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Commit c4ffaccc authored by Gerald Salin's avatar Gerald Salin
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Merge branch 'typo3V9' into 'master' 

Typo3 v9

See merge request !122
parents f63d77ab dff01ecc
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ui/nG6/class.tx_nG6_eid.php
View file @ c4ffaccc
......@@ -542,6 +542,7 @@ class tx_nG6_eid {
$password = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('password'));
$cruser_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('creator'));
$from_email = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('from_email'));
$envelope_sender_address = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('envelope_sender_address'));
$pid = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('pid'));
$project_url = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('project_url'));
$send_an_email = filter_var(trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('send_an_email')), FILTER_VALIDATE_BOOLEAN);
......@@ -582,7 +583,7 @@ class tx_nG6_eid {
$message = str_replace("###PROJECT_LINK###", $project_url, $message);
$msg_table = explode('\n', $message);
$message = implode("\n", $msg_table);
mail($email, $create_user_title, $message, "From: <".$from_email.">");
mail($email, $create_user_title, $message, "From: <".$from_email.">",'-f '.$envelope_sender_address);
}
print '2'; // ok
} elseif ($res_code == 1) {
......@@ -615,7 +616,7 @@ class tx_nG6_eid {
$message = str_replace("###PROJECT_LINK###", $project_url, $message);
$msg_table = explode('\n', $message);
$message = implode("\n", $msg_table);
mail($email, $add_user_title, $message, "From: <".$from_email.">");
mail($email, $add_user_title, $message, "From: <".$from_email.">",'-f '.$envelope_sender_address);
}
print '0';
......@@ -703,6 +704,7 @@ class tx_nG6_eid {
$cruser_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('creator'));
$send_an_email = filter_var(trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('send_an_email')), FILTER_VALIDATE_BOOLEAN);
$from_email = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('from_email'));
$envelope_sender_address = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('envelope_sender_address'));
$updated = tx_nG6_db::update_user($user_id, $first_name, $last_name, $email, $group_name, $organism, $location, tx_nG6_utils::hash_password($password)) ;
......@@ -733,7 +735,7 @@ class tx_nG6_eid {
}
}
$mail_content .= "\nThe NG6 team";
mail($email, $mail_title, $mail_content, "From: <".$from_email.">");
mail($email, $mail_title, $mail_content, "From: <".$from_email.">",'-f '.$envelope_sender_address);
}
}
......
ui/nG6/ext_emconf.php
View file @ c4ffaccc
......@@ -10,7 +10,7 @@
# "version" and "dependencies" must not be touched!
########################################################################
$EM_CONF[$_EXTKEY] = array(
$EM_CONF['nG6'] = array(
'title' => 'nG6',
'description' => 'Next Generation Sequencing Information System',
'category' => 'plugin',
......
ui/nG6/ext_localconf.php
View file @ c4ffaccc
......@@ -6,52 +6,52 @@ exec('chmod 777 '.\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('n
exec('chmod 777 '.\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'res/smarty/templates_c');
## Extending TypoScript from static template uid=43 to set up userdefined tag:
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript($_EXTKEY,'setup','
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript('nG6','setup','
tt_content.CSS_editor.ch.tx_nG6_pi1 = < plugin.tx_nG6_pi1.CSS_editor
',43);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43($_EXTKEY,'pi1/class.tx_nG6_pi1.php','_pi1','list_type',1);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43('nG6','pi1/class.tx_nG6_pi1.php','_pi1','list_type',1);
## Extending TypoScript from static template uid=43 to set up userdefined tag:
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript($_EXTKEY,'setup','
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript('nG6','setup','
tt_content.CSS_editor.ch.tx_nG6_pi2 = < plugin.tx_nG6_pi2.CSS_editor
',43);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43($_EXTKEY,'pi2/class.tx_nG6_pi2.php','_pi2','list_type',1);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43('nG6','pi2/class.tx_nG6_pi2.php','_pi2','list_type',1);
## Extending TypoScript from static template uid=43 to set up userdefined tag:
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript($_EXTKEY,'setup','
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript('nG6','setup','
tt_content.CSS_editor.ch.tx_nG6_pi3 = < plugin.tx_nG6_pi3.CSS_editor
',43);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43($_EXTKEY,'pi3/class.tx_nG6_pi3.php','_pi3','list_type',1);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43('nG6','pi3/class.tx_nG6_pi3.php','_pi3','list_type',1);
## Extending TypoScript from static template uid=43 to set up userdefined tag:
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript($_EXTKEY,'setup','
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript('nG6','setup','
tt_content.CSS_editor.ch.tx_nG6_pi4 = < plugin.tx_nG6_pi4.CSS_editor
',43);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43($_EXTKEY,'pi4/class.tx_nG6_pi4.php','_pi4','list_type',1);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43('nG6','pi4/class.tx_nG6_pi4.php','_pi4','list_type',1);
## Extending TypoScript from static template uid=43 to set up userdefined tag:
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript($_EXTKEY,'setup','
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript('nG6','setup','
tt_content.CSS_editor.ch.tx_nG6_pi5 = < plugin.tx_nG6_pi5.CSS_editor
',43);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43($_EXTKEY,'pi5/class.tx_nG6_pi5.php','_pi5','list_type',1);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43('nG6','pi5/class.tx_nG6_pi5.php','_pi5','list_type',1);
## Extending TypoScript from static template uid=43 to set up userdefined tag:
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript($_EXTKEY,'setup','
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addTypoScript('nG6','setup','
tt_content.CSS_editor.ch.tx_nG6_pi6 = < plugin.tx_nG6_pi6.CSS_editor
',43);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43($_EXTKEY,'pi6/class.tx_nG6_pi6.php','_pi6','list_type',1);
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPItoST43('nG6','pi6/class.tx_nG6_pi6.php','_pi6','list_type',1);
## Added to do some ajax
......
ui/nG6/ext_tables.php
View file @ c4ffaccc
<?php
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
if (!defined ('TYPO3_MODE')) die ('Access denied.');
$TCA["fe_rights_levels"] = Array(
......@@ -7,7 +8,7 @@ $TCA["fe_rights_levels"] = Array(
'label' => 'right_level_id',
"default_sortby" => "ORDER BY right_level_id",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php"
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6')."tca.php"
),
"feInterface" => Array (
"fe_admin_fieldList" => "right_level_id, right_level_label",
......@@ -20,7 +21,7 @@ $TCA["fe_rights"] = Array(
'label' => 'right_id, project_id, fe_user_id',
"default_sortby" => "ORDER BY right_id",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php"
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6')."tca.php"
),
"feInterface" => Array (
"fe_admin_fieldList" => "fe_user_id, right_id, project_id",
......@@ -46,8 +47,8 @@ $TCA["tx_nG6_run"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_run.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_run.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "hidden, name, date, directory, species, data_nature, type, nb_sequences, full_seq_size, description, sequencer",
......@@ -69,8 +70,8 @@ $TCA["tx_nG6_analyze"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_analyze.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_analyze.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "hidden, parent_uid, class, name, description, date, directory, software, version, params",
......@@ -92,8 +93,8 @@ $TCA["tx_nG6_sample"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_sample.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_sample.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "hidden, run_id, mid, description",
......@@ -115,8 +116,8 @@ $TCA["tx_nG6_result"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_result.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_result.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "analyze_id, file, rkey, rvalue, rgroup",
......@@ -138,8 +139,8 @@ $TCA["tx_nG6_project_run"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_project_run.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_project_run.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "hidden, project_id, run_id",
......@@ -161,8 +162,8 @@ $TCA["tx_nG6_project_analyze"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_project_analyze.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_project_analyze.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "hidden, project_id, analyze_id",
......@@ -184,8 +185,8 @@ $TCA["tx_nG6_run_analyze"] = Array (
"enablecolumns" => Array (
"disabled" => "hidden",
),
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY)."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::siteRelPath($_EXTKEY)."icon_tx_nG6_run_analyze.gif",
"dynamicConfigFile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."tca.php",
"iconfile" => \TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath('nG6'))."icon_tx_nG6_run_analyze.gif",
),
"feInterface" => Array (
"fe_admin_fieldList" => "hidden, run_id, analyze_id",
......@@ -195,32 +196,32 @@ $TCA["tx_nG6_run_analyze"] = Array (
//\TYPO3\CMS\Core\Utility\GeneralUtility::loadTCA('tt_content');
$TCA['tt_content']['types']['list']['subtypes_excludelist'][$_EXTKEY.'_pi1']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi1', $_EXTKEY.'_pi1'),'list_type', $_EXTKEY);
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi1_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY).'pi1/class.tx_nG6_pi1_wizicon.php';
$TCA['tt_content']['types']['list']['subtypes_excludelist']['nG6'.'_pi1']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi1', 'nG6'.'_pi1'),'list_type', 'nG6');
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi1_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'pi1/class.tx_nG6_pi1_wizicon.php';
//\TYPO3\CMS\Core\Utility\GeneralUtility::loadTCA('tt_content');
$TCA['tt_content']['types']['list']['subtypes_excludelist'][$_EXTKEY.'_pi2']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi2', $_EXTKEY.'_pi2'),'list_type', $_EXTKEY);
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi2_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY).'pi2/class.tx_nG6_pi2_wizicon.php';
$TCA['tt_content']['types']['list']['subtypes_excludelist']['nG6'.'_pi2']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi2', 'nG6'.'_pi2'),'list_type', 'nG6');
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi2_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'pi2/class.tx_nG6_pi2_wizicon.php';
//\TYPO3\CMS\Core\Utility\GeneralUtility::loadTCA('tt_content');
$TCA['tt_content']['types']['list']['subtypes_excludelist'][$_EXTKEY.'_pi3']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi3', $_EXTKEY.'_pi3'),'list_type', $_EXTKEY);
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi3_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY).'pi3/class.tx_nG6_pi3_wizicon.php';
$TCA['tt_content']['types']['list']['subtypes_excludelist']['nG6'.'_pi3']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi3', 'nG6'.'_pi3'),'list_type', 'nG6');
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi3_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'pi3/class.tx_nG6_pi3_wizicon.php';
//\TYPO3\CMS\Core\Utility\GeneralUtility::loadTCA('tt_content');
$TCA['tt_content']['types']['list']['subtypes_excludelist'][$_EXTKEY.'_pi4']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi4', $_EXTKEY.'_pi4'),'list_type', $_EXTKEY);
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi4_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY).'pi4/class.tx_nG6_pi4_wizicon.php';
$TCA['tt_content']['types']['list']['subtypes_excludelist']['nG6'.'_pi4']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi4', 'nG6'.'_pi4'),'list_type', 'nG6');
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi4_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'pi4/class.tx_nG6_pi4_wizicon.php';
//\TYPO3\CMS\Core\Utility\GeneralUtility::loadTCA('tt_content');
$TCA['tt_content']['types']['list']['subtypes_excludelist'][$_EXTKEY.'_pi5']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi5', $_EXTKEY.'_pi5'),'list_type', $_EXTKEY);
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi5_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY).'pi5/class.tx_nG6_pi5_wizicon.php';
$TCA['tt_content']['types']['list']['subtypes_excludelist']['nG6'.'_pi5']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi5', 'nG6'.'_pi5'),'list_type', 'nG6');
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi5_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'pi5/class.tx_nG6_pi5_wizicon.php';
//\TYPO3\CMS\Core\Utility\GeneralUtility::loadTCA('tt_content');
$TCA['tt_content']['types']['list']['subtypes_excludelist'][$_EXTKEY.'_pi6']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi6', $_EXTKEY.'_pi6'),'list_type', $_EXTKEY);
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi6_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath($_EXTKEY).'pi6/class.tx_nG6_pi6_wizicon.php';
$TCA['tt_content']['types']['list']['subtypes_excludelist']['nG6'.'_pi6']='layout,select_key';
\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::addPlugin(Array('LLL:EXT:nG6/locallang_db.xml:tt_content.list_type_pi6', 'nG6'.'_pi6'),'list_type', 'nG6');
if (TYPO3_MODE=="BE") $TBE_MODULES_EXT["xMOD_db_new_content_el"]["addElClasses"]["tx_nG6_pi6_wizicon"] = \TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('nG6').'pi6/class.tx_nG6_pi6_wizicon.php';
?>
ui/nG6/ext_tables.sql
View file @ c4ffaccc
......@@ -6,7 +6,7 @@ CREATE TABLE fe_rights_levels (
right_level_id int(11) NOT NULL,
right_level_label varchar(20) NOT NULL,
PRIMARY KEY (right_level_id),
) CHARSET=utf8 ;
);
/*
......@@ -17,7 +17,7 @@ CREATE TABLE fe_rights (
project_id int(11) NOT NULL,
right_id int(11) NOT NULL,
PRIMARY KEY (fe_user_id, project_id, right_id)
) CHARSET=utf8 ;
) ;
/*
......@@ -37,7 +37,7 @@ CREATE TABLE tx_nG6_project (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
......@@ -65,7 +65,7 @@ CREATE TABLE tx_nG6_run (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
/*
......@@ -92,7 +92,7 @@ CREATE TABLE tx_nG6_analyze (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
......@@ -114,7 +114,7 @@ CREATE TABLE tx_nG6_sample (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
/*
......@@ -137,7 +137,7 @@ CREATE TABLE tx_nG6_result (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
/*
......@@ -157,7 +157,7 @@ CREATE TABLE tx_nG6_project_run (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
/*
......@@ -177,7 +177,7 @@ CREATE TABLE tx_nG6_project_analyze (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
) ;
/*
......@@ -197,4 +197,4 @@ CREATE TABLE tx_nG6_run_analyze (
PRIMARY KEY (uid),
KEY parent (pid)
) CHARSET=utf8 ;
\ No newline at end of file
) ;
\ No newline at end of file
ui/nG6/lib/class.tx_nG6_utils.php
View file @ c4ffaccc
......@@ -234,7 +234,7 @@ class tx_nG6_utils {
}
$template_mail.='The nG6 purge process is undergoing an important overhaul.</br>
You can visit our FAQ at the following address : https://ng6.toulouse.inra.fr/index.php?id=57 .</br>
You can visit our FAQ at the following address : https://ng6.toulouse.inra.fr/faq .</br>
If you have any question or demand, do not hesitate to contact our support team at ng6-support@groupes.renater.fr.</br>';
$template_mail.='<p>Yours sincerely</p>
......@@ -298,12 +298,15 @@ $template_mail.='<p>Yours sincerely</p>
* @return hashed password
*/
static function hash_password($password){
if (\TYPO3\CMS\Crypto\PasswordHashing\SaltedPasswordsUtility::isUsageEnabled('FE')) {
$objSalt = \TYPO3\CMS\Core\Crypto\PasswordHashing\PasswordHashFactory::getSaltingInstance(NULL);
if (is_object($objSalt)) {
$saltedPassword = $objSalt->getHashedPassword($password);
}
}
$hashInstance = GeneralUtility::makeInstance(PasswordHashFactory::class)->getDefaultHashInstance('FE');
$hashedPassword = $hashInstance->getHashedPassword($password);
// if (\TYPO3\CMS\Crypto\PasswordHashing\SaltedPasswordsUtility::isUsageEnabled('FE')) {
// $objSalt = \TYPO3\CMS\Core\Crypto\PasswordHashing\PasswordHashFactory::getSaltingInstance(NULL);
// if (is_object($objSalt)) {
// $saltedPassword = $objSalt->getHashedPassword($password);
// }
// }
return $saltedPassword;
}
......
ui/nG6/pi1/class.tx_nG6_pi1.php
View file @ c4ffaccc
......@@ -200,6 +200,7 @@ class tx_nG6_pi1 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
$smarty->assign('user_login', $GLOBALS['TSFE']->fe_user->user['username']);
$smarty->assign('data_folder', $this->conf["data"]);
$smarty->assign('from_email', $this->conf["FromEmail"]);
$smarty->assign('envelope_sender_address', $this->conf["envelope_sender_address"]);
$smarty->assign('server_name', $this->conf["server_name"]);
$smarty->assign('project_ids', substr($project_ids,0,-1));
$smarty->assign('pid', $this->conf['userpidList']);
......
ui/nG6/pi1/class.tx_nG6_pi1_wizicon.php
View file @ c4ffaccc
......@@ -28,7 +28,7 @@
*/
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
class tx_nG6_pi1_wizicon {
/**
......
ui/nG6/pi1/project_view.tpl
View file @ c4ffaccc
......@@ -20,6 +20,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<input type="hidden" id="server_name" value="{$server_name}" />
<input type="hidden" id="from_email" value="{$from_email}" />
<input type="hidden" id="envelope_sender_address" value="{$envelope_sender_address}" />
<input type="hidden" id="user_id" value="{$user_id}" />
<input type="hidden" id="user_login" value="{$user_login}" />
<input type="hidden" id="pid" value="{$pid}" />
......
ui/nG6/pi2/class.tx_nG6_pi2_wizicon.php
View file @ c4ffaccc
......@@ -26,7 +26,7 @@
*
* @author PF bioinformatique de Toulouse <>
*/
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
class tx_nG6_pi2_wizicon {
/**
......
ui/nG6/pi3/class.tx_nG6_pi3_wizicon.php
View file @ c4ffaccc
......@@ -26,7 +26,7 @@
*
* @author PF bioinformatique de Toulouse <>
*/
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
class tx_nG6_pi3_wizicon {
/**
......
ui/nG6/pi4/class.tx_nG6_pi4_wizicon.php
View file @ c4ffaccc
......@@ -26,7 +26,7 @@
*
* @author PF bioinformatique de Toulouse <>
*/
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
class tx_nG6_pi4_wizicon {
/**
......
ui/nG6/pi5/class.tx_nG6_pi5_wizicon.php
View file @ c4ffaccc
......@@ -27,7 +27,7 @@
* @author PF bioinformatique de Toulouse <>
*/
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
class tx_nG6_pi5_wizicon {
/**
......
ui/nG6/pi6/class.tx_nG6_pi6.php
View file @ c4ffaccc
......@@ -239,7 +239,7 @@ class tx_nG6_pi6 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
$headers[] = 'MIME-Version: 1.0';
$headers[] = 'Content-type: text/html; charset=utf-8';
$headers[] = 'Cc: '.$GLOBALS['TSFE']->tmpl->setup["plugin."]["tx_nG6_pi6."]["email_copy"];
mail($to, $subject, $mail, implode("\r\n", $headers));
mail($to, $subject, $mail, implode("\r\n", $headers), '-f '. $GLOBALS['TSFE']->tmpl->setup["plugin."]["tx_nG6_pi6."]["envelope_sender_address"]);
//TODO check return function mail ok
}else{
//If the demand could not be inserted because another one already exists for the given project, we send a mail to the nG6 admins
......@@ -255,7 +255,7 @@ class tx_nG6_pi6 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
$headers[] = 'Content-type: text/html; charset=utf-8';
$headers[] = 'Cc: '.$GLOBALS['TSFE']->tmpl->setup["plugin."]["tx_nG6_pi6."]["email_copy"];
mail($to, $subject, $mail, implode("\r\n", $headers));
mail($to, $subject, $mail, implode("\r\n", $headers), '-f '. $GLOBALS['TSFE']->tmpl->setup["plugin."]["tx_nG6_pi6."]["envelope_sender_address"]);
}
}
return "Mail sent";
......@@ -319,7 +319,7 @@ class tx_nG6_pi6 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
$headers[] = 'Cc: '.$GLOBALS['TSFE']->tmpl->setup["plugin."]["tx_nG6_pi6."]["email_copy"];
$to= join(",",$res_demand["emails"]);
mail($to, $subject, $mail, implode("\r\n", $headers));
mail($to, $subject, $mail, implode("\r\n", $headers), '-f '. $GLOBALS['TSFE']->tmpl->setup["plugin."]["tx_nG6_pi6."]["envelope_sender_address"]);
}
}
}
......
ui/nG6/pi6/class.tx_nG6_pi6_wizicon.php
View file @ c4ffaccc
......@@ -26,7 +26,7 @@
*
* @author PF bioinformatique de Toulouse <>
*/
use \TYPO3\CMS\Core\Utility\ExtensionManagementUtility;
class tx_nG6_pi6_wizicon {
/**
......
ui/nG6/res/js/tx_nG6_pi1.js
View file @ c4ffaccc
......@@ -580,6 +580,7 @@ $(function () {
val_url += "&user_id=" + user_id ;
val_url += "&send_an_email=" + $("#send_email_chk")[0].checked;
val_url += "&from_email=" + $("#from_email").val();
val_url += "&envelope_sender_address=" + $("#envelope_sender_address").val();
$.ajax({
url: val_url,
......@@ -893,6 +894,7 @@ $(function () {
val_url += "&create_user_email=" + escape("Dear ###USER_FIRST_NAME### ###USER_LAST_NAME###,\nPlease find bellow your login/password required to log into the NG6 system (###PROJECT_LINK###): \n - login: ###USER_LOGIN###\n - password: ###USER_PASSWORD###\nThe NG6 team\nPS: this is an automatic e-mail message generated by the NG6 system. Please DO NOT RESPOND to this e-mail because the mail box is unattended.");
val_url += "&create_user_title=[NG6] Account creation";
val_url += "&from_email=" + $("#from_email").val();
val_url += "&envelope_sender_address=" + $("#envelope_sender_address").val();
val_url += "&project_url=" + escape(location.href);
val_url += "&send_an_email=" + $("#send_email_chk")[0].checked;
......
ui/nG6/template/index.html → ui/nG6/template/Resources/Private/Templates/NG6.html
View file @ c4ffaccc
<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xml:lang="fr" xmlns="http://www.w3.org/1999/xhtml" lang="fr">
<head>
<title>nG6 - next Generation Sequencing Information System</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
<!-- <link rel="stylesheet" type="text/css" href="styles.css"/> -->
<!--[if lte IE 6]><link type="text/css" rel="stylesheet" href="http://www.alsacreations.com/css/ie6.css" media="all" /><![endif]-->
<!--[if IE 7]><link type="text/css" rel="stylesheet" href="http://www.alsacreations.com/css/ie7.css" media="all" /><![endif]-->
<script type="text/javascript">
$(document).ready(function() {
$('[class^=tooltip]').poshytip({
className: 'tip-twitter',
showTimeout: 1,
alignTo: 'target',
alignX: 'center',
offsetY: 5,
allowTipHover: false
});
});
</script>
</head>
<body>
<!-- ###DOCUMENT### -->
<!-- bloc header, content header, header-inside, evitement, logo, menu, sous-menu, recherche -->
<div id="ng6-header">
......@@ -33,27 +11,26 @@
<div id="sous-menu">
<!-- ###SEARCHBOX### -->
<!-- ###SEARCHBOX### -->
<!-- ###MENU### -->
<f:format.htmlentitiesDecode>{SEARCHBOX}</f:format.htmlentitiesDecode>
<!-- ###MENU### -->
<f:format.htmlentitiesDecode>{MENU}</f:format.htmlentitiesDecode>
</div>
</div>
</div> <!-- fin de header -->
<!-- Header-sep, designe la bande graphique entre l'entête et le bloc central -->
<!-- Header-sep, designe la bande graphique entre l'entte et le bloc central -->
<div id="ng6-header-sep" class="ng6-sep">
<div class="ng6-sep-inside">
<!-- ###BROWSER### -->
<!-- ###BROWSER### -->
<f:format.htmlentitiesDecode>{BROWSER}</f:format.htmlentitiesDecode>
</div>
</div>
<div id="global">
<!-- Bloc Center, contient center, content, sidebar et center-sep -->
<div id="page">
<div id="content">
<!-- ###CONTENT### -->
<!-- ###CONTENT### -->
<f:format.htmlentitiesDecode>{CONTENT}</f:format.htmlentitiesDecode>
</div> <!-- content -->
</div> <!-- fin de page -->
</div> <!-- fin de global -->
......@@ -94,7 +71,7 @@
<div class="ng6-bottom">
<div class="ng6-bottom2">
Copyright &copy; 2013, INRA | Designed by <a class="ng6-footer-link" href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo</a>,
Copyright &copy; 2013, INRAe | Designed by <a class="ng6-footer-link" href="http://bioinfo.genotoul.fr/" target="_blank">GenoToul Bioinfo</a>,
<a class="ng6-footer-link" href="http://genomique.genotoul.fr/" target="_blank">GenoToul Genomic</a>
and <a class="ng6-footer-link" href="http://www.sigenae.org/" target="_blank">Sigenae</a> teams | Optimized for
<a class="tooltip-firefox firefox" href="http://www.mozilla.org/firefox" target="_blank" title="Mozilla Firefox"> </a>
......@@ -102,5 +79,3 @@
</div>
</div>
<!-- ###DOCUMENT### -->
</body>
</html>
\ No newline at end of file
ui/nG6/template/css/style.css → ui/nG6/template/Resources/Public/Css/style.css
View file @ c4ffaccc
......@@ -102,7 +102,7 @@ a img { border: 0; }
*
********************************/
#ng6-header { background: url(../images/bando-logo2.png) 50% 35px no-repeat #222426; border-bottom: 1px solid black;}
#ng6-header { background: url(../Images/bando-logo2.png) 50% 35px no-repeat #222426; border-bottom: 1px solid black;}
#ng6-header h1 { margin: 15px 0 0 0; padding: 0; height: 66px; font-size: 15px; line-height: 1; }
#ng6-header-inside { position: relative; width: 1200px; margin: 0 auto; }
......@@ -111,7 +111,7 @@ a img { border: 0; }
#evitement li a { color : #F1F1F1; text-decoration: none; font-weight: bold; }
#evitement li a:hover, #evitement li a:focus { color : #567f87; }
#sous-menu { width: 1200px; height: 66px; margin