Update collections inheritance & add minor polishing

README.md

@@ -1,6 +1,6 @@
 # Metis data management GUI: Backend for Frontend
 
-<p class="what_is_metis"><dfn>Metis</dfn> is an open scientific framework, materials data organizer, and collaborative online platform for the nanotechnology research. It was designed for the materials research teams at the physical and virtual laboratories. Metis is an AI-ready solution, aiming to bring the recent advances of computer science into a rather conservative area of new materials development and quality control. Metis currently focuses on the X-ray powder diffraction and atomistic simulations. It was started in 2021 in BASF (Ludwigshafen am Rhein, Germany) by Bernd Hinrichsen and Evgeny Blokhin.</p>
+<p class="what_is_metis"><dfn>Metis</dfn> is an open scientific framework, materials data organizer, and collaborative online platform for the nanotechnology research. It was designed for the offline physical and online virtual autonomous laboratories dealing with the materials science. Metis is an AI-ready solution, aiming to bring the recent advances of computer science into a rather conservative area of new materials development and quality control. Metis currently focuses on the X-ray powder diffraction and atomistic simulations. Its development was started in 2021 in BASF (Ludwigshafen am Rhein, Germany) by Bernd Hinrichsen and Evgeny Blokhin.</p>
 
 <p align="center"><img src="https://github.com/basf/metis-backend/blob/master/logo.png" width="300" /></p>
 

routes/[version]/calculations/_helpers.js

@@ -100,6 +100,7 @@ async function getAndPrepareCalcResults(userId, calculations, progress, result)
             const { id } = await db(USER_DATASOURCES_TABLE).where({ uuid: parent }).first('id');
             if (!id) return { error: 'Absent parent datasource' };
 
+            // collections inheritance
             const parentCollections = await selectUserCollections(
                 { id: userId },
                 { dataSourceIds: [id] }
@@ -112,7 +113,7 @@ async function getAndPrepareCalcResults(userId, calculations, progress, result)
             dataSources.data.push(dataSource);
         }
 
-        // get & prepare result datasources from sci. backend
+        // get & prepare result datasources from backend
         const preparedData = await getAndPrepareDataSources(dataSources);
         results = preparedData.data.map((dataSource) => ({ ...dataSource, progress }));
     }

routes/[version]/collections/_helpers.js

@@ -1,6 +1,7 @@
 const {
     COLLECTIONS_TYPES_TABLE,
     SHARED_COLLECTION_VISIBILITY,
+    PRIVATE_COLLECTION_VISIBILITY,
     USER_COLLECTIONS_TABLE,
     USER_SHARED_COLLECTIONS_TABLE,
     USER_DATASOURCES_TABLE,
@@ -97,7 +98,10 @@ async function changeOwnership(collectionId, userId) {
         .select('userId')
         .from(USER_COLLECTIONS_TABLE)
         .where('id', collectionId);
-    if (!ownerId || ownerId[0].userId !== SERVICE_UID) return 'Invalid collection selected';
+
+    if (!ownerId || ownerId[0].userId !== SERVICE_UID || userId === SERVICE_UID) {
+        throw new Error('Unsuitable collection selected');
+    }
 
     const targetIds = await db
         .select('dataSourceId')
@@ -110,7 +114,10 @@ async function changeOwnership(collectionId, userId) {
     });
 
     await db(USER_DATASOURCES_TABLE).whereIn('id', targets).update({ userId });
-    await db(USER_COLLECTIONS_TABLE).where('id', collectionId).update({ userId });
+    await db(USER_COLLECTIONS_TABLE).where('id', collectionId).update({
+        userId,
+        visibility: PRIVATE_COLLECTION_VISIBILITY,
+    });
 
     return false;
 }

routes/[version]/collections/index.js

@@ -10,7 +10,7 @@ module.exports = {
 };
 
 /**
- * @api {put} /v0/collections Create a collection
+ * @api {put} /v0/collections Create or update a collection
  * @apiName CreateCollection
  * @apiGroup Collections
  * @apiPermission API
@@ -25,6 +25,10 @@ async function put(req, res, next) {
         });
     }
 
+    if (req.body.id === null) {
+        return next({ status: StatusCodes.BAD_REQUEST, error: 'ID should be omitted.' });
+    }
+
     const reqId = req.id;
 
     res.status(StatusCodes.ACCEPTED).json({ reqId });

routes/[version]/collections/ownership.js

@@ -8,7 +8,7 @@ module.exports = {
 };
 
 /**
- * @api {post} /v0/collections/ownership Get data into work and change ownership (experimental)
+ * @api {post} /v0/collections/ownership Take on the data into work changing ownership
  * @apiName ListCollectionData
  * @apiGroup Collections
  * @apiPermission GUI_ONLY

routes/[version]/datasources/_helpers.js

@@ -2,6 +2,8 @@ const {
     insertUserDataSource,
     deleteUserDataSource,
     selectDataSourcesIdMap,
+    selectUserCollections,
+    delsertDataSourceCollections,
 } = require('../../../services/db');
 
 const {
@@ -28,7 +30,7 @@ async function createAndSaveDataSource(userId, content, fmt, name) {
     return insertUserDataSource(userId, { uuid: data.uuid });
 }
 
-async function importAndSaveDataSource(userId, externalId) {
+async function importAndSaveDataSource(userId, externalId, parentId) {
     let response;
     try {
         response = await importDataSource(externalId);
@@ -42,7 +44,17 @@ async function importAndSaveDataSource(userId, externalId) {
         throw 'Datasource cannot be used';
     }
 
-    return insertUserDataSource(userId, { uuid: response.data.uuid });
+    // collections inheritance
+    const parentCollections = await selectUserCollections(
+        { id: userId },
+        { dataSourceIds: [parentId] }
+    );
+    const collectionIds = parentCollections.data.map(({ id }) => id);
+    const dataSource = await insertUserDataSource(userId, { uuid: response.data.uuid });
+
+    await delsertDataSourceCollections(dataSource.id, collectionIds);
+
+    return dataSource;
 }
 
 /**

routes/[version]/datasources/index.js

@@ -2,6 +2,10 @@ const { StatusCodes } = require('http-status-codes');
 const { checkAuth } = require('../../../middlewares/auth');
 const { getUserDataSources } = require('../../../middlewares/db');
 
+const { USERS_TABLE, selectFirstUser, selectUserCollections } = require('../../../services/db');
+
+const { getAndPrepareCollections } = require('../collections/_helpers');
+
 const {
     createAndSaveDataSource,
     getAndPrepareDataSources,
@@ -94,17 +98,17 @@ async function get(req, res, next) {
  * @apiUse SSEStreamResponse
  */
 async function put(req, res, next) {
-    if (!req.body.id) {
+    if (!req.body.id || !req.body.parent) {
         return next({
             status: StatusCodes.BAD_REQUEST,
-            error: 'Required field *id* is not provided.',
+            error: 'Required fields are not provided.',
         });
     }
 
     const reqId = req.id;
     res.status(StatusCodes.ACCEPTED).json({ reqId });
 
-    const datasource = await importAndSaveDataSource(req.user.id, req.body.id);
+    const datasource = await importAndSaveDataSource(req.user.id, req.body.id, req.body.parent);
     if (!datasource)
         return next({
             status: StatusCodes.UNPROCESSABLE_ENTITY,
@@ -115,4 +119,10 @@ async function put(req, res, next) {
     const data = await getAndPrepareDataSources(req.session.datasources);
 
     res.sse.sendTo({ reqId, ...data }, 'datasources');
+
+    const user = await selectFirstUser({ [`${USERS_TABLE}.id`]: req.user.id });
+    const filters = await selectUserCollections(user);
+    const preparedFilters = await getAndPrepareCollections(filters);
+
+    res.sse.sendTo({ reqId, ...preparedFilters }, 'filters');
 }

routes/[version]/webhooks/calc_update.js

@@ -12,7 +12,6 @@ const {
 
 const { is_valid_uuid } = require('./_helpers');
 const { getAndPrepareCalcResults, deleteAndClearCalculation } = require('../calculations/_helpers');
-
 const { getAndPrepareDataSources } = require('../datasources/_helpers');
 const { getAndPrepareCollections } = require('../collections/_helpers');
 

services/db.js

@@ -81,6 +81,7 @@ const ADMIN_USER_ROLE = 'admin';
 const PUBLIC_COLLECTION_VISIBILITY = 'community';
 const SHARED_COLLECTION_VISIBILITY = 'shared';
 const PRIVATE_COLLECTION_VISIBILITY = 'private';
+
 const VISIBILITY_ENUM = [
     PRIVATE_COLLECTION_VISIBILITY,
     SHARED_COLLECTION_VISIBILITY,
@@ -114,8 +115,8 @@ module.exports = {
     insertUserDataSource,
     deleteUserDataSource,
     delsertDataSourceCollections,
-    selectDataSourceByUserId, // ??
-    selectDataSourcesByUserId, // ??
+    selectDataSourceByUserId, // FIXME?
+    selectDataSourcesByUserId, // FIXME?
 
     selectUserCollections,
     insertUserCollection,