Merge branch 'master' into 'issue#129'

# Conflicts:
#   ui/nG6/lib/class.tx_nG6_db.php

src/ng6/ng6workflow.py

@@ -190,9 +190,6 @@ class NG6Workflow (BasicNG6Workflow):
         pidx = 1
         nidx = 1
         for rang, sample in enumerate(self.samples) :
-            print(sample)
-            print("sample readsi")
-            print(sample.readsi)
             if sample.name :
                 self.samples_names.append(sample.name)
             else :
@@ -686,15 +683,15 @@ class CasavaNG6Workflow(NG6Workflow):
 
             # archive the files
             #TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
-            saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("readsi")
+
+            saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index")
             logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
             reads_prefixes = None
             if self.group_prefix != None :
                 # concatenate fastq
                 reads_prefixes = list((Utils.get_group_basenames(saved_files, "read")).keys())
-                logging.getLogger("CasavaNG6Workflow").debug("illumina_process reads_prefixes = " + ",".join(reads_prefixes))
                 logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
-                concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files, reads_prefixes])
+                concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files,reads_prefixes])
                 saved_files = concatenatefastq.concat_files
                 logging.getLogger("CasavaNG6Workflow").debug("illumina_process after concatenatefastq, saved_files = " + ",".join(saved_files))
 

ui/nG6/lib/class.tx_nG6_db.php

@@ -2174,7 +2174,7 @@ static function get_project_runs($project_id, $orderby='', $limit='') {
 	 * Returns a run's retention status and date
 	 * 
 	 * @param string  $r_id			    the analyze ids
-	 * @return['run_data_state']	    purged=> the date is purged, stored=> the data is stored
+	 * @return['run_data_state']	    purged=> the date is purged, stored=> the data is stored, extended=>retention extended and data still stored
 	 * @return['run_retention_date']	the unix epoch timestamp
 	 */
 	static function select_run_retention_status($r_id) {
@@ -2182,7 +2182,8 @@ static function get_project_runs($project_id, $orderby='', $limit='') {
 		// First select the run from the database
 		$queryParts = Array( 
 			'SELECT' => 'tx_nG6_run.data_state AS run_data_state, '. 
-    					'tx_nG6_run.retention_date AS run_retention_date ',
+    					'tx_nG6_run.retention_date AS run_retention_date, '.
+    					'tx_nG6_run.purged_date AS run_purged_date ',
 			'FROM' => 'tx_nG6_run ',
 			'WHERE' => 'tx_nG6_run.uid='.$r_id,
 			'GROUPBY' => '',
@@ -2194,8 +2195,9 @@ static function get_project_runs($project_id, $orderby='', $limit='') {
 		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
 		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {			
 			$result['run_data_state'] = $row['run_data_state'];
-			//$result['run_retention_date'] = $row['run_data_state'];
 			$result['run_retention_date'] = tx_nG6_utils::convert_epoch_timestamp_to_nice_date($row['run_retention_date']);
+			$result['run_purge_date'] = tx_nG6_utils::convert_epoch_timestamp_to_nice_date($row['run_purged_date']);
+			//$result['run_purge_date'] = $row['run_purged_date'];
 		}
 		return $result;
 	}
@@ -2565,14 +2567,16 @@ static function get_project_runs($project_id, $orderby='', $limit='') {
 	 * 
 	 * @param string  $a_id				  the analysis id
 	 * @return['analysis_data_state']	  purged=> the date is purged, stored=> the data is stored
-	 * @return['analysis_retention_date'] the unix epoch timestamp
+	 * @return['analysis_retention_date'] the retention unix epoch timestamp converted to a nice date
+	 * @return['analysis_purged_date']    the purge unix epoch timestamp converted to a nice date
 	 */
 	static function select_analysis_retention_status($a_id) {
 
 		// First select the analysis from the database
 		$queryParts = Array( 
 			'SELECT' => 'tx_nG6_analyze.data_state AS analysis_data_state, '. 
-    					'tx_nG6_analyze.retention_date AS analysis_retention_date ',
+    					'tx_nG6_analyze.retention_date AS analysis_retention_date, '.
+    					'tx_nG6_analyze.purged_date AS analysis_purged_date ',
 			'FROM' => 'tx_nG6_analyze ',
 			'WHERE' => 'tx_nG6_analyze.uid='.$a_id,
 			'GROUPBY' => '',
@@ -2584,8 +2588,8 @@ static function get_project_runs($project_id, $orderby='', $limit='') {
 		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
 		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {			
 			$result['analysis_data_state'] = $row['analysis_data_state'];
-			//$result['analysis_retention_date'] = $row['analysis_retention_date'];
 			$result['analysis_retention_date'] = tx_nG6_utils::convert_epoch_timestamp_to_nice_date($row['analysis_retention_date']);
+			$result['analysis_purge_date'] = tx_nG6_utils::convert_epoch_timestamp_to_nice_date($row['analysis_purged_date']);
 		}
 		return $result;
 	}

ui/nG6/lib/class.tx_nG6_utils.php

@@ -288,12 +288,10 @@ please have a look at our storage fees (<a href="###URL_PRICE###">###URL_PRICE##
     
     static function get_retention_policy_from_space_id($space_id = "default"){
     	$config_file_content = tx_nG6_utils::get_config_content("default");
-    	//file_put_contents("/work/ng6-test/jflow_rtherville/ng6_php.log", "tx_nG6_utils, get_retention_policy_from_space_id(), config_file_content: \n".$config_file_content."\n", FILE_APPEND);
-    	
+		
     	//To explode the file content by line, we use PHP_EOL
     	$array_config_content = explode(PHP_EOL, $config_file_content);
-    	//file_put_contents("/work/ng6-test/jflow_rtherville/ng6_php.log", "tx_nG6_utils, get_retention_policy_from_space_id(), array_config_content: \n".print_r($array_config_content,TRUE)."\n", FILE_APPEND);
-    	
+		
     	$space_id_retention_config = array();
     	$pattern_to_find = "[space_".$space_id."]";
     	$is_space_id_found = FALSE;

ui/nG6/pi1/analyzes/AnalysisTemplate.tpl

@@ -30,12 +30,14 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 		<div class="ng6-content-header-right">
 			{$analyse.description}
 			<br />
-			All data related to this analysis use <strong> {$analyse_size} </strong> on the hard drive.
+			All data related to this analysis use <strong> {$analyse_size} </strong> on the hard drive.<br />
 			{block name=description_update}{/block}
 			{if $analysis_data_state == 'stored'}
 				The analysis data is <strong>stored</strong>. It will be kept until {$analysis_retention_date}.<br/>
-			{else}
-				The analysis data has been <strong>purged</strong>.<br/>
+			{elseif $analysis_data_state == 'purged'}
+				The analysis data has been <strong>purged</strong> on {$analysis_purge_date}.<br/>
+			{elseif $analysis_data_state == 'extended'}
+				The analysis data retention has been <strong>extended</strong> to {$analysis_retention_date}.<br/>
 			{/if}
 		</div>
 		<div style="clear:both"></div>

ui/nG6/pi1/analyzes/FastQC.js

@@ -79,7 +79,7 @@ $(function () {
 			
 			//Build tbody
 			var tbody = "" ; 
-			var pattern_regexp = new RegExp( '<a[^>]+class="[^"]*imglink[^"]*"[^>]+href="(fileadmin\/data\/analyze\/[^"]+)' ) ;
+			var pattern_regexp = new RegExp( '<a[^>]+class="[^"]*imglink[^"]*"[^>]+href="(fileadmin\/data[_]*[a-z]*\/analyze\/[^"]+)' ) ;
 			for( var i = 0 ; i < samples.length ; i++ ) {
 				tbody += '<tr>' ; 
 				for( var j = 0 ; j < columns.length ; j++ ) {

ui/nG6/pi1/class.tx_nG6_pi1.php

@@ -325,6 +325,7 @@ class tx_nG6_pi1 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
 				$retention_policy = tx_nG6_db::select_run_retention_status($runs[key($runs)]['id']);
 				$smarty->assign('run_data_state', $retention_policy['run_data_state']);
 				$smarty->assign('run_retention_date', $retention_policy['run_retention_date']);
+				$smarty->assign('run_purge_date', $retention_policy['run_purge_date']);
 				
 				$run_analysis = tx_nG6_db::get_run_analysis($runs[key($runs)]['id']);
 				// Add some information to the table
@@ -404,6 +405,7 @@ class tx_nG6_pi1 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
 					$retention_policy = tx_nG6_db::select_analysis_retention_status($this->piVars['analyze_id']);
 					$smarty->assign('analysis_data_state', $retention_policy['analysis_data_state']);
 					$smarty->assign('analysis_retention_date', $retention_policy['analysis_retention_date']);
+					$smarty->assign('analysis_purge_date', $retention_policy['analysis_purge_date']);
 				
 					// Then select analyse results
 					$results = tx_nG6_db::select_analyse_results($this->piVars['analyze_id']);

ui/nG6/pi1/run_view.tpl

@@ -86,8 +86,10 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 			{/if}
 			{if $run_data_state == 'stored'}
 				The run data is <strong>stored</strong>. It will be kept until {$run_retention_date}.<br/>
-			{else}
-				The run data has been <strong>purged</strong>.<br/>
+			{elseif $run_data_state == 'purged'}
+				The run data has been <strong>purged</strong> on {$run_purge_date}.<br/>
+			{elseif $run_data_state == 'extended'}
+				The run data retention has been <strong>extended</strong> to {$run_retention_date}.<br/>
 			{/if}