Merge pull request #120 from common-workflow-language/cwltool

Cwltool parsing and API

Author: stain

Diff for: .travis.yml

@@ -7,13 +7,13 @@ services: mongodb
 
 before_install:
   - sudo apt-get -qq update
-  - sudo apt-get install graphviz
+  - sudo apt-get install graphviz python-pip
+  - sudo pip install cwltool
 
 notifications:
   webhooks:
     urls:
       - https://webhooks.gitter.im/e/abea7d67d180d37286b3
     on_success: change  # options: [always|never|change] default: always
     on_failure: always  # options: [always|never|change] default: always
-    on_start: never     # options: [always|never|change] default: always
-
+    on_start: never     # options: [always|never|change] default: always

Diff for: Dockerfile

@@ -1,4 +1,4 @@
-FROM maven:3.3-jdk-8-alpine
+FROM maven:3.5-jdk-8-alpine
 MAINTAINER Stian Soiland-Reyes <[email protected]>
 
 # Build-time metadata as defined at http://label-schema.org
@@ -16,7 +16,14 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
   org.label-schema.schema-version="1.0"
 
 
-RUN apk add --update graphviz ttf-freefont && rm -rf /var/cache/apk/*
+RUN apk add --update graphviz ttf-freefont py2-pip gcc python2-dev libc-dev && rm -rf /var/cache/apk/*
+
+
+#wheel needed by ruamel.yaml for some reason
+RUN pip install wheel
+RUN pip install cwltool html5lib ruamel.yaml==0.12.4
+
+RUN cwltool --version
 
 RUN mkdir /usr/share/maven/ref/repository
 
@@ -38,7 +45,4 @@ WORKDIR /tmp
 
 EXPOSE 8080
 
-# Expects mongodb on port 27017
-ENV SPRING_DATA_MONGODB_HOST=mongo
-ENV SPRING_DATA_MONGODB_PORT=27017
 CMD ["/usr/bin/java", "-jar", "/usr/lib/cwlviewer.jar"]

Diff for: LICENSE.md

@@ -199,24 +199,3 @@
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.
-
----------------------------------------------------------
-
-./src/main/resources/static/img/GitHub-Mark-32px.png
-
-GITHUB®, the GITHUB® logo design, OCTOCAT® and the OCTOCAT® logo design 
-are exclusive trademarks registered in the United States by GitHub, Inc.
-
-The OCTOCAT design is the exclusive property of GitHub, Inc and has 
-been federally registered with the United States Copyright Office. 
-All rights reserved.
-
-Use rules apply: https://github.com/logos
-
----------------------------------------------------------
-
-./src/main/resources/static/img/Docker-logo.png
-
-Copyright 2013-2015 Docker, Inc. All rights reserved.
-
-Use rules apply: https://www.docker.com/brand-guidelines

Diff for: NOTICE.md

@@ -76,6 +76,12 @@ For more information regarding the authorized uses of these items please [contac
 
 -----------
 
+# Git logo
+img/gitlogo.png
+Git Logo by Jason Long is licensed under the [Creative Commons Attribution 3.0 Unported License](https://creativecommons.org/licenses/by/3.0/)
+
+-----------
+
 # European Union flag
 img/Flag_of_Europe.svg
 Public Domain
@@ -170,4 +176,12 @@ https://github.com/ariutta/svg-pan-zoom
 
 [BSD 2-clause license](src/main/resources/static/bower_components/svg-pan-zoom/LICENSE)
 
------------
+----------
+
+# highlight.js
+bower_components/highlightjs
+https://highlightjs.org/
+
+[BSD 3-clause license](src/main/resources/static/bower_components/highlightjs/LICENSE)
+
+

Diff for: README.md

@@ -19,12 +19,11 @@ provide a [pull request](https://github.com/common-workflow-language/cwlviewer/p
 or join the [gitter chat for common-workflow-language](https://gitter.im/common-workflow-language/common-workflow-language)!
 
 
-## Running with Docker
+## Recommended - Running with Docker
 
 This application can be started with [Docker](https://www.docker.com/).
 
-If you have [Docker Compose](https://docs.docker.com/compose/install/), then to start
-MongoDB and CWLViewer exposed on port `8080`, run:
+If you have [Docker Compose](https://docs.docker.com/compose/install/), then to start CWLViewer exposed on port `8080`, run:
 
     docker-compose up
 
@@ -42,7 +41,6 @@ services:
     build: .
 ```
 
-
 See the [docker-compose.yml](docker-compose.yml) file for details.
 
 If you don't want to use Docker Compose, you can do the equivalent manually with `docker`
@@ -51,67 +49,33 @@ and the [commonworkflowlanguage/cwlviewer](https://hub.docker.com/r/commonworkfl
     docker run --name cwlviewer-mongo -p 27017:27017 -d mongo
     docker run --name cwlviewer -p 8080:8080 --link cwlviewer-mongo:mongo -d commonworkflowlanguage/cwlviewer
     docker logs -f cwlviewer
+    
+    
+**WARNING**: Please ensure that your MongoDB installation is not exposed to the world on port `27017`
 
 If you have modified the source code, then you may want to build the docker image locally first:
 
     docker build -t commonworkflowlanguage/cwlviewer .
 
+## Running without Docker
+
+### Requirements
 
-## Requirement: MongoDB
+#### MongoDB
 
 You will need to have [MongoDB](https://www.mongodb.com/) running,
-by default on `localhost:27017`.
+by default on `localhost:27017`
 
 If you are running from the command line, you can override this by supplying
 system properties like `-Dspring.data.mongodb.host=mongo.example.org` and
 `-Dspring.data.mongodb.port=1337`
 
-If you have Docker, but are not using the Docker Compose method above,
-you may start MongoDB with [Docker](https://www.docker.com/) using:
-
-    docker run --name cwlviewer-mongo -p 27017:27017 -d mongo
-
-**WARNING**: The above expose mongodb to the world on port `27017`.
-
-## Configuration
-
-There are a variety of configuration options detailed in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) which can be adjusted.
-
-When deploying with docker, these can be overriden externally by creating/modifying `docker-compose.override.yml` as follows:
-
-```yaml
-version: '2'
-services:
-  spring:
-    environment:
-            githubAPI.authentication: oauth
-            githubAPI.oauthToken: abcdefghhijklmnopqrstuvwxyz
-```
-
-The properties can alternatively be provided as system properties on the
-command line, e.g. `-DgithubAPI.authentication=oauth`
-`-DgithubAPI.oauthToken=abcdefghhijklmnopqrstuvwxyz` or via a [variety of other methods supported by Spring Boot](https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-external-config.html)
-
-### Github API
-
-If you run cwlviewer in production, you are likely to hit the GitHub API's rate limit of 60 requests/hr. This can be increased to 5000 requests/hr by using authentication (either basic or OAuth) by setting the `githubAPI.authentication` and either `githubAPI.oauthToken` or both `githubAPI.username` and `githubAPI.password` in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) depending on the method.
+#### Apache Jena Fuseki (or alternative SPARQL server)
 
-OAuth tokens can be obtained using the [Github authorizations API](https://developer.github.com/v3/oauth_authorizations/).
+You will also need to have a SPARQL server such as [Apache Jena Fuseki](https://jena.apache.org/documentation/fuseki2/) running, 
+by default on `localhost:3030`
 
-## Private Repositories
-
-If you wish to use cwlviewer to view private Github repositories, set
-
-```
-githubAPI.useForDownloads = true
-singleFileSizeLimit = 1048575
-```
-
-Along with an authentication method which has the privileges necessary to access the repository (see above).
-
-**WARNING**: This uses the [Github Contents API](https://developer.github.com/v3/repos/contents/) to download files instead of [Rawgit](https://rawgit.com/) which will increase API calls significantly.
-
-## Building and Running
+## Compiling and Running
 
 To compile you will need [Java 8](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or OpenJDK 8 (`apt install openjdk-8-jdk`),
 as well as [Apache Maven 3](https://maven.apache.org/download.cgi) (`apt install maven`).
@@ -145,6 +109,25 @@ org.researchobject.CwlViewerApplication  : Started CwlViewerApplication in 28.60
 
 Now check out http://localhost:8080/ to access CWL Viewer.
 
+## Configuration
+
+There are a variety of configuration options detailed in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) which can be adjusted.
+
+When deploying with docker, these can be overriden externally by creating/modifying `docker-compose.override.yml` as follows:
+
+```yaml
+version: '2'
+services:
+  spring:
+    environment:
+            githubAPI.authentication: oauth
+            githubAPI.oauthToken: abcdefghhijklmnopqrstuvwxyz
+```
+
+The properties can alternatively be provided as system properties on the
+command line, e.g. `-DgithubAPI.authentication=oauth`
+`-DgithubAPI.oauthToken=abcdefghhijklmnopqrstuvwxyz` or via a [variety of other methods supported by Spring Boot](https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-external-config.html)
+
 # Thanks
 
 Developers and [contributors](https://github.com/common-workflow-language/cwlviewer/graphs/contributors) include:

Diff for: docker-compose.yml

@@ -1,15 +1,27 @@
 version: '2'
 services:
   spring:
-    image: commonworkflowlanguage/cwlviewer
+    # To run from this source code instead of Docker hub,
+    # disable "image:"" and enable "build:" below
+    image: commonworkflowlanguage/cwlviewer    
     #build: .
     ports:
      - "8080:8080"
-# TODO:
-#    volumes:
-#     - .:/code
     links:
      - mongo
-
+     - sparql
+    environment:
+     - SPARQL_ENDPOINT=http://sparql:3030/cwlviewer/
+     - SPRING_DATA_MONGODB_HOST=mongo
+     - SPRING_DATA_MONGODB_PORT=27017
   mongo:
     image: mongo
+  sparql:
+## For debugging, expose the Fuseki port by enabling:
+#    ports:
+#     - "3030:3030"
+## To find the admin password, try:
+##   docker-compose exec sparql grep admin /fuseki/shiro.ini
+    image: stain/jena-fuseki
+    # FIXME: --loc=/fuseki/databases/cwlviewer fails as it needs empty dir
+    command: "/jena-fuseki/fuseki-server --loc=/fuseki/databases /cwlviewer"

Diff for: pom.xml

@@ -5,7 +5,7 @@
 
 	<groupId>org.commonwl.view</groupId>
 	<artifactId>cwlviewer</artifactId>
-	<version>0.0.1-SNAPSHOT</version>
+	<version>1.1.0-SNAPSHOT</version>
 	<packaging>jar</packaging>
 
 	<name>CWLViewer</name>
@@ -62,11 +62,6 @@
 			<artifactId>commons-io</artifactId>
 			<version>1.3.2</version>
 		</dependency>
-		<dependency>
-			<groupId>org.eclipse.mylyn.github</groupId>
-			<artifactId>org.eclipse.egit.github.core</artifactId>
-			<version>2.1.5</version>
-		</dependency>
 		<dependency>
 			<groupId>org.yaml</groupId>
 			<artifactId>snakeyaml</artifactId>
@@ -88,9 +83,24 @@
                 </exclusion>
             </exclusions>
         </dependency>
-	</dependencies>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>2.9.0.pr4</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-osgi</artifactId>
+            <version>3.3.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.jgit</groupId>
+            <artifactId>org.eclipse.jgit</artifactId>
+            <version>4.8.0.201706111038-r</version>
+        </dependency>
+    </dependencies>
 
-	<build>
+    <build>
 		<plugins>
 			<plugin>
 				<groupId>org.springframework.boot</groupId>

Diff for: src/main/java/org/commonwl/view/PageController.java

@@ -39,4 +39,24 @@ public String homePage(Model model, @RequestParam(value = "url", required = fals
         return "index";
     }
 
+    /**
+     * About page
+     * @param model The model for the about page
+     * @return The view for this page
+     */
+    @GetMapping("/about")
+    public String about(Model model) {
+        return "about";
+    }
+
+    /**
+     * API documentation page
+     * @param model The model for the API documentation page
+     * @return The view for this page
+     */
+    @GetMapping("/apidocs")
+    public String apiDocumentation(Model model) {
+        return "apidocs";
+    }
+
 }

Diff for: src/main/java/org/commonwl/view/cwl/CWLElement.java

@@ -19,22 +19,26 @@
 
 package org.commonwl.view.cwl;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
+
 import java.util.ArrayList;
 import java.util.List;
 
 /**
  * Represents the input/output of a workflow/tool
  */
+@JsonInclude(JsonInclude.Include.NON_EMPTY)
 public class CWLElement {
 
     private String label;
     private String doc;
     private String type;
+    private String format;
     private List<String> sourceID;
     private String defaultVal;
 
     public CWLElement() {
-        this.sourceID = new ArrayList<String>();
+        this.sourceID = new ArrayList<>();
     }
 
     public String getLabel() {
@@ -61,6 +65,22 @@ public void setType(String type) {
         this.type = type;
     }
 
+    public String getFormat() {
+        return format;
+    }
+
+    public void setFormat(String format) {
+        this.format = format;
+    }
+
+    public List<String> getSourceID() {
+        return sourceID;
+    }
+
+    public void setSourceID(List<String> sourceID) {
+        this.sourceID = sourceID;
+    }
+
     public List<String> getSourceIDs() {
         return sourceID;
     }