Merge remote-tracking branch 'origin/dev' into rc

README.md

@@ -1,5 +1,5 @@
 # ![](docs/images/glowingbear.png) Glowing Bear
-[![Build Status](https://travis-ci.org/thehyve/glowing-bear.svg?branch=dev)](https://travis-ci.org/thehyve/glowing-bear/branches)
+[![Build Status](https://travis-ci.com/thehyve/glowing-bear.svg?branch=dev)](https://travis-ci.com/thehyve/glowing-bear/branches)
 [![codecov](https://codecov.io/gh/thehyve/glowing-bear/branch/dev/graph/badge.svg)](https://codecov.io/gh/thehyve/glowing-bear)
 
 An [Angular]-based frontend application for clinical data selection and analysis 
@@ -92,7 +92,7 @@ gradle assemble
 gradle publish
 ```
 
-The latest release is [glowing-bear-2.0.14.tar](https://repo.thehyve.nl/service/local/repositories/releases/content/nl/thehyve/glowing-bear/2.0.14/glowing-bear-2.0.14.tar).
+The latest release is [glowing-bear-2.0.15.tar](https://repo.thehyve.nl/service/local/repositories/releases/content/nl/thehyve/glowing-bear/2.0.15/glowing-bear-2.0.15.tar).
 
 Published snapshot bundles are available in the `snapshots` repository
 on https://repo.thehyve.nl with id `nl.thehyve:glowing-bear:0.0.1-SNAPSNOT:tar`.
@@ -115,7 +115,7 @@ Glowing bear has a list of icons defined for basic subject dimensions:
 - diagnoses
 - biosources
 - biomaterials
-- images
+- radiology dimension and images
 
 If there is a new dimension, it will have a default icon. In order to customize this,
 for each new dimension that needs to be supported

docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM nginx:alpine
 
-ARG GB_VERSION="2.0.14"
+ARG GB_VERSION="2.0.15"
 ARG GB_SRC_REPOSITORY="releases"
 
 ENV GB_SRC_URL https://repo.thehyve.nl/service/local/artifact/maven/redirect?r=${GB_SRC_REPOSITORY}&g=nl.thehyve&a=glowing-bear&v=${GB_VERSION}&p=tar

docs/installation.md

@@ -187,7 +187,7 @@ curl -f --no-progress-meter \
   -d "password=${SYSTEM_PASSWORD}" \
   -d 'grant_type=password' \
   -d 'scope=offline_access' \
-  "${KEYCLOAK_SERVER_URL}/realms/${KEYCLOAK_REALM}/protocol/openid-connect/token' | jq -r '.refresh_token'
+  "${KEYCLOAK_SERVER_URL}/realms/${KEYCLOAK_REALM}/protocol/openid-connect/token" | jq -r '.refresh_token'
 ```
 
 The value of the `refresh_token` field in the response is the offline token.
@@ -252,7 +252,7 @@ Installation steps for TranSMART API server:
 
 4. Download the application in the `/home/transmart` directory:
    ```shell
-   TRANSMART_VERSION=17.2.8
+   TRANSMART_VERSION=17.2.11
    curl -f -L -o "/home/transmart/transmart-api-server-${TRANSMART_VERSION}.war" \
      "https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-api-server/${TRANSMART_VERSION}/transmart-api-server-${TRANSMART_VERSION}.war"
     ```
@@ -271,23 +271,8 @@ Installation steps for TranSMART API server:
      logSql: false
      formatql: false
      properties:
-       jmxEnabled: true
-       initialSize: 5
-       maxActive: 50
-       minIdle: 5
-       maxIdle: 25
-       maxWait: 10000
-       maxAge: 600000
-       timeBetweenEvictionRunsMillis: 5000
-       minEvictableIdleTimeMillis: 60000
-       validationQuery: select 1
-       validationQueryTimeout: 3
-       validationInterval: 15000
-       testOnBorrow: true
-       testWhileIdle: true
-       testOnReturn: false
-       jdbcInterceptors: ConnectionState
-       defaultTransactionIsolation: 2 # TRANSACTION_READ_COMMITTED
+       minimumIdle: 15
+       maximumPoolSize: 50
 
    keycloak:
      auth-server-url: https://keycloak.example.com  # CHANGE ME
@@ -316,7 +301,7 @@ Installation steps for TranSMART API server:
    [Service]
    User=transmart
    WorkingDirectory=/home/transmart
-   ExecStart=java -jar -server -Xms8g -Xmx8g -Djava.awt.headless=true -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true  -Dserver.port=8081 -Djava.security.egd=file:///dev/urandom -Dspring.config.location=/home/transmart/transmart-api-server.config.yml /home/transmart/transmart-api-server-17.2.8.war
+   ExecStart=java -jar -server -Xms8g -Xmx8g -Djava.awt.headless=true -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true  -Dserver.port=8081 -Djava.security.egd=file:///dev/urandom -Dspring.config.location=/home/transmart/transmart-api-server.config.yml /home/transmart/transmart-api-server-17.2.11.war
    StandardOutput=journal+console
    Restart=always
 
@@ -438,7 +423,7 @@ Installation steps for the Transmart Packer services:
    adduser --system packer
    ```
 
-2. Create a Python 3 virtual environment in `/home/gb/venv`:
+2. Create a Python 3 virtual environment in `/home/packer/venv`:
    ```shell
    python3 -m venv venv
    ```
@@ -519,21 +504,21 @@ Glowing Bear requires:
 
 1. Download the application and extract the contents in the `/var/www/glowingbear` directory:
    ```shell
-   GLOWING_BEAR_VERSION=2.0.13
+   GLOWING_BEAR_VERSION=2.0.15
    curl -f -L -o "glowing-bear-${GLOWING_BEAR_VERSION}.tar" \
      "https://repo.thehyve.nl/service/local/repositories/releases/content/nl/thehyve/glowing-bear/${GLOWING_BEAR_VERSION}/glowing-bear-${GLOWING_BEAR_VERSION}.tar"
    sudo mkdir -p /var/www/glowingbear
    sudo tar xf glowing-bear-${GLOWING_BEAR_VERSION}.tar -C /var/www/glowingbear
    ```
 
-2. Override environment file `/var/www/glowingbear/glowing-bear-2.0.13/app/config/env.json` with the following:
+2. Override environment file `/var/www/glowingbear/glowing-bear-2.0.15/app/config/env.json` with the following:
    ```json
    {
       "env": "default"
    }
    ```
 
-3. Edit configuration file `/var/www/glowingbear/glowing-bear-2.0.13/app/config/config.default.json` (overwrites the default config file in the `tar`):
+3. Edit configuration file `/var/www/glowingbear/glowing-bear-2.0.15/app/config/config.default.json` (overwrites the default config file in the `tar`):
    ```json
    {
      "oidc-server-url": "CHANGE ME",
@@ -574,7 +559,7 @@ Glowing Bear requires:
      error_log             /var/log/nginx/glowingbear.example.com:443.error.log;
 
      location / {
-       root /var/www/glowingbear/glowing-bear-2.0.13;
+       root /var/www/glowingbear/glowing-bear-2.0.15;
        index index.html index.htm;
        try_files $uri $uri/ /index.html =404;
      }

src/app/modules/gb-cohort-selection-module/constraint-components/gb-combination-constraint/gb-combination-constraint.component.html

@@ -7,10 +7,10 @@
                 [dropdownIcon]="disableDimensionDropdown ? '' : 'pi pi-chevron-down'"
                 (onChange)="onSelectedDimensionChange()" [autoWidth]="false" [style]="{'min-width':'10em'} ">
       <ng-template let-item pTemplate="selectedItem">
-        <i class="{{getDimensionIcon(item.label)}} gb-dimension-icon"></i>&nbsp;{{item.label}}
+        <i class="{{getDimensionIcon(item.value)}} gb-dimension-icon"></i>&nbsp;{{item.label}}
       </ng-template>
       <ng-template let-dimension pTemplate="item">
-        <i class="{{getDimensionIcon(dimension.label)}} gb-dimension-icon"></i>&nbsp;{{dimension.label}}
+        <i class="{{getDimensionIcon(dimension.value)}} gb-dimension-icon"></i>&nbsp;{{dimension.label}}
       </ng-template>
     </p-dropdown>
   </div>

src/app/modules/gb-cohort-selection-module/constraint-components/gb-combination-constraint/gb-combination-constraint.component.ts

@@ -37,7 +37,7 @@ export class GbCombinationConstraintComponent extends GbConstraintComponent impl
     let dimensions = [];
     for (let dim of subjectDimensions) {
       let ctype: SelectItem = {
-        label: dim,
+        label: dim === 'patient' ? 'Subject' : dim,
         value: dim
       };
       dimensions.push(ctype);

src/app/utilities/icon-helper.ts

@@ -30,7 +30,7 @@ export class IconHelper {
     if (/biomaterial/.test(dimension)) {
       return 'fa fa-leaf';
     }
-    if (/image/.test(dimension)) {
+    if (/image/.test(dimension) || /radiology/.test(dimension)) {
       return 'fa fa-image';
     }
     return 'fa fa-sticky-note';