Merge pull request #37 from 52North/develop

Merge develop
52North · Jul 16, 2019 · 2fee920 · 2fee920
2 parents 78a70c4 + 0290e59
commit 2fee920
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diff --git a/.gitignore b/.gitignore
@@ -1,141 +1,143 @@
-### https://raw.github.com/github/gitignore/master/Java.gitignore
-
-*.class
-
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
-
-# Package Files #
-*.jar
-*.war
-*.ear
-
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
-
-
-### https://raw.github.com/github/gitignore/master/Maven.gitignore
-
-target/
-pom.xml.tag
-pom.xml.releaseBackup
-pom.xml.versionsBackup
-pom.xml.next
-release.properties
-dependency-reduced-pom.xml
-
-
-### https://raw.github.com/github/gitignore/master/Global/NetBeans.gitignore
-
-nbproject/private/
-build/
-nbbuild/
-dist/
-nbdist/
-nbactions.xml
-nb-configuration.xml
-.nb-gradle/
-
-
-### https://raw.github.com/github/gitignore/master/Global/Eclipse.gitignore
-
-*.pydevproject
-.metadata
-.gradle
-bin/
-tmp/
-*.tmp
-*.bak
-*.swp
-*~.nib
-local.properties
-.settings/
-.loadpath
-
-# Eclipse Core
-.project
-
-# External tool builders
-.externalToolBuilders/
-
-# Locally stored "Eclipse launch configurations"
-*.launch
-
-# CDT-specific
-.cproject
-
-# JDT-specific (Eclipse Java Development Tools)
-.classpath
-
-# PDT-specific
-.buildpath
-
-# sbteclipse plugin
-.target
-
-# TeXlipse plugin
-.texlipse
-
-
-### https://raw.github.com/github/gitignore/master/Global/Windows.gitignore
-
-# Windows image file caches
-Thumbs.db
-ehthumbs.db
-
-# Folder config file
-Desktop.ini
-
-# Recycle Bin used on file shares
-$RECYCLE.BIN/
-
-# Windows Installer files
-*.cab
-*.msi
-*.msm
-*.msp
-
-# Windows shortcuts
-*.lnk
-
-
-### https://raw.github.com/github/gitignore/master/Global/Linux.gitignore
-
-*~
-
-# KDE directory preferences
-.directory
-
-# Linux trash folder which might appear on any partition or disk
-.Trash-*
-
-
-### https://raw.github.com/github/gitignore/master/Global/OSX.gitignore
-
-.DS_Store
-.AppleDouble
-.LSOverride
-
-# Icon must end with two \r
-Icon
-
-# Thumbnails
-._*
-
-# Files that might appear in the root of a volume
-.DocumentRevisions-V100
-.fseventsd
-.Spotlight-V100
-.TemporaryItems
-.Trashes
-.VolumeIcon.icns
-
-# Directories potentially created on remote AFP share
-.AppleDB
-.AppleDesktop
-Network Trash Folder
-Temporary Items
-.apdisk
-
-webapp/logs/
-
+### https://raw.github.com/github/gitignore/master/Java.gitignore
+
+*.class
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+
+### https://raw.github.com/github/gitignore/master/Maven.gitignore
+
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+
+
+### https://raw.github.com/github/gitignore/master/Global/NetBeans.gitignore
+
+nbproject/private/
+build/
+nbbuild/
+dist/
+nbdist/
+nbactions.xml
+nb-configuration.xml
+.nb-gradle/
+
+
+### https://raw.github.com/github/gitignore/master/Global/Eclipse.gitignore
+
+*.pydevproject
+.metadata
+.gradle
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+
+# Eclipse Core
+.project
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# CDT-specific
+.cproject
+
+# JDT-specific (Eclipse Java Development Tools)
+.classpath
+
+# PDT-specific
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# TeXlipse plugin
+.texlipse
+
+
+### https://raw.github.com/github/gitignore/master/Global/Windows.gitignore
+
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+
+### https://raw.github.com/github/gitignore/master/Global/Linux.gitignore
+
+*~
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+
+### https://raw.github.com/github/gitignore/master/Global/OSX.gitignore
+
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+webapp/logs/
+
+logs/
diff --git a/.travis.yml b/.travis.yml
@@ -1,7 +1,7 @@
 language: java
 sudo: false
 install: true
-script: mvn -fae -U -B clean install
+script: mvn -fae -U -B clean install -Pintegration-test
 jdk:
   - openjdk8
   - openjdk9

diff --git a/NOTICE b/NOTICE
@@ -58,6 +58,8 @@ This project includes:
   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
+  javaPS input/output handler under The Apache Software License, Version 2.0
+  javaps-test-processes under The Apache Software License, Version 2.0
   javax.inject under The Apache Software License, Version 2.0
   JCL 1.2 implemented over SLF4J under MIT License
   Joda-Time under Apache 2

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# javaPS
+# javaPS [![Maven Central](https://img.shields.io/maven-central/v/org.n52.wps/javaPS.svg)](https://search.maven.org/search?q=g:org.n52.wps%20and%20a:webapp) [![Total alerts](https://img.shields.io/lgtm/alerts/g/52North/javaPS.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/52North/javaPS/alerts/) [![Language grade: Java](https://img.shields.io/lgtm/grade/java/g/52North/javaPS.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/52North/javaPS/context:java)
 
 ## Description
 
@@ -16,7 +16,7 @@ javaPS implements the [OGC WPS specification, version 2.0](http://docs.opengeosp
 * General Features
   * Full java-based Open Source implementation.
   * Pluggable framework for algorithms and XML data handling and processing frameworks
-  * Built upon the [iceland project](https://github.com/52North/iceland)
+  * Built upon the [arctic-sea project](https://github.com/52North/arctic-sea)
   * Streaming de-/encoders for inputs and outputs
 
 ## License
@@ -25,8 +25,17 @@ This project is licensed under the Apache Software License, version 2.0.
 
 ## Changelog
 
-  * Changes since last release
-    * N/A First release
+### New features ---
+
+- Updated to arctic-sea v6
+- Added Dockerfile
+
+### Fixed issues ---
+
+- Test if inputs are null, This can be the case for optional inputs
+- Enabled storing of outputs encoded in base64
+- Removed test algorithm
+- Updated jackson-databind dependency
 
 ## Quick Start
 
@@ -78,4 +87,5 @@ https://52north.org/software/licensing/guidelines/
  * GLUES
  * TaMIS
  * OGC Testbeds
+ * RIESGOS
 
diff --git a/...e/src/main/java/org/n52/javaps/description/impl/TypedBoundingBoxInputDescriptionImpl.java b/...e/src/main/java/org/n52/javaps/description/impl/TypedBoundingBoxInputDescriptionImpl.java
@@ -25,7 +25,6 @@
 import org.n52.shetland.ogc.ows.OwsMetadata;
 import org.n52.shetland.ogc.wps.InputOccurence;
 import org.n52.shetland.ogc.wps.description.impl.BoundingBoxInputDescriptionImpl;
-import org.n52.shetland.ogc.wps.description.impl.BoundingBoxInputDescriptionImpl.AbstractBuilder;
 import org.n52.javaps.description.TypedBoundingBoxInputDescription;
 
 public class TypedBoundingBoxInputDescriptionImpl extends BoundingBoxInputDescriptionImpl implements

diff --git a/engine/src/main/java/org/n52/javaps/engine/impl/FileBasedResultPersistence.java b/engine/src/main/java/org/n52/javaps/engine/impl/FileBasedResultPersistence.java
@@ -300,8 +300,23 @@ private void persist(Path directory,
 
                         Encoder base64encoder = Base64.getEncoder();
 
-                        OutputStream outputStream = base64encoder.wrap(new FileOutputStream(outputFile.toFile()));
-                        IOUtils.copy(in, outputStream);
+                        OutputStream outputStream = null;
+                        OutputStream fileOutputStream = null;
+
+                        try {
+                            fileOutputStream = new FileOutputStream(outputFile
+                                    .toFile());
+
+                            outputStream = base64encoder.wrap(fileOutputStream);
+                            IOUtils.copy(in, outputStream);
+                        } finally {
+                            if (fileOutputStream != null) {
+                                fileOutputStream.close();
+                            }
+                            if (outputStream != null) {
+                                outputStream.close();
+                            }
+                        }
                     }
 
                 } else {

diff --git a/engine/src/main/java/org/n52/javaps/utils/IOUtils.java b/engine/src/main/java/org/n52/javaps/utils/IOUtils.java
@@ -178,7 +178,14 @@ public static List<File> unzipAll(File file) throws IOException {
 
         try (ZipInputStream zipInputStream = new ZipInputStream(new BufferedInputStream(new FileInputStream(file)))) {
             while ((entry = zipInputStream.getNextEntry()) != null) {
-                entryFile = new File(tempDir, entry.getName());
+                String entryName = entry.getName();
+                if (entryName.isEmpty()) {
+                    throw new IOException("Empty zip entry.");
+                }
+                entryFile = new File(tempDir, entryName);
+                if (!entryFile.toPath().normalize().startsWith(tempDir.toPath())) {
+                    throw new IOException("Bad zip entry: " + entryName);
+                }
                 boolean created = entryFile.createNewFile();
                 if (!created) {
                     LOGGER.info("File already exists: " + entryFile.getAbsolutePath());