first commit

.gitignore

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+.DS_Store
+*~
+*.swp
+test.php
+test-exec.php
+admin/config.ini
+admin/.htpasswd
+uploads/

.htaccess

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+# FORCE HTTPS
+RewriteEngine On
+RewriteCond %{HTTPS} !=on
+RewriteRule .* https://%{SERVER_NAME}%{REQUEST_URI} [R=301,L]

DOCUMENTATION

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+// HTML5
+// PHP5
+// PDO
+// jquery
+// vim
+
+// Licence Affero GPL v3
+
+// For PDF creation, we use fpdf http://www.fpdf.org
+// Accounts
+- Passwords are salted with a random salt, stored in SQL with the sha-512 hash.
+- Password forgotten => reset pass with password sent to email.

INSTALL

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+Thank you for choosing eLabFTW as a lab manager.
+
+Here is what you need in order to install it :
+
+- a server running GNU/Linux (although a Mac OS X or Windows server might work too, but I wouldn't recommand it)
+- with PHP5, MySQL5 (other relational database might work, as it uses PDO), Apache (other http servers might work)
+- basic knowledge of server administration, command line work
+- root access to the server ^^
+
+Have everything ?
+Now, let's begin :
+
+
+INSTALL
+*********************
+
+Connect to your server via SSH and fireup tmux (or screen).
+If you don't know what is SSH, maybe it's not a good idea to try and install eLabFTW.
+
+As root, cd to your public directory (/var/www generally) and enter these commands :
+
+PHP part
+*********
+
+(If you are behind a proxy :
+# export http_proxy=proxy-adress.company.org:3128
+)
+Get latest version
+# wget http://www.elabftw.net/downloads/latest.zip
+Extract it in the public folder
+# unzip latest.zip
+Now you have all the php files, we just need to add a library so the mails can be sent
+# pear channel-discover pear.swiftmailer.org
+# pear install swift/swift
+
+SQL part
+***********
+
+# mysql -uroot -ppassword < create_tables.sql
+

PASTIE

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+
+<!-- Redirect the user to the index after 2 secs -->
+<script>setTimeout('top.location = \'index.php\'', 2000);</script>

TODO

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+/////// Priority
+* search : selector should stay what it was
+* search : multiple critères( has file attached ?)
+* $_SESSION['groups']
+    with array of groups ?
+* put images in themes
+* most used protocoles get first in selecta ! 
+* remove "experiment" in zip file from prot
+* todo list on the side : with priorities (+/-)
+* templates for Exp (with blocks ?)
+* export by date range / tag
+* journal club : see past JC with papers
+* offline version !!
+
+** register
+* ask admin to validate new accounts
+* profile seeable by others
+* skype, tel, telperso, url
+* list protocols in exp to link them
+
+////// Features
+* dans ucp : tu choisis tes templates ! et tu choisis celle qui est créée par défaut, ensuite dans la page createXP, tu peux loader des templates
+* autosuggest on tags
+* announce birthday date of a team mb to other team mb
+* choose from tagcloud (need ajax for addtag, deltag)
+* statistics : make pie chart by tag
+* news feature, anyone can put a news up for evereybody to see
+* tree feature, tree in left pane, and manips related in right pane.
+* journal club
+* when click on file div, change file (with ajax ?)
+* add real calendar
+
+///// Osef
+* It's impossible to make a date before 2010 or after 2099
+* outcome is not kept if error
+* if two file field and file is only on the second one (first is empty) no file uploaded
+///// Longterm
+* un gestionnaire de musique à la ledjam
+* i18n
+
+///// SECURITY
+* check for flood register/login
+
+INSTALL
+put php files on server
+go to install.php
+asked for admin password
+admin password is generated and put inside sql file
+admin password for admin/.htpasswd
+sql create database
+import tables
+all running !

add_tag.php

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+<?php
+/********************************************************************************
+*                                                                               *
+*   Copyright 2012 Nicolas CARPi (nicolas.carpi@gmail.com)                      *
+*   http://www.elabftw.net/                                                     *
+*                                                                               *
+********************************************************************************/
+
+/********************************************************************************
+*  This file is part of eLabFTW.                                                *
+*                                                                               *
+*    eLabFTW is free software: you can redistribute it and/or modify            *
+*    it under the terms of the GNU Affero General Public License as             *
+*    published by the Free Software Foundation, either version 3 of             *
+*    the License, or (at your option) any later version.                        *
+*                                                                               *
+*    eLabFTW is distributed in the hope that it will be useful,                 *
+*    but WITHOUT ANY WARRANTY; without even the implied                         *
+*    warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR                    *
+*    PURPOSE.  See the GNU Affero General Public License for more details.      *
+*                                                                               *
+*    You should have received a copy of the GNU Affero General Public           *
+*    License along with eLabFTW.  If not, see <http://www.gnu.org/licenses/>.   *
+*                                                                               *
+********************************************************************************/
+/* addtag.php - for adding tags */
+require_once("inc/auth.php");
+require_once("inc/connect.php");
+
+// Check expid is valid and assign it to $expid
+if (filter_var($_POST['item_id'], FILTER_VALIDATE_INT)) {
+    $item_id = $_POST['item_id'];
+} else {
+    die("The experiment id parameter in the URL isn't a valid experiment ID");
+}
+// Sanitize tag
+$tag = filter_var($_POST['tag'], FILTER_SANITIZE_STRING);
+
+// Tag for experiment or protocol ?
+if ($_POST['type'] == 'exp' ){
+
+// Check expid is owned by connected user
+$sql = "SELECT userid FROM experiments WHERE id = ".$item_id;
+$req = $bdd->prepare($sql);
+$req->execute();
+$data = $req->fetch();
+if ($data['userid'] == $_SESSION['userid']) {
+    // SQL for addtag
+    $sql = "INSERT INTO experiments_tags (tag, item_id, userid) VALUES(:tag, :item_id, :userid)";
+    $req = $bdd->prepare($sql);
+    $result = $req->execute(array(
+        'tag' => $tag,
+        'item_id' => $item_id,
+        'userid' => $_SESSION['userid']
+    ));
+    if ($result) {
+        header("location: experiments.php?mode=edit&id=$item_id&tagadded=1");
+    } else {
+        die('Something went wrong in the database query. Check the flux capacitor.');
+    }
+}
+}elseif ($_POST['type'] == 'prot'){
+    // SQL for add tag to protocol
+    $sql = "INSERT INTO protocols_tags (tag, item_id) VALUES(:tag, :item_id)";
+    $req = $bdd->prepare($sql);
+    $result = $req->execute(array(
+        'tag' => $tag,
+        'item_id' => $item_id));
+    if ($result) {
+        header("location: protocols.php?mode=edit&id=$item_id&tagadded=1");
+    } else {
+        die('Something went wrong in the database query. Check the flux capacitor.');
+    }
+}else{
+    die('taggle');
+}

admin-exec.php

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+<?php
+/********************************************************************************
+*                                                                               *
+*   Copyright 2012 Nicolas CARPi (nicolas.carpi@gmail.com)                      *
+*   http://www.elabftw.net/                                                     *
+*                                                                               *
+********************************************************************************/
+
+/********************************************************************************
+*  This file is part of eLabFTW.                                                *
+*                                                                               *
+*    eLabFTW is free software: you can redistribute it and/or modify            *
+*    it under the terms of the GNU Affero General Public License as             *
+*    published by the Free Software Foundation, either version 3 of             *
+*    the License, or (at your option) any later version.                        *
+*                                                                               *
+*    eLabFTW is distributed in the hope that it will be useful,                 *
+*    but WITHOUT ANY WARRANTY; without even the implied                         *
+*    warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR                    *
+*    PURPOSE.  See the GNU Affero General Public License for more details.      *
+*                                                                               *
+*    You should have received a copy of the GNU Affero General Public           *
+*    License along with eLabFTW.  If not, see <http://www.gnu.org/licenses/>.   *
+*                                                                               *
+********************************************************************************/
+/* admin-exec.php - for administration of the elab */
+require_once('inc/common.php');
+if ($_SESSION['is_admin'] != 1) {die('You are not admin !');}
+
+// VALIDATE USERS
+if (isset($_POST['validate'])) {
+    $msg_arr = array();
+    $sql = "UPDATE users SET validated = 1 WHERE userid = :userid";
+    $req = $bdd->prepare($sql);
+    foreach ($_POST['validate'] as $user) {
+        $req->execute(array(
+            'userid' => $user
+        ));
+            $msg_arr[] = 'Validated user with user ID : '.$user;
+    }
+    $_SESSION['infos'] = $msg_arr;
+    header('Location: admin.php');
+    exit();
+}
+
+// MANAGE USERS
+if (isset($_GET['deluser']) && filter_var($_GET['deluser'], FILTER_VALIDATE_INT)) {
+    $userid = $_GET['deluser'];
+    $msg_arr = array();
+    // DELETE USER
+    $sql = "DELETE FROM users WHERE userid = ".$userid;
+    $req = $bdd->prepare($sql);
+    $req->execute();
+    $msg_arr[] = 'Deleted user with user ID : '.$userid;
+    $_SESSION['infos'] = $msg_arr;
+    header('Location: admin.php');
+    exit();
+}

admin.php

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+<?php
+/********************************************************************************
+*                                                                               *
+*   Copyright 2012 Nicolas CARPi (nicolas.carpi@gmail.com)                      *
+*   http://www.elabftw.net/                                                     *
+*                                                                               *
+********************************************************************************/
+
+/********************************************************************************
+*  This file is part of eLabFTW.                                                *
+*                                                                               *
+*    eLabFTW is free software: you can redistribute it and/or modify            *
+*    it under the terms of the GNU Affero General Public License as             *
+*    published by the Free Software Foundation, either version 3 of             *
+*    the License, or (at your option) any later version.                        *
+*                                                                               *
+*    eLabFTW is distributed in the hope that it will be useful,                 *
+*    but WITHOUT ANY WARRANTY; without even the implied                         *
+*    warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR                    *
+*    PURPOSE.  See the GNU Affero General Public License for more details.      *
+*                                                                               *
+*    You should have received a copy of the GNU Affero General Public           *
+*    License along with eLabFTW.  If not, see <http://www.gnu.org/licenses/>.   *
+*                                                                               *
+********************************************************************************/
+/* admin.php - for administration of the elab */
+require_once('inc/common.php');
+if ($_SESSION['is_admin'] != 1) {die('You are not admin !');}
+$title = 'Admin Panel';
+require_once('inc/head.php');
+require_once('inc/menu.php');
+require_once('inc/info_box.php');
+?>
+<h2>ADMIN PANEL</h2>
+<?php
+// SQL to get all unvalidated users
+$sql = "SELECT userid, lastname, firstname, email FROM users WHERE validated = 0";
+$req = $bdd->prepare($sql);
+$req->execute();
+$count = $req->rowCount();
+// only show the frame if there is some users to validate
+if ($count > 0) {
+    echo "
+<section class='fail'>
+<h3>USERS WAITING FOR VALIDATION</h3>";
+echo "<form method='post' action='admin-exec.php'><ul>";
+while ($data = $req->fetch()) {
+    echo "<li><input type='checkbox' name='validate[]' value='".$data['userid']."'> ".$data['firstname']." ".$data['lastname']." (".$data['email'].")</li>";
+}
+echo "</ul><input type='submit' name='submit' value='Validate users' /></form>";
+echo "</section>";
+}
+?>
+
+<section class='item'>
+<h3>TEAM MEMBERS</h3>
+<?php
+// TODO different colors for different groups
+// SQL to get all users
+$sql = "SELECT userid, lastname, firstname, email FROM users WHERE validated = 1";
+$req = $bdd->prepare($sql);
+$req->execute();
+echo "<form method='post' action='admin-exec.php'><ul>";
+while ($data = $req->fetch()) {
+    echo "<li>".$data['firstname']." ".$data['lastname']." (".$data['email'].") :: <a href='admin-exec.php?deluser=".$data['userid']."'>delete</a> <a href='admin-exec.php?edituser=".$data['userid']."'>edit</a></li>";
+}
+echo "</section>";
+require_once('inc/footer.php') ?>

admin/.htaccess

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+AuthUserFile /Applications/MAMP/htdocs/admin/.htpasswd
+AuthName "Are you admin ?"
+AuthType Basic
+Require user admin

admin/version.ini

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+; Version file for eLabFTW
+version = 0.5