[Imaging Browser] Fix caveat bug not showing when there are pipeline protocol violations (#8661)

cmadjar · web-flow · commit cb67330ba72f · 2023-05-02T10:37:00.000-04:00
This fixes a bug where the Caveat link was not showing when a file has protocol violations logged automatically by the pipeline in the MRI violation module. It also fixes the link to the MRI violation module with the new react links.
diff --git a/modules/imaging_browser/jsx/ImagePanel.js b/modules/imaging_browser/jsx/ImagePanel.js
@@ -320,7 +320,7 @@ class ImageQCDropdown extends Component {
     } else {
       dropdown = (
         <div className="col-xs-12">
-          {this.props.defaultValue}
+          {this.props.options[this.props.defaultValue]}
         </div>
       );
     }
@@ -491,24 +491,18 @@ class ImagePanelQCCaveatSelector extends Component {
   render() {
     // Link caveat to MRI Violations if set true
     let mriViolationsLink = null;
-    if (this.props.SeriesUID && this.props.Caveat === '1') {
-        // If there is a manual caveat that was set, the link
-        // will take you to it, even though there might also
-        // be a caveat that was set by the MRI piepline (i.e
-        // not manual). Note that manual caveat are always
-        // resolved
-        if (this.props.CaveatViolationsResolvedID) {
-            mriViolationsLink = '/mri_violations/resolved_violations/?' +
-              'SeriesUID=' + this.props.SeriesUID + '&filter=true';
-        }
+    if (this.props.FullName && this.props.Caveat === '1') {
+        mriViolationsLink = '/mri_violations/?' +
+          'mincFile=' + this.props.FullName +
+          '&seriesUID=' + this.props.SeriesUID;
     }
 
     return (
       <ImageQCDropdown
         Label="Caveat"
         FormName="caveat"
         FileID={this.props.FileID}
-        editable={this.props.HasQCPerm}
+        editable={this.props.HasQCPerm && this.props.EditableCaveat}
         options={
           {
             '': '',
@@ -527,7 +521,8 @@ ImagePanelQCCaveatSelector.propTypes = {
   HasQCPerm: PropTypes.bool,
   SeriesUID: PropTypes.string,
   Caveat: PropTypes.string,
-  CaveatViolationsResolvedID: PropTypes.string,
+  EditableCaveat: PropTypes.bool,
+  FullName: PropTypes.string,
 };
 
 
@@ -605,7 +600,8 @@ class ImagePanelQCPanel extends Component {
           HasQCPerm={this.props.HasQCPerm}
           Caveat={this.props.Caveat}
           SeriesUID={this.props.SeriesUID}
-          CaveatViolationsResolvedID={this.props.CaveatViolationsResolvedID}
+          EditableCaveat={this.props.EditableCaveat}
+          FullName={this.props.FullName}
         />
         <ImagePanelQCSNRValue
           FileID={this.props.FileID}
@@ -624,7 +620,8 @@ ImagePanelQCPanel.propTypes = {
   Caveat: PropTypes.string,
   SeriesUID: PropTypes.string,
   SNR: PropTypes.string,
-  CaveatViolationsResolvedID: PropTypes.string,
+  EditableCaveat: PropTypes.bool,
+  FullName: PropTypes.string,
 };
 
 
@@ -924,10 +921,11 @@ class ImagePanelBody extends Component {
               HasQCPerm={this.props.HasQCPerm}
               QCStatus={this.props.QCStatus}
               Caveat={this.props.Caveat}
-              CaveatViolationsResolvedID={this.props.CaveatViolationsResolvedID}
               Selected={this.props.Selected}
               SNR={this.props.SNR}
               SeriesUID={this.props.SeriesUID}
+              EditableCaveat={this.props.EditableCaveat}
+              FullName={this.props.Fullname}
             />
           </div>
         </div>
@@ -971,8 +969,8 @@ ImagePanelBody.propTypes = {
   JsonFile: PropTypes.string,
   OtherTimepoints: PropTypes.string,
   HeadersExpanded: PropTypes.bool,
-  CaveatViolationsResolvedID: PropTypes.string,
   HeaderInfo: PropTypes.object,
+  EditableCaveat: PropTypes.bool,
 };
 
 
@@ -1049,7 +1047,7 @@ class ImagePanel extends Component {
               HasQCPerm={this.props.HasQCPerm}
               QCStatus={this.props.QCStatus}
               Caveat={this.props.Caveat}
-              CaveatViolationsResolvedID={this.props.CaveatViolationsResolvedID}
+              EditableCaveat={this.props.EditableCaveat}
               Selected={this.props.Selected}
               SNR={this.props.SNR}
 
@@ -1092,7 +1090,7 @@ ImagePanel.propTypes = {
   HeaderInfo: PropTypes.object,
   HeadersExpanded: PropTypes.string,
   APIFile: PropTypes.string,
-  CaveatViolationsResolvedID: PropTypes.string,
+  EditableCaveat: PropTypes.bool,
 };
 
 let RImagePanel = React.createFactory(ImagePanel);
diff --git a/modules/imaging_browser/php/viewsession.class.inc b/modules/imaging_browser/php/viewsession.class.inc
@@ -317,57 +317,63 @@ class ViewSession extends \NDB_Form
                 (int)$FileObj->getParameter('AcquisitionProtocolID')
             );
 
-            $caveatViolationsResolvedID
+            $manualCaveatViolationsResolvedID
                 = $this->_getManualCaveatViolationsResolvedID($FileID);
-            $caveat = $caveatViolationsResolvedID ? 1 : 0;
-            $file   = [
-                'FileID'                     => $FileID,
-                'Filename'                   => $Filename,
-                'APIFile'                    => $APIFile,
-                'FullFilename'               => $FullFilename,
-                'New'                        => $New,
-                'OutputType'                 => $OutputType,
-                'AcquisitionProtocol'        => $AcquisitionProtocol,
-                'CoordinateSpace'            => $CoordinateSpace,
-                'AcquisitionDate'            => $AcquisitionDate,
-                'ProcDate'                   => $ProcDate,
-                'FileInsertDate'             => $FileInsertDate,
-                'SeriesDescription'          => $SeriesDescription,
-                'SeriesNumber'               => $SeriesNumber,
-                'SeriesUID'                  => $SeriesUID,
-                'EchoTime'                   => $EchoTime,
-                'InversionTime'              => $InversionTime,
-                'RepetitionTime'             => $RepetitionTime,
-                'SliceThickness'             => $SliceThickness,
-                'Time'                       => $Time,
-                'ImageType'                  => $ImageType,
-                'PhaseEncodingDirection'     => $PhaseEncodingDirection,
-                'EchoNumber'                 => $EchoNumber,
-                'Comment'                    => $Comment,
-                'ProcessingPipeline'         => $ProcessingPipeline,
-                'TotalRejected'              => $TotalRejected,
-                'SourceFile'                 => $SourceFile,
-                'Tool'                       => $Tool,
-                'SlicewiseRejected'          => $SlicewiseRejected,
-                'InterlaceRejected'          => $InterlaceRejected,
-                'IntergradientRejected'      => $IntergradientRejected,
-                'Xstep'                      => $Xstep,
-                'Ystep'                      => $Ystep,
-                'Zstep'                      => $Zstep,
-                'Selected'                   => $Selected,
-                'QCStatus'                   => $QCStatus,
-                'QCDate'                     => $QCDate,
-                'Caveat'                     => $caveat,
-                'SNR'                        => $SNR,
-                'XMLreport'                  => $XMLreport,
-                'XMLprotocol'                => $XMLprotocol,
-                'NrrdFile'                   => $NrrdFile,
-                'NiiFile'                    => $NiiFile,
-                'BvalFile'                   => $BvalFile,
-                'BvecFile'                   => $BvecFile,
-                'JsonFile'                   => $JsonFile,
-                'OtherTimepoints'            => $OtherTimepoints,
-                'CaveatViolationsResolvedID' => $caveatViolationsResolvedID,
+            $caveat = $manualCaveatViolationsResolvedID ? 1 : 0;
+            $foundProtocolViolations = $this->_getProtocolViolations($FileID);
+            $editableCaveat          = true;
+            if ($foundProtocolViolations) {
+                $caveat         = 1;
+                $editableCaveat = false;
+            }
+            $file = [
+                'FileID'                 => $FileID,
+                'Filename'               => $Filename,
+                'APIFile'                => $APIFile,
+                'FullFilename'           => $FullFilename,
+                'New'                    => $New,
+                'OutputType'             => $OutputType,
+                'AcquisitionProtocol'    => $AcquisitionProtocol,
+                'CoordinateSpace'        => $CoordinateSpace,
+                'AcquisitionDate'        => $AcquisitionDate,
+                'ProcDate'               => $ProcDate,
+                'FileInsertDate'         => $FileInsertDate,
+                'SeriesDescription'      => $SeriesDescription,
+                'SeriesNumber'           => $SeriesNumber,
+                'SeriesUID'              => $SeriesUID,
+                'EchoTime'               => $EchoTime,
+                'InversionTime'          => $InversionTime,
+                'RepetitionTime'         => $RepetitionTime,
+                'SliceThickness'         => $SliceThickness,
+                'Time'                   => $Time,
+                'ImageType'              => $ImageType,
+                'PhaseEncodingDirection' => $PhaseEncodingDirection,
+                'EchoNumber'             => $EchoNumber,
+                'Comment'                => $Comment,
+                'ProcessingPipeline'     => $ProcessingPipeline,
+                'TotalRejected'          => $TotalRejected,
+                'SourceFile'             => $SourceFile,
+                'Tool'                   => $Tool,
+                'SlicewiseRejected'      => $SlicewiseRejected,
+                'InterlaceRejected'      => $InterlaceRejected,
+                'IntergradientRejected'  => $IntergradientRejected,
+                'Xstep'                  => $Xstep,
+                'Ystep'                  => $Ystep,
+                'Zstep'                  => $Zstep,
+                'Selected'               => $Selected,
+                'QCStatus'               => $QCStatus,
+                'QCDate'                 => $QCDate,
+                'Caveat'                 => $caveat,
+                'SNR'                    => $SNR,
+                'XMLreport'              => $XMLreport,
+                'XMLprotocol'            => $XMLprotocol,
+                'NrrdFile'               => $NrrdFile,
+                'NiiFile'                => $NiiFile,
+                'BvalFile'               => $BvalFile,
+                'BvecFile'               => $BvecFile,
+                'JsonFile'               => $JsonFile,
+                'OtherTimepoints'        => $OtherTimepoints,
+                'EditableCaveat'         => $editableCaveat,
             ];
 
             $this->tpl_data['files'][] = $file;
@@ -402,6 +408,29 @@ class ViewSession extends \NDB_Form
         return $this->_DB->pselectOneInt($query, ['fileID' => $fileID]);
     }
 
+    /**
+     * Gets the ID of the record in table violations_resolved associated
+     * to the manual caveat set on a given file.
+     *
+     * @param $fileID int the ID of the record in table files.
+     *
+     * @return ?array array of IDs of the associated records in table
+     *              mri_violations_log or null if there is none.
+     */
+    function _getProtocolViolations(int $fileID): ?array
+    {
+        $query = "
+            SELECT mvl.LogID
+            FROM files f
+            JOIN mri_violations_log mvl
+              ON (mvl.MincFile = f.File)
+            WHERE f.FileID =:fileID
+            AND mvl.Header NOT LIKE 'Manual Caveat Set by %';
+        ";
+
+        return $this->_DB->pselect($query, ['fileID' => $fileID]);
+    }
+
     /**
      * Gets a rejected parameter according to its type
      *
@@ -537,11 +566,11 @@ class ViewSession extends \NDB_Form
                     ['FileID' => $curFileID]
                 );
 
-                $caveatViolationsResolvedID
+                $manualCaveatViolationsResolvedID
                     = $this->_getManualCaveatViolationsResolvedID($curFileID);
                 // If Caveat was set to true and there is not already a manual
                 // caveat for that scan, then the user wants to create one
-                if ($curCaveat === '1' && !$caveatViolationsResolvedID) {
+                if ($curCaveat === '1' && !$manualCaveatViolationsResolvedID) {
                     //----------------------------------------------------------//
                     // Insert a record in mri_violations_log to indicate that   //
                     // there is an MRI violation for that scan. The Header      //
@@ -622,9 +651,9 @@ class ViewSession extends \NDB_Form
                         ['Caveat' => 1],
                         ['FileID' => $curFileID],
                     );
-                } elseif ($curCaveat === '0' && $caveatViolationsResolvedID) {
+                } elseif ($curCaveat === '0' && $manualCaveatViolationsResolvedID) {
                     $quotedViolationsResolvedID
-                        = $this->_DB->quote("$caveatViolationsResolvedID");
+                        = $this->_DB->quote("$manualCaveatViolationsResolvedID");
                     $query = "
                         DELETE FROM mri_violations_log
                         WHERE LogID = (
@@ -638,7 +667,7 @@ class ViewSession extends \NDB_Form
 
                     $this->_DB->delete(
                         'violations_resolved',
-                        ['ID' => $caveatViolationsResolvedID]
+                        ['ID' => $manualCaveatViolationsResolvedID]
                     );
 
                     $quotedFileID = $this->_DB->quote($curFileID);
diff --git a/modules/imaging_browser/templates/form_viewSession.tpl b/modules/imaging_browser/templates/form_viewSession.tpl
@@ -34,7 +34,7 @@
                 "Selected" : "{if $files[file].Selected}{$files[file].Selected}{/if}",
 
                 "Caveat" : "{$files[file].Caveat}",
-                "CaveatViolationsResolvedID" : "{$files[file].CaveatViolationsResolvedID}",
+                "EditableCaveat": "{$files[file].EditableCaveat}",
                 "SNR" : "{if $files[file].SNR}{$files[file].SNR}{/if}",
                 'HeaderInfo' : {
                   "SeriesUID" : "{$files[file].SeriesUID}",
diff --git a/modules/imaging_browser/test/TestPlan.md b/modules/imaging_browser/test/TestPlan.md
@@ -31,37 +31,39 @@
 ### Main panel:  Per Acquisition
 16. Files can be downloaded (links clickable) if and only if user has at least one of the module permissions. Ensure that DICOM downloads are
 prepended with the Patient Name.
-17. Scan-level QC flags (Selected, pass/fail, Caveat emptor) are viewable to all, modifiable if and only if user has permission `imaging_browser_qc`.  
-18. There will be a Caveat link just above the Caveat drop-down in the image panel of a given scan if and only if there is an MRI violation with:
+17. Scan-level QC flags (Selected, pass/fail) are viewable to all, modifiable if and only if user has permission `imaging_browser_qc`.
+18. Scan-level Caveat emptor are viewable to all, modifiable if and only if user has permission `imaging_browser_qc` and there are no
+    pipeline protocol violations associated to the image in the MRI violation module (`Manual Caveat Set by...` protocol violation
+    with no other protocol violations can be modified). Example in raisinbread: `OTT170_300170_V1` `fieldmapBOLD` images have
+    pipeline protocol violations associated to the image in the MRI violation module and therefore Caveat should not be editable.
+19. There will be a Caveat link just above the Caveat drop-down in the image panel of a given scan if and only if there is an MRI violation with:
        i) the same path as the image file
        ii) the same SeriesUID as the image's SeriesUID
-       iii) header set to 'Manual Caveat set by <username>'
-       iv) resolution type set to 'Inserted with flag'
     Search in the MRI violations' Resolved tab using the scan's SeriesUID and image file path to verify this. Note that you can see the header
     of an MRI violation by clicking on the 'Protocol Violation' link in the 'Problem' column.
-19. In the imaging browser, pick a scan that does not have a Caveat link. Use the drop-down to set the Caveat to true and save your modification.
+20. In the imaging browser, pick a scan that does not have a Caveat link. Use the drop-down to set the Caveat to true and save your modification.
     Ensure that there is now a link to your newly created caveat and verify that when you click on it it redirects to the MRI violations' violations
     resolved submenu with your caveat displayed in the search result table.
-20. In the imaging browser, pick a scan that has a Caveat link. Use the drop-down to set the Caveat to false and save your modification.
+21. In the imaging browser, pick a scan that has a Caveat link. Use the drop-down to set the Caveat to false and save your modification.
     Ensure that there is no Caveat link for that scan now. Using the MRI violation module and the technique described in 17, validate that there
     are no MRI violations that would justify the presence of a link for that scan.
-21. Selected:  can be set back to Null (blank).
-22. Clicking on an image launches the BrainBrowser.
-23. Clicking on the "QC Comments" button opens the QC comments window.
-24. Longitudinal View button launches the BrainBrowser with images of the chosen modality for that specific candidate across visits/timepoints.
+22. Selected:  can be set back to Null (blank).
+23. Clicking on an image launches the BrainBrowser.
+24. Clicking on the "QC Comments" button opens the QC comments window.
+25. Longitudinal View button launches the BrainBrowser with images of the chosen modality for that specific candidate across visits/timepoints.
 
 ### MRI-QC : Scan-level (QC Comments) dialog window
-25. With the permission `imaging_browser_qc`, edit comments, checkboxes, and dropdown values. 
-26. Clicking Save should update the values.
-27. Data should not be editable without this permission.
+26. With the permission `imaging_browser_qc`, edit comments, checkboxes, and dropdown values. 
+27. Clicking Save should update the values.
+28. Data should not be editable without this permission.
 
 ### Visit-level QC feedback dialog window
-28. On the view session page, click the button "Visit Level Feedback".
-29. The entries in this dialog should be editable when a user has the permission `imaging_browser_qc`.
-30. Try editing comments (adding new ones, deleting old ones). Click Save and ensure the data is saved.
+29. On the view session page, click the button "Visit Level Feedback".
+30. The entries in this dialog should be editable when a user has the permission `imaging_browser_qc`.
+31. Try editing comments (adding new ones, deleting old ones). Click Save and ensure the data is saved.
 
 ### Test the Candidate Dashboard widget
-31. Go to the candidate dashboard in the candidate module and check the Imaging QC Summary widget.
+32. Go to the candidate dashboard in the candidate module and check the Imaging QC Summary widget.
     - For each visit, check that the QC status displayed matches the Imaging Browser Module by hovering over any visit to see detailed modality breakdown for visit.
     - Click on a visit from the graph to access the imaging browser. Check that the link redirects to the correct scans in the imaging browser.
     - For a few candidate/visits, check that all the files from the Imaging Browser Module appear in the widget for all the visits.
