Migrate helpers in NDB_Menu_Filter

aces · Aug 18, 2021 · 27821bc · 27821bc
1 parent 1a067ea
commit 27821bc
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Showing 7 changed files with 104 additions and 96 deletions.
diff --git a/modules/electrophysiology_browser/php/electrophysiology_browser.class.inc b/modules/electrophysiology_browser/php/electrophysiology_browser.class.inc
@@ -81,7 +81,11 @@ class Electrophysiology_Browser extends \DataFrameworkMenu
         }
 
         return [
-            'sites'    => $this->getSiteOptions($user, false),
+            'sites'    => $this->getSiteOptions(
+                $user,
+                false,
+                $this->allSitePermissionNames()
+            ),
             'projects' => $this->getProjectOptions($user, false),
             'types'    => $list_of_types
         ];

diff --git a/modules/genomic_browser/php/cnvbrowser.class.inc b/modules/genomic_browser/php/cnvbrowser.class.inc
@@ -96,7 +96,7 @@ class CnvBrowser extends \DataFrameworkMenu implements ETagCalculator
 
         return (new \LORIS\genomic_browser\Views\CNV(
             $platform_options,
-            $this->getSiteOptions($user, false),
+            $this->getSiteOptions($user, false, $this->allSitePermissionNames()),
             $this->getSubprojectOptions($user),
         ))->toArray();
     }

diff --git a/modules/genomic_browser/php/methylation.class.inc b/modules/genomic_browser/php/methylation.class.inc
@@ -84,7 +84,7 @@ class Methylation extends \DataFrameworkMenu implements ETagCalculator
         $user = \NDB_Factory::singleton()->user();
 
         return (new \LORIS\genomic_browser\Views\Methylation(
-            $this->getSiteOptions($user, false),
+            $this->getSiteOptions($user, false, $this->allSitePermissionNames()),
             $this->getSubprojectOptions($user),
         ))->toArray();
     }

diff --git a/modules/genomic_browser/php/profiles.class.inc b/modules/genomic_browser/php/profiles.class.inc
@@ -83,7 +83,7 @@ class Profiles extends \DataFrameworkMenu implements ETagCalculator
         $user = \NDB_Factory::singleton()->user();
 
         return (new \LORIS\genomic_browser\Views\Profiles(
-            $this->getSiteOptions($user, false),
+            $this->getSiteOptions($user, false, $this->allSitePermissionNames()),
             $this->getSubprojectOptions($user, false),
         ))->toArray();
     }

diff --git a/modules/genomic_browser/php/snpbrowser.class.inc b/modules/genomic_browser/php/snpbrowser.class.inc
@@ -92,7 +92,7 @@ class SnpBrowser extends \DataFrameworkMenu implements ETagCalculator
             $platform_options[$name] = $name;
         }
         return (new \LORIS\genomic_browser\Views\SNP(
-            $this->getSiteOptions($user, false),
+            $this->getSiteOptions($user, false, $this->allSitePermissionNames()),
             $this->getSubprojectOptions($user, false),
             $platform_options,
         ))->toArray();

diff --git a/php/libraries/DataFrameworkMenu.class.inc b/php/libraries/DataFrameworkMenu.class.inc
@@ -187,96 +187,5 @@ abstract class DataFrameworkMenu extends NDB_Menu_Filter
         return new \LORIS\Http\DataIteratorBinaryStream($rows);
 
     }
-
-    /**
-     * Format the user's projects to display the module filter options
-     *
-     * @param \User $user        User
-     * @param bool  $numericKeys If the returned projects keys
-     *                           should be numeric (ProjectID) or project name
-     *
-     * @return array - an associative array of the form (ID|mame => name)
-     */
-    public function getProjectOptions(
-        \User $user,
-        bool  $numericKeys = true
-    ): array {
-        $projects     = $user->getProjects();
-        $projectNames = array_map(
-            fn($project) => $project->getName(),
-            $projects
-        );
-
-        if ($numericKeys) {
-            $projectIDs = array_map(
-                fn($project) => strval($project->getId()),
-                $projects
-            );
-            return array_combine($projectIDs, $projectNames);
-        }
-
-        return array_combine($projectNames, $projectNames);
-    }
-
-    /**
-     * Format the user's subprojects to display the module filter options
-     *
-     * @param \User $user        User
-     * @param bool  $numericKeys If the returned subprojects keys
-     *                           should be numeric (SubprojectID)
-     *                           or strings (subproject name)
-     *
-     * @return array - an associative array of the form (ID => name)
-     */
-    public function getSubprojectOptions(
-        \User $user,
-        bool $numericKeys = true
-    ): array {
-        $subprojectOptions = array_reduce(
-            $user->getProjects(),
-            fn($subprojects, $project) =>
-                $subprojects
-                + array_column($project->getSubprojects(), 'title', 'subprojectId'),
-            []
-        );
-
-        if (!$numericKeys) {
-            $subprojectNames = array_values($subprojectOptions);
-            return array_combine($subprojectNames, $subprojectNames);
-        }
-
-        return $subprojectOptions;
-    }
-
-    /**
-     * Format the user's sites to display the module filter options
-     *
-     * @param \User $user        User
-     * @param bool  $numericKeys If the returned sites keys should be
-                                 numeric (CenterID) or strings (site name)
-     * @param bool  $studySite   If the returned sites should be study sites only
-     *
-     * @return array An associative array of the form (ID|name => name)
-     */
-    public function getSiteOptions(
-        \User $user,
-        bool $numericKeys = true,
-        bool $studySite = true
-    ): array {
-        // If the user has any of the All Site permissions,
-        // get the list of all study sites
-        if ($user->hasAnyPermission($this->allSitePermissionNames())) {
-            $siteOptions = \Utility::getSiteList($studySite);
-        } else {
-            $siteOptions = $user->getStudySites();
-        }
-
-        if (!$numericKeys) {
-            $siteNames = array_values($siteOptions);
-            return array_combine($siteNames, $siteNames);
-        }
-
-        return $siteOptions;
-    }
 }
 
diff --git a/php/libraries/NDB_Menu_Filter.class.inc b/php/libraries/NDB_Menu_Filter.class.inc
@@ -849,5 +849,100 @@ class NDB_Menu_Filter extends NDB_Menu
             ]
         );
     }
+
+    /**
+     * Format the user's projects to display the module filter options
+     *
+     * @param \User $user        User
+     * @param bool  $numericKeys If the returned projects keys
+     *                           should be numeric (ProjectID) or project name
+     *
+     * @return array - an associative array of the form (ID|mame => name)
+     */
+    public function getProjectOptions(
+        \User $user,
+        bool  $numericKeys = true
+    ): array {
+        $projects     = $user->getProjects();
+        $projectNames = array_map(
+            fn($project) => $project->getName(),
+            $projects
+        );
+
+        if ($numericKeys) {
+            $projectIDs = array_map(
+                fn($project) => strval($project->getId()),
+                $projects
+            );
+            return array_combine($projectIDs, $projectNames);
+        }
+
+        return array_combine($projectNames, $projectNames);
+    }
+
+    /**
+     * Format the user's subprojects to display the module filter options
+     *
+     * @param \User $user        User
+     * @param bool  $numericKeys If the returned subprojects keys
+     *                           should be numeric (SubprojectID)
+     *                           or strings (subproject name)
+     *
+     * @return array - an associative array of the form (ID => name)
+     */
+    public function getSubprojectOptions(
+        \User $user,
+        bool $numericKeys = true
+    ): array {
+        $subprojectOptions = array_reduce(
+            $user->getProjects(),
+            fn($subprojects, $project) =>
+                $subprojects
+                + array_column($project->getSubprojects(), 'title', 'subprojectId'),
+            []
+        );
+
+        if (!$numericKeys) {
+            $subprojectNames = array_values($subprojectOptions);
+            return array_combine($subprojectNames, $subprojectNames);
+        }
+
+        return $subprojectOptions;
+    }
+
+    /**
+     * Format the user's sites to display the module filter options
+     *
+     * @param \User $user                User
+     * @param bool  $numericKeys         If the returned sites keys should be
+                                         numeric (CenterID) or strings (site name)
+     * @param ?array $allsitesPermission A list of permission
+     *                                   which gives access to all sites
+     * @param bool  $studySite           If the returned sites should be
+     *                                   study sites only
+     *
+     * @return array An associative array of the form (ID|name => name)
+     */
+    public function getSiteOptions(
+        \User $user,
+        bool $numericKeys = true,
+        ?array $allsitesPermission = ['access_all_profiles'],
+        bool $studySite = true
+    ): array {
+        // If the user has any of the All Site permissions,
+        // get the list of all study sites
+        if ($allsitesPermission && $user->hasAnyPermission($allsitesPermission)) {
+            $siteOptions = \Utility::getSiteList($studySite);
+        } else {
+            $siteOptions = $user->getStudySites();
+        }
+
+        if (!$numericKeys) {
+            $siteNames = array_values($siteOptions);
+            return array_combine($siteNames, $siteNames);
+        }
+
+        return $siteOptions;
+    }
 }