Merge branch 'main' into purge-old-queuedworkflows

Author: mr-c

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+- package-ecosystem: maven
+  directory: "/"
+  schedule:
+    interval: daily
+  open-pull-requests-limit: 10
+  ignore:
+  - dependency-name: org.springframework.boot:spring-boot-starter-parent
+    versions:
+    - "> 1.5.22.RELEASE"
+  - dependency-name: com.fasterxml.jackson.core:jackson-core
+    versions:
+    - 2.12.1
+    - 2.12.2
+  - dependency-name: org.eclipse.jgit:org.eclipse.jgit
+    versions:
+    - 5.10.0.202012080955-r
+  - dependency-name: org.apache.jena:jena-osgi
+    versions:
+    - 3.17.0

.github/workflows/codeql-analysis.yml

@@ -2,7 +2,9 @@ name: "Code scanning - action"
 
 on:
   push:
+    branches: [main]
   pull_request:
+    branches: [main]
   schedule:
     - cron: '0 9 * * 0'
 

README.md

@@ -38,19 +38,19 @@ This application can be started with [Docker](https://www.docker.com/) and [Dock
 
 Then run the following commands to clone the project in your local system.
 
-   ``` 
+   ```
     git clone https://github.com/common-workflow-language/cwlviewer.git
-    cd cwlviewer 
+    cd cwlviewer
   ```
 
 In the project directory, to start CWLViewer exposed on port `8080`, run:
 
     docker-compose up
-     
-The web server will connect to a local host, you'll see the message saying "Tomacat started on port(s):8080". 
 
-To see the locally running CWL Viewer app, visit http://localhost:8080/ in your web browser.  
-   
+The web server will connect to a local host, you'll see the message saying "Tomacat started on port(s):8080".
+
+To see the locally running CWL Viewer app, visit http://localhost:8080/ in your web browser.
+
 To stop and remove:
 
     docker-compose down
@@ -72,6 +72,44 @@ If you have modified the source code, then you may want to build the docker imag
 
     docker build -t commonworkflowlanguage/cwlviewer .
 
+## Running Spring Boot locally for development, with MongoDB and Jena Fuseki in Docker
+
+Create `docker-compose.override.yml`:
+
+```
+version: '3.2'
+services:
+  mongo:
+    ports:
+     - "27017:27017"
+  sparql:
+    ports:
+     - "3030:3030"
+```
+
+Then start the containers:
+
+```
+docker-compose up
+```
+
+Then start Spring Boot locally:
+
+```
+mvn spring-boot:run -Dserver.port=7999
+```
+
+Now you can connect to http://localhost:7999 in your browser.
+
+## Deleting the data volumes to reset state
+
+To completely reset the state, you must delete the data volumes:
+
+```
+docker-compose down
+docker volume rm  cwlviewer_bundle cwlviewer_git cwlviewer_graphviz cwlviewer_mongo cwlviewer_sparql
+```
+
 ## Running without Docker
 
 ### Requirements

pom.xml

@@ -23,10 +23,10 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<java.version>1.8</java.version>
-		<jena.version>3.15.0</jena.version>
+		<jena.version>4.0.0</jena.version>
 		<!-- BEGIN should correspond to https://repo1.maven.org/maven2/org/apache/jena/jena/3.9.0/jena-3.9.0.pom -->
-		<ver.jsonldjava>0.13.0</ver.jsonldjava>
-		<ver.jackson>2.11.1</ver.jackson>
+		<ver.jsonldjava>0.13.3</ver.jsonldjava>
+		<ver.jackson>2.12.3</ver.jackson>
 		<!-- END -->
 	</properties>
 
@@ -70,7 +70,7 @@
 		<dependency>
 			<groupId>org.yaml</groupId>
 			<artifactId>snakeyaml</artifactId>
-			<version>1.26</version>
+			<version>1.28</version>
 		</dependency>
 		<dependency>
 			<groupId>com.github.jabbalaci</groupId>
@@ -106,7 +106,7 @@
 		<dependency>
 			<groupId>org.eclipse.jgit</groupId>
 			<artifactId>org.eclipse.jgit</artifactId>
-			<version>5.8.0.202006091008-r</version>
+			<version>5.11.1.202105131744-r</version>
 		</dependency>
 		<dependency>
 			<groupId>org.mockito</groupId>
@@ -117,7 +117,7 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-compress</artifactId>
-			<version>1.19</version>
+			<version>1.20</version>
 		</dependency>
 	</dependencies>