Merge pull request #767 from sfu-ireceptor/master

Merge master into production-v4

app/Bookmark.php

@@ -41,7 +41,7 @@ public static function findGroupedByMonthForUser($user_id)
 
     public static function get($id, $user_id)
     {
-        $b = static::where(['user_id' => $user_id, 'id'=> $id])->first();
+        $b = static::where(['user_id' => $user_id, 'id' => $id])->first();
 
         return $b;
     }

app/CachedSample.php

@@ -2,6 +2,7 @@
 
 namespace App;
 
+use Illuminate\Support\Facades\Log;
 use Illuminate\Support\Str;
 use Jenssegers\Mongodb\Eloquent\Model;
 
@@ -14,25 +15,52 @@ class CachedSample extends Model
     // cache samples from REST services
     public static function cache()
     {
-        // get data
+        // delete any previously cached data
+        self::truncate();
+
+        // Keep track of number of samples cached.
+        $sample_count = 0;
+        // get sequnce data
         $sample_data = Sample::find([], 'titi');  // use Jérôme's username (titi) for now
         $sample_list = $sample_data['items'];
 
-        // delete any previously cached data
-        self::truncate();
+        // cache data
+        foreach ($sample_list as $s) {
+            $s->ir_repertoire_type = 'sequence';
+            self::create(json_decode(json_encode($s), true));
+        }
+        $sample_count += count($sample_list);
+
+        // get clone data
+        $sample_data = Sample::find([], 'titi', true, 'clone');
+        $sample_list = $sample_data['items'];
+
+        // cache data
+        foreach ($sample_list as $s) {
+            $s->ir_repertoire_type = 'clone';
+            self::create(json_decode(json_encode($s), true));
+        }
+        $sample_count += count($sample_list);
+
+        // get cell data
+        $sample_data = Sample::find([], 'titi', true, 'cell');  // use Jérôme's username (titi) for now
+        $sample_list = $sample_data['items'];
 
         // cache data
         foreach ($sample_list as $s) {
+            $s->ir_repertoire_type = 'cell';
             self::create(json_decode(json_encode($s), true));
         }
+        $sample_count += count($sample_list);
 
-        return count($sample_list);
+        return $sample_count;
     }
 
     // return cached samples
-    public static function cached()
+    public static function cached($sample_type = 'sequence')
     {
-        return self::all();
+        return self::where('ir_repertoire_type', '=', $sample_type)->get();
+        //return self::all();
     }
 
     // return metadata by querying cached samples
@@ -60,12 +88,31 @@ public static function metadata()
         // list of REST services
         $t['rest_service_list'] = RestService::findEnabled(['id', 'name', 'rest_service_group_code'])->toArray();
 
-        // stats
+        // Get the total number of repositories.
         $t['total_repositories'] = count(self::distinctValuesGrouped(['rest_service_id']));
+        $t['total_repositories_sequences'] = count(self::distinctValuesFiltered('rest_service_id', 'ir_repertoire_type', 'sequence'));
+        $t['total_repositories_clones'] = count(self::distinctValuesFiltered('rest_service_id', 'ir_repertoire_type', 'clone'));
+        $t['total_repositories_cells'] = count(self::distinctValuesFiltered('rest_service_id', 'ir_repertoire_type', 'cell'));
+
+        // Get the total number of labs.
         $t['total_labs'] = count(self::distinctValuesGrouped(['rest_service_id', 'lab_name']));
+
+        // Get the study counts for total, sequence, clone, and cell studies.
         $t['total_projects'] = count(self::distinctValuesGrouped(['rest_service_id', 'study_title']));
+        $t['total_projects_sequences'] = count(self::distinctValuesFiltered('study_title', 'ir_repertoire_type', 'sequence'));
+        $t['total_projects_cells'] = count(self::distinctValuesFiltered('study_title', 'ir_repertoire_type', 'cell'));
+        $t['total_projects_clones'] = count(self::distinctValuesFiltered('study_title', 'ir_repertoire_type', 'clone'));
+
+        // Get the repertoire counts for all, sequence, clone, and cell repertoires.
         $t['total_samples'] = self::count();
+        $t['total_samples_sequences'] = self::where('ir_repertoire_type', '=', 'sequence')->count();
+        $t['total_samples_clones'] = self::where('ir_repertoire_type', '=', 'clone')->count();
+        $t['total_samples_cells'] = self::where('ir_repertoire_type', '=', 'cell')->count();
+
+        // Get the total counts for sequences, clones, and cells.
         $t['total_sequences'] = self::sum('ir_sequence_count');
+        $t['total_clones'] = self::sum('ir_clone_count');
+        $t['total_cells'] = self::sum('ir_cell_count');
 
         return $t;
     }
@@ -90,18 +137,41 @@ public static function distinctValues($fieldName)
         return $t;
     }
 
+    public static function distinctValuesFiltered($fieldName, $filterField, $filterValue)
+    {
+        $l = self::where($filterField, '=', $filterValue)->whereNotNull($fieldName)->distinct($fieldName)->get();
+        $l = $l->toArray();
+
+        // replace each array item (a one-item array) by the value directly
+        // Ex: [0]=>[[0]=> "Unknown"] is replaced by [0]=> "Unknown"
+        $t = [];
+        foreach ($l as $lt) {
+            if (! empty(trim($lt[0]))) {
+                $val = trim($lt[0]);
+                if (! in_array($val, $t)) {
+                    $t[] = $val;
+                }
+            }
+        }
+
+        return $t;
+    }
+
     public static function distinctValuesGrouped($fields)
     {
         $l = self::groupBy($fields);
+        //Log::debug('distinctValuesGrouped: l = ' . json_encode($l));
 
         // exclude null values
         foreach ($fields as $fieldName) {
             $l = $l->whereNotNull($fieldName);
         }
+        //Log::debug('distinctValuesGrouped: l = ' . json_encode($l));
 
         // do query
         $l = $l->get();
         $l = $l->toArray();
+        //Log::debug('distinctValuesGrouped: l = ' . json_encode($l));
 
         // remove useless '_id' key
         foreach ($l as $k => $v) {