Merge branch 'master' into issue_tracker_major_leigh_features

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,34 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: Bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is
+
+**To Reproduce**
+Steps to reproduce the behavior (attach screenshots if applicable):
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**What did you expect to happen?**
+A clear and concise description of what you expected to happen.
+
+**Browser Environment (please complete the following information):**
+- OS: [e.g. Plan9, HURD, Oberon, etc]
+- Browser [e.g. chrome, firefox] (note that only these two browsers are supported)
+- Version [e.g. 22]
+
+**Server Environment (if known):**
+- LORIS Version: [e.g. 21.0.0]
+- Linux distribution and Version: [e.g. Ubuntu 16.04, CentOS 7]
+- MySQL/MariaDB Version: [e.g. MySQL 5.7, MariaDB 10.3]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: Proposal
+assignees: ''
+
+---
+
+**Is your feature request related to an existing module?**
+Tell us the name of the module you'd like to have a feature added to, or if you'd like a new module.
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,6 +5,6 @@
 
 1.
 
-#### Links to related tickets (GitHub, Redmine, ...)
+#### Link(s) to related issue(s)
 
-*
+* Resolves #  (Reference the issue this fixes, if any.)

CHANGELOG.md

@@ -0,0 +1,16 @@
+## CHANGELOG
+
+- ***When adding content to this document, make sure to create a section for each module 
+if the changes only impact a single module and that section does not already exist in
+the document. When changes affect the entire software, make sure to add them in the 
+core section.***
+
+- ***When possible please provide the number of the pull request(s) containing the 
+changes in the following format: PR #1234***
+
+### VERSION
+
+#### Core
+
+#### Modules 
+##### module1

CONTRIBUTING.md

@@ -17,35 +17,12 @@ some of the factors we'll consider when reviewing your code.
 
 ## Development branches
 
-Please create a fork of the LORIS repository on your own GitHub account and
-push changes to local branches rather than pushing new branches directly 
-to our repository.
-
-You should base your pull requests on one of the following branches
-depending on the kind of change you are making:
-
-#### Bug Fixes
-   - Branch: `bugfix` 
-   - Content: Generally these changes do not require SQL scripts
-   and are concise with the sole objective to correct a single problem
-   in the code.
-
-#### Minor Changes and Small Features
-   - Branch: `minor` 
-   - Content: Features affecting self-contained components such
-   as modules. Additions to Libraries, API, or modules that do not change
-   any function signatures.
-
-#### Major Changes, Non Backwards-Compatible Changes and Large Features
-   - Branch: `major` 
-   - Content: Any change modifying a function signature in a
-   library class. Features require extensive LORIS-wide testing. New
-   complex systems and features spanning across multiple modules and
-   libraries. Deprecated functions clean-up.
-
-For more information about making well-organized pull requests,
-please read our in-depth Wiki page, 
-["Contributing to the Code"](https://github.com/aces/Loris/wiki/Contributing-to-the-Code).
+For the most part, changes to the codebase should be sent to the `master`
+branch, which is the default.
+
+Small bug fixes for a given version of LORIS should be sent to the branch named
+for that version. For example, fixing a bug in LORIS version 22 should be sent
+to the `22.0-release` branch.
 
 ## Pull Request Title and Description
 

README.md

@@ -1,4 +1,6 @@
-# [![Build Status](https://travis-ci.org/aces/Loris.svg?branch=master)](https://travis-ci.org/aces/Loris) [![Documentation Status](https://readthedocs.org/projects/acesloris/badge/?version=latest)](https://acesloris.readthedocs.io/en/latest/?badge=latest)
+<img src="./htdocs/images/LORIS_logo.svg" width="35%">
+
+[![Build Status](https://travis-ci.org/aces/Loris.svg?branch=master)](https://travis-ci.org/aces/Loris) [![Documentation Status](https://readthedocs.org/projects/acesloris/badge/?version=latest)](https://acesloris.readthedocs.io/en/latest/?badge=latest)
 
 # LORIS Neuroimaging Platform
 
@@ -27,7 +29,7 @@ Deploy and log in with username *admin* and the password that's set up during de
  * Apache **2.4** or higher
  * MySQL >= 5.7 (or MariaDB >= 10.3) 
  * PHP <b>7.2</b> or higher
- * [Composer](https://getcomposer.org/)
+ * [Composer](https://getcomposer.org/) <b>1.4</b> or higher
  * NodeJS <b>8.0</b> or higher
  * NPM
  * make
@@ -86,6 +88,8 @@ sudo service apache2 reload
 
 6. Go to http://localhost/installdb.php and follow the instructions to finalize LORIS installation, then restart apache.
 
+If you use MySQL 8, please read [this link](https://www.php.net/manual/en/mysqli.requirements.php) and also [this](https://dev.mysql.com/doc/refman/8.0/en/upgrading-from-previous-series.html#upgrade-caching-sha2-password-compatible-connectors).
+
 7. Follow the [Setup Guide in the LORIS Wiki](https://github.com/aces/Loris/wiki/Setup) to complete your post-installation setup and configuration, and for more documentation.
 
 ## Community
@@ -112,4 +116,3 @@ LORIS is made by staff developers at the McGill Centre for Integrative Neuroscie
 See [LORIS.ca](www.loris.ca) for our current team, the history of LORIS, and our **Technical Papers**.
 
 The original (pre-GitHub) LORIS development team from 1999-2010 included: Dario Vins, Alex Zijdenbos, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, and Samir Das.  
-

SQL/0000-00-03-ConfigTables.sql

@@ -75,6 +75,8 @@ INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType,
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'publication_uploads', 'Path to uploaded publications', 1, 0, 'web_path', ID, 'Publications', 10 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'publication_deletions', 'Path to deleted publications', 1, 0, 'web_path', ID, 'Deleted Publications', 11 FROM ConfigSettings WHERE Name="paths";
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'MINCToolsPath', 'Path to the MINC tools', 1, 0, 'web_path', ID, 'Path to the MINC tools', 12 FROM ConfigSettings WHERE Name="paths";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'documentRepositoryPath', 'Path to uploaded document repository files', 1, 0, 'web_path', ID, 'Document Repository Upload Path', 13 FROM ConfigSettings WHERE Name="paths";
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataReleasePath', 'Path to uploaded data release files', 1, 0, 'web_path', ID, 'Data release Upload Path', 14 FROM ConfigSettings WHERE Name="paths";
 
 
 INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, Label, OrderNumber) VALUES ('gui', 'Settings related to the overall display of LORIS', 1, 0, 'GUI', 3);

SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql

@@ -0,0 +1,9 @@
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'documentRepositoryPath', 'Path to uploaded document repository files', 1, 0, 'text', cs1.ID, 'Document Repository Upload Path', MAX(cs2.OrderNumber)+1 FROM ConfigSettings cs1 JOIN ConfigSettings cs2 WHERE cs1.Name="paths" AND cs2.parent=cs1.ID;
+INSERT INTO ConfigSettings (Name, Description, Visible, AllowMultiple, DataType, Parent, Label, OrderNumber) SELECT 'dataReleasePath', 'Path to uploaded data release files', 1, 0, 'text', cs1.ID, 'Data Release Upload Path', MAX(cs2.OrderNumber)+1 FROM ConfigSettings cs1 JOIN ConfigSettings cs2 WHERE cs1.Name="paths" AND cs2.parent=cs1.ID;
+
+-- For backwards compatibility, check the previous base and default to same folder as previous setting
+SELECT Value INTO @base FROM Config c JOIN ConfigSettings cs ON cs.ID=c.ConfigID WHERE cs.Name="base";
+
+INSERT INTO Config (ConfigID, Value) SELECT ID, CONCAT(@base,"modules/document_repository/user_uploads/") FROM ConfigSettings WHERE Name="documentRepositoryPath";
+INSERT INTO Config (ConfigID, Value) SELECT ID, CONCAT(@base,"modules/data_release/user_uploads/") FROM ConfigSettings WHERE Name="dataReleasePath";
+

composer.json

@@ -17,7 +17,7 @@
     },
     "require-dev" : {
         "squizlabs/php_codesniffer" : "3.5.1",
-        "phpunit/phpunit" : "6.5.*",
+        "phpunit/phpunit" : "7.0.0",
         "facebook/webdriver" : "dev-master",
         "phan/phan": ">=2.3.0",
         "phpmd/phpmd": "~2.7"