[genomic_browser] Fix several issues including misaligned table columns, broken filters, and multilingual code

modules/genomic_browser/jsx/tabs_content/cnv.js

@@ -151,10 +151,6 @@ class CNV extends Component {
           options: options.Cohorts,
         },
       },
-      {
-        label: t('Date of Birth', {ns: 'loris'}),
-        show: false,
-      },
       {
         label: t('External ID', {ns: 'genomic_browser'}),
         show: false,
@@ -179,8 +175,8 @@ class CNV extends Component {
           name: 'Strand',
           type: 'select',
           options: {
-            F: 'Forward',
-            R: 'Reverse',
+            '+': t('Forward', {ns: 'genomic_browser'}),
+            '-': t('Reverse', {ns: 'genomic_browser'}),
           },
         },
       },

modules/genomic_browser/jsx/tabs_content/methylation.js

@@ -152,10 +152,6 @@ class Methylation extends Component {
           options: options.Cohorts,
         },
       },
-      {
-        label: t('Date of Birth', {ns: 'loris'}),
-        show: false,
-      },
       {
         label: t('Sample', {ns: 'genomic_browser'}),
         show: true,
@@ -183,8 +179,8 @@ class Methylation extends Component {
           name: 'Strand',
           type: 'select',
           options: {
-            F: 'Forward',
-            R: 'Reverse',
+            '+': t('Forward', {ns: 'genomic_browser'}),
+            '-': t('Reverse', {ns: 'genomic_browser'}),
           },
         },
       },

modules/genomic_browser/jsx/tabs_content/snp.js

@@ -152,10 +152,6 @@ class SNP extends Component {
           options: options.Cohorts,
         },
       },
-      {
-        label: t('Date of Birth', {ns: 'loris'}),
-        show: false,
-      },
       {
         label: t('External ID', {ns: 'genomic_browser'}),
         show: false,
@@ -182,8 +178,8 @@ class SNP extends Component {
           name: 'Strand',
           type: 'select',
           options: {
-            F: 'Forward',
-            R: 'Reverse',
+            '+': t('Forward', {ns: 'genomic_browser'}),
+            '-': t('Reverse', {ns: 'genomic_browser'}),
           },
         },
       },

modules/genomic_browser/locale/fr/LC_MESSAGES/genomic_browser.po

@@ -314,3 +314,9 @@ msgstr "non classé"
 
 msgid "Upload error!"
 msgstr "Erreur de téléversement !"
+
+msgid "Forward"
+msgstr "Sens"
+
+msgid "Reverse"
+msgstr "Antisens"

modules/genomic_browser/locale/genomic_browser.pot

@@ -315,3 +315,9 @@ msgstr ""
 
 msgid "Upload error!"
 msgstr ""
+
+msgid "Forward"
+msgstr ""
+
+msgid "Reverse"
+msgstr ""

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

@@ -212,10 +212,10 @@ class CnvDTO implements DataInstance, SiteHaver
     public function jsonSerialize() : array
     {
         return [
-            'PSC'               => $this->_PSC,
+            'PSC'               => dgettext("psc", $this->_PSC),
             'DCCID'             => $this->_DCCID,
             'PSCID'             => $this->_PSCID,
-            'Sex'               => $this->_Sex,
+            'Sex'               => dgettext("sex", $this->_Sex),
             'Cohort'            => $this->_Cohort,
             'ExternalID'        => $this->_ExternalID,
             'Chromosome'        => $this->_Chromosome,
@@ -226,12 +226,14 @@ class CnvDTO implements DataInstance, SiteHaver
             'Gene_Symbol'       => $this->_Gene_Symbol,
             'Gene_Name'         => $this->_Gene_Name,
             'CNV_Description'   => $this->_CNV_Description,
-            'CNV_Type'          => $this->_CNV_Type,
+            'CNV_Type'          => $this->_CNV_Type === "unknown"
+                ? dgettext("loris", $this->_CNV_Type)
+                : dgettext("genomic_browser", $this->_CNV_Type),
             'Copy_Num_Change'   => $this->_Copy_Num_Change,
             'Event_Name'        => $this->_Event_Name,
             'Common_CNV'        => $this->_Common_CNV,
             'Characteristics'   => $this->_Characteristics,
-            'Inheritance'       => $this->_Inheritance,
+            'Inheritance'       => dgettext("loris", $this->_Inheritance),
             'Array_Report'      => $this->_Array_Report,
             'Markers'           => $this->_Markers,
             'Validation_Method' => $this->_Validation_Method,

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

@@ -271,7 +271,7 @@ class MethylationDTO implements DataInstance, SiteHaver
             'PSC'              => $this->_PSC,
             'DCCID'            => $this->_DCCID,
             'PSCID'            => $this->_PSCID,
-            'Sex'              => $this->_Sex,
+            'Sex'              => dgettext("sex", $this->_Sex),
             'Cohort'           => $this->_Cohort,
             'Sample'           => $this->_Sample,
             'cpg_name'         => $this->_cpg_name,
@@ -284,7 +284,7 @@ class MethylationDTO implements DataInstance, SiteHaver
             'Probe_Loc_B'      => $this->_Probe_Loc_B,
             'Probe_Seq_B'      => $this->_Probe_Seq_B,
             'Design'           => $this->_Design,
-            'Color'            => $this->_Color,
+            'Color'            => dgettext("genomics_browser", $this->_Color),
             'Assembly'         => $this->_Assembly,
             'SNP_10'           => $this->_SNP_10,
             'Gene'             => $this->_Gene,
@@ -299,7 +299,7 @@ class MethylationDTO implements DataInstance, SiteHaver
             'Reg_Feature_Loc'  => $this->_Reg_Feature_Loc,
             'Reg_Feature_Grp'  => $this->_Reg_Feature_Grp,
             'DHS'              => $this->_DHS,
-            'Platform'         => $this->_Platform,
+            'Platform'         => dgettext("genotyping_platform", $this->_Platform),
         ];
     }
 

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

@@ -126,11 +126,12 @@ class ProfileDTO implements DataInstance, SiteHaver
     public function jsonSerialize(): array
     {
         return [
-            'centerID'   => $this->_PSC,
+            'centerID'   => dgettext("psc", $this->_PSC),
             'DCCID'      => $this->_DCCID,
             'PSCID'      => $this->_PSCID,
-            'Sex'        => $this->_Sex,
-            'Cohort'     => $this->_Cohort,
+            'Sex'        => dgettext("sex", $this->_Sex),
+            'Cohort'     => $this->_Cohort ? dgettext("cohort", $this->_Cohort)
+                : $this->_Cohort,
             'externalID' => $this->_externalID,
             'File'       => $this->_File,
             'SNP'        => $this->_SNP,

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

@@ -257,12 +257,14 @@ class SnpDTO implements DataInstance, SiteHaver
      */
     public function jsonSerialize(): array
     {
+        $cohort = $this->_Cohort;
         return [
-            'PSC'                 => $this->_PSC,
+            'PSC'                 => dgettext("psc", $this->_PSC),
             'DCCID'               => $this->_DCCID,
             'PSCID'               => $this->_PSCID,
-            'Sex'                 => $this->_Sex,
-            'Cohort'              => $this->_Cohort,
+            'Sex'                 => dgettext("sex", $this->_Sex),
+            'Cohort'              => $cohort ?
+                dgettext("cohort", $cohort) : $cohort,
             'externalID'          => $this->_externalID,
             'Chromosome'          => $this->_Chromosome,
             'Strand'              => $this->_Strand,

modules/genomic_browser/php/snpbrowser.class.inc

@@ -89,7 +89,7 @@ class SnpBrowser extends \DataFrameworkMenu implements ETagCalculator
             );
         $platform_options = [];
         foreach ($platform_results as $row) {
-            $name = $row['Name'];
+            $name = dgettext('genotyping_platform', $row['Name']);
             $platform_options[$name] = $name;
         }
         return (new \LORIS\genomic_browser\Views\SNP(

modules/genomic_browser/php/views/cnv.class.inc

@@ -40,11 +40,13 @@ class CNV
      */
     public function __construct($platform_options, $sites, $cohorts)
     {
+        $sexes = \Utility::getSexList();
+        $sexes = array_combine($sexes, $sexes);
         $this->_formElement = [
             'Sites'    => $sites,
             'Cohorts'  => $cohorts,
             'Platform' => $platform_options,
-            'Sex'      => \Utility::getSexList(),
+            'Sex'      => $sexes,
         ];
     }
 

modules/genomic_browser/php/views/methylation.class.inc

@@ -39,6 +39,8 @@ class Methylation
      */
     public function __construct($sites, $cohorts)
     {
+        $sexes = \Utility::getSexList();
+        $sexes = array_combine($sexes, $sexes);
         $this->_formElement = [
             'Sites'           => $sites,
             'Cohorts'         => $cohorts,
@@ -58,7 +60,7 @@ class Methylation
                 'genotyping_platform',
                 'Name'
             ),
-            'Sex'             => \Utility::getSexList(),
+            'Sex'             => $sexes,
         ];
     }
 

modules/genomic_browser/php/views/profiles.class.inc

@@ -39,10 +39,12 @@ class Profiles
      */
     public function __construct($sites, $cohorts)
     {
+        $sexes = \Utility::getSexList();
+        $sexes = array_combine($sexes, $sexes);
         $this->_formElement = [
             'Sites'   => $sites,
             'Cohorts' => $cohorts,
-            'Sex'     => \Utility::getSexList(),
+            'Sex'     => $sexes,
         ];
     }
 

modules/genomic_browser/php/views/snp.class.inc

@@ -40,11 +40,13 @@ class SNP
      */
     public function __construct($sites, $cohorts, $platform_options)
     {
+        $sexes = \Utility::getSexList();
+        $sexes = array_combine($sexes, $sexes);
         $this->_formElement = [
             'Sites'    => $sites,
             'Cohorts'  => $cohorts,
             'Platform' => $platform_options,
-            'Sex'      => \Utility::getSexList(),
+            'Sex'      => $sexes,
         ];
     }
 

php/libraries/DataFrameworkMenu.class.inc

@@ -269,6 +269,13 @@ abstract class DataFrameworkMenu extends NDB_Menu_Filter
             []
         );
 
+        $cohortOptions = array_map(
+            function ($name) {
+                return dgettext("cohort", $name);
+            },
+            $cohortOptions
+        );
+
         if (!$numericKeys) {
             $cohortNames = array_values($cohortOptions);
             return array_combine($cohortNames, $cohortNames);

raisinbread/locale/fr/LC_MESSAGES/genotyping_platform.po

@@ -0,0 +1,20 @@
+msgid ""
+msgstr ""
+
+"Project-Id-Version: LORIS 29\n"
+"Report-Msgid-Bugs-To: https://github.com/aces/Loris/issues\n"
+"POT-Creation-Date: 2025-04-08 14:37-0400\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: fr\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+"Plural-Forms: nplurals=2; plural=(n > 1);\n"
+
+msgid "Custom CNV array"
+msgstr "Puce CNV personnalisée"
+
+msgid "Custom SNP array"
+msgstr "Puce SNP personnalisée"

raisinbread/locale/genotyping_platform.pot

@@ -0,0 +1,19 @@
+msgid ""
+msgstr ""
+
+"Project-Id-Version: LORIS 29\n"
+"Report-Msgid-Bugs-To: https://github.com/aces/Loris/issues\n"
+"POT-Creation-Date: 2025-04-08 14:37-0400\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+msgid "Custom CNV array"
+msgstr ""
+
+msgid "Custom SNP array"
+msgstr ""