Transfer mri violations to resolved tab in bulk

tools/mri_violations_resolver.php

@@ -0,0 +1,160 @@
+<?php
+/**
+ * This script is used to move mri violations to the resolved tab in bulk.
+ * This is the first step for a project that wants to insert scans that were
+ * previously excluded.
+ * Just modify the where clause and test on the front end with same filter first.
+ *
+ * Usage: php mri_violations_resolver.php [confirm]
+ *
+ * PHP Version 5
+ *
+ * @category MRI
+ * @package  Main
+ * @author   Gregory Luneau <gregory.luneau@mcgill.ca>
+ * @license  Loris License
+ * @link     https://www.github.com/aces/Loris/
+ */
+
+set_include_path(get_include_path().":../project/libraries:../php/libraries:");
+
+// path to config file
+$configFile = "../project/config.xml";
+
+require_once __DIR__ . "/../vendor/autoload.php";
+require_once "NDB_Client.class.inc";
+
+
+$confirm = false;
+if (isset($argv[1]) && $argv[1] === "confirm") {
+    $confirm = true;
+}
+
+$client = new NDB_Client();
+$client->makeCommandLine();
+$client->initialize($configFile);
+
+$DB =& Database::singleton();
+
+// Query as it is in the mri violation module
+// It is complete as it apears in the module for two reasons:
+//   1. for reproducibility, this tools expects that you have validated your search
+//      in LORIS front end first.
+//   2. for future feature improvements that will use currently unused part of this
+//      query.
+$query = "SELECT v.PatientName, v.Project, v.Subproject, v.Site, v.TimeRun,
+          v.MincFile, v.Series_Description as Series_Description_Or_Scan_Type,
+          v.Problem, v.SeriesUID, v.hash, v.join_id, v.Resolved FROM (
+            SELECT PatientName as PatientName,
+                time_run as TimeRun,
+                c.ProjectID as Project,
+                s.SubprojectID as Subproject,
+                minc_location as MincFile,
+                series_description as Series_Description,
+                'Could not identify scan type' as Problem,
+                SeriesUID,
+            md5(concat_WS(':',minc_location,PatientName,SeriesUID,time_run)) as hash,
+                mri_protocol_violated_scans.ID as join_id,
+                p.CenterID as Site,
+                violations_resolved.Resolved as Resolved
+            FROM mri_protocol_violated_scans
+            LEFT JOIN violations_resolved
+            ON (violations_resolved.ExtID=mri_protocol_violated_scans.ID
+            AND violations_resolved.TypeTable='mri_protocol_violated_scans')
+            LEFT JOIN candidate c
+            ON (mri_protocol_violated_scans.CandID = c.CandID)
+            LEFT JOIN session s
+            ON (mri_protocol_violated_scans.CandID = s.CandID)
+            LEFT JOIN psc p
+            ON (p.CenterID = c.CenterID)
+            WHERE Resolved is NULL UNION SELECT PatientName,
+                TimeRun,
+                c.ProjectID as Project,
+                s.SubprojectID as Subproject,
+                MincFile,
+                mri_scan_type.Scan_type,
+                'Protocol Violation',
+                SeriesUID,
+                md5(concat_WS(':',MincFile,PatientName,SeriesUID,TimeRun)) as hash,
+                mri_violations_log.LogID as join_id,
+                p.CenterID as Site,
+                violations_resolved.Resolved as Resolved
+            FROM mri_violations_log
+            LEFT JOIN mri_scan_type
+            ON (mri_scan_type.ID=mri_violations_log.Scan_type)
+            LEFT JOIN violations_resolved
+            ON (violations_resolved.ExtID=mri_violations_log.LogID
+            AND violations_resolved.TypeTable='mri_violations_log')
+            LEFT JOIN candidate c
+            ON (mri_violations_log.CandID=c.CandID)
+            LEFT JOIN session s
+            ON (mri_violations_log.CandID = s.CandID)
+            LEFT JOIN psc p
+            ON (p.CenterID = c.CenterID)
+            WHERE Resolved is NULL UNION SELECT PatientName,
+                TimeRun,
+                c.ProjectID as Project,
+                s.SubprojectID as Subproject,
+                MincFile,
+                null,
+                Reason,
+                SeriesUID,
+                md5(concat_WS(':',MincFile,PatientName,SeriesUID,TimeRun)) as hash,
+                MRICandidateErrors.ID as join_id,
+                p.CenterID as Site,
+                violations_resolved.Resolved as Resolved
+            FROM MRICandidateErrors
+            LEFT JOIN violations_resolved
+            ON (violations_resolved.ExtID=MRICandidateErrors.ID
+            AND violations_resolved.TypeTable='MRICandidateErrors')
+            LEFT JOIN candidate c
+            ON (SUBSTRING_INDEX(MRICandidateErrors.PatientName,'_',1)=c.PSCID)
+            LEFT JOIN session s
+            ON (c.CandID = s.CandID)
+            LEFT JOIN psc p
+            ON (p.CenterID = c.CenterID)
+            WHERE Resolved is NULL)
+            as v WHERE
+            v.problem = :pr and
+            v.series_description like :sd
+            ORDER BY v.TimeRun DESC";
+
+// Filter values to modify
+$where   = array(
+            'pr' => 'Protocol Violation',
+            'sd' => '%t1%',
+           );
+$results = $DB->pselect($query, $where);
+
+foreach ($results AS $result) {
+
+    $newlyResolved         = array();
+    $newlyResolved['hash'] = $result['hash'];
+    $newlyResolved['Resolved']   = 'inserted_flag';
+    $newlyResolved['User']       = get_current_user();
+    $newlyResolved['ChangeDate'] = date("Y-m-d H:i:s");
+    $newlyResolved['TypeTable']  = 'mri_violations_log';
+    $newlyResolved['ExtID']      = $result['join_id'];
+
+    // Does a hash and a ExtID already exists?
+    $row = $DB->pselectRow(
+        "SELECT * FROM violations_resolved
+        WHERE hash = :ha and ExtID = :ex ",
+        array(
+         'ha' => $result['hash'],
+         'ex' => $result['join_id'],
+        )
+    );
+
+    // Insert if new
+    if (empty($row)) {
+        if ($confirm) {
+            $DB->insert('violations_resolved', $newlyResolved);
+            print "inserting\t";
+        }
+        print_r($newlyResolved);
+    } else {
+        print "skip\n";
+    }
+
+}