Merge branch 'develop' of https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa

2bbaa8d2 · jlopez · c19068c7 · 5a75029d · 2bbaa8d2 · c19068c7
Commit 2bbaa8d2 authored May 24, 2019 by jlopez
--- a/.docker/db/wicopa/.gitkeep
+++ b/.docker/db/wicopa/.gitkeep
--- a/.docker/web/Dockerfile
+++ b/.docker/web/Dockerfile
-FROM alpine:3.9
-
-LABEL Author remyd1 - https://github.com/remyd1
-RUN apk --update add php-apache2 php7-session php7-mysqli && rm -f /var/cache/apk/*
-
-
-RUN mkdir /app && cd /app && \
-  wget https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/archive/v0.3/wicopa-v0.3.tar.gz && \
-  tar -xf wicopa-v0.3.tar.gz && ln -s wicopa-v0.3 wicopa && \
-  cp wicopa/conf/Conf.php.sample wicopa/conf/Conf.php && \
-  chown -R apache:apache /app && \
-  sed -i "s#DB_NAME       = ''#DB_NAME       = 'wicopa'#" wicopa/conf/Conf.php && \
-  sed -i "s#DB_HOSTNAME   = ''#DB_HOSTNAME   = 'wicopadb'#" wicopa/conf/Conf.php && \
-  sed -i "s#DB_USERNAME   = ''#DB_USERNAME   = 'wicopauser'#" wicopa/conf/Conf.php && \
-  sed -i "s#DB_PP         = ''#DB_PP         = 'w1c0Pa5s'#" wicopa/conf/Conf.php && \
-  sed -i "s#'to_replace_with_your_admin_pass'#'450cb0c92db35549cb926efc391df2ceae4b48d1'#" wicopa/conf/Conf.php
-
-RUN sed -i 's/^#ServerName .*/ServerName localhost:80/g' /etc/apache2/httpd.conf && \
-  sed -i 's#/var/www/localhost/htdocs#/app/wicopa#g' /etc/apache2/httpd.conf && \
-  sed -i 's/^LoadModule php7_module.*/LoadModule php7_module modules\/libphp7\.so/g' /etc/apache2/httpd.conf && \
-  sed -i 's/DirectoryIndex index\.html/DirectoryIndex index\.php/g' /etc/apache2/httpd.conf && \
-  sed -ri 's#^DocumentRoot .*#DocumentRoot "/app/wicopa"#g' /etc/apache2/httpd.conf && \
-  sed -i 's#AllowOverride None#AllowOverride All#g' /etc/apache2/httpd.conf && \
-  echo "AddType application/x-httpd-php .php" >> /etc/apache2/httpd.conf
-
-RUN echo "Success"
-
-EXPOSE 80
-
-ENTRYPOINT httpd -D FOREGROUND && /bin/bash
--- a/.docker/web/Dockerfile
+++ b/.docker/web/Dockerfile
+Dockerfile.develop
\ No newline at end of file
--- a/.docker/web/Dockerfile.develop
+++ b/.docker/web/Dockerfile.develop
+FROM alpine:3.9
+
+LABEL Author remyd1 - https://github.com/remyd1
+RUN apk --update add php-apache2 php7-session php7-mysqli git && rm -f /var/cache/apk/*
+
+
+RUN mkdir /app && cd /app && \
+  git clone https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa.git
+
+WORKDIR /app/wicopa
+
+RUN git checkout develop && \
+  cp inc/conf/Conf.php.sample inc/conf/Conf.php && \
+  chown -R apache:apache /app && \
+  sed -i "s#DB_NAME       = ''#DB_NAME       = 'wicopa'#"      inc/conf/Conf.php && \
+  sed -i "s#DB_HOSTNAME   = ''#DB_HOSTNAME   = 'wicopadb'#"    inc/conf/Conf.php && \
+  sed -i "s#DB_USERNAME   = ''#DB_USERNAME   = 'wicopauser'#"  inc/conf/Conf.php && \
+  sed -i "s#DB_PP         = ''#DB_PP         = 'w1c0Pa5s'#"    inc/conf/Conf.php && \
+  sed -i "s#'to_replace_with_your_admin_pass'#'450cb0c92db35549cb926efc391df2ceae4b48d1'#" inc/conf/Conf.php
+
+RUN sed -i 's/^#ServerName .*/ServerName localhost:80/g' /etc/apache2/httpd.conf && \
+  sed -i 's#/var/www/localhost/htdocs#/app/wicopa#g' /etc/apache2/httpd.conf && \
+  sed -i 's/^LoadModule php7_module.*/LoadModule php7_module modules\/libphp7\.so/g' /etc/apache2/httpd.conf && \
+  sed -i 's/DirectoryIndex index\.html/DirectoryIndex index\.php/g' /etc/apache2/httpd.conf && \
+  sed -ri 's#^DocumentRoot .*#DocumentRoot "/app/wicopa"#g' /etc/apache2/httpd.conf && \
+  sed -i 's#AllowOverride None#AllowOverride All#g' /etc/apache2/httpd.conf && \
+  echo "AddType application/x-httpd-php .php" >> /etc/apache2/httpd.conf
+
+RUN echo "Success"
+
+EXPOSE 80
+
+ENTRYPOINT httpd -D FOREGROUND && /bin/bash
--- a/.docker/web/Dockerfile.stable
+++ b/.docker/web/Dockerfile.stable
+FROM alpine:3.9
+
+LABEL Author remyd1 - https://github.com/remyd1
+RUN apk --update add php-apache2 php7-session php7-mysqli && rm -f /var/cache/apk/*
+
+
+RUN mkdir /app && cd /app && \
+  wget https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/archive/v0.4/wicopa-v0.4.tar.gz && \
+  tar -xf wicopa-v0.4.tar.gz && ln -s wicopa-v0.4 wicopa && \
+  cp wicopa/inc/conf/Conf.php.sample wicopa/inc/conf/Conf.php && \
+  chown -R apache:apache /app && \
+  sed -i "s#DB_NAME       = ''#DB_NAME       = 'wicopa'#" wicopa/inc/conf/Conf.php && \
+  sed -i "s#DB_HOSTNAME   = ''#DB_HOSTNAME   = 'wicopadb'#" wicopa/inc/conf/Conf.php && \
+  sed -i "s#DB_USERNAME   = ''#DB_USERNAME   = 'wicopauser'#" wicopa/inc/conf/Conf.php && \
+  sed -i "s#DB_PP         = ''#DB_PP         = 'w1c0Pa5s'#" wicopa/inc/conf/Conf.php && \
+  sed -i "s#'to_replace_with_your_admin_pass'#'450cb0c92db35549cb926efc391df2ceae4b48d1'#" wicopa/inc/conf/Conf.php
+
+RUN sed -i 's/^#ServerName .*/ServerName localhost:80/g' /etc/apache2/httpd.conf && \
+  sed -i 's#/var/www/localhost/htdocs#/app/wicopa#g' /etc/apache2/httpd.conf && \
+  sed -i 's/^LoadModule php7_module.*/LoadModule php7_module modules\/libphp7\.so/g' /etc/apache2/httpd.conf && \
+  sed -i 's/DirectoryIndex index\.html/DirectoryIndex index\.php/g' /etc/apache2/httpd.conf && \
+  sed -ri 's#^DocumentRoot .*#DocumentRoot "/app/wicopa"#g' /etc/apache2/httpd.conf && \
+  sed -i 's#AllowOverride None#AllowOverride All#g' /etc/apache2/httpd.conf && \
+  echo "AddType application/x-httpd-php .php" >> /etc/apache2/httpd.conf
+
+RUN echo "Success"
+
+EXPOSE 80
+
+ENTRYPOINT httpd -D FOREGROUND && /bin/bash
--- a/.gitignore
+++ b/.gitignore
 wicopa.sql
-conf/Conf.php
+inc/conf/Conf.php
 *.swp
+.docker/db/wicopa/*
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
+stages:
+  - build
+  - test
+  - deploy
+
+image: docker:latest
+
+services:
+  - docker:dind
+
+PrebuildJob:
+  stage: build
+  tags:
+    - bioco
+  script:
+    - apk update
+    - apk add --no-cache py-pip python-dev libffi-dev openssl-dev gcc libc-dev make wget gzip git net-tools
+    - git clone https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa.git
+    - cd wicopa
+    - wget -q http://web.mbb.univ-montp2.fr/download/wicopa.sql.gz
+    - gunzip -d wicopa.sql.gz
+    - pip install docker-compose
+
+
+BuildJob:
+  stage: build
+  script:
+    - docker-compose --version
+    - docker info
+    - docker-compose build
+
+TestJob:
+  stage: test
+  script:
+    - docker info
+
+RunDeployment:
+  stage: deploy
+  tags:
+    - bioco
+  script:
+    - docker-compose up
+    - netstat -naptu |grep -E "80|3306"
+    - wget http://127.0.0.1:8000
+    - cat index.*
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -9,7 +9,7 @@ a2enmod php7.0

 cd /var/www/html/wicopa

-cp conf/Conf.php.sample conf/Conf.php
+cp inc/conf/Conf.php.sample inc/conf/Conf.php

 chown -R www-data /var/www/html/wicopa
 chmod -R o-r /var/www/html/wicopa
@@ -30,7 +30,7 @@ wget http://web.mbb.univ-montp2.fr/download/wicopa.sql.gz

 pv wicopa.sql.gz | gunzip | mysql -uwicopauser -p wicopa

-vim conf/Conf.php
+vim inc/conf/Conf.php
 ```

 # Using Docker
@@ -38,13 +38,13 @@ vim conf/Conf.php
 ```bash
 git clone https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa.git
 # you need to have wicopa.sql here
-wget http://web.mbb.univ-montp2.fr/download/wicopa.sql.gz
-gunzip -d wicopa.sql.gz
-
-mkdir -p /data/mysql/wicopa
+cd wicopa
+wget http://web.mbb.univ-montp2.fr/download/wicopa.sql.gz && gunzip -d wicopa.sql.gz

-docker-compose up --build
+sudo docker-compose up --build
 # you can access to it at http://127.0.0.1:8000
 # you can login as "admin" with password w1c0Pa5s
 ```

+Your database will be located in `.docker/db/wicopa`.
+Note: the `:z` option on your volumes in the docker-compose file is needed if you run it on RedHat-like distros, due to some selinux problems [See here for more informations](https://www.projectatomic.io/blog/2015/06/using-volumes-with-docker-can-cause-problems-with-selinux/).
--- a/README.md
+++ b/README.md
 # wicopa

-Web Interface Container Packaging
+Wicopa means **Web Interface for Container PAckaging**
+
+This Web UI application can generate Dockerfiles or definition files for Singularity.

 # Install

 Check [INSTALL](INSTALL.md)
+
+You can test it easily with Docker, using `docker-compose` ([See here](INSTALL.md#using-docker)).
+
+# Roadmap
+
+  - Tags to search recipes ([see issue #11](https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/issues/11)),
+  - Loading and sharing recipes ([see issue #10](https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/issues/10)),
+  - Adding a custom local configuration to all recipes. Indeed, HPC administrator could occasionnally allow Singularity containers on their cluster. Thus, they usually need to edit the recipe to add custom contents, in order to rebuild the image ([see issue #7](https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/issues/7)),
+  - Convert the functions to retrieve specific language packages in pure PHP to be able to upgrade it directly from the admin panel ([see issue #2](https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/issues/2)),
+  - adding a connection to a personal Gitlab/Github profile ([see issue #13](https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/issues/13)).
\ No newline at end of file
--- a/container.php
+++ b/container.php
@@ -21,8 +21,13 @@ $containers = $db->getContainers();
    <!-- Bootstrap CSS -->
    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
    <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/jquery.dataTables.min.css" crossorigin="anonymous">
-    <link rel="stylesheet" href="./css/style.css">
-    <script src="./js/jscolor.js"></script>
+
+    <!-- local fallbacks -->
+    <!--link rel="stylesheet" href="./inc/css/bootstrap.min.css">
+    <link rel="stylesheet" href="./inc/css/jquery.dataTables.min.css"-->
+
+    <link rel="stylesheet" href="./inc/css/style.css">
+    <script src="./inc/js/jscolor.js"></script>
    <title>wicopa</title>

 </head>
@@ -181,10 +186,13 @@ $containers = $db->getContainers();

 <!-- jQuery Version 1.11.1 -->
 <script src="http://code.jquery.com/jquery-latest.min.js" type="text/javascript"></script>
-
 <!-- Latest compiled and minified JavaScript -->
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>

+<!-- local fallbacks -->
+<!--script src="inc/js/jquery-latest.min.js" type="text/javascript"></script>
+<script src="inc/js/bootstrap.min.js" type="text/javascript"></script-->
+
 <script type="text/javascript">
 </script>


--- a/dao/DBquery.php
+++ b/dao/DBquery.php
@@ -6,7 +6,7 @@
 * Time: 16:38
 */

-require_once(__DIR__.'/../conf/Conf.php');
+require_once(__DIR__.'/../inc/conf/Conf.php');
 require_once(__DIR__.'/../model/Section.php');
 require_once(__DIR__.'/../model/Manager.php');
 require_once(__DIR__.'/../model/Distribution.php');

--- a/dao/LDAPquery.php
+++ b/dao/LDAPquery.php
@@ -4,7 +4,7 @@
 * Connection to ldap
 */

-require_once(__DIR__.'/../conf/Conf.php');
+require_once(__DIR__.'/../inc/conf/Conf.php');

 class LDAPquery {


--- a/docker-compose.yml
+++ b/docker-compose.yml
 version: '3'

 services:
-  apache:
+  web:
    build: 
-      context: .
-      dockerfile: .docker/web/Dockerfile
+      context: .docker/web
    container_name: wicopaweb
    restart: always
    ports:
      - "8000:80"
    depends_on: 
-      - mariadb
-  mariadb:
+      - db
+  db:
    image: mariadb:10.3
    restart: always
    container_name: wicopadb
    volumes:
-      - /data/mysql/wicopa:/var/lib/mysql
-      - ./wicopa.sql:/docker-entrypoint-initdb.d/wicopa.sql
+            - ./.docker/db/wicopa:/var/lib/mysql:z
+            - ./wicopa.sql:/docker-entrypoint-initdb.d/wicopa.sql:z
    environment:
      MYSQL_ROOT_PASSWORD: w1c0Pa5s
      MYSQL_DATABASE: wicopa

--- a/conf/Conf.php.sample
+++ b/conf/Conf.php.sample
--- a/css/.DS_Store
+++ b/css/.DS_Store
--- a/css/bootstrap-grid.css
+++ b/css/bootstrap-grid.css
--- a/css/bootstrap-grid.css.map
+++ b/css/bootstrap-grid.css.map
--- a/css/bootstrap-grid.min.css
+++ b/css/bootstrap-grid.min.css
--- a/css/bootstrap-grid.min.css.map
+++ b/css/bootstrap-grid.min.css.map
--- a/css/bootstrap-reboot.css
+++ b/css/bootstrap-reboot.css