added some mpi endpoints

hicsail · Sep 13, 2024 · f849e19 · f849e19
1 parent 9c23f40
commit f849e19
Show file tree

Hide file tree

Showing 3 changed files with 201 additions and 8 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,5 @@
 # Scripts
 /scripts/node_modules/
 /scripts/dist/
+
+/.vscode/
diff --git a/src/mpi/mpi.controller.ts b/src/mpi/mpi.controller.ts
@@ -1,6 +1,8 @@
-import { Controller, Get, Query } from '@nestjs/common';
+import { Controller, Get, Query, Post, Body } from '@nestjs/common';
 import { MPIService } from './mpi.service';
 
+type eLabsStatus = 'PENDING' | 'PROGRESS' | 'COMPLETED';
+
 @Controller('mpi')
 export class MPIController {
   constructor(private readonly mpiService: MPIService) {}
@@ -10,13 +12,50 @@ export class MPIController {
     return await this.mpiService.exchangeCodeForToken(code);
   }
 
-  @Get('sequences')
-  async getSequences(): Promise<string> {
-    return this.mpiService.getSequences();
+  @Get('is_logged_in')
+  isLoggedIn(): { loggedIn: boolean } {
+    return { loggedIn: this.mpiService.isLoggedIn() };
   }
 
   @Get('auth0_logout')
   async logout(): Promise<string> {
     return this.mpiService.logout();
   }
+
+  @Get('sequences')
+  async getSequences(): Promise<string> {
+    return this.mpiService.getSequences();
+  }
+
+  @Get('azentaSeqOrder/:id')
+  async azentaSeqOrder(id: string): Promise<string> {
+    return this.mpiService.azentaSeqOrder(id);
+  }
+
+  @Get('azentaSeqOrders')
+  async azentaSeqOrders(): Promise<string> {
+    return this.mpiService.azentaSeqOrders();
+  }
+
+  @Get('azentaCreateSeqOrder')
+  async azentaCreateSeqOrder(): Promise<string> {
+    return this.mpiService.azentaCreateSeqOrder();
+  }
+
+  @Post('e-labs/create-study')
+  async createELabsStudy(@Body('bearerToken') bearerToken: string, @Body('projectID') projectID: number, @Body('name') name: string): Promise<number | undefined> {
+    return this.mpiService.createELabsStudy(bearerToken, projectID, name);
+  }
+
+  @Post('e-labs/create-experiment')
+  async createELabsExperiment(
+    @Body('bearerToken') bearerToken: string,
+    @Body('studyID') studyID: number,
+    @Body('name') name: string,
+    @Body('status') status: eLabsStatus,
+    @Body('templateID') templateID?: number,
+    @Body('autoCollaborate') autoCollaborate?: boolean
+  ): Promise<number | undefined> {
+    return this.mpiService.createELabsExperiment(bearerToken, studyID, name, status, templateID, autoCollaborate);
+  }
 }
diff --git a/src/mpi/mpi.service.ts b/src/mpi/mpi.service.ts
@@ -1,6 +1,33 @@
 import { BadRequestException, Injectable } from '@nestjs/common';
 import axios from 'axios';
 
+// type ELabsStudyResponse = {
+//   studyID      : number;
+//   projectID    : number;
+//   groupID      : number;
+//   subGroupID   : number;
+//   userID       : number;
+//   name         : string;
+//   statusChanged: string;
+//   description  : string;
+//   notes        : string;
+//   approve      : string;
+//   created      : string;
+//   deleted      : boolean;
+// };
+
+type eLabsStatus = 'PENDING' | 'PROGRESS' | 'COMPLETED';
+
+// type ELabsExperimentResponse = {
+//   bearerToken     : string,
+//   experimentID    : number,
+//   studyID         : number,
+//   name            : string,
+//   status          : eLabsStatus,
+//   templateID?     : number,
+//   autoCollaborate?: boolean
+// }
+
 @Injectable()
 export class MPIService {
   private tokenStore = new Map<string, { accessToken: string; refreshToken: string; accessTokenExpiration: Date }>();
@@ -13,10 +40,10 @@ export class MPIService {
   private currentUserId = 'mpitest';
 
   // To log in use:
-  // NOTE THAT THIS SERVER IS RUNNING ON PORT 3000
-  // https://mpi-dev.us.auth0.com/authorize?response_type=code&scope=offline_access&client_id=tZSXM9f8WUiPIpNGt1kXlGqzZVYvWNEF&redirect_uri=http://127.0.0.1:3000/mpi/auth0_redirect&audience=https://mpi.com
+  // NOTE THAT THIS SERVER IS RUNNING ON PORT 5100
+  // https://mpi-dev.us.auth0.com/authorize?response_type=code&scope=offline_access&client_id=tZSXM9f8WUiPIpNGt1kXlGqzZVYvWNEF&redirect_uri=http://127.0.0.1:5100/mpi/auth0_redirect&audience=https://mpi.com
   // To log out use:
-  // https://mpi-dev.us.auth0.com/oidc/logout?post_logout_redirect_uri=http://127.0.0.1:3000/mpi/auth0_logout&client_id=tZSXM9f8WUiPIpNGt1kXlGqzZVYvWNEF
+  // https://mpi-dev.us.auth0.com/oidc/logout?post_logout_redirect_uri=http://127.0.0.1:5100/mpi/auth0_logout&client_id=tZSXM9f8WUiPIpNGt1kXlGqzZVYvWNEF
 
   async exchangeCodeForToken(code: string): Promise<string> {
     const tokenUrl = `https://mpi-dev.us.auth0.com/oauth/token`;
@@ -25,7 +52,7 @@ export class MPIService {
       client_id: this.client_id,
       client_secret: this.client_secret,
       code,
-      redirect_uri: 'http://127.0.0.1:3000/mpi/auth0_redirect' // URL in this server that was used to redirect to after Auth0 login
+      redirect_uri: 'http://127.0.0.1:5100/mpi/auth0_redirect' // URL in this server that was used to redirect to after Auth0 login
     };
 
     const response = await axios.post(tokenUrl, payload, {
@@ -85,15 +112,39 @@ export class MPIService {
     const user = this.tokenStore.get(this.currentUserId);
     if (user && user.accessToken && user.accessTokenExpiration) {
       if (user.accessTokenExpiration > new Date(Date.now())) {
+        console.log('user ', user, ' has valid token');
         return user.accessToken;
       } else {
+        console.log('user ', user, ' has expired token; requesting refreshed token');
         await this.exchangeRefreshTokenForToken();
         return this.tokenStore.get(this.currentUserId)!.accessToken;
       }
     }
     return '';
   }
 
+  isLoggedIn(): boolean {
+    const user = this.tokenStore.get(this.currentUserId);
+    if (user && user.accessToken && user.accessTokenExpiration) {
+      console.log('user ', user, ' is already logged in');
+      return user.accessTokenExpiration > new Date();
+    }
+    return false;
+  }
+
+  async createSequence(): Promise<any> {
+    const token = await this.getAccessToken();
+    if (!token) {
+      return new BadRequestException('No token found, log in to MPI first');
+    }
+    const sequences = await axios.get('http://localhost:5000/sequences', {
+      headers: {
+        Authorization: `Bearer ${token}`
+      }
+    });
+    return sequences.data;
+  }
+
   async getSequences(): Promise<any> {
     const token = await this.getAccessToken();
     if (!token) {
@@ -106,4 +157,105 @@ export class MPIService {
     });
     return sequences.data;
   }
+
+  // Azenta endpoints
+  async azentaSeqOrder(id: string): Promise<any> {
+    const token = await this.getAccessToken();
+    if (!token) {
+      return new BadRequestException('No token found, log in to MPI first');
+    }
+    const azentaSeqOrder = await axios.get(`http://localhost:5000/azenta/seqOrder/${id}`, {
+      headers: {
+        Authorization: `Bearer ${token}`
+      }
+    });
+    return azentaSeqOrder.data;
+  }
+
+  async azentaSeqOrders(): Promise<any> {
+    const token = await this.getAccessToken();
+    if (!token) {
+      return new BadRequestException('No token found, log in to MPI first');
+    }
+    const azentaSeqOrders = await axios.get('http://localhost:5000/azenta/seqOrder', {
+      headers: {
+        Authorization: `Bearer ${token}`
+      }
+    });
+    return azentaSeqOrders.data;
+  }
+
+  async azentaCreateSeqOrder(): Promise<any> {
+    const token = await this.getAccessToken();
+    const order = {
+      orderName: 'DAMP_Azenta_Order'
+    };
+    if (!token) {
+      throw new BadRequestException('No token found, log in to MPI first');
+    }
+    const azentaSeqOrders = await axios.post('http://localhost:5000/azenta/seqOrder', order, {
+      headers: {
+        Authorization: `Bearer ${token}`,
+        'Content-Type': 'application/json'
+      }
+    });
+    return azentaSeqOrders.data;
+  }
+
+  // eLabs
+  async createELabsStudy(bearerToken: string, projectID: number, name: string): Promise<number | undefined> {
+    const token = await this.getAccessToken();
+    if (!token) {
+      throw new BadRequestException('No token found, log in to MPI first');
+    }
+    try {
+      const response = await axios.post(
+        'http://localhost:5000/e-labs/create-study',
+        { bearerToken, projectID, name },
+        {
+          headers: {
+            Authorization: `Bearer ${token}`,
+            'Content-Type': 'application/json; charset=utf-8'
+          }
+        }
+      );
+
+      if (!response.data || !response.data.studyID) {
+        throw new Error('Error creating eLabs Study from Canvas Workflow...');
+      }
+
+      return response.data.studyID;
+    } catch (error) {
+      console.error(error);
+      return undefined;
+    }
+  }
+
+  async createELabsExperiment(bearerToken: string, studyID: number, name: string, status: eLabsStatus, templateID?: number, autoCollaborate?: boolean): Promise<number | undefined> {
+    const token = await this.getAccessToken();
+    if (!token) {
+      throw new BadRequestException('No token found, log in to MPI first');
+    }
+    try {
+      const response = await axios.post(
+        'http://localhost:5000/e-labs/create-experiment',
+        { bearerToken, studyID, name, status, templateID, autoCollaborate },
+        {
+          headers: {
+            Authorization: `Bearer ${token}`,
+            'Content-Type': 'application/json; charset=utf-8'
+          }
+        }
+      );
+
+      if (!response.data || !response.data.experimentID) {
+        throw new Error('Error creating eLabs Experiment from Canvas Service...');
+      }
+
+      return response.data.experimentID;
+    } catch (error) {
+      console.error(error);
+      return undefined;
+    }
+  }
 }