Merge pull request #2432 from ideafast/feat/trpc-drive

Feat/trpc drive
ideafast · Jul 10, 2024 · 34ec740 · 34ec740
2 parents 9bf7b93 + b4fbe08
commit 34ec740
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Showing 22 changed files with 2,209 additions and 194 deletions.
diff --git a/package.json b/package.json
@@ -105,6 +105,7 @@
         "@ideafast/idgen": "0.1.1",
         "@swc/helpers": "0.5.10",
         "@trpc/server": "10.45.2",
+        "JSONStream": "1.3.5",
         "antd": "5.16.4",
         "apollo-upload-client": "18.0.1",
         "axios": "1.6.8",
@@ -133,12 +134,12 @@
         "hi-base32": "0.5.1",
         "http-proxy-middleware": "3.0.0",
         "https-browserify": "1.0.0",
-        "JSONStream": "1.3.5",
         "jsonwebtoken": "9.0.2",
         "jstat": "1.9.6",
         "lint-staged": "15.2.2",
         "minio": "7.1.3",
         "mongodb": "6.5.0",
+        "multer": "1.4.3",
         "nodemailer": "6.9.13",
         "passport": "0.7.0",
         "path-browserify": "1.0.1",

diff --git a/packages/itmat-commons/src/utils/objStore.ts b/packages/itmat-commons/src/utils/objStore.ts
@@ -71,6 +71,25 @@ export class ObjectStore {
         return result.etag;
     }
 
+    public async copyObject(sourceBucket: string, sourceUri: string, targetBucket: string, targetUri: string) {
+        if (!this.client) {
+            throw new Error('Connection failed.');
+        }
+
+        const lowerSourceBucket = sourceBucket.toLowerCase();
+        const lowerTargetBucket = targetBucket.toLowerCase();
+
+        // Ensure target bucket exists
+        const bucketExists = await this.client.bucketExists(lowerTargetBucket);
+        if (!bucketExists) {
+            await this.client.makeBucket(lowerTargetBucket, this.config?.bucketRegion ?? '');
+        }
+        // Copy the object
+        const conds = new Minio.CopyConditions();
+        const result = await this.client.copyObject(lowerTargetBucket, targetUri, `/${lowerSourceBucket}/${sourceUri}`, conds);
+        return result.etag;
+    }
+
     public async downloadFile(studyId: string, uri: string): Promise<Readable> {
         if (!this.client) {
             throw new Error('Connection failed.');

diff --git a/packages/itmat-cores/src/GraphQLCore/studyCore.ts b/packages/itmat-cores/src/GraphQLCore/studyCore.ts
@@ -379,10 +379,10 @@ export class StudyCore {
                 }
             }
 
-            fieldRecords = await this.db.collections.field_dictionary_collection.aggregate<IField>([{
-                $match: { studyId: studyId, dateDeleted: null, dataVersion: { $in: availableDataVersions } }
+            fieldRecords = (await this.db.collections.field_dictionary_collection.aggregate<IField>([{
+                $match: { studyId: studyId, dataVersion: { $in: availableDataVersions } }
             }, {
-                $sort: { dateAdded: -1 }
+                $sort: { 'life.createdTime': -1 }
             }, {
                 $group: {
                     _id: '$fieldId',
@@ -394,7 +394,7 @@ export class StudyCore {
                 }
             }, {
                 $sort: { fieldId: 1 }
-            }]).toArray();
+            }]).toArray()).filter(el => el.life.deletedTime === null);
             if (queryString.data_requested && queryString.data_requested.length > 0) {
                 fieldRecords = fieldRecords.filter(el => (queryString.data_requested || []).includes(el.fieldId));
             }
@@ -409,10 +409,10 @@ export class StudyCore {
             // unversioned data: metadatafilter for versioned data and all unversioned tags
             if (versionId === null && aggregatedPermissions.hasVersioned) {
                 availableDataVersions.push(null);
-                fieldRecords = await this.db.collections.field_dictionary_collection.aggregate<IField>([{
-                    $match: { studyId: studyId, dateDeleted: null, dataVersion: { $in: availableDataVersions } }
+                fieldRecords = (await this.db.collections.field_dictionary_collection.aggregate<IField>([{
+                    $match: { studyId: studyId, dataVersion: { $in: availableDataVersions } }
                 }, {
-                    $sort: { dateAdded: -1 }
+                    $sort: { 'life.createdTime': -1 }
                 }, {
                     $match: {
                         $or: [
@@ -431,18 +431,18 @@ export class StudyCore {
                     }
                 }, {
                     $sort: { fieldId: 1 }
-                }]).toArray();
+                }]).toArray()).filter(el => el.life.deletedTime === null);
                 if (queryString.data_requested && queryString.data_requested?.length > 0) {
                     fieldRecords = fieldRecords.filter(el => (queryString.data_requested || []).includes(el.fieldId));
                 }
             } else if (versionId === undefined || versionId === '-1') {
                 if (versionId === '-1') {
                     availableDataVersions = availableDataVersions.length !== 0 ? [availableDataVersions[availableDataVersions.length - 1]] : [];
                 }
-                fieldRecords = await this.db.collections.field_dictionary_collection.aggregate<IField>([{
-                    $match: { studyId: studyId, dateDeleted: null, dataVersion: { $in: availableDataVersions } }
+                fieldRecords = (await this.db.collections.field_dictionary_collection.aggregate<IField>([{
+                    $match: { studyId: studyId, dataVersion: { $in: availableDataVersions } }
                 }, {
-                    $sort: { dateAdded: -1 }
+                    $sort: { 'life.createdTime': -1 }
                 }, {
                     $match: {
                         $or: [
@@ -460,7 +460,7 @@ export class StudyCore {
                     }
                 }, {
                     $sort: { fieldId: 1 }
-                }]).toArray();
+                }]).toArray()).filter(el => el.life.deletedTime === null);
                 if (queryString.data_requested && queryString.data_requested?.length > 0) {
                     fieldRecords = fieldRecords.filter(el => (queryString.data_requested || []).includes(el.fieldId));
                 }
@@ -492,7 +492,7 @@ export class StudyCore {
                     fieldRecords = fieldRecords.filter(el => (queryString.data_requested || []).includes(el.fieldId));
                 }
             }
-
+            console.log(fieldRecords);
             // TODO: placeholder for metadata filter
             // if (queryString.metadata) {
             //     metadataFilter = { $and: queryString.metadata.map((el) => translateMetadata(el)) };

diff --git a/packages/itmat-cores/src/database/database.ts b/packages/itmat-cores/src/database/database.ts
@@ -1,4 +1,4 @@
-import type { IField, IFile, IJobEntry, ILogEntry, IOrganisation, IProject, IPubkey, IQueryEntry, IRole, IStudy, IUser, IStandardization, IConfig, IData } from '@itmat-broker/itmat-types';
+import type { IField, IFile, IJobEntry, ILogEntry, IOrganisation, IProject, IPubkey, IQueryEntry, IRole, IStudy, IUser, IStandardization, IConfig, IData, IDrive } from '@itmat-broker/itmat-types';
 import { Database as DatabaseBase, IDatabaseBaseConfig } from '@itmat-broker/itmat-commons';
 import type { Collection } from 'mongodb';
 
@@ -17,7 +17,8 @@ export interface IDatabaseConfig extends IDatabaseBaseConfig {
         pubkeys_collection: string,
         data_collection: string,
         standardizations_collection: string,
-        configs_collection: string
+        configs_collection: string,
+        drives_collection: string
     };
 }
 
@@ -35,6 +36,7 @@ export interface IDatabaseCollectionConfig {
     pubkeys_collection: Collection<IPubkey>,
     data_collection: Collection<IData>,
     standardizations_collection: Collection<IStandardization>,
-    configs_collection: Collection<IConfig>
+    configs_collection: Collection<IConfig>,
+    drives_collection: Collection<IDrive>
 }
 export type DBType = DatabaseBase<IDatabaseBaseConfig, IDatabaseCollectionConfig>;
diff --git a/packages/itmat-cores/src/index.ts b/packages/itmat-cores/src/index.ts
@@ -10,6 +10,10 @@ export * from './GraphQLCore/standardizationCore';
 export * from './GraphQLCore/studyCore';
 export * from './GraphQLCore/userCore';
 // TRPCCore
+export * from './trpcCore/configCore';
+export * from './trpcCore/driveCore';
+export * from './trpcCore/fileCore';
+export * from './trpcCore/studyCore';
 export * from './trpcCore/userCore';
 export * from './rest/fileDownload';
 export * from './authentication/pubkeyAuthentication';