Merge branch 'develop' into bugFixMySQLdb

Author: BLasan

.docker/volumes/mysql/create-schema.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+SCHEMA_DIR=/tmp/schema
+
+mysql_exec=( mysql -uroot -p${MYSQL_ROOT_PASSWORD} )
+
+if [[ -z "$BASSA_DB_NAME" ]]
+then
+    echo "BASSA_DB_NAME is not defined."
+    exit 1
+fi
+
+echo "Creating database ${BASSA_DB_NAME}..."
+echo "DROP DATABASE IF EXISTS ${BASSA_DB_NAME}; CREATE DATABASE ${BASSA_DB_NAME};" | "${mysql_exec[@]}" &> /dev/null
+
+mysql_exec_in_db=("${mysql_exec[@]}" "${BASSA_DB_NAME}")
+
+for sql_file in $SCHEMA_DIR/*
+do
+    sql_file_name=$(basename $sql_file)
+    echo "Dumping file ${sql_file_name} to ${BASSA_DB_NAME}..."
+    "${mysql_exec_in_db[@]}" < ${sql_file} &> /dev/null
+done
+
+echo "Initial schema created!"

.gitattributes

@@ -0,0 +1,203 @@
+## GITATTRIBUTES
+#
+# Details per file setting:
+#   text    These files should be normalized (i.e. convert CRLF to LF).
+#   binary  These files are binary and should be left untouched.
+#
+# Note that binary is a macro for -text -diff.
+######################################################################
+
+## AUTO-DETECT
+##   Handle line endings automatically for files detected as
+##   text and leave all files detected as binary untouched.
+##   This will handle all files NOT defined below.
+* text=auto
+
+# Source files
+# ============
+*.pxd		text
+*.py 		text
+*.py3 		text
+*.pyw 		text
+*.pyx  		text
+
+# Binary files
+# ============
+*.db		binary
+*.p 		binary
+*.pkl 		binary
+*.pyc 		binary
+*.pyd		binary
+*.pyo 		binary
+
+## SOURCE CODE
+*.bat      text eol=crlf
+*.coffee   text
+*.css      text
+*.htm      text
+*.html     text
+*.inc      text
+*.ini      text
+*.js       text
+*.json     text
+*.jsx      text
+*.less     text
+*.od       text
+*.onlydata text
+*.php      text
+*.pl       text
+*.py       text
+*.rb       text
+*.sass     text
+*.scm      text
+*.scss     text
+*.sh       text eol=lf
+*.sql      text
+*.styl     text
+*.tag      text
+*.ts       text
+*.tsx      text
+*.xml      text
+*.xhtml    text
+
+## DOCKER
+*.dockerignore    text
+Dockerfile    text
+
+## DOCUMENTATION
+*.markdown   text
+*.md         text
+*.mdwn       text
+*.mdown      text
+*.mkd        text
+*.mkdn       text
+*.mdtxt      text
+*.mdtext     text
+*.txt        text
+AUTHORS      text
+CHANGELOG    text
+CHANGES      text
+CONTRIBUTING text
+COPYING      text
+copyright    text
+*COPYRIGHT*  text
+INSTALL      text
+license      text
+LICENSE      text
+NEWS         text
+readme       text
+*README*     text
+TODO         text
+
+## TEMPLATES
+*.dot        text
+*.ejs        text
+*.haml       text
+*.handlebars text
+*.hbs        text
+*.hbt        text
+*.jade       text
+*.latte      text
+*.mustache   text
+*.njk        text
+*.phtml      text
+*.tmpl       text
+*.tpl        text
+*.twig       text
+
+## LINTERS
+.csslintrc    text
+.eslintrc     text
+.htmlhintrc   text
+.jscsrc       text
+.jshintrc     text
+.jshintignore text
+.stylelintrc  text
+
+## CONFIGS
+*.bowerrc      text
+*.cnf          text
+*.conf         text
+*.config       text
+.browserslistrc    text
+.editorconfig  text
+.gitattributes text
+.gitconfig     text
+.htaccess      text
+*.npmignore    text
+*.yaml         text
+*.yml          text
+browserslist   text
+Makefile       text
+makefile       text
+
+## GRAPHICS
+*.ai   binary
+*.bmp  binary
+*.eps  binary
+*.gif  binary
+*.ico  binary
+*.jng  binary
+*.jp2  binary
+*.jpg  binary
+*.jpeg binary
+*.jpx  binary
+*.jxr  binary
+*.pdf  binary
+*.png  binary
+*.psb  binary
+*.psd  binary
+*.svg  text
+*.svgz binary
+*.tif  binary
+*.tiff binary
+*.wbmp binary
+*.webp binary
+
+## AUDIO
+*.kar  binary
+*.m4a  binary
+*.mid  binary
+*.midi binary
+*.mp3  binary
+*.ogg  binary
+*.ra   binary
+
+## VIDEO
+*.3gpp binary
+*.3gp  binary
+*.as   binary
+*.asf  binary
+*.asx  binary
+*.fla  binary
+*.flv  binary
+*.m4v  binary
+*.mng  binary
+*.mov  binary
+*.mp4  binary
+*.mpeg binary
+*.mpg  binary
+*.ogv  binary
+*.swc  binary
+*.swf  binary
+*.webm binary
+
+## ARCHIVES
+*.7z  binary
+*.gz  binary
+*.jar binary
+*.rar binary
+*.tar binary
+*.zip binary
+
+## FONTS
+*.ttf   binary
+*.eot   binary
+*.otf   binary
+*.woff  binary
+*.woff2 binary
+
+## EXECUTABLES
+*.pyc binary
+
+

.github/ISSUE_TEMPLATE.md

@@ -1,32 +1,36 @@
 <!--- Provide a general summary of the issue in the Title above -->
 
-## Expected Behavior
+#### Expected Behavior
 <!--- If you're describing a bug, tell us what should happen -->
 <!--- If you're suggesting a change/improvement, tell us how it should work -->
 
-## Current Behavior
+#### Current Behavior
 <!--- If describing a bug, tell us what happens instead of the expected behavior -->
 <!--- If suggesting a change/improvement, explain the difference from current behavior -->
 
-## Possible Solution
+#### Possible Solution
 <!--- Not obligatory, but suggest a fix/reason for the bug, -->
 <!--- or ideas how to implement the addition or change -->
 
-## Steps to Reproduce (for bugs)
+#### Steps to Reproduce (for bugs)
 <!--- Provide a link to a live example, or an unambiguous set of steps to -->
 <!--- reproduce this bug. Include code to reproduce, if relevant -->
 1.
 2.
 3.
 4.
 
-## Context
+#### Context
 <!--- How has this issue affected you? What are you trying to accomplish? -->
 <!--- Providing context helps us come up with a solution that is most useful in the real world -->
 
-## Your Environment
+#### Your Environment
 <!--- Include as many relevant details about the environment you experienced the bug in -->
 * Version used:
 * Environment name and version (e.g. Chrome 39, node.js 5.4):
 * Operating System and version (desktop or mobile):
 * Link to your project:
+
+
+# Pull Requests to this issue
+If you are planning to create a PR for this issue, please make sure you first discuss with the maintainers of the project about ths issue well and get the 'Go' from them first.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,31 +1,31 @@
 <!--- Provide a general summary of your changes in the Title above -->
 
-## Description
+#### Description
 <!--- Describe your changes in detail -->
 
-## Related Issue
+#### Related Issue
 <!--- This project only accepts pull requests related to open issues -->
 <!--- If suggesting a new feature or change, please discuss it in an issue first -->
 <!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
 <!--- Please link to the issue here: -->
 
-## Motivation and Context
+#### Motivation and Context
 <!--- Why is this change required? What problem does it solve? -->
 
-## How Has This Been Tested?
+#### How Has This Been Tested?
 <!--- Please describe in detail how you tested your changes. -->
 <!--- Include details of your testing environment, and the tests you ran to -->
 <!--- see how your change affects other areas of the code, etc. -->
 
-## Screenshots (In case of UI changes):
+#### Screenshots (In case of UI changes):
 
-## Types of changes
+#### Types of changes
 <!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
 - [ ] Bug fix (non-breaking change which fixes an issue)
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Breaking change (fix or feature that would cause existing functionality to change)
 
-## Checklist:
+#### Checklist:
 <!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
 <!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
 - [ ] My code follows the code style of this project.

.gitignore

@@ -1,6 +1,9 @@
 
 # Created by https://www.gitignore.io/api/vim,node,python,sublimetext,visualstudiocode
 
+### Mac Junk ###
+.DS_Store
+
 ### Node ###
 # Logs
 logs
@@ -42,7 +45,7 @@ jspm_packages/
 
 *.log
 components/core/debug-server.log
-downloads/
+
 
 # UI
 ui/dist
@@ -226,4 +229,9 @@ tags
 !.vscode/extensions.json
 .history
 
+### IDEs
+
+.idea/*
+.vscode/*
+
 # End of https://www.gitignore.io/api/vim,node,python,sublimetext,visualstudiocode

.travis.yml

@@ -1,34 +1,29 @@
 dist: trusty
-language: node_js
-node_js:
-  - "6.10.0"
-python:
-  - "3.6"
+language: minimal
+
 sudo: required
 
 services:
   - docker
 
-cache:
-  directories:
-    - ui/node_modules
-
 before_install:
-  - export CHROME_BIN=chromium-browser
-  - export DISPLAY=:99.0
-  - sh -e /etc/init.d/xvfb start
-  
+  - |
+      if ! git diff --name-only $TRAVIS_COMMIT_RANGE | grep -qvE '(.md)|(.png)|(.)|^(LICENSE)|^(docs)|^(robots.txt)|^(package-list-yum)|^(package-list-pacman)|^(package-list-dnf)|^(package-list-brew)|^(package-list-aptget)|^(humans.txt)|^(docker-compose.yml)|^(docker-compose.dev.yml)|^(bassa)|^(.gitignore)|^(.gitattributes)|^(bassa-ui.yaml)|^(bassa-ingress.yaml)|^(bassa-api.yaml)|^(deploy_rds.sh)|^(rds-dev.json)|^(template.json)|^(setup-mysql.sh)|^(setup-database.sh)|^(create-schema.sh)|^(Bassa.sql)'
+      then
+        echo "Files changed not related to dockerfile, therefore travis build ends"
+        exit
+      fi
+
 script: 
-  - ./setup.sh 
-  - cd ui && npm install && npm test
-  - cd $TRAVIS_BUILD_DIR
-  - cd components/core && python setup.py test
-  - docker build --build-arg VCS_REF=`git rev-parse --short HEAD`   --build-arg BUILD_DATE=`date -u +”%Y-%m-%dT%H:%M:%SZ”` -t scoreucsc/bassa  .
+  - docker build --build-arg VCS_REF=`git rev-parse --short HEAD`   --build-arg BUILD_DATE=`date -u +”%Y-%m-%dT%H:%M:%SZ”` -t scoreucsc/bassa-ui  ui
+  - docker build --build-arg VCS_REF=`git rev-parse --short HEAD`   --build-arg BUILD_DATE=`date -u +”%Y-%m-%dT%H:%M:%SZ”` -t scoreucsc/bassa   components/core
 
 after_success:
   - if [ "$TRAVIS_BRANCH" == "master" -a "$TRAVIS_PULL_REQUEST" == "false" ]; then
     docker login -u "$DOCKER_USERNAME" -p "$DOCKER_PASSWORD";
     docker push scoreucsc/bassa;
     curl -X POST 'https://hooks.microbadger.com/images/scoreucsc/bassa/Wbi5zehDMooS3ri2bgC8LETGGuQ=';
+    docker push scoreucsc/bassa-ui;
+    curl -X POST 'https://hooks.microbadger.com/images/scoreucsc/bassa-ui/et6pa2aJq-tEvwFoW-PL8ixNxr0=';
     fi
 

code_of_conduct.md renamed to CODE_OF_CONDUCT.md

@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    {project}  Copyright (C) {year}  {fullname}
+    Bassa Project Copyright (C) 2019 , ScoreLab
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.