[Tools] delete_physiological_file.php

Author: laemtl

tools/delete_candidate.php renamed to tools/data_integrity/data_deletion/delete_candidate.php

@@ -14,19 +14,13 @@
  *
  * @category Main
  * @package  Loris
- * @author   Various <example@example.com>
+ * @author   Loris Team <loris-dev@bic.mni.mcgill.ca>
  * @license  Loris license
  * @link     https://www.github.com/aces/Loris/
  */
 
-set_include_path(
-    get_include_path().":".
-    __DIR__."/../project/tools:".
-    __DIR__."/../php/tools:"
-);
-
-require_once __DIR__ . "/../vendor/autoload.php";
-require_once "generic_includes.php";
+require_once __DIR__ . "/../../../vendor/autoload.php";
+require_once __DIR__ . "/../../generic_includes.php";
 use \LORIS\StudyEntities\Candidate\CandID;
 
 /**
@@ -82,7 +76,7 @@
     break;
 }
 
-$DB =& Database::singleton();
+$DB = \NDB_Factory::singleton()->database();
 
 /*
  * Perform validations on arguments
@@ -135,7 +129,7 @@ function showHelp()
     echo <<<USAGE
 *** Delete Candidate Info ***
 
-Usage: php delete_candidate.php delete_candidate CandID PSCID [confirm]
+Usage: php delete_candidate.php delete_candidate CandID PSCID [confirm] [tosql]
 Example: php delete_candidate.php delete_candidate 965327 dcc0007
 Example: php delete_candidate.php delete_candidate 965327 dcc0007 confirm
 Example: php delete_candidate.php delete_candidate 965327 dcc0007 tosql
@@ -315,25 +309,25 @@ function deleteCandidate($CandID, $PSCID, $confirm, $printToSQL, $DB, &$output)
         $DB->delete("parameter_candidate", ["CandID" => $CandID]);
 
         //delete from SNP_candidate_rel
-        $result = $DB->delete("SNP_candidate_rel", ["CandID" => $CandID]);
+        $DB->delete("SNP_candidate_rel", ["CandID" => $CandID]);
 
         //delete from CNV
-        $result = $DB->delete("CNV", ["CandID" => $CandID]);
+        $DB->delete("CNV", ["CandID" => $CandID]);
 
         //delete from genomic_candidate_files_rel
-        $result = $DB->delete(
+        $DB->delete(
             "genomic_candidate_files_rel",
             ["CandID" => $CandID]
         );
 
         //delete from genomic_sample_candidate_rel
-        $result = $DB->delete(
+        $DB->delete(
             "genomic_sample_candidate_rel",
             ["CandID" => $CandID]
         );
 
         //delete from issues
-        $result = $DB->delete("issues", ["candID" => $CandID]);
+        $DB->delete("issues", ["candID" => $CandID]);
 
         //delete from candidate
         $DB->delete("candidate", ["CandID" => $CandID]);

tools/delete_ignored_conflicts.php renamed to tools/data_integrity/data_deletion/delete_ignored_conflicts.php

@@ -28,12 +28,16 @@
  * @package  Loris
  * @author   Loris Team <loris-dev@bic.mni.mcgill.ca>
  * @license  Loris license
- * @link     https://www.github.com/aces/Loris-Trunk/
+ * @link     https://www.github.com/aces/Loris/
  */
 
-set_include_path(get_include_path().":../project/libraries:../php/libraries:");
+set_include_path(
+    get_include_path().":".
+    __DIR__."../../../project/libraries:" .
+    __DIR__."../../../php/libraries:"
+);
 
-require_once __DIR__ . "/../vendor/autoload.php";
+require_once __DIR__ . "/../../../vendor/autoload.php";
 require_once "NDB_Client.class.inc";
 $client = new NDB_Client();
 $client->makeCommandLine();
@@ -131,18 +135,18 @@ function detectIgnoreColumns($instruments)
  */
 function defaultIgnoreColumns()
 {
-    $db =& Database::singleton();
+    $db = \NDB_Factory::singleton()->database();
 
     if ($this->confirm) {
         foreach ($this->defaultFields as $field) {
-            $defaultQuery = "DELETE FROM conflicts_unresolved 
+            $defaultQuery = "DELETE FROM conflicts_unresolved
                 WHERE FieldName = '$field'";
             $changes      = $db->run($defaultQuery);
             echo $changes . "\n";
         }
     } else {
         foreach ($this->defaultFields as $field) {
-            $defaultQuery  = "SELECT TableName, FieldName, Value1, Value2 
+            $defaultQuery  = "SELECT TableName, FieldName, Value1, Value2
           FROM conflicts_unresolved WHERE FieldName = '$field'";
             $defaultColumn = $db->pselectOne($defaultQuery, []);
             echo "TableName, FieldName, Value1, Value2: ";