Rc/0.3.0

.dockerignore

@@ -1,4 +1,6 @@
 .env.local
+.env.test
+.env.schema
 .next
 node_modules
 Dockerfile

.env.schema

@@ -7,4 +7,5 @@ NEXT_PUBLIC_EGO_CLIENT_ID=dms-ui-dev
 ######### Arranger
 NEXT_PUBLIC_ARRANGER_PROJECT_ID=
 NEXT_PUBLIC_ARRANGER_GRAPHQL_FIELD=
-NEXT_PUBLIC_ARRANGER_INDEX=
+NEXT_PUBLIC_ARRANGER_INDEX=
+NEXT_PUBLIC_ARRANGER_API_URL=

Jenkinsfile.groovy

@@ -55,88 +55,83 @@ spec:
 			}
 		}
 
-        stage('Build & Publish Develop') {
-            when {
-                anyOf {
-                    branch 'develop'
-                }
-            }
-            steps {
-                container('docker') {
-                    withCredentials([usernamePassword(credentialsId:'OvertureDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
-                        sh 'docker login -u $USERNAME -p $PASSWORD'
-                    }
-                    // DNS error if --network is default
-                    sh "docker build --network=host -f Dockerfile . -t ${dockerHubRepo}:${version}-${commit} -t ${dockerHubRepo}:edge"
-                    sh "docker push ${dockerHubRepo}:${version}-${commit}"
-                    sh "docker push ${dockerHubRepo}:edge"
-                }
-            }
-        }
+		stage('Build & Publish Develop') {
+			when {
+				anyOf {
+					branch 'develop'
+				}
+			}
+			steps {
+				container('docker') {
+					withCredentials([usernamePassword(credentialsId:'OvertureDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
+						sh 'docker login -u $USERNAME -p $PASSWORD'
+					}
+					// DNS error if --network is default
+					sh "docker build --network=host -f Dockerfile . -t ${dockerHubRepo}:${version}-${commit} -t ${dockerHubRepo}:edge"
+					sh "docker push ${dockerHubRepo}:${version}-${commit}"
+					sh "docker push ${dockerHubRepo}:edge"
+				}
+			}
+		}
 
-        stage('Release & Tag') {
-            when {
-                anyOf {
-                    branch 'master'
-                }
-            }
-            steps {
-                container('docker') {
-                    withCredentials([usernamePassword(credentialsId: 'OvertureBioGithub', passwordVariable: 'GIT_PASSWORD', usernameVariable: 'GIT_USERNAME')]) {
-                        sh "git tag ${version}"
-                        sh "git push https://${GIT_USERNAME}:${GIT_PASSWORD}@github.com/${githubRepo} --tags"
-                    }
-                    withCredentials([usernamePassword(credentialsId:'OvertureDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
-                        sh 'docker login -u $USERNAME -p $PASSWORD'
-                    }
-                    // DNS error if --network is default
-                    sh "docker build --network=host -f Dockerfile . -t ${dockerHubRepo}:${version} -t ${dockerHubRepo}:latest"
-                    sh "docker push ${dockerHubRepo}:${version}"
-                    sh "docker push ${dockerHubRepo}:latest"
-                }
-            }
-        }
-        
+		stage('Release & Tag') {
+			when {
+				anyOf {
+					branch 'master'
+				}
+			}
+			steps {
+				container('docker') {
+					withCredentials([usernamePassword(credentialsId: 'OvertureBioGithub', passwordVariable: 'GIT_PASSWORD', usernameVariable: 'GIT_USERNAME')]) {
+						sh "git tag ${version}"
+						sh "git push https://${GIT_USERNAME}:${GIT_PASSWORD}@github.com/${githubRepo} --tags"
+					}
+					withCredentials([usernamePassword(credentialsId:'OvertureDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
+						sh 'docker login -u $USERNAME -p $PASSWORD'
+					}
+					// DNS error if --network is default
+					sh "docker build --network=host -f Dockerfile . -t ${dockerHubRepo}:${version} -t ${dockerHubRepo}:latest"
+					sh "docker push ${dockerHubRepo}:${version}"
+					sh "docker push ${dockerHubRepo}:latest"
+				}
+			}
+		}
+		
 
-        //stage('Deploy to overture-qa') {
-            //when {
-                //branch "develop"
-            //}
-            //steps {
-                //container('helm') {
-                    //withCredentials([file(credentialsId:'4ed1e45c-b552-466b-8f86-729402993e3b', variable: 'KUBECONFIG')]) {
-                        //sh 'env'
-                        //sh 'helm init --client-only'
-                        //sh "helm ls --kubeconfig $KUBECONFIG"
-                        //sh "helm repo add overture https://overture-stack.github.io/charts-server/"
-                        //sh """
-                            //helm upgrade --kubeconfig $KUBECONFIG --install --namespace=overture-qa ego \\
-                            //overture/ego --reuse-values --set-string image.tag=${version}-${commit}
-                           //"""
-                    //}
-                //}
-            //}
-        //}
+		stage('Deploy to overture-qa') {
+			when {
+				branch "develop"
+			}
+			steps {
+				build(job: "/Overture.bio/provision/helm", parameters: [
+						[$class: 'StringParameterValue', name: 'OVERTURE_ENV', value: 'qa' ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_CHART_NAME', value: 'dms-ui'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_RELEASE_NAME', value: 'dms-ui'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_CHART_VERSION', value: ''], // use latest
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REPO_URL', value: "https://overture-stack.github.io/charts-server/"],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REUSE_VALUES', value: "false" ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_ARGS_LINE', value: "--set-string image.tag=${version}-${commit}"]
+				])
+			}
+		}
+
+		stage('Deploy to overture-staging') {
+			when {
+				branch "master"
+			}
+			steps {
+				build(job: "/Overture.bio/provision/helm", parameters: [
+						[$class: 'StringParameterValue', name: 'OVERTURE_ENV', value: 'staging' ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_CHART_NAME', value: 'dms-ui'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_RELEASE_NAME', value: 'dms-ui'],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_CHART_VERSION', value: ''], // use latest
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REPO_URL', value: "https://overture-stack.github.io/charts-server/"],
+						[$class: 'StringParameterValue', name: 'OVERTURE_HELM_REUSE_VALUES', value: "false" ],
+						[$class: 'StringParameterValue', name: 'OVERTURE_ARGS_LINE', value: "--set-string image.tag=${version}"]
+				])
+			}
+		}
 
-        //stage('Deploy to overture-staging') {
-            //when {
-                //branch "master"
-            //}
-            //steps {
-                //container('helm') {
-                    //withCredentials([file(credentialsId:'4ed1e45c-b552-466b-8f86-729402993e3b', variable: 'KUBECONFIG')]) {
-                        //sh 'env'
-                        //sh 'helm init --client-only'
-                        //sh "helm ls --kubeconfig $KUBECONFIG"
-                        //sh "helm repo add overture https://overture-stack.github.io/charts-server/"
-                        //sh """
-                            //helm upgrade --kubeconfig $KUBECONFIG --install --namespace=overture-qa ego \\
-                            //overture/ego --reuse-values --set-string image.tag=${version}
-                           //"""
-                    //}
-                //}
-            //}
-        //}
     }
     post {
         unsuccessful {

components/Footer.tsx

@@ -22,6 +22,8 @@ const Footer = () => {
         justify-content: flex-end;
         align-items: center;
         padding-right: 18px;
+        ${theme.shadow.default};
+        z-index: 10;
       `}
     >
       <StyledLink

components/PageLayout.tsx

@@ -3,6 +3,7 @@ import { css } from '@emotion/core';
 
 import defaultTheme from './theme';
 import NavBar from './NavBar';
+import Footer from './Footer';
 
 const PageLayout = ({ children }: { children: React.ReactNode }) => {
   return (
@@ -18,6 +19,7 @@ const PageLayout = ({ children }: { children: React.ReactNode }) => {
     >
       <NavBar />
       {children}
+      <Footer />
     </div>
   );
 };

components/pages/login/index.tsx

@@ -23,8 +23,12 @@ const LoginButton = ({
   title: string;
   path: string;
 }) => {
-  const { EGO_API_ROOT, EGO_CLIENT_ID } = getConfig();
-  const url = `${urlJoin(EGO_API_ROOT, '/oauth/login', path)}?client_id=${EGO_CLIENT_ID}`;
+  const { NEXT_PUBLIC_EGO_API_ROOT, NEXT_PUBLIC_EGO_CLIENT_ID } = getConfig();
+  const url = `${urlJoin(
+    NEXT_PUBLIC_EGO_API_ROOT,
+    '/oauth/login',
+    path,
+  )}?client_id=${NEXT_PUBLIC_EGO_CLIENT_ID}`;
   const disabled = !path;
   return (
     <a
@@ -97,7 +101,6 @@ const LoginPage = () => {
           flex: 1;
           flex-direction: row;
           position: relative;
-          min-width: 1440px;
         `}
       >
         <div

components/pages/repository/PageContent.tsx

@@ -37,8 +37,8 @@ const PageContent = (props: PageContentProps) => {
             min-width: 250px;
             max-width: 270px;
             background-color: ${theme.colors.white};
-            ${theme.shadow.default}
             z-index: 1;
+            ${theme.shadow.right};
           `}
         >
           <Facets {...props} />
@@ -60,7 +60,6 @@ const PageContent = (props: PageContentProps) => {
             <QueryBar {...props} />
             <RepoTable {...props} />
           </div>
-          <Footer />
         </div>
       </div>
     </div>

components/pages/repository/index.tsx

@@ -6,6 +6,7 @@ import PageLayout from '../../PageLayout';
 import { RepoFiltersType } from './sqonTypes';
 import { getConfig } from '../../../global/config';
 import { css } from '@emotion/core';
+import createArrangerFetcher from '../../utils/arrangerFetcher';
 
 const Arranger = dynamic(
   () => import('@arranger/components/dist/Arranger').then((comp) => comp.Arranger),
@@ -33,13 +34,23 @@ export interface PageContentProps {
   fetchData?: (projectId: string) => Promise<any>;
 }
 
+const arrangerFetcher = createArrangerFetcher({});
+
 const RepositoryPage = () => {
-  const { ARRANGER_PROJECT_ID, ARRANGER_GRAPHQL_FIELD, ARRANGER_INDEX } = getConfig();
+  const {
+    NEXT_PUBLIC_ARRANGER_PROJECT_ID,
+    NEXT_PUBLIC_ARRANGER_GRAPHQL_FIELD,
+    NEXT_PUBLIC_ARRANGER_INDEX,
+  } = getConfig();
 
   return (
     <PageLayout>
       {/* TODO: arranger config error handling tbd */}
-      {!(ARRANGER_PROJECT_ID && ARRANGER_GRAPHQL_FIELD && ARRANGER_INDEX) ? (
+      {!(
+        NEXT_PUBLIC_ARRANGER_PROJECT_ID &&
+        NEXT_PUBLIC_ARRANGER_GRAPHQL_FIELD &&
+        NEXT_PUBLIC_ARRANGER_INDEX
+      ) ? (
         <div
           css={css`
             display: flex;
@@ -56,19 +67,20 @@ const RepositoryPage = () => {
               `
             }
           >
-            Arranger is missing configuration values. Please check your ".env.local" file.
+            Arranger is missing configuration values. Please check your ".env" file.
             <ul>
-              <li>Project ID: {ARRANGER_PROJECT_ID || 'missing'}</li>
-              <li>GraphQL Field: {ARRANGER_GRAPHQL_FIELD || 'missing'}</li>
-              <li>Index: {ARRANGER_INDEX || 'missing'}</li>
+              <li>Project ID: {NEXT_PUBLIC_ARRANGER_PROJECT_ID || 'missing'}</li>
+              <li>GraphQL Field: {NEXT_PUBLIC_ARRANGER_GRAPHQL_FIELD || 'missing'}</li>
+              <li>Index: {NEXT_PUBLIC_ARRANGER_INDEX || 'missing'}</li>
             </ul>
           </div>
         </div>
       ) : (
         <Arranger
-          projectId={ARRANGER_PROJECT_ID}
-          graphqlField={ARRANGER_GRAPHQL_FIELD}
-          index={ARRANGER_INDEX}
+          api={arrangerFetcher}
+          projectId={NEXT_PUBLIC_ARRANGER_PROJECT_ID}
+          graphqlField={NEXT_PUBLIC_ARRANGER_GRAPHQL_FIELD}
+          index={NEXT_PUBLIC_ARRANGER_INDEX}
           render={(props: PageContentProps) => {
             return <PageContent {...props} />;
           }}

components/theme/shadow.ts

@@ -2,6 +2,11 @@ const defaultShadow = `
   box-shadow: 0 1px 6px 0 rgba(0, 0, 0, 0.1), 0 1px 5px 0 rgba(0, 0, 0, 0.08);
 `;
 
+const rightShadow = `
+  box-shadow: 3px 0 5px -2px rgba(0, 0, 0, 0.1), 3px 0 5px -2px rgba(0, 0, 0, 0.08);
+`;
+
 export default {
   default: defaultShadow,
+  right: rightShadow,
 };

components/utils/ajax.ts

@@ -0,0 +1,25 @@
+/***************
+Arranger does not work with fetch lib right out of the box, so using this implementation from
+https://github.com/IHCC-cohorts/ihcc-ui/blob/develop/src/pages/cohortRepo/arrangerFetcher/ajax.ts
+for now
+ ***************/
+
+import axios from 'axios';
+
+const ajax = axios.create();
+
+ajax.interceptors.request.use(
+  (config) => {
+    // set Authorization headers on a per request basis
+    // setting headers on axios get/put/post or common seems to be shared accross all axios instances
+    config.headers = {
+      ...config.headers,
+    };
+    return config;
+  },
+  (err) => {
+    return Promise.reject(err);
+  },
+);
+
+export default ajax;

components/utils/arrangerFetcher.ts

@@ -0,0 +1,27 @@
+import urlJoin from 'url-join';
+import { getConfig } from '../../global/config';
+import ajax from './ajax';
+
+const createArrangerFetcher = ({
+  onError = (err: any) => Promise.reject(err),
+  defaultHeaders = {},
+} = {}) => ({ method = 'post', body = {}, headers = {} }) => {
+  const { NEXT_PUBLIC_ARRANGER_API, NEXT_PUBLIC_ARRANGER_PROJECT_ID } = getConfig();
+  const uri = urlJoin(NEXT_PUBLIC_ARRANGER_API, NEXT_PUBLIC_ARRANGER_PROJECT_ID, '/graphql');
+  return ajax
+    .post(uri, body, {
+      headers: {
+        'Content-Type': 'application/json',
+        ...(defaultHeaders || {}),
+        ...headers,
+      },
+    })
+    .then((response: { data: any }) => {
+      return response.data;
+    })
+    .catch((err: { response: any }) => {
+      return onError(err);
+    });
+};
+
+export default createArrangerFetcher;