[genomic_browser] Solve the issues

modules/genomic_browser/help/genomic_browser.md

@@ -0,0 +1,18 @@
+# Genomic Browser
+
+This module allows you to visualize the results of already analyzed genetic tests cross-linked with behavioral and imaging candidate data.
+
+It is designed for researchers and study personnel who are browsing and reviewing summary data. This module presents summary genomic data of several types, enabling you to review and explore data available for study participants in a cross-modal context. Supported data types include SNP, CNV, and methylation (epigenomic) data.
+
+### Usage
+You can switch between the different tabs to view different types of genomic data. The tabs are:
+- Profile, GWAS, SNP, CNV, Methylation and Files
+- **Profiles**: This tab allows you to get a brief summary of the data available for each participant, including whether SNPs, CNVs and CPGs were found or not.
+- **GWAS**: This tab allows you to visualize the results of a genome-wide association study (GWAS) for each participant.
+- **SNP**: This tab allows you to visualize the results of a single nucleotide polymorphism (SNP) analysis for each participant.
+- **CNV**: This tab allows you to visualize the results of a copy number variation (CNV) analysis for each participant.
+- **Methylation**: This tab allows you to visualize the results of a methylation analysis for each participant.
+- **Files**: This tab allows you to upload and download files related to the genomic data.
+
+### Uploading Data
+To upload data, you can use the "Upload" button in the "Files" tab. This will allow you to select a file from your computer and upload it to the server. The file should be in a format that is compatible with the module, such as CSV.

modules/genomic_browser/jsx/tabs_content/filemanager/uploadForm.js

@@ -10,6 +10,7 @@ import {
   SelectElement,
   ButtonElement,
 } from 'jsx/Form';
+import swal from 'sweetalert2';
 
 /**
  * Genomic Upload Form
@@ -200,7 +201,8 @@ class GenomicUploadForm extends Component {
           }, // reset form data after successful file upload
           uploadProgress: -1,
         });
-        swal('Upload Successful!', '', 'success');
+        swal.fire('Upload Successful!', '', 'success');
+        this.props.closeFileUploadModal();
       }
       ).catch((error) => {
         console.error(error);
@@ -211,14 +213,15 @@ class GenomicUploadForm extends Component {
           errorMessage: msg,
           uploadProgress: -1,
         });
-        swal(msg, '', 'error');
+        swal.fire(msg, '', 'error');
       });
   }
 }
 GenomicUploadForm.propTypes = {
   action: PropTypes.string,
   permissions: PropTypes.object,
   baseURL: PropTypes.string.isRequired,
+  closeFileUploadModal: PropTypes.func.isRequired,
 };
 
 export default GenomicUploadForm;

modules/genomic_browser/jsx/tabs_content/files.js

@@ -37,7 +37,6 @@ class Files extends Component {
     this.formatColumn = this.formatColumn.bind(this);
     this.openFileUploadModal = this.openFileUploadModal.bind(this);
     this.closeFileUploadModal = this.closeFileUploadModal.bind(this);
-    this.renderFileUploadForm = this.renderFileUploadForm.bind(this);
     this.setFileUploadFormData = this.setFileUploadFormData.bind(this);
   }
 
@@ -116,26 +115,7 @@ class Files extends Component {
       },
       showFileUploadModal: false,
     });
-  }
-
-  /**
-   * Render File Upload Form
-   *
-   * @return {JSX} react upload form modal
-   */
-  renderFileUploadForm() {
-    return (
-      <Modal
-        title='Upload File'
-        onClose={this.closeFileUploadModal}
-        show={this.state.showFileUploadModal}
-      >
-        <GenomicUploadForm
-          permissions={this.state.data.permissions}
-          baseURL={this.props.baseURL}
-        />
-      </Modal>
-    );
+    this.fetchData();
   }
 
   /**
@@ -252,7 +232,17 @@ class Files extends Component {
 
     return (
       <React.Fragment>
-        {this.renderFileUploadForm()}
+        <Modal
+          title='Upload File'
+          onClose={this.closeFileUploadModal}
+          show={this.state.showFileUploadModal}
+        >
+          <GenomicUploadForm
+            permissions={this.state.data.permissions}
+            baseURL={this.props.baseURL}
+            closeFileUploadModal={this.closeFileUploadModal}
+          />
+        </Modal>
         <FilterableDataTable
           name={'filterableDataTableFiles'}
           data={this.state.data.Data}

modules/genomic_browser/jsx/tabs_content/gwas.js

@@ -79,8 +79,7 @@ class GWAS extends Component {
     const hiddenHeaders = [
       'PSC',
       'DCCID',
-      'externalID',
-      'DoB',
+      'externalID'
     ];
     let reactElement;
     if (-1 === hiddenHeaders.indexOf(column)) {

modules/genomic_browser/jsx/tabs_content/profiles.js

@@ -180,10 +180,6 @@ class Profiles extends Component {
           options: options.Cohorts,
         },
       },
-      {
-        label: 'Date of Birth',
-        show: false,
-      },
       {
         label: 'External ID',
         show: false,

modules/genomic_browser/jsx/tabs_content/snp.js

@@ -198,10 +198,10 @@ class SNP extends Component {
         show: false,
       },
       {
-        label: 'Name',
+        label: 'Gene Name',
         show: false,
         filter: {
-          name: 'Name',
+          name: 'Gene Name',
           type: 'text',
         },
       },
@@ -223,10 +223,10 @@ class SNP extends Component {
         },
       },
       {
-        label: 'Name',
+        label: 'SNP Name',
         show: false,
         filter: {
-          name: 'Name',
+          name: 'SNP Name',
           type: 'text',
         },
       },

modules/genomic_browser/php/filemanager.class.inc

@@ -57,7 +57,7 @@ class FileManager extends \NDB_Page implements ETagCalculator
         // Parse GET query params.
         $values = $request->getQueryParams();
         // GET request for downloading file by ID.
-        if ($values['filename']) {
+        if ($values['filename'] ?? false) {
             $factory  = \NDB_Factory::singleton();
             $config   = $factory->config();
             $filesDir = \Utility::appendForwardSlash(
@@ -129,7 +129,7 @@ class FileManager extends \NDB_Page implements ETagCalculator
         // handles upload process - returns status of file upload.
         $response = $genomicFile->setupUploading(
             $request->getAttribute('user'), // user
-            $_FILES, // file data
+            $request->getUploadedFiles(), // file data
             $values // post request values.
         );
 

modules/genomic_browser/php/models/cnvdto.class.inc

@@ -71,13 +71,6 @@ class CnvDTO implements DataInstance, SiteHaver
      */
     private $_Cohort = "";
 
-    /**
-     * The DoB
-     *
-     * @var string
-     */
-    private $_DoB = "";
-
     /**
      * The ExternalID
      *
@@ -224,7 +217,6 @@ class CnvDTO implements DataInstance, SiteHaver
             'PSCID'             => $this->_PSCID,
             'Sex'               => $this->_Sex,
             'Cohort'            => $this->_Cohort,
-            'DoB'               => $this->_DoB,
             'ExternalID'        => $this->_ExternalID,
             'Chromosome'        => $this->_Chromosome,
             'Strand'            => $this->_Strand,

modules/genomic_browser/php/models/methylationdto.class.inc

@@ -71,13 +71,6 @@ class MethylationDTO implements DataInstance, SiteHaver
      */
     private $_Cohort = "";
 
-    /**
-     * The DoB
-     *
-     * @var string
-     */
-    private $_DoB = "";
-
     /**
      * The Sample
      *
@@ -280,7 +273,6 @@ class MethylationDTO implements DataInstance, SiteHaver
             'PSCID'            => $this->_PSCID,
             'Sex'              => $this->_Sex,
             'Cohort'           => $this->_Cohort,
-            'DoB'              => $this->_DoB,
             'Sample'           => $this->_Sample,
             'cpg_name'         => $this->_cpg_name,
             'Beta_value'       => $this->_Beta_value,

modules/genomic_browser/php/models/profiledto.class.inc

@@ -83,13 +83,6 @@ class ProfileDTO implements DataInstance, SiteHaver
      */
     private $_Cohort = "";
 
-    /**
-     * The DoB
-     *
-     * @var string
-     */
-    private $_DoB = "";
-
     /**
      * The externalID
      *
@@ -138,7 +131,6 @@ class ProfileDTO implements DataInstance, SiteHaver
             'PSCID'      => $this->_PSCID,
             'Sex'        => $this->_Sex,
             'Cohort'     => $this->_Cohort,
-            'DoB'        => $this->_DoB,
             'externalID' => $this->_externalID,
             'File'       => $this->_File,
             'SNP'        => $this->_SNP,

modules/genomic_browser/php/models/snpdto.class.inc

@@ -82,13 +82,6 @@ class SnpDTO implements DataInstance, SiteHaver
      */
     private $_Cohort = "";
 
-    /**
-     * The DoB
-     *
-     * @var string
-     */
-    private $_DoB = "";
-
     /**
      * The externalID
      *
@@ -270,7 +263,6 @@ class SnpDTO implements DataInstance, SiteHaver
             'PSCID'               => $this->_PSCID,
             'Sex'                 => $this->_Sex,
             'Cohort'              => $this->_Cohort,
-            'DoB'                 => $this->_DoB,
             'externalID'          => $this->_externalID,
             'Chromosome'          => $this->_Chromosome,
             'Strand'              => $this->_Strand,

modules/genomic_browser/php/provisioners/cnvprovisioner.class.inc

@@ -29,7 +29,6 @@ class CnvProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                 candidate.PSCID AS _PSCID,
                 candidate.Sex AS _Sex,
                 cohort.CohortID AS _Cohort,
-                DATE_FORMAT(candidate.DoB, '%Y-%m-%d') AS _DoB,
                 candidate.ExternalID AS _ExternalID,
                 candidate.RegistrationCenterID as _centerID,
                 candidate.RegistrationProjectID as _projectID,

modules/genomic_browser/php/provisioners/methylationprovisioner.class.inc

@@ -31,7 +31,6 @@ class MethylationProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisione
                 candidate.RegistrationCenterID as _centerID,
                 candidate.RegistrationProjectID as _projectID,
                 cohort.CohortID AS _Cohort,
-                DATE_FORMAT(candidate.DoB, '%Y-%m-%d') AS _DoB,
                 gscr.sample_label AS _Sample,
                 cpg.cpg_name AS _cpg_name,
                 cpg.beta_value AS _Beta_value,

modules/genomic_browser/php/provisioners/profileprovisioner.class.inc

@@ -29,7 +29,6 @@ class ProfileProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                 candidate.PSCID AS _PSCID,
                 candidate.Sex AS _Sex,
                 subproj.title AS _Cohort,
-                DATE_FORMAT(candidate.DoB, '%Y-%m-%d') AS _DoB,
                 candidate.ExternalID AS _externalID,
                 candidate.RegistrationCenterID as _centerID,
                 candidate.RegistrationProjectID as _projectID,

modules/genomic_browser/php/provisioners/snpprovisioner.class.inc

@@ -28,8 +28,7 @@ class SnpProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                 LPAD(candidate.CandID, 10, '0') AS _DCCID,
                 candidate.PSCID AS _PSCID,
                 candidate.Sex AS _Sex,
-                subproj.title AS _Cohort,
-                DATE_FORMAT(candidate.DoB, '%Y-%m-%d') AS _DoB,
+                cohort.title AS _Cohort,
                 candidate.ExternalID AS _externalID,
                 candidate.RegistrationCenterID as _centerID,
                 candidate.RegistrationProjectID as _projectID,
@@ -66,8 +65,8 @@ class SnpProvisioner extends \LORIS\Data\Provisioners\DBObjectProvisioner
                     JOIN candidate c ON c.ID=s.CandidateID
                     GROUP BY
                         c.CandID) AS cohort ON (cohort.CandID = candidate.CandID)
-                LEFT JOIN cohort AS subproj
-                    ON (cohort.CohortID = subproj.CohortID)
+                LEFT JOIN cohort
+                    ON (cohort.CohortID = CohortID)
                 LEFT JOIN psc ON (psc.CenterID = candidate.RegistrationCenterID)
                 JOIN SNP_candidate_rel
                     ON (candidate.ID = SNP_candidate_rel.CandidateID)

modules/genomic_browser/php/uploading/genomicfile.class.inc

@@ -58,20 +58,25 @@ class Genomicfile
      */
     function setupUploading($user, $files, $values) : array
     {
-        $this->_user   = $user;
-        $this->_bytes  = $files['file']['size'];
-        $this->_values = $values;
-
+        if (!isset($files['file'])
+            || empty($files['file']->getStream()->getMetadata('uri'))
+        ) {
+            return false;
+        }
+        $this->_user         = $user;
+        $this->_bytes        = $files['file']->getSize();
+        $this->_values       = $values;
         $this->_fileToUpload
             = (object) [
-                'file_type'         => $files['file']['type'],
-                'file_name'         => $files['file']['name'],
-                'tmp_name'          => $files['file']['tmp_name'],
+                'file_type'         => $files['file']->getClientMediaType(),
+                'file_name'         => $files['file']->getClientFilename(),
+                'tmp_name'          => $files['file']
+                    ->getStream()->getMetadata('uri'),
                 'size'              => round($this->_bytes / 1048576, 0),
                 'inserted_by'       => $this->_user->getData('UserID'),
                 'genomic_file_type' => empty($this->_values['fileType']) ?
                 null : str_replace('_', ' ', $this->_values['fileType']),
-                'description'       => $this->_values['fileDescription'],
+                'description'       => $this->_values['fileDescription'] ?? '',
             ];
 
         $this->setFullPath($this->_fileToUpload);