Merge branch 'user_management' into 'master'

User management

See merge request !15

application.properties.example

@@ -28,6 +28,8 @@ server_socket_host = 127.0.0.1
 # on which socket port should run the web server
 server_socket_port = 8080
 #server_socket_port = 8083
+# protocol used to access web server (http|https)
+server_socket_protocol = https
 # date format
 date_format = %d/%m/%Y
 # data retention time (in years)

src/jflow/config_reader.py

@@ -112,9 +112,9 @@ class JFlowConfigReader(object):
           
     def get_socket_options(self):
         try:
-            return [self.reader.get("global", "server_socket_host"), int(self.reader.get("global", "server_socket_port"))]
+            return [self.reader.get("global", "server_socket_host"), int(self.reader.get("global", "server_socket_port")), self.reader.get("global", "server_socket_protocol")]
         except:
-            return ["127.0.0.1", 8080]
+            return ["127.0.0.1", 8080,"http"]
         
     def get_ssl_files(self):
         try:

src/jflow/server.py

@@ -530,7 +530,7 @@ class JFlowServer (object):
         socket_opt = self.jflow_config_reader.get_socket_options()
         if not os.path.isdir(path):
             return {
-                    'url':'http://' + socket_opt[0] + ':' + str(socket_opt[1]) + '/' + path.replace(work_dir, web_path),
+                    'url':socket_opt[2]+'://' + socket_opt[0] + ':' + str(socket_opt[1]) + '/' + path.replace(work_dir, web_path),
                     'size': get_octet_string_representation(os.path.getsize(os.path.abspath(path))),
                     'extension': os.path.splitext(path)[1]
                    }

src/ng6/config_reader.py

@@ -159,12 +159,13 @@ class NG6ConfigReader(object):
     def get_server_parameters(self):
         """
         return the server parameters
-          @return:    server_socket_host, server_socket_port
+          @return:    server_socket_host, server_socket_port, server_socket_protocol
         """
 #        try:
         server_params = []
         server_params.append(self.reader.get('global', 'server_socket_host'))
         server_params.append(self.reader.get('global', 'server_socket_port'))
+        server_params.append(self.reader.get("global", 'server_socket_protocol'))
         return server_params
 #        except :
 #            raise Error("Failed when parsing the config file !") 

ui/nG6/class.tx_nG6_eid.php

@@ -61,7 +61,7 @@ class tx_nG6_eid {
     	//error_log("tx_nG6_eid ".$type." \n ", 3, "/work/tmp/mes-erreurs.log");
     	// If the type of data requested is project
     	if ($type == 'project') {
-    		$project_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('id'));
+    		$project_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('object_id'));
 	    	// Select all runs linked to the project
 	    	$project_runs = tx_nG6_db::get_user_project_runs($user_id, $project_id, 'tx_nG6_run.date DESC');
 	    	// for each run
@@ -79,7 +79,7 @@ class tx_nG6_eid {
 	    	
 	    // If the type of data requested is run
     	} else if ($type == 'run'){
-			$run_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('id'));
+			$run_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('object_id'));
 			// Select all analysis linked to the run and the run information
 			$run_analysis = tx_nG6_db::get_user_run_analysis($user_id, $run_id, 'tx_nG6_analyze.name');
 			$run_info = tx_nG6_db::select_run($run_id);
@@ -639,7 +639,7 @@ class tx_nG6_eid {
     		$group_name	= trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('title'));
     		$location	= trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('location'));
     		$organism	= trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('organism'));
-    		$user_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('id'));
+    		$user_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('user_id'));
     		$password = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('password'));
     		$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);
@@ -681,7 +681,7 @@ class tx_nG6_eid {
     		print $nb_updated;
     	}
     	else if ($type == 'get_user_group'){
-    		$id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('id'));
+    		$id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('user_id'));
     		print json_encode(tx_nG6_db::get_group_informations(tx_nG6_db::get_user_usergroup($id)));
     	}
     	elseif($type == 'runs_table') {

ui/nG6/pi1/analyzes/BasicAnalyse.tpl

+{*
+Copyright (C) 2009 INRA
+ 
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program 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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*}
+
+{extends file='AnalysisTemplate.tpl'}
+
+{block name=description_update}
+	<br/>
+	<div  style="float:right;">
+		{if $is_project_admin }
+			<button id="add_file" type="button" class="btn btn-sm btn-primary"><i class="glyphicon glyphicon-plus"></i> add files</button>
+		{/if}
+	</div>
+{/block}
+
+{* No result tab*}
+{block name=nav_menu_results}{/block}
+{block name=tab_content_results}{/block}
\ No newline at end of file

ui/nG6/res/js/tx_nG6_pi1.js

@@ -394,7 +394,7 @@ $(function () {
   			console.log("update_pwd " + update_pwd);
   			// get title laboratory and organism from ajax query
   			$.ajax({
-				url: "index.php?eID=tx_nG6&type=get_user_group&id=" + user_id ,
+				url: "index.php?eID=tx_nG6&type=get_user_group&user_id=" + user_id ,
 				dataType: 'json',
 				success: function (data) {
 					update_user_call_back(data, first_name);

ui/nG6/res/js/tx_nG6_pi5.js

@@ -398,7 +398,7 @@ $(function () {
 						run_description : "Run ###SPAN_NAME### (###SPAN_SPECIES###) - (###SPAN_DATE###) produced ###SPAN_NB_SEQ### reads",
 						analyse_description : "Analyse ###SPAN_NAME###",
 						user_id : $("#user_id").val(),
-						id : n.attr("id").split("_")[1],
+						object_id : n.attr("id").split("_")[1],
 						type : n.attr("id").split("_")[0]
 					};
             	}

workflows/components/subsetAssignation.py

@@ -16,6 +16,7 @@
 #
 
 import os, sys
+import logging
 from subprocess import Popen, PIPE
 
 from jflow.utils import get_argument_pattern
@@ -96,7 +97,7 @@ class SubsetAssignation (Analysis):
         self.use_index = "true"
         if not os.path.exists( self.databank + ".00.idx" ) :
             self.use_index = "false"
-            sys.stderr.write("[WARNING] " + self.__class__.__name__ + " works more quickly with megablast index.\n")
+            logging.getLogger("SubsetAssignation").warn("would work more quickly with megablast index")
         
         if group_prefix == None :
             self.add_parameter_list("group_prefixes", "group_prefix", default=list(map(os.path.basename, self.get_outputs('{basename_woext}', self.sequence_files))))