

From 3acf7dd7fafb4b8a3d2eb47b2e4de4733db5755d Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 18 Jul 2018 16:22:50 +0100
Subject: [PATCH 06/16] Update README

---
 centos74-matlab-fludetector/README.adoc | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/centos74-matlab-fludetector/README.adoc b/centos74-matlab-fludetector/README.adoc
index 16ced9f..942ec49 100644
--- a/centos74-matlab-fludetector/README.adoc
+++ b/centos74-matlab-fludetector/README.adoc
@@ -1,5 +1,7 @@
 = centos74-matlab-fludetector
 
+This Ansible playbook provisions a CentOS 7.4 machine with a single-node instance of the FluDetector app (https://github.com/UCL/fludetector-flask)
+
 == Requirements
 
 - Ansible (version 2.4.2) - https://www.ansible.com/
@@ -8,11 +10,16 @@
 
 == Installation
 
-Save the FluDetector model tarball archive in this directory
+Save the FluDetector model tarball archive in this directory, edit `hosts.ini` inventory file to set the hostname of the productive system 
+and execute the ansible playbook to install the FluDetector app.
+
+....
+ansible-playbook -i hosts.ini --limit 'productive' -u [remoteuser] -b -k -K playbook.yml
+....
 
 == Testing
 
-A Vagrant (https://www.vagrantup.com/) file is provided for local testing
+A Vagrant (https://www.vagrantup.com/) file is provided for local testing. It requires a CentOS 7.4 box installed with the name 'centos-7.4'. Fire up the vagrant up to test the installation:
 
 ....
 vagrant up
@@ -32,6 +39,7 @@ tar xfO /tmp/FluDetectorModel-Google201804.tar.gz --wildcards '*.sql' | sudo sql
 
 === Calculate model scores 
 
+Install the Google API key in the `.env` file and run a model score calculation for dates in the past.
 ....
 cd /opt/fludetector
 sudo sed -i 's/^\(GOOGLE_API_KEY=\).*/\1APIKEY/' .env
@@ -40,6 +48,7 @@ sudo ./scripts/run.sh runmodel 1 --start [yyyy-mm-dd] --end [yyyy-mm-dd]
 
 === Start scheduler for calculation of model scores
 
+Once the calculation of scores for past dates is completed, start the scheduler to run these calculations automatically on a daily basis.
 ....
 sudo supervisorctl restart fludetector fludetector-google
 ....
\ No newline at end of file

From 9aece19570c17d2a5afdb54379da33e4232bd911 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 18 Jul 2018 16:50:29 +0100
Subject: [PATCH 07/16] Update README with information about installation of
 Matlab

---
 centos74-matlab-fludetector/README.adoc | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/centos74-matlab-fludetector/README.adoc b/centos74-matlab-fludetector/README.adoc
index 942ec49..38bc4de 100644
--- a/centos74-matlab-fludetector/README.adoc
+++ b/centos74-matlab-fludetector/README.adoc
@@ -8,6 +8,20 @@ This Ansible playbook provisions a CentOS 7.4 machine with a single-node instanc
 - Matlab (version R2017a) - https://uk.mathworks.com/products/matlab.html
 - FluDetector model artifacts (version 2018.04) - tarball archive available by request
 
+=== Matlab
+
+The playbook installs Matlab from the DVD iso files. Make sure the following files are present in the playbook directory:
+
+- `R2017a_glnxa64_dvd1.iso`
+- `R2017a_glnxa64_dvd2.iso`
+- `installationKey.txt` (https://uk.mathworks.com/help/install/ug/install-and-activate-without-an-internet-connection.html)
+- `license.txt` (http://uk.mathworks.com/help/install/ug/install-license-manager-using-a-file-installation-key.html)
+
+[NOTE]
+====
+The `license.txt` file is required for networked installations of Matlab. Edit the playbook if using a different installation method for Matlab.
+====
+
 == Installation
 
 Save the FluDetector model tarball archive in this directory, edit `hosts.ini` inventory file to set the hostname of the productive system 

From e940cd047401e7dc59be655d09d85601becc556a Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 18 Jul 2018 16:54:51 +0100
Subject: [PATCH 08/16] Configure admonitions

---
 centos74-matlab-fludetector/README.adoc | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/centos74-matlab-fludetector/README.adoc b/centos74-matlab-fludetector/README.adoc
index 38bc4de..f3cb6f5 100644
--- a/centos74-matlab-fludetector/README.adoc
+++ b/centos74-matlab-fludetector/README.adoc
@@ -1,3 +1,11 @@
+ifdef::env-github[]
+:tip-caption: :bulb:
+:note-caption: :information_source:
+:important-caption: :heavy_exclamation_mark:
+:caution-caption: :fire:
+:warning-caption: :warning:
+endif::[]
+
 = centos74-matlab-fludetector
 
 This Ansible playbook provisions a CentOS 7.4 machine with a single-node instance of the FluDetector app (https://github.com/UCL/fludetector-flask)

From 1453d9576c7870d5332c79e956b38a1a9720cddf Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 8 Aug 2018 17:26:57 +0100
Subject: [PATCH 09/16] New fludetector version

---
 centos74-fludetector3/Vagrantfile            | 17 +++++
 centos74-fludetector3/conf/nginx.conf        | 19 ++++++
 centos74-fludetector3/conf/supervisor.ini.j2 |  4 ++
 centos74-fludetector3/playbook.yml           | 65 ++++++++++++++++++++
 4 files changed, 105 insertions(+)
 create mode 100644 centos74-fludetector3/Vagrantfile
 create mode 100644 centos74-fludetector3/conf/nginx.conf
 create mode 100644 centos74-fludetector3/conf/supervisor.ini.j2
 create mode 100644 centos74-fludetector3/playbook.yml

diff --git a/centos74-fludetector3/Vagrantfile b/centos74-fludetector3/Vagrantfile
new file mode 100644
index 0000000..8c733de
--- /dev/null
+++ b/centos74-fludetector3/Vagrantfile
@@ -0,0 +1,17 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+Vagrant.configure("2") do |config|
+
+  config.vm.box = "centos-7.4"
+
+  config.vm.provision "ansible" do |ansible|
+    ansible.playbook = "playbook.yml"
+    ansible.compatibility_mode = "2.0"
+  end
+
+  config.vm.network "forwarded_port", guest: 80, host: 10080
+
+  config.ssh.insert_key = false
+  
+end
diff --git a/centos74-fludetector3/conf/nginx.conf b/centos74-fludetector3/conf/nginx.conf
new file mode 100644
index 0000000..64a4468
--- /dev/null
+++ b/centos74-fludetector3/conf/nginx.conf
@@ -0,0 +1,19 @@
+upstream gunicorn_server {
+  server unix:/var/run/gunicorn.sock fail_timeout=0;
+}
+
+server {
+
+  server_name localhost;
+
+  add_header X-Frame-Options "SAMEORIGIN";
+  add_header X-XSS-Protection "1; mode=block";
+  add_header X-Content-Type-Options nosniff;
+  
+  location / {
+    proxy_pass http://gunicorn_server;
+    proxy_set_header Host localhost;
+    proxy_set_header X-Forwarded-For $remote_addr;
+  }
+
+}
\ No newline at end of file
diff --git a/centos74-fludetector3/conf/supervisor.ini.j2 b/centos74-fludetector3/conf/supervisor.ini.j2
new file mode 100644
index 0000000..9f52897
--- /dev/null
+++ b/centos74-fludetector3/conf/supervisor.ini.j2
@@ -0,0 +1,4 @@
+[program:fludetector]
+command = /opt/fludetector/scripts/serve.sh
+directory = /opt/fludetector
+user = {{fludetector_user}}
\ No newline at end of file
diff --git a/centos74-fludetector3/playbook.yml b/centos74-fludetector3/playbook.yml
new file mode 100644
index 0000000..15a869c
--- /dev/null
+++ b/centos74-fludetector3/playbook.yml
@@ -0,0 +1,65 @@
+---
+- hosts: localhost
+  user: vagrant
+
+- hosts: all
+  become: True
+  become_method: sudo
+  vars:
+    virtualenv_dir: /opt/fludetector/venv
+    listen_as: http
+    fludetector_user: root
+    fludetector_model: FluDetectorModel-Google201804.tar.gz
+    fludetector_sql: model_data_google_2018_04.sql
+    installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
+    license_file: license.txt
+    fludetector_version: v2.0
+    model_id: 1
+  tasks:
+    - name: Install EPEL repository
+      yum: name=epel-release state=present
+
+    - name: Install Python 3.4 and Pip
+      yum: name={{item}} state=present
+      with_items:
+        - python34
+        - python34-pip
+
+    - name: Install SQLite3 and lzop
+      yum: name={{item}} state=latest
+      with_items:
+        - sqlite
+        - lzop
+
+    - name: Setup a Python 3.4 environment
+      shell: pyvenv {{virtualenv_dir}}
+
+    - name: Create fludetector log directory
+      file: path=/opt/fludetector/logs state=directory
+
+    - name: Deploy fludetector Flask app
+      unarchive: src=https://github.com/UCL/fludetector-api-flask/archive/v1.0-cr1.tar.gz dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
+
+    - name: Install Supervisor
+      yum: name=supervisor state=present
+
+    - name: Deploy Supervisor configuration for Flask-Gunicorn app
+      template: src=conf/supervisor.ini.j2 dest=/etc/supervisord.d/fludetector.ini
+      
+    - name: Install Nginx
+      yum: name=nginx state=present
+
+    - name: Upload Nginx configuration for fludetector
+      copy: src=conf/nginx.conf dest=/etc/nginx/conf.d/fludetector.conf
+
+    - name: Enable nginx port in firewall
+      command: firewall-cmd --zone=public --permanent --add-service={{listen_as}}
+
+    - name: Enable nginx
+      systemd: name=nginx state=started enabled=yes
+
+    - name: Start supervisord
+      systemd: name=supervisord state=started enabled=yes
+
+    - name: Restart firewalld
+      systemd: name=firewalld state=restarted

From 78b02e6e66c7f1b5b1dfd8183fe808f44804de06 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Thu, 9 Aug 2018 13:04:14 +0100
Subject: [PATCH 10/16] Complete installation of Flask app

---
 centos74-fludetector3/playbook.yml | 161 ++++++++++++++++++++++++++---
 1 file changed, 146 insertions(+), 15 deletions(-)

diff --git a/centos74-fludetector3/playbook.yml b/centos74-fludetector3/playbook.yml
index 15a869c..80d7296 100644
--- a/centos74-fludetector3/playbook.yml
+++ b/centos74-fludetector3/playbook.yml
@@ -6,27 +6,34 @@
   become: True
   become_method: sudo
   vars:
-    virtualenv_dir: /opt/fludetector/venv
+    virtualenv_dir: /opt/fludetector/flask/venv
     listen_as: http
     fludetector_user: root
-    fludetector_model: FluDetectorModel-Google201804.tar.gz
-    fludetector_sql: model_data_google_2018_04.sql
+    fludetector_model: FluDetectorModel-Google201807.tar.gz
+    fludetector_sql: model_data_google_2018_07.sql
+    matlab_localdir: /Volumes/cs-iso/Linux-Software/Matlab/
     installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
     license_file: license.txt
     fludetector_version: v2.0
     model_id: 1
   tasks:
     - name: Install EPEL repository
-      yum: name=epel-release state=present
+      yum:
+        name: epel-release
+        state: present
 
     - name: Install Python 3.4 and Pip
-      yum: name={{item}} state=present
+      yum:
+        name: "{{item}}"
+        state: present
       with_items:
         - python34
         - python34-pip
 
     - name: Install SQLite3 and lzop
-      yum: name={{item}} state=latest
+      yum:
+        name: "{{item}}"
+        state: latest
       with_items:
         - sqlite
         - lzop
@@ -35,31 +42,155 @@
       shell: pyvenv {{virtualenv_dir}}
 
     - name: Create fludetector log directory
-      file: path=/opt/fludetector/logs state=directory
+      file:
+        path: /opt/fludetector/flask/logs
+        state: directory
 
     - name: Deploy fludetector Flask app
-      unarchive: src=https://github.com/UCL/fludetector-api-flask/archive/v1.0-cr1.tar.gz dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
+      unarchive:
+        src: https://github.com/UCL/fludetector-api-flask/archive/v1.0-cr1.tar.gz
+        dest: /opt/fludetector/flask/
+        remote_src: yes
+        extra_opts: "--strip-components=1"
 
     - name: Install Supervisor
-      yum: name=supervisor state=present
+      yum:
+        name: supervisor
+        state: present
 
     - name: Deploy Supervisor configuration for Flask-Gunicorn app
-      template: src=conf/supervisor.ini.j2 dest=/etc/supervisord.d/fludetector.ini
+      template:
+        src: conf/supervisor.ini.j2
+        dest: /etc/supervisord.d/fludetector.ini
       
     - name: Install Nginx
-      yum: name=nginx state=present
+      yum:
+        name: nginx
+        state: present
 
     - name: Upload Nginx configuration for fludetector
-      copy: src=conf/nginx.conf dest=/etc/nginx/conf.d/fludetector.conf
+      copy:
+        src: conf/nginx.conf
+        dest: /etc/nginx/conf.d/fludetector.conf
 
     - name: Enable nginx port in firewall
       command: firewall-cmd --zone=public --permanent --add-service={{listen_as}}
 
     - name: Enable nginx
-      systemd: name=nginx state=started enabled=yes
+      systemd:
+        name: nginx
+        state: started
+        enabled: yes
 
     - name: Start supervisord
-      systemd: name=supervisord state=started enabled=yes
+      systemd:
+        name: supervisord
+        state: started
+        enabled: yes
 
     - name: Restart firewalld
-      systemd: name=firewalld state=restarted
+      systemd:
+        name: firewalld
+        state: restarted
+
+    - name: Install requirements for Matlab
+      yum:
+        name: "{{item}}"
+        state: present
+      with_items:
+        - libX11
+        - libXext
+        - libXt
+
+    - name: Create Downloads directory if it doesn't exist
+      file:
+        path: /root/Downloads
+        state: directory
+        
+    - name: Copy Matlab DVDs
+      copy:
+        src: "{{matlab_localdir}}/{{item}}"
+        dest: /root/Downloads/
+      with_items:
+        - R2017a_glnxa64_dvd1.iso
+        - R2017a_glnxa64_dvd2.iso
+
+    - name: Mount Matlab DVD 1
+      mount:
+        path: /mnt
+        src: /root/Downloads/R2017a_glnxa64_dvd1.iso
+        fstype: auto
+        opts: loop
+        state: mounted
+
+    - name: Create directory for Matlab archives install
+      file:
+        path: /root/Downloads/MathWorks/R2017a
+        state: directory
+
+    - name: Mount Matlab DVD 2
+      mount:
+        path: /root/Downloads/MathWorks/R2017a
+        src: /root/Downloads/R2017a_glnxa64_dvd1.iso
+        fstype: auto
+        opts: loop
+        state: mounted
+
+    - name: Copy license file
+      copy:
+        src: "{{license_file}}"
+        dest: /root/
+
+    - name: Install Matlab
+      command: /mnt/install -mode silent -agreeToLicense yes -destinationFolder /opt/MATLAB -fileInstallationKey {{installation_key_file}} -licensePath /root/{{license_file}} -product.MATLAB
+
+    - name: Create symlink to Matlab executable
+      file:
+        path: /usr/local/bin/matlab
+        src: /opt/MATLAB/bin/matlab
+        state: link
+
+    - name: Unmount DVDs and remove from fstab
+      mount:
+        path: "{{item}}"
+        state: absent
+      with_items:
+        - /root/Downloads/MathWorks/R2017a
+        - /mnt
+
+    - name: Delete Matlab iso files
+      file:
+        path: "/root/Downloads/{{item}}"
+        state: absent
+      with_items:
+        - R2017a_glnxa64_dvd1.iso
+        - R2017a_glnxa64_dvd2.iso
+
+    - name: Install Matlab engine for Python
+      command: python3 setup.py install --prefix {{virtualenv_dir}}
+      args:
+        chdir: /opt/MATLAB/extern/engines/python
+
+    - name: Create directory for GPML package
+      file:
+        path: "/opt/fludetector/flask/matlab/gpml"
+        state: directory
+
+    - name: Download GPML package
+      unarchive:
+        src: http://gaussianprocess.org/gpml/code/matlab/release/gpml-matlab-v4.2-2018-06-11.tar.gz
+        dest: "/opt/fludetector/flask/matlab/gpml"
+        remote_src: yes
+        extra_opts: "--strip-components=1"
+
+    - name: Upload FluDetector artifacts
+      copy:
+        src: "{{fludetector_model}}"
+        dest: /tmp
+
+    - name: Deploy Matlab artifacts
+      unarchive:
+        src: "/tmp/{{fludetector_model}}"
+        exclude: "{{fludetector_sql}}"
+        dest: /opt/fludetector/flask/matlab
+        remote_src: yes

From f29a0e490cc6d241470835414d7ca3059b2335d4 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Thu, 13 Sep 2018 18:31:16 +0100
Subject: [PATCH 11/16] WIP: Playbook for installing FluDetector app and Octave

---
 centos74-octave-fludetector/.gitignore        |   4 +
 centos74-octave-fludetector/README.adoc       |  66 +++++++++++
 centos74-octave-fludetector/Vagrantfile       |  15 +++
 centos74-octave-fludetector/conf/env          |   4 +
 centos74-octave-fludetector/conf/nginx.conf   |  19 ++++
 centos74-octave-fludetector/conf/seed.sql     |  13 +++
 .../conf/supervisor.ini.j2                    |   9 ++
 centos74-octave-fludetector/hosts.ini         |   6 +
 centos74-octave-fludetector/playbook.yml      | 105 ++++++++++++++++++
 9 files changed, 241 insertions(+)
 create mode 100644 centos74-octave-fludetector/.gitignore
 create mode 100644 centos74-octave-fludetector/README.adoc
 create mode 100644 centos74-octave-fludetector/Vagrantfile
 create mode 100644 centos74-octave-fludetector/conf/env
 create mode 100644 centos74-octave-fludetector/conf/nginx.conf
 create mode 100644 centos74-octave-fludetector/conf/seed.sql
 create mode 100644 centos74-octave-fludetector/conf/supervisor.ini.j2
 create mode 100644 centos74-octave-fludetector/hosts.ini
 create mode 100644 centos74-octave-fludetector/playbook.yml

diff --git a/centos74-octave-fludetector/.gitignore b/centos74-octave-fludetector/.gitignore
new file mode 100644
index 0000000..7ec3e16
--- /dev/null
+++ b/centos74-octave-fludetector/.gitignore
@@ -0,0 +1,4 @@
+.DS_Store
+
+FluDetectorModel-Google201804.tar.gz
+*.rpm
diff --git a/centos74-octave-fludetector/README.adoc b/centos74-octave-fludetector/README.adoc
new file mode 100644
index 0000000..8e33ee0
--- /dev/null
+++ b/centos74-octave-fludetector/README.adoc
@@ -0,0 +1,66 @@
+ifdef::env-github[]
+:tip-caption: :bulb:
+:note-caption: :information_source:
+:important-caption: :heavy_exclamation_mark:
+:caution-caption: :fire:
+:warning-caption: :warning:
+endif::[]
+
+= centos74-octave-fludetector
+
+This Ansible playbook provisions a CentOS 7.4 machine with a single-node instance of the FluDetector app (https://github.com/UCL/fludetector-flask)
+
+== Requirements
+
+- Ansible (version 2.4.2) - https://www.ansible.com/
+- Octave 4.x for CentOS - rpm archives available
+- FluDetector model artifacts (version 2018.04) - tarball archive available by request
+
+=== Octave
+
+The playbook installs Octave from the rpm file. Make sure the file `octave-4.2.2-6.el7.centos.1.x86_64.rpm` is present in the playbook directory:
+
+== Installation
+
+Save the FluDetector model tarball archive in this directory, edit `hosts.ini` inventory file to set the hostname of the productive system 
+and execute the ansible playbook to install the FluDetector app.
+
+....
+ansible-playbook -i hosts.ini --limit 'productive' -u [remoteuser] -b -k -K playbook.yml
+....
+
+== Testing
+
+A Vagrant (https://www.vagrantup.com/) file is provided for local testing. It requires a CentOS 7.4 box installed with the name 'centos-7.4'. Fire up the vagrant up to test the installation:
+
+....
+vagrant up
+....
+
+The web interface is available on http://localhost:10080/
+
+== Configuration of FluDetector model
+
+=== Install model data in SQLite instance
+
+An SQL script with all the parameters required to run the model is provided in the tarball archive.
+....
+cd /opt/fludetector
+tar xfO /tmp/FluDetectorModel-Google201804.tar.gz --wildcards '*.sql' | sudo sqlite3 data.db
+....
+
+=== Calculate model scores 
+
+Install the Google API key in the `.env` file and run a model score calculation for dates in the past.
+....
+cd /opt/fludetector
+sudo sed -i 's/^\(GOOGLE_API_KEY=\).*/\1APIKEY/' .env
+sudo ./scripts/run.sh runmodel 1 --start [yyyy-mm-dd] --end [yyyy-mm-dd]
+....
+
+=== Start scheduler for calculation of model scores
+
+Once the calculation of scores for past dates is completed, start the scheduler to run these calculations automatically on a daily basis.
+....
+sudo supervisorctl restart fludetector fludetector-google
+....
\ No newline at end of file
diff --git a/centos74-octave-fludetector/Vagrantfile b/centos74-octave-fludetector/Vagrantfile
new file mode 100644
index 0000000..1c01328
--- /dev/null
+++ b/centos74-octave-fludetector/Vagrantfile
@@ -0,0 +1,15 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+Vagrant.configure("2") do |config|
+
+  config.vm.box = "centos-7.4"
+
+  config.vm.provision "ansible" do |ansible|
+    ansible.playbook = "playbook.yml"
+    ansible.compatibility_mode = "2.0"
+  end
+
+  config.vm.network "forwarded_port", guest: 80, host: 10080
+
+end
diff --git a/centos74-octave-fludetector/conf/env b/centos74-octave-fludetector/conf/env
new file mode 100644
index 0000000..258de38
--- /dev/null
+++ b/centos74-octave-fludetector/conf/env
@@ -0,0 +1,4 @@
+GOOGLE_API_KEY=invalidcredential
+ADMIN_USERNAME=invalidcredential
+ADMIN_PASSWORD=invalidcredential
+SECRET_KEY=invalidcredential
\ No newline at end of file
diff --git a/centos74-octave-fludetector/conf/nginx.conf b/centos74-octave-fludetector/conf/nginx.conf
new file mode 100644
index 0000000..64a4468
--- /dev/null
+++ b/centos74-octave-fludetector/conf/nginx.conf
@@ -0,0 +1,19 @@
+upstream gunicorn_server {
+  server unix:/var/run/gunicorn.sock fail_timeout=0;
+}
+
+server {
+
+  server_name localhost;
+
+  add_header X-Frame-Options "SAMEORIGIN";
+  add_header X-XSS-Protection "1; mode=block";
+  add_header X-Content-Type-Options nosniff;
+  
+  location / {
+    proxy_pass http://gunicorn_server;
+    proxy_set_header Host localhost;
+    proxy_set_header X-Forwarded-For $remote_addr;
+  }
+
+}
\ No newline at end of file
diff --git a/centos74-octave-fludetector/conf/seed.sql b/centos74-octave-fludetector/conf/seed.sql
new file mode 100644
index 0000000..8ef649b
--- /dev/null
+++ b/centos74-octave-fludetector/conf/seed.sql
@@ -0,0 +1,13 @@
+BEGIN TRANSACTION;
+INSERT INTO "model" VALUES(1,'Dummy Google Data','google',1,'nonexistent_function,1');
+INSERT INTO "model_score" VALUES('2018-01-01','e',0.0,1);
+INSERT INTO "model_score" VALUES('2018-01-02','e',0.2,1);
+INSERT INTO "model_score" VALUES('2018-01-03','e',0.4,1);
+INSERT INTO "model_score" VALUES('2018-01-04','e',0.6,1);
+INSERT INTO "model_score" VALUES('2018-01-05','e',0.8,1);
+INSERT INTO "model_score" VALUES('2018-01-06','e',0.9,1);
+INSERT INTO "model_score" VALUES('2018-01-07','e',0.7,1);
+INSERT INTO "model_score" VALUES('2018-01-08','e',0.5,1);
+INSERT INTO "model_score" VALUES('2018-01-09','e',0.3,1);
+INSERT INTO "model_score" VALUES('2018-01-10','e',0.1,1);
+COMMIT;
diff --git a/centos74-octave-fludetector/conf/supervisor.ini.j2 b/centos74-octave-fludetector/conf/supervisor.ini.j2
new file mode 100644
index 0000000..f0f64f9
--- /dev/null
+++ b/centos74-octave-fludetector/conf/supervisor.ini.j2
@@ -0,0 +1,9 @@
+[program:fludetector]
+command = /opt/fludetector/scripts/serve.sh
+directory = /opt/fludetector
+user = {{fludetector_user}}
+
+[program:fludetector-google]
+command = /opt/fludetector/scripts/run.sh runmodelscheduler {{model_id}} '30 14 * * *'
+directory = /opt/fludetector
+user = {{fludetector_user}}
diff --git a/centos74-octave-fludetector/hosts.ini b/centos74-octave-fludetector/hosts.ini
new file mode 100644
index 0000000..78f4ece
--- /dev/null
+++ b/centos74-octave-fludetector/hosts.ini
@@ -0,0 +1,6 @@
+[vagrant]
+127.0.0.1:2222 ansible_connection=local
+localhost:2222 ansible_connection=local
+
+[production]
+fmdetect.cs.ucl.ac.uk
diff --git a/centos74-octave-fludetector/playbook.yml b/centos74-octave-fludetector/playbook.yml
new file mode 100644
index 0000000..2a2922f
--- /dev/null
+++ b/centos74-octave-fludetector/playbook.yml
@@ -0,0 +1,105 @@
+---
+- hosts: localhost
+  user: vagrant
+
+- hosts: all
+  become: True
+  become_method: sudo
+  vars:
+    virtualenv_dir: /opt/fludetector/venv
+    listen_as: http
+    fludetector_user: root
+    fludetector_model: FluDetectorModel-Google201804.tar.gz
+    fludetector_sql: model_data_google_2018_04.sql
+    installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
+    license_file: license.txt
+    fludetector_version: v2.0
+    model_id: 1
+  tasks:
+    - name: Install EPEL repository
+      yum: name=epel-release state=present
+
+    - name: Install Python 2.7 and Pip
+      yum: name={{item}} state=present
+      with_items:
+        - python
+        - python-pip
+
+    - name: Install SQLite3 and lzop
+      yum: name={{item}} state=latest
+      with_items:
+        - sqlite
+        - lzop
+
+    - name: Update pip and virtualenv
+      pip: name={{item}} state=latest
+      with_items:
+        - pip
+        - virtualenv
+      
+    - name: Setup a Python 2.7 environment
+      shell: virtualenv -p /usr/bin/python2.7 {{virtualenv_dir}}
+
+    - name: Create fludetector log directory
+      file: path=/opt/fludetector/logs state=directory
+
+    - name: Deploy fludetector Flask app
+      unarchive: src="https://github.com/UCL/fludetector-flask/archive/{{fludetector_version}}.tar.gz" dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
+
+    - name: Copy env file
+      copy: src=conf/env dest=/opt/fludetector/.env
+
+    - name: Install Nginx
+      yum:
+        name: nginx
+        state: present
+
+    - name: Upload Nginx configuration for fludetector
+      copy:
+        src: conf/nginx.conf
+        dest: /etc/nginx/conf.d/fludetector.conf
+
+    - name: Enable nginx port in firewall
+      command: firewall-cmd --zone=public --permanent --add-service={{listen_as}}
+
+    - name: Restart firewalld
+      systemd:
+        name: firewalld
+        state: restarted
+
+    - name: Upload Octave rpm
+      copy:
+        src: octave-4.2.2-6.el7.centos.1.x86_64.rpm
+        dest: /tmp/
+
+    - name: Install Octave
+      yum:
+        name: /tmp/octave-4.2.2-6.el7.centos.1.x86_64.rpm
+        state: present
+
+    - name: Create directory for GPML package
+      file:
+        path: "/opt/fludetector/octave/gpml"
+        state: directory
+
+    - name: Download GPML package
+      unarchive:
+        src: http://gaussianprocess.org/gpml/code/matlab/release/gpml-matlab-v4.2-2018-06-11.tar.gz
+        dest: "/opt/fludetector/octave/gpml"
+        remote_src: yes
+        extra_opts: "--strip-components=1"
+
+    - name: Upload FluDetector artifacts
+      copy:
+        src: "{{fludetector_model}}"
+        dest: /tmp
+
+    - name: Deploy Matlab artifacts
+      unarchive:
+        src: "/tmp/{{fludetector_model}}"
+        exclude: "{{fludetector_sql}}"
+        dest: /opt/fludetector/octave
+        remote_src: yes
+
+    - name: Start nginx
+      systemd: name=nginx state=started enabled=yes

From 5bc8e5ed93ed80fb262ac677924dd6311af37fb6 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Fri, 14 Sep 2018 14:16:49 +0100
Subject: [PATCH 12/16] Add installation of Octave

---
 centos74-octave-fludetector/README.adoc  | 9 +++++++++
 centos74-octave-fludetector/conf/env     | 3 ++-
 centos74-octave-fludetector/playbook.yml | 2 +-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/centos74-octave-fludetector/README.adoc b/centos74-octave-fludetector/README.adoc
index 8e33ee0..f500817 100644
--- a/centos74-octave-fludetector/README.adoc
+++ b/centos74-octave-fludetector/README.adoc
@@ -41,6 +41,15 @@ The web interface is available on http://localhost:10080/
 
 == Configuration of FluDetector model
 
+=== Initial configuration
+
+A script is provided to configure the application
+
+````
+cd /opt/fludetector
+./scripts/init.sh
+````
+
 === Install model data in SQLite instance
 
 An SQL script with all the parameters required to run the model is provided in the tarball archive.
diff --git a/centos74-octave-fludetector/conf/env b/centos74-octave-fludetector/conf/env
index 258de38..1ac8a83 100644
--- a/centos74-octave-fludetector/conf/env
+++ b/centos74-octave-fludetector/conf/env
@@ -1,4 +1,5 @@
 GOOGLE_API_KEY=invalidcredential
 ADMIN_USERNAME=invalidcredential
 ADMIN_PASSWORD=invalidcredential
-SECRET_KEY=invalidcredential
\ No newline at end of file
+SECRET_KEY=invalidcredential
+MODEL_ENGINE=octave
diff --git a/centos74-octave-fludetector/playbook.yml b/centos74-octave-fludetector/playbook.yml
index 2a2922f..ce64428 100644
--- a/centos74-octave-fludetector/playbook.yml
+++ b/centos74-octave-fludetector/playbook.yml
@@ -13,7 +13,7 @@
     fludetector_sql: model_data_google_2018_04.sql
     installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
     license_file: license.txt
-    fludetector_version: v2.0
+    fludetector_version: v2.1
     model_id: 1
   tasks:
     - name: Install EPEL repository

From 9c42b210a485cc4ddaab9403283c23e9acd68b43 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Fri, 14 Sep 2018 14:20:40 +0100
Subject: [PATCH 13/16] Add installation of Octave

---
 centos74-octave-fludetector/README.adoc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/centos74-octave-fludetector/README.adoc b/centos74-octave-fludetector/README.adoc
index f500817..c50c29d 100644
--- a/centos74-octave-fludetector/README.adoc
+++ b/centos74-octave-fludetector/README.adoc
@@ -45,10 +45,10 @@ The web interface is available on http://localhost:10080/
 
 A script is provided to configure the application
 
-````
+....
 cd /opt/fludetector
 ./scripts/init.sh
-````
+....
 
 === Install model data in SQLite instance
 

From 74875d1218d5d86dd3b4493d5a2bc02b04b242d8 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Fri, 14 Sep 2018 16:05:04 +0100
Subject: [PATCH 14/16] Add installation and configuration of Supervisor

---
 centos74-octave-fludetector/README.adoc  |  2 +-
 centos74-octave-fludetector/playbook.yml | 52 ++++++++++++++++++------
 2 files changed, 41 insertions(+), 13 deletions(-)

diff --git a/centos74-octave-fludetector/README.adoc b/centos74-octave-fludetector/README.adoc
index c50c29d..573ef7a 100644
--- a/centos74-octave-fludetector/README.adoc
+++ b/centos74-octave-fludetector/README.adoc
@@ -71,5 +71,5 @@ sudo ./scripts/run.sh runmodel 1 --start [yyyy-mm-dd] --end [yyyy-mm-dd]
 
 Once the calculation of scores for past dates is completed, start the scheduler to run these calculations automatically on a daily basis.
 ....
-sudo supervisorctl restart fludetector fludetector-google
+sudo systemctl start supervisord
 ....
\ No newline at end of file
diff --git a/centos74-octave-fludetector/playbook.yml b/centos74-octave-fludetector/playbook.yml
index ce64428..65fe128 100644
--- a/centos74-octave-fludetector/playbook.yml
+++ b/centos74-octave-fludetector/playbook.yml
@@ -11,28 +11,35 @@
     fludetector_user: root
     fludetector_model: FluDetectorModel-Google201804.tar.gz
     fludetector_sql: model_data_google_2018_04.sql
-    installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
-    license_file: license.txt
     fludetector_version: v2.1
+    octave_version: 4.2.2-6.el7.centos.1
     model_id: 1
   tasks:
     - name: Install EPEL repository
-      yum: name=epel-release state=present
+      yum:
+        name: epel-release
+        state: present
 
     - name: Install Python 2.7 and Pip
-      yum: name={{item}} state=present
+      yum:
+        name: "{{item}}"
+        state: present
       with_items:
         - python
         - python-pip
 
     - name: Install SQLite3 and lzop
-      yum: name={{item}} state=latest
+      yum:
+        name: "{{item}}"
+        state: latest
       with_items:
         - sqlite
         - lzop
 
     - name: Update pip and virtualenv
-      pip: name={{item}} state=latest
+      pip:
+        name: "{{item}}"
+        state: latest
       with_items:
         - pip
         - virtualenv
@@ -41,13 +48,31 @@
       shell: virtualenv -p /usr/bin/python2.7 {{virtualenv_dir}}
 
     - name: Create fludetector log directory
-      file: path=/opt/fludetector/logs state=directory
+      file:
+        path: /opt/fludetector/logs
+        state: directory
 
     - name: Deploy fludetector Flask app
-      unarchive: src="https://github.com/UCL/fludetector-flask/archive/{{fludetector_version}}.tar.gz" dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
+      unarchive:
+        src: "https://github.com/UCL/fludetector-flask/archive/{{fludetector_version}}.tar.gz"
+        dest: /opt/fludetector/
+        remote_src: yes
+        extra_opts: "--strip-components=1"
 
     - name: Copy env file
-      copy: src=conf/env dest=/opt/fludetector/.env
+      copy:
+        src: conf/env
+        dest: /opt/fludetector/.env
+
+    - name: Install Supervisor
+      yum:
+        name: supervisor
+        state: present
+
+    - name: Deploy Supervisor configuration for Flask-Gunicorn app
+      template:
+        src: conf/supervisor.ini.j2
+        dest: /etc/supervisord.d/fludetector.ini
 
     - name: Install Nginx
       yum:
@@ -69,12 +94,12 @@
 
     - name: Upload Octave rpm
       copy:
-        src: octave-4.2.2-6.el7.centos.1.x86_64.rpm
+        src: "octave-{{octave_version}}.x86_64.rpm"
         dest: /tmp/
 
     - name: Install Octave
       yum:
-        name: /tmp/octave-4.2.2-6.el7.centos.1.x86_64.rpm
+        name: "/tmp/octave-{{octave_version}}.x86_64.rpm"
         state: present
 
     - name: Create directory for GPML package
@@ -102,4 +127,7 @@
         remote_src: yes
 
     - name: Start nginx
-      systemd: name=nginx state=started enabled=yes
+      systemd:
+        name: nginx
+        state: started
+        enabled: yes

From 3ac36100439317a4f81817b57e53d11b17ddd876 Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Wed, 19 Sep 2018 14:41:07 +0100
Subject: [PATCH 15/16] Update version of FluDetector app

---
 centos74-fludetector/playbook.yml        | 2 +-
 centos74-matlab-fludetector/playbook.yml | 2 +-
 centos74-octave-fludetector/playbook.yml | 8 +++++++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/centos74-fludetector/playbook.yml b/centos74-fludetector/playbook.yml
index d4ec63b..1f10fed 100644
--- a/centos74-fludetector/playbook.yml
+++ b/centos74-fludetector/playbook.yml
@@ -38,7 +38,7 @@
       file: path=/opt/fludetector/logs state=directory
 
     - name: Deploy fludetector Flask app
-      unarchive: src=https://github.com/UCL/fludetector-flask/archive/v1.1.tar.gz dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
+      unarchive: src=https://github.com/UCL/fludetector-flask/archive/v2.2.tar.gz dest=/opt/fludetector/ remote_src=yes extra_opts="--strip-components=1"
 
     - name: Copy env file
       copy: src=conf/env dest=/opt/fludetector/.env
diff --git a/centos74-matlab-fludetector/playbook.yml b/centos74-matlab-fludetector/playbook.yml
index 164b5a1..1e6748d 100644
--- a/centos74-matlab-fludetector/playbook.yml
+++ b/centos74-matlab-fludetector/playbook.yml
@@ -13,7 +13,7 @@
     fludetector_sql: model_data_google_2018_04.sql
     installation_key_file: "{{lookup('file', 'installationKey.txt')}}"
     license_file: license.txt
-    fludetector_version: v2.0
+    fludetector_version: v2.2
     model_id: 1
   tasks:
     - name: Install EPEL repository
diff --git a/centos74-octave-fludetector/playbook.yml b/centos74-octave-fludetector/playbook.yml
index 65fe128..9ff930f 100644
--- a/centos74-octave-fludetector/playbook.yml
+++ b/centos74-octave-fludetector/playbook.yml
@@ -11,7 +11,7 @@
     fludetector_user: root
     fludetector_model: FluDetectorModel-Google201804.tar.gz
     fludetector_sql: model_data_google_2018_04.sql
-    fludetector_version: v2.1
+    fludetector_version: v2.2
     octave_version: 4.2.2-6.el7.centos.1
     model_id: 1
   tasks:
@@ -131,3 +131,9 @@
         name: nginx
         state: started
         enabled: yes
+
+    - name: Start supervisord
+      systemd:
+        name: supervisord
+        state: started
+        enabled: yes

From cbb55db91479a2f8425e64f82c068797b1061baf Mon Sep 17 00:00:00 2001
From: David Guzman <d.guzman@ucl.ac.uk>
Date: Thu, 17 Jan 2019 18:50:27 +0000
Subject: [PATCH 16/16] Test box for the Takeout app

---
 centos75-node-glassfish/README.md             |  25 +++
 centos75-node-glassfish/Vagrantfile           |  18 ++
 .../conf/glassfish.service                    |  13 ++
 centos75-node-glassfish/conf/nginx.conf       |  41 ++++
 .../conf/takeout-react.service                |  14 ++
 centos75-node-glassfish/playbook.yml          | 185 ++++++++++++++++++
 6 files changed, 296 insertions(+)
 create mode 100644 centos75-node-glassfish/README.md
 create mode 100644 centos75-node-glassfish/Vagrantfile
 create mode 100644 centos75-node-glassfish/conf/glassfish.service
 create mode 100644 centos75-node-glassfish/conf/nginx.conf
 create mode 100644 centos75-node-glassfish/conf/takeout-react.service
 create mode 100644 centos75-node-glassfish/playbook.yml

diff --git a/centos75-node-glassfish/README.md b/centos75-node-glassfish/README.md
new file mode 100644
index 0000000..7b7b25e
--- /dev/null
+++ b/centos75-node-glassfish/README.md
@@ -0,0 +1,25 @@
+# CentOS 7.5 with Node and Glassfish
+
+## Software versions:
+
+- Node 10 
+- Glassfish 5
+
+## Installation 
+
+Define Ansible host for apiclient and run with `ansible-playbook`
+```
+ansible-playbook -u dguzman -k -K playbook.yml --extra-vars "target=searchapp"
+```
+
+## Testing (connection to CS network required)
+
+For local testing, just start a VM using vagrant.
+
+```
+vagrant up --no-provision
+
+ansible-playbook --private-key=.vagrant/machines/default/virtualbox/private_key -u vagrant -i .vagrant/provisioners/ansible/inventory --extra-vars "target=all" --connection=ssh --ssh-extra-args="-o UserKnownHostsFile=/dev/null -o IdentitiesOnly=yes -o StrictHostKeyChecking=no -o Port=2222 -o KbdInteractiveAuthentication=no -o PreferredAuthentications=gssapi-with-mic,gssapi-keyex,hostbased,publickey -o PasswordAuthentication=no -o User=vagrant -o ConnectTimeout=30" playbook.yml
+```
+
+Once the provisioning has completed, open http://localhost:10080 with a web browser
\ No newline at end of file
diff --git a/centos75-node-glassfish/Vagrantfile b/centos75-node-glassfish/Vagrantfile
new file mode 100644
index 0000000..45b40dd
--- /dev/null
+++ b/centos75-node-glassfish/Vagrantfile
@@ -0,0 +1,18 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+Vagrant.configure("2") do |config|
+
+  config.vm.box = "centos-7.5"
+
+  config.vm.provision "ansible" do |ansible|
+    ansible.playbook = "playbook.yml"
+    ansible.compatibility_mode = "2.0"
+    ansible.extra_vars = {
+      target: "all"
+    }
+  end
+  
+  config.vm.network "forwarded_port", guest: 80, host: 10080
+
+end
diff --git a/centos75-node-glassfish/conf/glassfish.service b/centos75-node-glassfish/conf/glassfish.service
new file mode 100644
index 0000000..f370e3c
--- /dev/null
+++ b/centos75-node-glassfish/conf/glassfish.service
@@ -0,0 +1,13 @@
+[Unit]
+Description = GlassFish Server v5
+After = syslog.target network.target
+
+[Service]
+User = glassfish
+ExecStart = /usr/bin/java -jar /opt/glassfish/glassfish/lib/client/appserver-cli.jar start-domain
+ExecStop = /usr/bin/java -jar /opt/glassfish/glassfish/lib/client/appserver-cli.jar stop-domain
+ExecReload = /usr/bin/java -jar /opt/glassfish/glassfish/lib/client/appserver-cli.jar restart-domain
+Type = forking
+
+[Install]
+WantedBy = multi-user.target
\ No newline at end of file
diff --git a/centos75-node-glassfish/conf/nginx.conf b/centos75-node-glassfish/conf/nginx.conf
new file mode 100644
index 0000000..df71a4c
--- /dev/null
+++ b/centos75-node-glassfish/conf/nginx.conf
@@ -0,0 +1,41 @@
+server {
+
+    server_name localhost;
+
+    add_header X-Frame-Options "SAMEORIGIN";
+    add_header X-XSS-Protection "1; mode=block";
+    add_header X-Content-Type-Options nosniff;
+
+    location /api/ {
+
+        if ($request_method = 'OPTIONS') {
+            add_header 'Access-Control-Allow-Origin' '$http_referer';
+            add_header 'Access-Control-Allow-Methods' 'OPTIONS,PUT';
+            add_header 'Access-Control-Allow-Headers' 'Content-Type';
+            add_header 'Access-Control-Max-Age' 1728000;
+            add_header 'Content-Type' 'text/plain; charset=utf-8';
+            add_header 'Content-Length' 0;
+            return 204;
+        }
+
+        if ($request_method = 'PUT') {
+            add_header 'Access-Control-Allow-Origin' '$http_referer';
+            add_header 'Access-Control-Allow-Methods' 'PUT';
+            add_header 'Access-Control-Allow-Headers' 'Content-Type';
+        }
+
+        proxy_pass http://localhost:8080/;
+        proxy_set_header Host $http_host;
+        proxy_set_header X-Forwarded-For $remote_addr;
+        
+    }
+
+    location / {
+        
+        proxy_pass http://localhost:5000/;
+        proxy_set_header Host localhost;
+        proxy_set_header X-Forwarded-For $remote_addr;
+        
+    }
+
+}
diff --git a/centos75-node-glassfish/conf/takeout-react.service b/centos75-node-glassfish/conf/takeout-react.service
new file mode 100644
index 0000000..2a3512b
--- /dev/null
+++ b/centos75-node-glassfish/conf/takeout-react.service
@@ -0,0 +1,14 @@
+[Unit]
+Description=Takeout React app - web interface
+Documentation=https://www.github.com/UCL/takeout-app-react
+After=network.target
+
+[Service]
+Type=simple
+User=root
+WorkingDirectory=/opt/node/takeout-app-react
+ExecStart=/usr/bin/serve -s build
+Restart=on-failure
+
+[Install]
+WantedBy=multi-user.target
diff --git a/centos75-node-glassfish/playbook.yml b/centos75-node-glassfish/playbook.yml
new file mode 100644
index 0000000..587a31b
--- /dev/null
+++ b/centos75-node-glassfish/playbook.yml
@@ -0,0 +1,185 @@
+---
+- hosts: '{{ target }}'
+  become: True
+  become_method: sudo
+  vars:
+    glassfish_version: '5.0'
+    nodeapp_version: '0.4'
+    javaeeapp_tag: '0.3'
+    javaeeapp_version: '1.0-SNAPSHOT'
+    pgjdbc_version: '42.2.5'
+  vars_prompt:
+    - name: pg_user
+      prompt: Enter the user for connecting to the database
+      private: no
+    - name: pg_pass
+      prompt: Enter the password for connecting to the database
+      private: yes
+    - name: pg_dbname
+      prompt: Enter the name of the database
+      private: no
+    - name: pg_host
+      prompt: Enter the hostname for the database
+      private: no
+  tasks:
+  - name: Install NodeSource yum repository
+    shell: curl -sL https://rpm.nodesource.com/setup_10.x | sudo bash -
+    args:
+      warn: false
+
+  - name: Install EPEL repository
+    yum:
+      name: epel-release
+      state: present
+
+  - name: Install Node.js and npm
+    yum:
+      name: nodejs
+      state: present
+
+  - name: Create system user for Node
+    user:
+      name: node
+      system: yes
+      local: yes
+      createhome: yes
+      home: /opt/node
+      shell: /sbin/nologin
+
+  - name: Install serve package
+    npm:
+      name: serve
+      global: yes
+
+  - name: Download and unpack Node app
+    unarchive:
+      src: "https://github.com/UCL/takeout-app-react/archive/{{nodeapp_version}}.tar.gz"
+      dest: /opt/node
+      remote_src: yes
+    become_user: node
+
+  - name: Rename Node app directory
+    command: "mv /opt/node/takeout-app-react-{{nodeapp_version}} /opt/node/takeout-app-react"
+    become_user: node
+
+  - name: Install packages from package.json
+    npm:
+      path: /opt/node/takeout-app-react
+      state: present
+      production: yes
+    become_user: node
+
+  - name: Build Node app
+    command: "npm run build"
+    args:
+      chdir: /opt/node/takeout-app-react
+    become_user: node
+    environment:
+      REACT_APP_API_HOST: '/api/takeout-api-javaee'
+
+  - name: Upload systemd configuration file for the Takeout app
+    copy:
+      src: conf/takeout-react.service
+      dest: /etc/systemd/system/takeout-react.service
+
+  - name: Start Node app
+    service:
+      name: takeout-react
+      state: started
+      enabled: yes
+    
+  - name: Create system user for Glassfish
+    user:
+      name: glassfish
+      system: yes
+      local: yes
+      createhome: yes
+      home: /opt/glassfish
+      shell: /sbin/nologin
+
+  - name: Install OpenJDK 8
+    yum:
+      name: java-1.8.0-openjdk-devel
+      state: present
+        
+  - name: Install unzip
+    yum:
+      name: unzip
+      state: present
+
+  - name: Download and unpack Glassfish
+    unarchive:
+      src: 'http://download.oracle.com/glassfish/{{glassfish_version}}/release/glassfish-{{glassfish_version}}.zip'
+      dest: /opt
+      creates: /opt/glassfish5
+      remote_src: yes
+      owner: glassfish
+      group: glassfish
+
+  - name: Move Glassfish files to HOME
+    shell: mv /opt/glassfish5/* /opt/glassfish
+    become_user: glassfish
+
+  - name: Remove glassfish5 directory
+    file:
+      path: /opt/glassfish5
+      state: absent
+
+  - name: Upload Systemd unit file for Glassfish
+    copy:
+      src: conf/glassfish.service
+      dest: /usr/lib/systemd/system/glassfish.service
+
+  - name: Download PostgreSQL JDBC driver
+    get_url:
+      url: 'https://jdbc.postgresql.org/download/postgresql-{{pgjdbc_version}}.jar'
+      dest: /opt/glassfish/glassfish/lib
+      owner: glassfish
+      group: glassfish
+
+  - name: Start Glassfish
+    service:
+      name: glassfish
+      state: started
+      enabled: yes
+
+  - name: Configure JDBC connection pool
+    command: '/opt/glassfish/bin/asadmin create-jdbc-connection-pool --restype javax.sql.ConnectionPoolDataSource --datasourceclassname org.postgresql.ds.PGConnectionPoolDataSource --property portNumber=5432:user={{pg_user}}:password={{pg_pass}}:databaseName={{pg_dbname}}:serverName={{pg_host}} dataPool'
+    become_user: glassfish
+
+  - name: Configure JDBC resource
+    command: '/opt/glassfish/bin/asadmin create-jdbc-resource --connectionpoolid dataPool jdbc/takeout'
+    become_user: glassfish
+
+  - name: Download Takeout API
+    get_url:
+      url: 'https://github.com/UCL/takeout-api-javaee/releases/download/v{{javaeeapp_tag}}/takeout-api-javaee-{{javaeeapp_version}}.war'
+      dest: /tmp
+      owner: glassfish
+      group: glassfish
+
+  - name: Deploy Takeout API
+    command: '/opt/glassfish/bin/asadmin deploy --name takeout-api-javaee --contextroot takeout-api-javaee /tmp/takeout-api-javaee-{{javaeeapp_version}}.war'
+    become_user: glassfish
+
+  - name: Install NGINX
+    yum:
+      name: nginx
+      state: present
+
+  - name: Upload NGINX configuration file
+    copy:
+      src: conf/nginx.conf
+      dest: /etc/nginx/conf.d/takeout.conf
+
+  - name: Start NGINX
+    service:
+      name: nginx
+      state: started
+      enabled: yes
+
+  - name: Configure firewall
+    command: 'firewall-cmd --zone=public --permanent --add-service=http'
+
+  - name: Reload firewall rules
+    command: firewall-cmd --reload