Bump symfony/http-foundation from 6.2.8 to 6.4.16

app/SequenceCell.php → app/Cell.php

@@ -9,7 +9,7 @@
 use Illuminate\Support\Facades\Storage;
 use ZipArchive;
 
-class SequenceCell
+class Cell
 {
     public static function summary($filters, $username)
     {
@@ -77,7 +77,7 @@ public static function summary($filters, $username)
         return $data;
     }
 
-    public static function expectedSequenceCellsByRestSevice($filters, $username)
+    public static function expectedCellsByRestSevice($filters, $username)
     {
         $response_list = RestService::sequences_summary($filters, $username, false, 'cell');
         $expected_nb_cells_by_rs = [];
@@ -133,7 +133,7 @@ public static function cellsTSVFolder($filters, $username, $url = '',
 
         // do extra cell summary request to get expected number of cells
         // for sanity check after download
-        $expected_nb_cells_by_rs = self::expectedSequenceCellsByRestSevice($filters, $username);
+        $expected_nb_cells_by_rs = self::expectedCellsByRestSevice($filters, $username);
 
         // get filtered list of repertoires ids
         $filtered_samples_by_rs = self::filteredSamplesByRestService($response_list);
@@ -197,7 +197,7 @@ public static function cellsTSVFolder($filters, $username, $url = '',
             // sequence data
             $sequence_response_list = RestService::sequences_data_from_cell_ids($filters, $folder_path, $username, $expected_nb_cells_by_rs, $cell_id_list_by_rs);
         } else {
-            Log::debug('SequenceCell::cellTSVFolder - SKIPPING DOWNLOAD');
+            Log::debug('Cell::cellTSVFolder - SKIPPING DOWNLOAD');
         }
 
         $file_stats = self::file_stats($cell_response_list, $expression_response_list, $metadata_response_list, $sequence_response_list, $expected_nb_cells_by_rs, $download_data);

app/Http/Controllers/CellController.php

@@ -3,11 +3,11 @@
 namespace App\Http\Controllers;
 
 use App\Bookmark;
+use App\Cell;
 use App\Download;
 use App\FieldName;
 use App\QueryLog;
 use App\Sample;
-use App\SequenceCell;
 use App\System;
 use App\Tapis;
 use Facades\App\Query;
@@ -59,17 +59,23 @@ public function index(Request $request)
         // allow only Cell filters, or only GEX filters, based on currently opened panel
         if (isset($filters['open_filter_panel_list'])) {
             $open_filter_panel_list = $filters['open_filter_panel_list'];
+            //Log::debug($open_filter_panel_list);
+            //blah;
             if ($open_filter_panel_list[0] == 0) {
                 unset($filters['property_expression']);
                 unset($filters['value_expression']);
-            } else {
+            } elseif ($open_filter_panel_list[1] == 0) {
+                unset($filters['antigen']);
+                unset($filters['antigen_source_species']);
+                unset($filters['peptide_sequence_aa']);
+            } elseif ($open_filter_panel_list[2] == 0) {
                 unset($filters['expression_study_method_cell']);
                 unset($filters['virtual_pairing_cell']);
             }
         }
 
         // retrieve data
-        $cell_data = SequenceCell::summary($filters, $username);
+        $cell_data = Cell::summary($filters, $username);
 
         // store data size in user query log
         $query_log_id = $request->get('query_log_id');

app/Jobs/DownloadSequences.php

@@ -2,11 +2,11 @@
 
 namespace App\Jobs;
 
+use App\Cell;
 use App\LocalJob;
 use App\Query;
 use App\QueryLog;
 use App\Sequence;
-use App\SequenceCell;
 use App\SequenceClone;
 use App\User;
 use Carbon\Carbon;
@@ -102,7 +102,7 @@ public function handle()
         } elseif ($this->type == 'clone') {
             $t = SequenceClone::clonesTSV($filters, $this->username, $this->url, $sample_filter_fields);
         } elseif ($this->type == 'cell') {
-            $t = SequenceCell::cellsTSV($filters, $this->username, $this->url, $sample_filter_fields);
+            $t = Cell::cellsTSV($filters, $this->username, $this->url, $sample_filter_fields);
         }
 
         //$file_path = $t['public_path'];

app/Jobs/LaunchJob.php

@@ -2,11 +2,11 @@
 
 namespace App\Jobs;
 
+use App\Cell;
 use App\Job;
 use App\LocalJob;
 use App\Query;
 use App\Sequence;
-use App\SequenceCell;
 use App\SequenceClone;
 use App\System;
 use App\Tapis;
@@ -132,7 +132,7 @@ public function handle()
                 $zip_info = SequenceClone::clonesTSV($filters, $gw_username, $job->url,
                     $sample_filter_fields, $download_data);
             } elseif ($jobType == 'cell') {
-                $zip_info = SequenceCell::cellsTSV($filters, $gw_username, $job->url,
+                $zip_info = Cell::cellsTSV($filters, $gw_username, $job->url,
                     $sample_filter_fields, $download_data);
             }