[mindlogger] Implementation ML integration POC1

SQL/0000-00-01-Modules.sql

@@ -52,5 +52,6 @@ INSERT INTO modules (Name, Active) VALUES ('user_accounts', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('electrophysiology_browser', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('dqt', 'Y');
 INSERT INTO modules (Name, Active) VALUES ('electrophysiology_uploader', 'Y');
+INSERT INTO modules (Name, Active) VALUES ('mindlogger', 'Y');
 
 ALTER TABLE issues ADD CONSTRAINT `fk_issues_7` FOREIGN KEY (`module`) REFERENCES `modules` (`ID`);

SQL/0000-00-02-Permission.sql

@@ -131,7 +131,8 @@ INSERT INTO `permissions` VALUES
     (60,'behavioural_quality_control_view','Flagged Behavioural Entries',(SELECT ID FROM modules WHERE Name='behavioural_qc'),'View','2'),
     (61,'api_docs','API documentation',(SELECT ID FROM modules WHERE Name='api_docs'),'View','2'),
     (62,'electrophysiology_browser_edit_annotations','Annotations',(SELECT ID FROM modules WHERE Name='electrophysiology_browser'),'Create/Edit','2'),
-    (63,'monitor_eeg_uploads','Monitor EEG uploads',(SELECT ID FROM modules WHERE Name='electrophysiology_uploader'),NULL,'2');
+    (63,'monitor_eeg_uploads','Monitor EEG uploads',(SELECT ID FROM modules WHERE Name='electrophysiology_uploader'),NULL,'2'),
+    (64, 'mindlogger_schema_create', 'Mindlogger applet schemas and instruments thru API', (SELECT ID FROM modules WHERE Name='mindlogger'), 'Create', 2);
 
 INSERT INTO `user_perm_rel` (userID, permID)
   SELECT u.ID, p.permID

SQL/New_patches/2023-11-21-Mindlogger.sql

@@ -0,0 +1,25 @@
+-- Enable Mindlogger module
+INSERT INTO modules (Name, Active)
+VALUES ('mindlogger', 'Y');
+
+
+-- Add Mindlogger module permissions
+INSERT INTO `permissions` (code, description, moduleID, action, categoryID)
+VALUES ('mindlogger_schema_create', 'Mindlogger applet schemas and instruments thru API',
+        (SELECT ID FROM modules WHERE Name = 'mindlogger'), 'Create', 2);
+
+
+-- Create Mindlogger schema table
+CREATE TABLE `instrument_mindlogger_schema`
+(
+    `AppletID`     varchar(36) NOT NULL,
+    `AppletSchema` text        NOT NULL,
+    `CreatedDate`  timestamp   NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    `UpdatedDate`  timestamp   NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+    PRIMARY KEY (AppletId)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+-- Add Mindlogger instruments subgroup
+INSERT INTO test_subgroups (Subgroup_name)
+VALUES ('Mindlogger instruments');
+

modules/dictionary/php/datadictrow.class.inc

@@ -64,7 +64,6 @@ class DataDictRow implements \LORIS\Data\DataInstance,
             'datascope'          => $scope,
             'type'               => $this->getDataType(),
             'cardinality'        => $this->getCardinality(),
-            'visits'             => $this->visits,
         ];
 
         $itype = $this->item->getDataType();

modules/mindlogger/README.md

@@ -0,0 +1,24 @@
+# Mindlogger
+
+## Purpose
+The API module is intended to provide a stable, versioned REST interface for receiving Mindlogger Applet schemas saving to the DB and creating instruments.
+
+## Intended Users
+The module has 1 intended use cases:
+
+1. Interactions with data coming from outside the LORIS core softwar
+
+
+## Scope
+
+## Permissions
+
+Accessing the `mindlogger` module requires the `mindlogger_schema_create` permission (_"Create Mindlogger applet schemas and instruments thru API"_)
+
+Users with the `mindlogger_schema_create ` permission can create new ML applet schema entries and related instruments in the Loris.
+
+## Configurations
+
+
+## Interactions with LORIS
+

modules/mindlogger/php/endpoint.class.inc

@@ -0,0 +1,71 @@
+<?php declare(strict_types=1);
+/**
+ * An API endpoint is an endpoint which abstracts away common element
+ * of different Mindlogger API endpoints.
+ *
+ * PHP Version 7
+ *
+ * @category Mindlogger
+ * @package  Mindlogger
+ * @author   Dzmitry Yahur <dyagur@scnsoft.com>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://github.com/aces/Loris
+ */
+
+namespace LORIS\mindlogger;
+
+use \Psr\Http\Message\ServerRequestInterface;
+use \Psr\Http\Server\RequestHandlerInterface;
+use \Psr\Http\Message\ResponseInterface;
+use \LORIS\Http\Endpoint as LORISEndpoint;
+
+/**
+ * An abstract class for common concerns of different API endpoints.
+ *
+ * @category Mindlogger
+ * @package  Mindlogger
+ * @author   Dzmitry Yahur <dyagur@scnsoft.com>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://github.com/aces/Loris
+ */
+abstract class Endpoint extends LORISEndpoint implements RequestHandlerInterface
+{
+    /**
+     * Return an array of valid HTTP methods for this endpoint
+     *
+     * @return string[] Valid versions
+     */
+    abstract protected function allowedMethods(): array;
+
+    /**
+     * Return a list of Mindlog API versions which this endpoint
+     * supports.
+     *
+     * @return string[] LORIS API Versions
+     */
+    abstract protected function supportedVersions(): array;
+
+    /**
+     * An API endpoint overrides the default Mindlog Endpoint to add checks for
+     * supported version(s).
+     *
+     * @param ServerRequestInterface  $request The incoming PSR7 request
+     * @param RequestHandlerInterface $handler The PSR15 request handler
+     *
+     * @return ResponseInterface
+     */
+    public function process(
+        ServerRequestInterface  $request,
+        RequestHandlerInterface $handler
+    ): ResponseInterface {
+        $versions = $this->supportedVersions() ?? [];
+        $version  = $request->getAttribute("Mindlogger-API-Version") ?? "unknown";
+        if (!in_array($version, $versions)) {
+            // If it's not supported by a version of the API, that means the
+            // endpoint for that version should be not found
+            return new \LORIS\Http\Response\JSON\NotFound('Unsupported version');
+        }
+
+        return parent::process($request, $handler);
+    }
+}

modules/mindlogger/php/endpoints/schema.class.inc

@@ -0,0 +1,165 @@
+<?php declare(strict_types=1);
+/**
+ * This implements the Schema endpoint class
+ *
+ * PHP Version 8
+ *
+ * @category Mindlogger
+ * @package  Mindlogger
+ * @author   Dzmitry Yahur <dyagur@scnsoft.com>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://github.com/aces/Loris
+ */
+
+namespace LORIS\mindlogger\Endpoints;
+
+use \Psr\Http\Message\ServerRequestInterface;
+use \Psr\Http\Message\ResponseInterface;
+use \LORIS\mindlogger\Endpoint;
+
+/**
+ * A class for handling the /schema endpoint.
+ *
+ * @category Mindlogger
+ * @package  Mindlogger
+ * @author   Dzmitry Yahur <dyagur@scnsoft.com>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://github.com/aces/Loris
+ */
+class Schema extends Endpoint
+{
+    const INSTRUMENT_SUBGROUP_NAME = "Mindlogger instruments";
+
+    /**
+     * Permission checks
+     *
+     * @param \User $user The requesting user
+     *
+     * @return boolean true if access is permitted
+     */
+    private function _hasAccess(\User $user)
+    {
+        return $user->hasPermission('mindlogger_schema_create');
+    }
+
+    /**
+     * Return which methods are supported by this endpoint.
+     *
+     * @return array supported HTTP methods
+     */
+    protected function allowedMethods(): array
+    {
+        return ['POST'];
+    }
+
+    /**
+     * Versions of the Mindlogger API which are supported by this
+     * endpoint.
+     *
+     * @return array a list of supported API versions.
+     */
+    protected function supportedVersions(): array
+    {
+        return ["v1",];
+    }
+
+
+    /**
+     * Handles a request starts with /schema
+     *
+     * @param ServerRequestInterface $request The incoming PSR7 request
+     *
+     * @return ResponseInterface The outgoing PSR7 response
+     */
+    public function handle(ServerRequestInterface $request): ResponseInterface
+    {
+        $user = $request->getAttribute('user');
+
+        if ($user instanceof \LORIS\AnonymousUser) {
+            return new \LORIS\Http\Response\JSON\Unauthorized();
+        }
+
+        if (!$this->_hasAccess($user)) {
+            return new \LORIS\Http\Response\JSON\Forbidden();
+        }
+
+        switch ($request->getMethod()) {
+        case 'POST':
+            return $this->_handlePOST($request);
+
+        case 'OPTIONS':
+            return (new \LORIS\Http\Response())
+                ->withHeader('Allow', $this->allowedMethods());
+
+        default:
+            return new \LORIS\Http\Response\JSON\MethodNotAllowed(
+                $this->allowedMethods()
+            );
+        }
+    }
+
+    /**
+     * Handle a POST request to the /schema endpoint
+     *
+     * @param ServerRequestInterface $request The incoming PSR7 request
+     *
+     * @return ResponseInterface The outgoing PSR7 response
+     */
+    private function _handlePOST(ServerRequestInterface $request): ResponseInterface
+    {
+        $data = json_decode((string)$request->getBody(), true);
+        $db   = \NDB_Factory::singleton()->database();
+
+        $appletId     = $data["id"];
+        $appletSchema = $data;
+
+        if ($db->pselectOneInt("SELECT COUNT(*) FROM instrument_mindlogger_schema WHERE AppletID = ?", [$appletId])) {
+            return new \LORIS\Http\Response\JsonResponse(["status" => "failed", "message" => "Applet already exists"]);
+        }
+
+        try {
+            $db->beginTransaction();
+            $db->unsafeInsert(
+                "instrument_mindlogger_schema",
+                [
+                    "AppletID"     => $appletId,
+                    "AppletSchema" => json_encode($appletSchema),
+                ]
+            );
+            $this->makeInstrument($appletId, $appletSchema["displayName"]);
+            $db->commit();
+
+            return new \LORIS\Http\Response\JsonResponse(["status" => "OK"]);
+        } catch (\Exception $e) {
+            $db->rollback();
+            return new \LORIS\Http\Response\JSON\BadRequest(
+                $e->getMessage()
+            );
+        }
+    }
+
+
+    /**
+     * Create an instrument in the database
+     *
+     * @param string $testName The name of the instrument
+     * @param string $fullName The full name of the instrument
+     *
+     * @return void
+     */
+    protected function makeInstrument(string $testName, string $fullName): void
+    {
+        $db         = \NDB_Factory::singleton()->database();
+        $subgroupId = $db->pselectOneInt("SELECT ID FROM test_subgroups WHERE Subgroup_name = ?", [self::INSTRUMENT_SUBGROUP_NAME]);
+
+        $db->insert(
+            "test_names",
+            [
+                "Test_name"     => $testName,
+                "Full_name"     => $fullName,
+                "Sub_group"     => $subgroupId,
+                "IsDirectEntry" => 0,
+            ]
+        );
+    }
+}