Merge pull request #373 from hms-dbmi-cellenics/1932-remove-account-s…

…pecific-hardcodings Remove account specific hardcodings in the api code
hms-dbmi-cellenics · Jun 20, 2022 · ca85234 · ca85234
2 parents 1ac8311 + b50af10
commit ca85234
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Showing 19 changed files with 317 additions and 19 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -205,7 +205,7 @@ jobs:
         uses: aws-actions/configure-aws-credentials@v1
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} 
           aws-region: eu-west-1
 
       - id: login-ecr

diff --git a/src/api.v2/helpers/pipeline/pipelineConstruct/constructors/createNewJobIfNotExist.js b/src/api.v2/helpers/pipeline/pipelineConstruct/constructors/createNewJobIfNotExist.js
@@ -1,3 +1,5 @@
+const config = require('../../../../../config');
+
 const createNewJobIfNotExist = (context, step) => {
   const { accountId, activityArn, processName } = context;
 
@@ -6,7 +8,7 @@ const createNewJobIfNotExist = (context, step) => {
     Type: 'Task',
     Resource: 'arn:aws:states:::lambda:invoke',
     Parameters: {
-      FunctionName: `arn:aws:lambda:eu-west-1:${accountId}:function:local-container-launcher`,
+      FunctionName: `arn:aws:lambda:${config.awsRegion}:${accountId}:function:local-container-launcher`,
       Payload: {
         image: 'biomage-pipeline-runner',
         name: `${processName}-runner`,

diff --git a/src/api.v2/helpers/pipeline/pipelineConstruct/constructors/deleteCompleteJobs.js b/src/api.v2/helpers/pipeline/pipelineConstruct/constructors/deleteCompleteJobs.js
@@ -1,3 +1,5 @@
+const config = require('../../../../../config');
+
 const constructDeleteCompletedJobs = (context, step) => {
   const { accountId } = context;
 
@@ -7,7 +9,7 @@ const constructDeleteCompletedJobs = (context, step) => {
     Comment: 'Removes Docker containers with pipeline runs on the local machine.',
     Resource: 'arn:aws:states:::lambda:invoke',
     Parameters: {
-      FunctionName: `arn:aws:lambda:eu-west-1:${accountId}:function:remove-previous-pipeline-containers`,
+      FunctionName: `arn:aws:lambda:${config.awsRegion}:${accountId}:function:remove-previous-pipeline-containers`,
     },
   };
 };

diff --git a/src/api.v2/helpers/pipeline/pipelineConstruct/constructors/requestAssignPodToPipeline.js b/src/api.v2/helpers/pipeline/pipelineConstruct/constructors/requestAssignPodToPipeline.js
@@ -23,7 +23,6 @@ const buildPodRequest = (sandboxId, experimentId, taskName, processName, activit
   },
 });
 
-
 const requestPod = (context, step) => {
   const {
     environment, accountId, sandboxId, activityArn, experimentId, processName,

diff --git a/src/config/default-config.js b/src/config/default-config.js
@@ -11,6 +11,7 @@ const githubOrganisationName = 'hms-dbmi-cellenics';
 // If we are, assign NODE_ENV based on the Github (AWS/k8s cluster) environment.
 // If NODE_ENV is set, that will take precedence over the Github
 // environment.
+
 if (process.env.K8S_ENV && !process.env.NODE_ENV) {
   switch (process.env.K8S_ENV) {
     case 'staging':
@@ -20,6 +21,7 @@ if (process.env.K8S_ENV && !process.env.NODE_ENV) {
     case 'production':
       process.env.NODE_ENV = 'production';
       process.env.CLUSTER_ENV = process.env.K8S_ENV;
+
       break;
     default:
       // We are probably on a review branch or other deployment.
@@ -35,10 +37,14 @@ if (!process.env.K8S_ENV) {
   process.env.NODE_ENV = process.env.NODE_ENV || 'development';
 }
 
-const awsRegion = process.env.AWS_DEFAULT_REGION || 'eu-west-1';
+const awsRegion = process.env.AWS_REGION || process.env.AWS_DEFAULT_REGION || 'eu-west-1';
+
+const domainName = process.env.DOMAIN_NAME || 'localhost:5000';
+
 const cognitoISP = new AWS.CognitoIdentityServiceProvider({
   region: awsRegion,
 });
+
 async function getAwsPoolId() {
   const { UserPools } = await cognitoISP.listUserPools({ MaxResults: 60 }).promise();
   // when k8s is undefined we are in development where we use staging user pool so we set
@@ -59,6 +65,8 @@ async function getAwsAccountId() {
   return data.Account;
 }
 
+
+
 const config = {
   port: parseInt(process.env.PORT, 10) || 3000,
   clusterEnv: process.env.CLUSTER_ENV || 'development',
@@ -68,6 +76,7 @@ const config = {
   workerNamespace: `worker-${process.env.SANDBOX_ID || 'default'}`,
   pipelineNamespace: `pipeline-${process.env.SANDBOX_ID || 'default'}`,
   awsRegion,
+  domainName,
   awsAccountIdPromise: getAwsAccountId(),
   awsUserPoolIdPromise: getAwsPoolId(),
   cognitoISP,
@@ -78,7 +87,7 @@ const config = {
   workerInstanceConfigUrl: `https://raw.githubusercontent.com/${githubOrganisationName}/iac/master/releases/production/worker.yaml`,
   pipelineInstanceConfigUrl: `https://raw.githubusercontent.com/${githubOrganisationName}/iac/master/releases/production/pipeline.yaml`,
   cachingEnabled: true,
-  corsOriginUrl: 'https://scp.biomage.net',
+  corsOriginUrl: `https://${domainName}`,
   adminSub: '032abd44-0cd3-4d58-af21-850ca0b95ac7',
 };
 
@@ -88,7 +97,7 @@ if (config.clusterEnv === 'staging' && config.sandboxId === 'default') {
   config.workerInstanceConfigUrl = `https://raw.githubusercontent.com/${githubOrganisationName}/iac/master/releases/staging/worker.yaml`;
   config.pipelineInstanceConfigUrl = `https://raw.githubusercontent.com/${githubOrganisationName}/iac/master/releases/staging/pipeline.yaml`;
   config.cachingEnabled = false;
-  config.corsOriginUrl = 'https://ui-default.scp-staging.biomage.net';
+  config.corsOriginUrl = `https://ui-default.${domainName}`;
   config.adminSub = '0b17683f-363b-4466-b2e2-5bf11c38a76e';
 }
 
@@ -97,7 +106,7 @@ if (config.clusterEnv === 'staging' && config.sandboxId !== 'default') {
   config.workerInstanceConfigUrl = `https://raw.githubusercontent.com/${githubOrganisationName}/iac/master/releases/staging/${config.sandboxId}.yaml`;
   config.pipelineInstanceConfigUrl = `https://raw.githubusercontent.com/${githubOrganisationName}/iac/master/releases/staging/${config.sandboxId}.yaml`;
   config.cachingEnabled = false;
-  config.corsOriginUrl = `https://ui-${config.sandboxId}.scp-staging.biomage.net`;
+  config.corsOriginUrl = `https://ui-${config.sandboxId}.${domainName}`;
   config.adminSub = '0b17683f-363b-4466-b2e2-5bf11c38a76e';
 }
 

diff --git a/src/config/test-config.js b/src/config/test-config.js
@@ -12,6 +12,8 @@ module.exports = {
   port: 3000,
   clusterEnv: 'test',
   awsRegion: 'eu-west-1',
+  corsOriginUrl: 'https://scp.mockDomainName.com',
+  domainName: 'scp.mockDomainName.com',
   podName: 'test',
   sandboxId: 'default',
   adminSub: 'mockAdminSub',

diff --git a/src/utils/__mocks__/getLogger.js b/src/utils/__mocks__/getLogger.js
@@ -0,0 +1,9 @@
+const mockLogger = {
+  log: jest.fn(() => { }),
+  error: jest.fn(() => { }),
+  debug: jest.fn(() => { }),
+  trace: jest.fn(() => { }),
+  warn: jest.fn(() => { }),
+};
+
+module.exports = jest.fn(() => mockLogger);
diff --git a/src/utils/emailTemplates/buildPipelineStatusEmailBody.js b/src/utils/emailTemplates/buildPipelineStatusEmailBody.js
@@ -1,10 +1,11 @@
+const config = require('../../config');
 const {
   SUCCEEDED,
 } = require('../../api/general-services/pipeline-manage/constants');
 
 const buildPipelineStatusEmailBody = (experimentId, status, user) => {
   const firstname = user.name.split(' ')[0];
-  const link = `scp.biomage.net/experiments/${experimentId}/data-processing`;
+  const link = `${config.corsOriginUrl}/experiments/${experimentId}/data-processing`;
   const successMessage = `
       The data processing pipeline has completed successfully and your data is now ready to explore:<br/>
       <a href="${link}">${link}</a>

diff --git a/src/utils/emailTemplates/buildUserInvitedEmailBody.js b/src/utils/emailTemplates/buildUserInvitedEmailBody.js
@@ -1,5 +1,7 @@
+const config = require('../../config');
+
 const buildUserInvitedEmailBody = (email, experimentId, inviterUser) => {
-  const link = `scp.biomage.net/experiments/${experimentId}/data-exploration`;
+  const link = `${config.domainName}/experiments/${experimentId}/data-exploration`;
 
   const messageToSend = `
         <html>

diff --git a/src/utils/emailTemplates/buildUserInvitedNotRegisteredEmailBody.js b/src/utils/emailTemplates/buildUserInvitedNotRegisteredEmailBody.js
@@ -1,3 +1,5 @@
+const config = require('../../config');
+
 const buildUserInvitedNotRegisteredEmailBody = (email, inviterUser) => {
   const messageToSend = `
         <html>
@@ -8,7 +10,7 @@ const buildUserInvitedNotRegisteredEmailBody = (email, inviterUser) => {
               Hello, <br/>
               Your collaborator ${inviterUser.email} has invited you to explore their single cell RNA-seq project in Cellenics. <br/><br/>
               You need to create a Cellenics account in order to access the project. <br/>
-              Register at <a href="https://scp.biomage.net">scp.biomage.net</a> using this email address.<br/> <br/>
+              Register at <a href="${config.corsOriginUrl}">${config.corsOriginUrl}</a> using this email address.<br/> <br/>
 
               Cellenics is a user-friendly online tool for single cell RNA-seq data analysis. <br/>
               The platform is designed specifically for biologists, and it's completely free for academic researchers.<br/><br/>

diff --git a/src/utils/isPromise.js b/src/utils/isPromise.js
@@ -0,0 +1,5 @@
+function isPromise(value) {
+  return Boolean(value && typeof value.then === 'function');
+}
+
+module.exports = isPromise;
diff --git a/tests/api.v2/helpers/access/__snapshots__/createUserInvite.test.js.snap b/tests/api.v2/helpers/access/__snapshots__/createUserInvite.test.js.snap
@@ -20,7 +20,7 @@ Object {
               Hello, <br/>
               Your collaborator [email protected] has invited you to explore their single cell RNA-seq project in Cellenics. <br/><br/>
               Access it with the link below: <br/>
-              <a href=\\"scp.biomage.net/experiments/experimentId/data-exploration\\">scp.biomage.net/experiments/experimentId/data-exploration</a> <br/> <br/>
+              <a href=\\"scp.mockDomainName.com/experiments/experimentId/data-exploration\\">scp.mockDomainName.com/experiments/experimentId/data-exploration</a> <br/> <br/>
               Cellenics is a user-friendly online tool for single cell RNA-seq data analysis. <br/>
               The platform is designed specifically for biologists, and it's completely free for academic researchers.<br/><br/>
               More information about Cellenics can be found at <a href=\\"https://biomage.net\\">biomage.net</a>.<br/><br/>
@@ -42,7 +42,7 @@ Object {
               Hello, <br/>
               Your collaborator [email protected] has invited you to explore their single cell RNA-seq project in Cellenics. <br/><br/>
               Access it with the link below: <br/>
-              <a href=\\"scp.biomage.net/experiments/experimentId/data-exploration\\">scp.biomage.net/experiments/experimentId/data-exploration</a> <br/> <br/>
+              <a href=\\"scp.mockDomainName.com/experiments/experimentId/data-exploration\\">scp.mockDomainName.com/experiments/experimentId/data-exploration</a> <br/> <br/>
               Cellenics is a user-friendly online tool for single cell RNA-seq data analysis. <br/>
               The platform is designed specifically for biologists, and it's completely free for academic researchers.<br/><br/>
               More information about Cellenics can be found at <a href=\\"https://biomage.net\\">biomage.net</a>.<br/><br/>
@@ -83,7 +83,7 @@ Object {
               Hello, <br/>
               Your collaborator [email protected] has invited you to explore their single cell RNA-seq project in Cellenics. <br/><br/>
               You need to create a Cellenics account in order to access the project. <br/>
-              Register at <a href=\\"https://scp.biomage.net\\">scp.biomage.net</a> using this email address.<br/> <br/>
+              Register at <a href=\\"https://scp.mockDomainName.com\\">https://scp.mockDomainName.com</a> using this email address.<br/> <br/>
 
               Cellenics is a user-friendly online tool for single cell RNA-seq data analysis. <br/>
               The platform is designed specifically for biologists, and it's completely free for academic researchers.<br/><br/>
@@ -106,7 +106,7 @@ Object {
               Hello, <br/>
               Your collaborator [email protected] has invited you to explore their single cell RNA-seq project in Cellenics. <br/><br/>
               You need to create a Cellenics account in order to access the project. <br/>
-              Register at <a href=\\"https://scp.biomage.net\\">scp.biomage.net</a> using this email address.<br/> <br/>
+              Register at <a href=\\"https://scp.mockDomainName.com\\">https://scp.mockDomainName.com</a> using this email address.<br/> <br/>
 
               Cellenics is a user-friendly online tool for single cell RNA-seq data analysis. <br/>
               The platform is designed specifically for biologists, and it's completely free for academic researchers.<br/><br/>

diff --git a/tests/config/__snapshots__/default-config-production.test.js.snap b/tests/config/__snapshots__/default-config-production.test.js.snap
@@ -0,0 +1,29 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`default-config Returns correct values for production 1`] = `
+Object {
+  "adminSub": "032abd44-0cd3-4d58-af21-850ca0b95ac7",
+  "api": Object {
+    "prefix": "/",
+  },
+  "awsRegion": "eu-west-1",
+  "cachingEnabled": true,
+  "clusterEnv": "production",
+  "cognitoISP": Object {
+    "listUserPools": Object {
+      "promise": [MockFunction],
+    },
+  },
+  "corsOriginUrl": "https://localhost:5000",
+  "domainName": "localhost:5000",
+  "githubToken": undefined,
+  "pipelineInstanceConfigUrl": "https://raw.githubusercontent.com/hms-dbmi-cellenics/iac/master/releases/production/pipeline.yaml",
+  "pipelineNamespace": "pipeline-default",
+  "podName": "local",
+  "port": 3000,
+  "rdsSandboxId": "default",
+  "sandboxId": "default",
+  "workerInstanceConfigUrl": "https://raw.githubusercontent.com/hms-dbmi-cellenics/iac/master/releases/production/worker.yaml",
+  "workerNamespace": "worker-default",
+}
+`;
diff --git a/tests/config/__snapshots__/default-config-staging-sandboxid.test.js.snap b/tests/config/__snapshots__/default-config-staging-sandboxid.test.js.snap
@@ -0,0 +1,29 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`default-config Returns correct values for staging sandboxid 1`] = `
+Object {
+  "adminSub": "0b17683f-363b-4466-b2e2-5bf11c38a76e",
+  "api": Object {
+    "prefix": "/",
+  },
+  "awsRegion": "eu-west-1",
+  "cachingEnabled": false,
+  "clusterEnv": "staging",
+  "cognitoISP": Object {
+    "listUserPools": Object {
+      "promise": [MockFunction],
+    },
+  },
+  "corsOriginUrl": "https://ui-mockedSandboxId.scp-staging.biomage.net",
+  "domainName": "scp-staging.biomage.net",
+  "githubToken": undefined,
+  "pipelineInstanceConfigUrl": "https://raw.githubusercontent.com/hms-dbmi-cellenics/iac/master/releases/staging/mockedSandboxId.yaml",
+  "pipelineNamespace": "pipeline-mockedSandboxId",
+  "podName": "local",
+  "port": 3000,
+  "rdsSandboxId": "default",
+  "sandboxId": "mockedSandboxId",
+  "workerInstanceConfigUrl": "https://raw.githubusercontent.com/hms-dbmi-cellenics/iac/master/releases/staging/mockedSandboxId.yaml",
+  "workerNamespace": "worker-mockedSandboxId",
+}
+`;
diff --git a/tests/config/__snapshots__/default-config-staging.test.js.snap b/tests/config/__snapshots__/default-config-staging.test.js.snap
@@ -0,0 +1,29 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`default-config Returns correct values for staging default 1`] = `
+Object {
+  "adminSub": "0b17683f-363b-4466-b2e2-5bf11c38a76e",
+  "api": Object {
+    "prefix": "/",
+  },
+  "awsRegion": "eu-west-1",
+  "cachingEnabled": false,
+  "clusterEnv": "staging",
+  "cognitoISP": Object {
+    "listUserPools": Object {
+      "promise": [MockFunction],
+    },
+  },
+  "corsOriginUrl": "https://ui-default.scp-staging.biomage.net",
+  "domainName": "scp-staging.biomage.net",
+  "githubToken": undefined,
+  "pipelineInstanceConfigUrl": "https://raw.githubusercontent.com/hms-dbmi-cellenics/iac/master/releases/staging/pipeline.yaml",
+  "pipelineNamespace": "pipeline-default",
+  "podName": "local",
+  "port": 3000,
+  "rdsSandboxId": "default",
+  "sandboxId": "default",
+  "workerInstanceConfigUrl": "https://raw.githubusercontent.com/hms-dbmi-cellenics/iac/master/releases/staging/worker.yaml",
+  "workerNamespace": "worker-default",
+}
+`;
diff --git a/tests/config/default-config-production.test.js b/tests/config/default-config-production.test.js
@@ -0,0 +1,54 @@
+// @ts-nocheck
+const _ = require('lodash');
+
+const AWS = require('aws-sdk');
+const isPromise = require('../../src/utils/isPromise');
+
+jest.mock('aws-sdk');
+jest.mock('../../src/utils/getLogger');
+
+describe('default-config', () => {
+  const OLD_ENV = _.cloneDeep(process.env);
+
+  beforeEach(() => {
+    jest.clearAllMocks();
+    process.env = OLD_ENV;
+  });
+
+  afterAll(() => {
+    jest.clearAllMocks();
+    process.env = OLD_ENV;
+  });
+
+  it('Returns correct values for production', () => {
+    const prodEnvironment = 'production';
+    process.env.K8S_ENV = prodEnvironment;
+    process.env.CLUSTER_ENV = prodEnvironment;
+    process.env.AWS_DEFAULT_REGION = 'eu-west-1';
+
+    const userPoolId = 'mockUserPoolId';
+    const accountId = 'mockAccountId';
+
+    AWS.CognitoIdentityServiceProvider = jest.fn(() => ({
+      listUserPools: {
+        promise: jest.fn(() => Promise.resolve(
+          { UserPools: [{ id: userPoolId, Name: `biomage-user-pool-case-insensitive-${prodEnvironment}` }] },
+        )),
+      },
+    }));
+
+    AWS.STS = jest.fn(() => ({
+      getCallerIdentity: {
+        promise: jest.fn(() => Promise.resolve({ Account: accountId })),
+      },
+    }));
+
+    const defaultConfig = jest.requireActual('../../src/config/default-config');
+
+    const defaultConfigEntries = Object.entries(defaultConfig);
+    const filteredEntries = defaultConfigEntries.filter(([, value]) => !isPromise(value));
+    const defaultConfigFiltered = Object.fromEntries(filteredEntries);
+
+    expect(defaultConfigFiltered).toMatchSnapshot();
+  });
+});
-Original file line number
+Diff line change
@@ Expand Up @@
       },
     });
     const requestPod = (context, step) => {
       const {
         environment, accountId, sandboxId, activityArn, experimentId, processName,
@@ Expand Down @@