Merge pull request #28 from 52North/develop

Merge develop

.travis.yml

@@ -3,7 +3,9 @@ sudo: false
 install: true
 script: mvn -fae -U -B clean install
 jdk:
-  - oraclejdk8
+  - openjdk8
+  - openjdk9
+  - openjdk10
 cache:
   directories:
     - $HOME/.m2

NOTICE

@@ -33,14 +33,14 @@ This project includes:
   Animal Sniffer Annotations under MIT license
   Apache Commons Codec under Apache License, Version 2.0
   Apache Commons Configuration under Apache License, Version 2.0
-  Apache Commons Lang under The Apache Software License, Version 2.0
+  Apache Commons Lang under Apache License, Version 2.0
   Apache Commons Logging under The Apache Software License, Version 2.0
   Apache HttpClient under Apache License, Version 2.0
-  Apache HttpCore under Apache License, Version 2.0
   Apache Log4j API under The Apache Software License, Version 2.0
   Apache Log4j Core under The Apache Software License, Version 2.0
   Apache Log4j SLF4J Binding under The Apache Software License, Version 2.0
   Apache Log4j Web under The Apache Software License, Version 2.0
+  Checker Qual under The MIT License
   ClassLoader Leak Prevention library under Apache 2
   Commons Lang under The Apache Software License, Version 2.0
   Cross-Origin Resource Sharing (CORS) Filter under The Apache Software License, Version 2.0
@@ -49,15 +49,22 @@ This project includes:
   EXIficient-Core under MIT License
   EXIficient-Grammars under MIT License
   FindBugs-jsr305 under The Apache Software License, Version 2.0
+  geolatte-geom under LGPL 3.0
+  Guava InternalFutureFailureAccess and InternalFutures under The Apache Software License, Version 2.0
+  Guava ListenableFuture only under The Apache Software License, Version 2.0
   Guava: Google Core Libraries for Java under The Apache Software License, Version 2.0
   J2ObjC Annotations under The Apache Software License, Version 2.0
   Jackson-annotations under The Apache Software License, Version 2.0
   Jackson-core under The Apache Software License, Version 2.0
   jackson-databind under The Apache Software License, Version 2.0
+  Java Architecture for XML Binding under CDDL 1.1 or GPL2 w/ CPE
   Java Property Utility under The Apache Software License, Version 2.0
+  JavaBeans(TM) Activation Framework under COMMON DEVELOPMENT AND DISTRIBUTION LICENSE (CDDL) Version 1.0
   javax.inject under The Apache Software License, Version 2.0
   JCL 1.2 implemented over SLF4J under MIT License
   Joda-Time under Apache 2
+  Old JAXB Core under CDDL+GPL License
+  Old JAXB Runtime under CDDL+GPL License
   org.locationtech.jts:jts-core under Eclipse Publish License, Version 1.0 or Eclipse Distribution License - v 1.0
   PJL Compressing Filter under Apache Software License V2.0
   SLF4J API Module under MIT License
@@ -73,5 +80,6 @@ This project includes:
   StAX API under The Apache Software License, Version 2.0
   Xerces2-j under The Apache Software License, Version 2.0
   XML Commons External Components XML APIs under The Apache Software License, Version 2.0 or The SAX License or The W3C License
+  XML Pull Parsing API under Public Domain
   XmlBeans under The Apache Software License, Version 2.0
 

README.md

@@ -58,15 +58,14 @@ Try out the latest javaPS alpha-release on on our [Geoprocessing Demo Server](ht
 ## Support
 
 You can get support in the community mailing list and forums:
-http://52north.org/resources/mailing-lists-and-forums/
+https://52north.org/discuss/#mailing-lists
 
 ## Contribute
 
 Are you are interesting in contributing to javaPS and you want to pull your changes to the 52°North repository to make it available to all?
 In that case we need your official permission and for this purpose we have a so called contributors license agreement (CLA) in place. With this agreement you grant us the rights to use and publish your code under an open source license.
 A link to the contributors license agreement and further explanations are available here:
-http://52north.org/about/licensing/cla-guideline
-
+https://52north.org/software/licensing/guidelines/
 ## Credits
 
  * Christian Autermann, @autermann

docs/documentation_markdown/docs/algorithm_definition/algorithm_definition.markdown

@@ -10,44 +10,81 @@ How to add custom Processes/Algorithms to JavaPS
 
 As described in the [Architectural Details Page](../architecture/architecture.markdown), processes are implementations of the interface ***IAlgorithm***, which prescribes an *execute()* method and a ***TypedProcessDescription***, the Java representation of a process description. The abstract component ***AbstractAlgorithm*** implements the interface and thus provides the rudimentary skeleton for any ***Algorithm*** implementation. However, algorithm developers do not have to extend ***AbstractAlgorithm*** themselves. Instead, **JavaPS** offers a more elegant and simple way of implementing custom ***Algorithms***. Through suitable *Java annotations*, any Java class may become an ***Algorithm*** that is found at application start-up by **JavaPS**. This functionality is provided by component ***AnnotatedAlgorithm***, which extends ***AbstractAlgorithm*** and thus provides a full implementation of the requirements (*process description* and *execute()* method). The necessary information is automatically parsed and derived from the *annotations*.
 
-The following example demonstrates the definition of an *annotated algorithm*. The exemplar *"TestAlgorithm"* is marked as an implementation of ***IAlgorithm*** by annotating certain methods with key annotation, such as **@Algorithm**, **@LiteralInput**, **@LiteralOutput** and **@Execute**.
+The following example demonstrates the definition of an *annotated algorithm*. The exemplar *"EchoProcess"* is marked as an implementation of ***IAlgorithm*** by annotating certain methods with key annotation, such as **@Algorithm**, **@LiteralInput**, **@LiteralOutput** and **@Execute**.
 
 ```
-package org.n52.javaps.service;
+package org.n52.wps.echoprocess;
 
 //import statements omitted
 
 @Algorithm(version = "1.0.0")
-public class TestAlgorithm {
-    private String input1;
-    private String input2;
-    private String output1;
-    private String output2;
-
-    @LiteralInput(identifier = "input1")
-    public void setInput1(String value) {
-         this.input1 = value;
+public class EchoProcess {
+
+    private static final Logger log = LoggerFactory.getLogger(EchoProcess.class);
+
+    private List<XmlObject> complexInput;
+    private List<String> literalInput;
+
+    private XmlObject complexOutput;
+    private String literalOutput;
+
+    private OwsBoundingBox boundingboxInput;
+    private OwsBoundingBox boundingboxOutput;
+
+    @Execute
+    public void echo() {
+        
+        log.debug("Running echo process");
+
+        if (literalInput != null && literalInput.size() > 0){
+            literalOutput = literalInput.get(0);
+        } else{
+            log.debug("No literal input");
+        }
+
+        if (complexInput != null && complexInput.size() > 0){
+            complexOutput = complexInput.get(0);
+        } else{
+            log.debug("No complex input");
+        }
+        
+        if (boundingboxInput != null){
+            boundingboxOutput = boundingboxInput;
+        } else{
+            log.debug("No bounding box input");
+        }
+
+        log.debug("Finished echo process, literal output is '{}', complex output is : {}", literalOutput, complexOutput);
     }
 
-    @LiteralInput(identifier = "input2")
-    public void setInput2(String value) {
-         this.input2 = value;
+    @LiteralOutput(identifier = "literalOutput")
+    public String getLiteralOutput() {
+        return literalOutput;
     }
 
-    @Execute
-    public void execute() {
-         this.output1 = input1;
-         this.output2 = input2;
+    @LiteralInput(identifier = "literalInput", maxOccurs = 1)
+    public void setLiteralInput(List<String> literalInput) {
+        this.literalInput = literalInput;
+    }
+
+    @BoundingBoxInput(defaultCRSString="EPSG:4326", identifier = "boundingboxInput")
+    public void setBoundingBox(OwsBoundingBox data){
+        this.boundingboxInput = data;
+    }
+
+    @BoundingBoxOutput(defaultCRSString="EPSG:4326", identifier = "boundingboxOutput")
+    public OwsBoundingBox getBoundingBox(){
+        return this.boundingboxOutput;
     }
 
-    @LiteralOutput(identifier = "output1")
-    public String getOutput1() {
-         return this.output1;
+    @ComplexOutput(identifier="complexOutput", binding=GenericXMLDataBinding.class)
+    public XmlObject getComplexOutput() {
+        return complexOutput;
     }
 
-    @LiteralOutput(identifier = "output2")
-    public String getOutput2() {
-         return this.output2;
+    @ComplexInput(identifier="complexInput", binding=GenericXMLDataBinding.class)
+    public void setComplexInput(List<XmlObject> complexInput) {
+        this.complexInput = complexInput;
     }
 
 }
@@ -96,6 +133,18 @@ Annotation `@ComplexInput` Properties
 -	long **maximumMegaBytes**: a limitation of the maximum size of the complex input's payload
 -	Class **binding**: reference to a *binding* class that implements/extends *ComplexData.class* and thus is able to parse the complex input from an *Execute* request correctly; basically this *binding* component acts as a wrapper for the input; more information about *binding* is provided in section [The Role of the Binding Implementations](#the-role-of-the-binding-implementations)
 
+#### Setter Annotation **@BoundingBoxInput**
+
+Annotation `@ComplexInput` Properties
+
+-	String **identifier**: specifies the unique *input identifier* of the input
+-	String **title**: the title of the input; can be chosen arbitrarily
+-	String **abstrakt**: a description of the input
+-	long **minOccurs**: the minimum number of occurrences within an *Execute* request; default value is "1"
+-	long **maxOccurs**: the maximum number of occurrences within an *Execute* request; default value is "1"
+-   String **defaultCRSString**: the default CRS as String; default value is "http://www.opengis.net/def/crs/EPSG/0/4326"
+-   String[] **supportedCRSStringArray**: String array of supported CRS; default value is {"http://www.opengis.net/def/crs/EPSG/0/4326"}
+
 ### Annotations for the Definition of *Process Outputs*
 
 #### Setter Annotation **@LiteralOutput**
@@ -117,6 +166,16 @@ Annotation `@ComplexOutput` Properties
 -	String **abstrakt**: a description of the output
 -	Class **binding**: reference to a *binding* class that implements/extends *ComplexData.class* and thus is able to encode the output correctly; basically this *binding* component acts as a wrapper for the output; more information about *binding* is provided in section [The Role of the Binding Implementations](#the-role-of-the-binding-implementations)
 
+#### Setter Annotation **@BoundingBoxOutput**
+
+Annotation `@BoundingBoxOutput` Properties
+
+-	String **identifier**: specifies the unique *output identifier* of the output
+-	String **title**: the title of the output; can be chosen arbitrarily
+-	String **abstrakt**: a description of the output
+-   String **defaultCRSString**: the default CRS as String; default value is "http://www.opengis.net/def/crs/EPSG/0/4326"
+-   String[] **supportedCRSStringArray**: String array of supported CRS; default value is {"http://www.opengis.net/def/crs/EPSG/0/4326"}
+
 ### The Role of the Binding Implementations
 
 During the previous explanation of the annotations for *in-* and *outputs*, a specific annotation called **binding** was introduced. Its purpose and relevance will be described in this section. In general, a **WPS** process defines several process *in-* and *outputs*. When a client constructs and sends an **Execute request**, the *inputs* are specified using a certain **format/encoding**. Also the client may request the process *output(s)* to be **encoded in a certain format**. While the available **formats** are predefined by the **JavaPS** implementation of that process, the ***Algorithm*** implementation uses a single internal representation of the *in-* and *outputs*. Hence, transformation between the different data representations is necessary.

engine/pom.xml

@@ -94,6 +94,10 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+        </dependency>
         <dependency>
         	<groupId>xml-apis</groupId>
         	<artifactId>xml-apis</artifactId>

engine/src/main/java/org/n52/javaps/algorithm/annotation/BoundingBoxInput.java

@@ -46,8 +46,6 @@
 
     long maxOccurs() default 1;
 
-    String boundingBoxString() default "";
-
     String defaultCRSString() default CRS_EPSG_4326;
 
     String[] supportedCRSStringArray() default { CRS_EPSG_4326 };

engine/src/main/java/org/n52/javaps/algorithm/annotation/BoundingBoxInputAnnotationParser.java

@@ -20,6 +20,8 @@
 import java.lang.reflect.Member;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.function.Function;
 
 import org.n52.javaps.description.TypedBoundingBoxInputDescription;
@@ -41,6 +43,7 @@ class BoundingBoxInputAnnotationParser<M extends AccessibleObject & Member, B ex
         AbstractInputAnnotationParser<BoundingBoxInput, M, B> {
 
     private static final Logger LOG = LoggerFactory.getLogger(BoundingBoxInputAnnotationParser.class);
+    private static final String COULD_NOT_CREATE_URI_FROM_STRING = "Could not create URI from String: ";
 
     BoundingBoxInputAnnotationParser(Function<M, B> bindingFunction) {
         super(bindingFunction);
@@ -55,16 +58,27 @@ protected TypedBoundingBoxInputDescription createDescription(BoundingBoxInput an
         try {
             defaultCRSURI = new URI(annotation.defaultCRSString());
         } catch (URISyntaxException e) {
-            LOG.error("Could not create URI from String: " + annotation.defaultCRSString());
+            LOG.error(COULD_NOT_CREATE_URI_FROM_STRING + annotation.defaultCRSString());
             defaultCRSURI = URI.create("http://www.opengis.net/def/crs/EPSG/0/4326");
         }
 
+        List<OwsCRS> supportedCRSList = new ArrayList<>();
+
+        String [] supportedCRSArray = annotation.supportedCRSStringArray();
+
+        for (String crsString : supportedCRSArray) {
+            try {
+                supportedCRSList.add(new OwsCRS(new URI(crsString)));
+            } catch (URISyntaxException e) {
+                LOG.error(COULD_NOT_CREATE_URI_FROM_STRING + crsString);
+            }
+        }
         // TODO add supported CRSs
 
         return new TypedProcessDescriptionFactory().boundingBoxInput().withIdentifier(annotation.identifier())
                 .withAbstract(annotation.abstrakt()).withTitle(annotation.title()).withMinimalOccurence(annotation
                         .minOccurs()).withMaximalOccurence(annotation.maxOccurs()).withDefaultCRS(new OwsCRS(
-                                defaultCRSURI)).build();
+                                defaultCRSURI)).withSupportedCRS(supportedCRSList).build();
     }
 
     @Override

engine/src/main/java/org/n52/javaps/engine/impl/ProcessInputDecoderImpl.java

@@ -104,6 +104,15 @@ private Data<?> decodeReference(TypedProcessInputDescription<?> description,
     private Data<?> decodeValueInput(TypedProcessInputDescription<?> description,
             ValueProcessData input) throws InputDecodingException {
         Format format = input.getFormat();
+
+        if (format.isEmpty()) {
+            if (description.isComplex()) {
+                format = description.asComplex().getDefaultFormat();
+            } else {
+                format = Format.TEXT_XML;
+            }
+        }
+
         Class<? extends Data<?>> bindingType = description.getBindingType();
 
         InputHandler handler = this.inputHandlerRepository.getInputHandler(format, bindingType).orElseThrow(

engine/src/main/java/org/n52/javaps/engine/impl/ProcessOutputEncoderImpl.java

@@ -26,6 +26,7 @@
 import javax.inject.Inject;
 
 import org.n52.shetland.ogc.ows.OwsCode;
+import org.n52.shetland.ogc.wps.Format;
 import org.n52.shetland.ogc.wps.OutputDefinition;
 import org.n52.shetland.ogc.wps.data.GroupProcessData;
 import org.n52.shetland.ogc.wps.data.ProcessData;
@@ -79,7 +80,18 @@ private void createData(TypedProcessOutputDescriptionContainer description,
     private ProcessData createValueData(TypedProcessOutputDescription<?> outputDescription,
             OutputDefinition outputDefinition,
             Data<?> data) throws OutputEncodingException {
-        OutputHandler outputHandler = this.outputHandlerRepository.getOutputHandler(outputDefinition.getFormat(), data)
+
+        Format format = outputDefinition.getFormat();
+
+        if (format.isEmpty()) {
+            if (outputDescription.isComplex()) {
+                format = outputDescription.asComplex().getDefaultFormat();
+            } else {
+                format = Format.TEXT_XML;
+            }
+        }
+
+        OutputHandler outputHandler = this.outputHandlerRepository.getOutputHandler(format, data)
                 .orElseThrow(noHandlerFound(outputDescription.getId()));
         return new GeneratingProcessData(outputDescription, outputDefinition, outputHandler, data);
     }

engine/src/main/java/org/n52/javaps/engine/impl/ResolvableReferenceProcessData.java

@@ -83,8 +83,9 @@ public ValueProcessData resolve() throws IOException {
 
     private byte[] getFromLocalDisc() throws IOException {
         URL fileURL = getURI().toURL();
-        InputStream is = new FileInputStream(fileURL.getFile());
-        return ByteStreams.toByteArray(is);
+        try (InputStream is = new FileInputStream(fileURL.getFile())) {
+           return ByteStreams.toByteArray(is);
+        }
     }
 
 }

engine/src/main/java/org/n52/javaps/io/bbox/BoundingBoxData.java

@@ -16,8 +16,15 @@
  */
 package org.n52.javaps.io.bbox;
 
-import org.n52.shetland.ogc.ows.OwsBoundingBox;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.commons.io.IOUtils;
 import org.n52.javaps.io.Data;
+import org.n52.javaps.io.DecodingException;
+import org.n52.shetland.ogc.ows.OwsBoundingBox;
+import org.n52.shetland.ogc.wps.Format;
 
 public final class BoundingBoxData implements Data<OwsBoundingBox> {
     private static final long serialVersionUID = -3219612972795621553L;
@@ -37,4 +44,18 @@ public OwsBoundingBox getPayload() {
     public Class<?> getSupportedClass() {
         return OwsBoundingBox.class;
     }
+
+    private synchronized void writeObject(java.io.ObjectOutputStream oos) throws IOException {
+        ByteArrayOutputStream out = new ByteArrayOutputStream();
+        BoundingBoxInputOutputHandler generator = new BoundingBoxInputOutputHandler();
+        InputStream in = generator.generate(null, this, new Format());
+        IOUtils.copy(in, out);
+    }
+
+    private void readObject(java.io.ObjectInputStream oos) throws IOException, ClassNotFoundException,
+            DecodingException {
+        BoundingBoxInputOutputHandler parser  = new BoundingBoxInputOutputHandler();
+        BoundingBoxData data = (BoundingBoxData) parser.parse(null, oos, new Format());
+        this.boundingBox = data.boundingBox;
+    }
 }

engine/src/main/java/org/n52/javaps/io/bbox/BoundingBoxInputOutputHandler.java

@@ -179,9 +179,8 @@ public InputStream generate(TypedProcessOutputDescription<?> description,
             InputStream stream = new ByteArrayInputStream(bytes);
 
             if (format.isBase64()) {
-                stream = new Base64InputStream(stream, true);
+                return new Base64InputStream(stream, true);
             }
-
             return stream;
         } catch (XMLStreamException ex) {
             throw new IOException(ex);