2018 01 17 tara perm roles

.travis.yml

@@ -1,15 +1,13 @@
 language: php
 
+
 cache:
     directories:
         - vendor
-
 php:
-    - "7"
+    - "7.0"
     - "7.1"
 
-sudo: false
-
 addons:
     firefox: "44.0"
 
@@ -24,20 +22,21 @@ before_install:
     - nvm install node
     - mkdir -p project project/libraries
     - phpenv config-rm xdebug.ini
-
+    - if [[ ${TRAVIS_PHP_VERSION:0:3} == "7.0" ]]; then Dir="router.php" ; fi
+    - if [[ ${TRAVIS_PHP_VERSION:0:3} == "7.1" ]]; then Dir="htdocs/router.php" ; fi
+    - php -S localhost:8000 -t htdocs $Dir 2>1 > /dev/null &
 install:
     # Install composer modules
     - composer install
+    - composer require --dev
     - phpenv rehash
 
+
     # Install node modules specified in package.json
     - npm install
 
     # Download a Selenium Web Driver release
     - wget "http://selenium-release.storage.googleapis.com/2.52/selenium-server-standalone-2.52.0.jar"
-
-    - php -S localhost:8000 -t htdocs htdocs/router.php 2>1 > /dev/null &
-
     # Extracting firefox and setting PATH variable...
     - tar -xjf /tmp/firefox-44.0.tar.bz2 --directory /tmp
     - export PATH="/tmp/firefox:$PATH"
@@ -49,6 +48,8 @@ install:
     - DISPLAY=:99.0 java -jar selenium-server-standalone-2.52.0.jar  2>1 > /dev/null &
 
 before_script:
+
+
     # Set up the Loris environment
     - mkdir -p project smarty/templates_c project/instruments project/tables_sql
     - chmod 777 smarty/templates_c project/instruments project/tables_sql
@@ -62,6 +63,8 @@ before_script:
     - mysql LorisTest < SQL/0000-00-03-ConfigTables.sql
     - mysql LorisTest < SQL/0000-00-04-Help.sql
     - mysql LorisTest < docs/instruments/radiology_review.sql
+    - mysql LorisTest < test/RBdata.sql
+    - mysql LorisTest < test/test_instrument/medical_history.sql
     - mysql LorisTest -u root -e "GRANT UPDATE,INSERT,SELECT,DELETE,DROP,CREATE TEMPORARY TABLES ON LorisTest.* TO 'SQLTestUser'@'localhost' IDENTIFIED BY 'TestPassword' WITH GRANT OPTION"
     - cp docs/config/config.xml project/config.xml
     - cp docs/config/config.xml test/config.xml
@@ -91,10 +94,6 @@ before_script:
  # - "LORIS_DB_CONFIG=test/config.xml"
 
 script:
-    - npm run lint:php
-    - npm run lint:javascript
-
-    # Run unit tests to make sure functions still do what they should.
-    - vendor/bin/phpunit --configuration test/phpunit.xml
+    - npm run lint:php && npm run lint:javascript && vendor/bin/phpunit --configuration test/phpunit.xml
 
 dist: precise

Dockerfile.MySQL

@@ -5,6 +5,9 @@ COPY SQL/0000-00-01-Permission.sql /0000-00-01-Permission.sql
 COPY SQL/0000-00-02-Menus.sql /0000-00-02-Menus.sql
 COPY SQL/0000-00-03-ConfigTables.sql /0000-00-03-ConfigTables.sql
 COPY SQL/0000-00-04-Help.sql /0000-00-04-Help.sql
+COPY test/RBdata.sql /RBdata.sql
+COPY test/test_instrument/testtest.sql /test_instrument.sql
+COPY test/test_instrument/medical_history.sql  /medical_history.sql
 
 ADD docs/Docker/LorisDB-EntryPoint.sh /entrypoint.sh
 

Dockerfile.test.db

@@ -8,7 +8,8 @@ COPY SQL/0000-00-02-Menus.sql /0000-00-02-Menus.sql
 COPY SQL/0000-00-03-ConfigTables.sql /0000-00-03-ConfigTables.sql
 COPY SQL/0000-00-04-Help.sql /0000-00-04-Help.sql
 COPY test/test_instrument/testtest.sql /test_instrument.sql
-
+COPY test/RBdata.sql /RBdata.sql
+COPY test/test_instrument/medical_history.sql /medical_history.sql
 COPY docs/instruments/radiology_review.sql /radiology_review.sql
 
 RUN echo "Use LorisTest;" | cat - \
@@ -18,7 +19,9 @@ RUN echo "Use LorisTest;" | cat - \
     0000-00-03-ConfigTables.sql \
     0000-00-04-Help.sql \
     test_instrument.sql \
-    radiology_review.sql > /docker-entrypoint-initdb.d/0000-compiled.sql
+    RBdata.sql \
+    medical_history.sql \
+    radiology_review.sql > /docker-entrypoint-initdb.d/0000-compiled.sql 
 
 RUN echo "Use LorisTest;" >> /docker-entrypoint-initdb.d/0001-paths.sql
 RUN echo "UPDATE Config SET Value='${BASE_DIR}/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');" >> /docker-entrypoint-initdb.d/0001-paths.sql

README.Mac.md

@@ -1,4 +1,4 @@
-#LORIS Mac Install Guide
+# LORIS Mac Install Guide
 ### Mac is no longer supported as of 15.10. 
 
 This is a guide on how to get a LORIS instance Running on your Mac computer. It is designed for installation in a sandbox environment. 
@@ -87,11 +87,11 @@ SET PASSWORD FOR 'root'@'localhost' = PASSWORD('$newpwd');
 
 ## 1.5 Smarty 3
 
-###1.5.1 Obtaining Smarty 3
+### 1.5.1 Obtaining Smarty 3
 
 Go to [http://www.smarty.net/download](http://www.smarty.net/download) and download the latest stable release of Smarty 3.x.x
 
-###1.5.2 Setting up Smarty 3
+### 1.5.2 Setting up Smarty 3
 
 Create the following directories if they do not already exist:
 
@@ -108,18 +108,18 @@ sudo mv /path/to/Smarty-3.x.x/libs/ /usr/local/lib/php/Smarty/smarty3
 
 After you have moved the directory ensure to add the path ```/usr/local/lib/php/Smarty``` to the ```include_path``` in the php.ini file (see [section 1.3.4](#include_path) part 3).
 
-#2. Installing LORIS Code Base
+# 2. Installing LORIS Code Base
 
 This section goes over how to obtain the LORIS code base and setup the database on your local machine.
 
-##2.1 Obtaining the LORIS code
+## 2.1 Obtaining the LORIS code
 
 Download the latest release from the [releases page](https://github.com/aces/Loris/releases) and
 extract it to `~/Sites/$projectname`
 
 <i>$projectname ⇾ “loris” or one-word project name</i>
 
-##2.2 Installing LORIS
+## 2.2 Installing LORIS
 
 Run installer script to install core code, libraries, and MySQL schema (see Loris Installation Schematic). 
 The script will prompt for information, including usernames and folders which it will create automatically.
@@ -131,7 +131,7 @@ cd ~/Sites/$projectname/tools
 The install script may not fully execute on Mac OS systems.  It is recommended to carefully review and execute manually the steps in the install.sh script on your system.  A few MySQL statement examples are provided in section 2.3. 
 Since the install script was created for LINUX OS, its apache2 setup steps won’t work. Section 3 describes how to set up the apache2 server for Mac.
 
-##2.3 Manually running install script steps
+## 2.3 Manually running install script steps
 
 Since you may not be able to fully execute the install.sh script at step 2.2, the following examples may help in manually executing the sequence of commands found in the install script.
 

README.md

@@ -1,4 +1,4 @@
-# LORIS Neuroimaging Platform [![Build Status](https://travis-ci.org/aces/Loris.svg?branch=17.1-dev)](https://travis-ci.org/aces/Loris)
+# LORIS Neuroimaging Platform
 
 LORIS (Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research. LORIS makes it easy to manage large datasets including behavioural, clinical, neuroimaging and genetic data acquired over time or at different sites.
 
@@ -7,10 +7,17 @@ NEW <b>⇾  Try LORIS on Heroku</b> before installing it on your system<br>
 Test out the project management and clinical data management side of LORIS (complete Imaging features not yet available)<br>
 Deploy and log in with username <i>admin</i> and the password that's set up during deployment via ClearDB.
 
-[![Deploy](https://www.herokucdn.com/deploy/button.png)](https://heroku.com/deploy?template=https://github.com/aces/Loris/tree/17.1-dev)
+[![Deploy](https://www.herokucdn.com/deploy/button.png)](https://heroku.com/deploy?template=https://github.com/aces/Loris/tree/master)
 <hr>
 
-This Readme covers installation of the <b>18.0</b> LORIS release on <b>Ubuntu</b>.
+| Branch | Status |
+| ------ | ------ |
+| master | [![Build Status](https://travis-ci.org/aces/Loris.svg?branch=master)](https://travis-ci.org/aces/Loris)
+| major  | [![Build Status](https://travis-ci.org/aces/Loris.svg?branch=major)](https://travis-ci.org/aces/Loris)
+| minor  | [![Build Status](https://travis-ci.org/aces/Loris.svg?branch=minor)](https://travis-ci.org/aces/Loris)
+| bugfix | [![Build Status](https://travis-ci.org/aces/Loris.svg?branch=bugfix)](https://travis-ci.org/aces/Loris)
+
+This Readme covers installation of the LORIS <b>v18.0.0</b> release on <b>Ubuntu</b>.
 ([CentOS Readme also available](https://github.com/aces/Loris/blob/master/README.CentOS6.md)).
 
 Please consult the [LORIS Wiki Setup Guide](https://github.com/aces/Loris/wiki/Setup) notes on this [Install process](https://github.com/aces/Loris/wiki/Installing-Loris) for more information not included in this Readme. The [LORIS Developers mailing list](http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev) may also provide installation guidance not covered in the Wiki.