add general relationship methods

biotorrents · May 29, 2024 · 46659c2 · 46659c2
1 parent 2b66810
commit 46659c2
Show file tree

Hide file tree

Showing 83 changed files with 3,992 additions and 815 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,7 @@
+# Contributing to BioGazelle
+
+Thanks for your interest in improving BioGazelle's codebase.
+
+## General application layout
+
+todo
diff --git a/app/Auth.php b/app/Auth.php
@@ -387,12 +387,13 @@ public function login(array $data)
 
         $username = \Gazelle\Escape::username($data["username"] ?? null);
         $passphrase = \Gazelle\Escape::passphrase($data["passphrase"] ?? null);
-        $rememberMe = \Gazelle\Escape::bool($data["rememberMe"] ?? null);
-
-        # 2fa code needs to be a string (RobThree)
         $twoFactor = \Gazelle\Escape::string($data["twoFactor"] ?? null);
+        $rememberMe = \Gazelle\Escape::bool($data["rememberMe"] ?? null);
 
         try {
+            # start a transaction
+            $app->dbNew->beginTransaction();
+
             # validate userId and 2fa
             $query = "
                 select users.id, users_main.twoFactor from users
@@ -410,30 +411,12 @@ public function login(array $data)
             if ($row["twoFactor"] && empty($twoFactor)) {
                 throw new Exception("2fa code required");
             }
-        } catch (Throwable $e) {
-            return $e->getMessage();
-            return $message;
-        }
 
-        # gazelle 2fa
-        if (!empty($twoFactor)) {
-            try {
+            if (!empty($twoFactor)) {
                 $this->verify2FA($userId, $twoFactor);
-            } catch (Throwable $e) {
-                return $e->getMessage();
-                return $message;
             }
-        }
-
-        try {
-            /*
-            # todo: we're just updating users_main.id, it's technically wrong
-            # also this executes on every login, kinda lazy and not ideal
-            $query = "update users_main set id = userId where userId = ?";
-            $app->dbNew->do($query, [$userId]);
-            */
 
-            # todo: same as above
+            # are there any unencrypted emails left?
             $query = "select email from users where id = ?";
             $email = $app->dbNew->single($query, [$userId]);
 
@@ -443,7 +426,7 @@ public function login(array $data)
                 $app->dbNew->do($query, [ \Gazelle\Crypto::encrypt($email), $userId ]);
             }
 
-            # legacy: remove after 2024-04-01
+            # legacy isPassphraseMigrated: remove after 2025-04-01
             $query = "select isPassphraseMigrated from users_info where userId = ?";
             $isPassphraseMigrated = $app->dbNew->single($query, [$userId]);
 
@@ -482,36 +465,42 @@ public function login(array $data)
                 $response = $this->library->loginWithUsername($username, $passphrase, $this->remember($rememberMe));
             }
             */
-        } catch (\Delight\Auth\InvalidEmailException $e) {
-            return $e->getMessage();
-            return $message;
-        } catch (\Delight\Auth\InvalidPasswordException $e) {
-            return $e->getMessage();
-            return $message;
+            /*
+            } catch (\Delight\Auth\InvalidEmailException $e) {
+                return $e->getMessage();
+                return $message;
+            } catch (\Delight\Auth\InvalidPasswordException $e) {
+                return $e->getMessage();
+                return $message;
+            */
         } catch (\Delight\Auth\EmailNotVerifiedException $e) {
             # this throws to provide a "resend confirmation email" link
             throw new \Delight\Auth\EmailNotVerifiedException($e->getMessage());
-        } catch (\Delight\Auth\TooManyRequestsException $e) {
-            return $e->getMessage();
-            return $message;
-        } catch (\Delight\Auth\UnknownUsernameException $e) {
-            return $e->getMessage();
-            return $message;
-        } catch (\Delight\Auth\AmbiguousUsernameException $e) {
-            return $e->getMessage();
-            return $message;
+            /*
+            } catch (\Delight\Auth\TooManyRequestsException $e) {
+                return $e->getMessage();
+                return $message;
+            } catch (\Delight\Auth\UnknownUsernameException $e) {
+                return $e->getMessage();
+                return $message;
+            } catch (\Delight\Auth\AmbiguousUsernameException $e) {
+                return $e->getMessage();
+                return $message;
+            */
         } catch (Throwable $e) {
             return $e->getMessage();
             return $message;
         }
 
+        /*
         try {
             # gazelle session
             $this->createSession($userId, $rememberMe);
         } catch (Throwable $e) {
             return $e->getMessage();
             return $message;
         }
+        */
     } # login
 
 

diff --git a/app/Better.php b/app/Better.php
@@ -128,7 +128,7 @@ public static function missingCitations(bool $snatchedOnly = false): array
             from torrents_group
             {$subQuery}
             where torrents_group.id not in
-            (select distinct group_id from literature)
+            (select distinct groupId from literature_groups)
             order by rand() limit {$resultCount}
         ";
 

diff --git a/app/Models/Collages.php b/app/Models/Collages.php
@@ -129,7 +129,7 @@ public function relationships(): array
      *
      * @return array
      */
-    public function relatedTorrentGroups(): array
+    private function relatedTorrentGroups(): array
     {
         $app = App::go();
 
@@ -145,30 +145,6 @@ public function relatedTorrentGroups(): array
     }
 
 
-    /** accessors */
-
-
-    /**
-     * getTorrentGroups
-     *
-     * @return array
-     */
-    public function getTorrentGroups(): array
-    {
-        $app = App::go();
-
-        # get related id's
-        $ref = $this->relatedTorrentGroups();
-
-        $data = [];
-        foreach ($ref as $row) {
-            $data[] = new TorrentGroups($row["id"]);
-        }
-
-        return $data;
-    }
-
-
     /** methods */
 
 

diff --git a/app/Models/Conversations.php b/app/Models/Conversations.php
@@ -90,7 +90,7 @@ public function relationships(): ?array
      *
      * @return ?array
      */
-    public function relatedMessages(): ?array
+    private function relatedMessages(): ?array
     {
         $app = App::go();
 

diff --git a/app/Models/Creators.php b/app/Models/Creators.php
@@ -83,7 +83,7 @@ public function relationships(): array
      *
      * @return array
      */
-    public function relatedTorrentGroups(): array
+    private function relatedTorrentGroups(): array
     {
         $app = App::go();
 
@@ -104,7 +104,7 @@ public function relatedTorrentGroups(): array
      *
      * @return array
      */
-    public function relatedRequests(): array
+    private function relatedRequests(): array
     {
         $app = App::go();
 
@@ -123,55 +123,6 @@ public function relatedRequests(): array
     /** methods */
 
 
-    /**
-     * getTorrentGroups
-     *
-     * Gets the torrent groups for a creator.
-     *
-     * @return array
-     */
-    public function getTorrentGroups(): array
-    {
-        $app = App::go();
-
-        # get related id's
-        $ref = $this->relatedTorrentGroups();
-
-        $data = [];
-        foreach ($ref as $row) {
-            $data[] = new TorrentGroups($row["id"]);
-        }
-
-        return $data;
-    }
-
-
-    /**
-     * getRequests
-     *
-     * Gets the requests for a creator.
-     *
-     * @return array
-     */
-    public function getRequests(): array
-    {
-        $app = App::go();
-
-        # get related id's
-        $ref = $this->relatedRequests();
-
-        $data = [];
-        foreach ($ref as $row) {
-            $data[] = new Requests($row["id"]);
-        }
-
-        return $data;
-    }
-
-
-    /** */
-
-
     /**
      * hydrateFromSemanticScholar
      *
@@ -209,11 +160,12 @@ public function hydrateFromSemanticScholar(): ?array
         # prepare the data for the database
         $data = [
             "id" => $this->id,
+            "orcid" => $canonicalCreator["externalIds"]["ORCID"] ?? null,
             "semanticScholarId" => $canonicalCreator["authorId"] ?? null,
             "name" => $canonicalCreator["name"] ?? null,
             "slug" => \Illuminate\Support\Str::slug($canonicalCreator["name"] ?? null),
-            "aliases" => json_encode($canonicalCreator["aliases"] ?? null),
-            "affiliations" => json_encode($canonicalCreator["affiliations"] ?? null),
+            "aliases" => json_encode($canonicalCreator["aliases"] ?? []),
+            "affiliations" => json_encode($canonicalCreator["affiliations"] ?? []),
             "homepage" => $canonicalCreator["homepage"] ?? null,
             "hIndex" => $canonicalCreator["hIndex"] ?? null,
             "paperCount" => $canonicalCreator["paperCount"] ?? null,