basic framework for reading Json/GeoJson data (#1042)

ING-3128
* fix: fix Groovy compiler level in Eclipse projects
* build: fix missing package import for test bundle
* refactor: delete obsolete JSON related classes
* refactor: rename JSON writer package
* refactor: stub implementation of reading JSON instances
* refactor: don't use outdated jackson library for Json processing
* feat: improve content type matching based on extension
Value matches related to file extensions higher depending on the number
if dots they contain.
Goal is to for example not match a `.xml.gz` file to a random content
type with a `gz` extension, but to prefer the one with `xml.gz`.

common/plugins/eu.esdihumboldt.hale.common.align.tgraph.test/.settings/org.eclipse.jdt.groovy.core.prefs

@@ -1,2 +1,2 @@
 eclipse.preferences.version=1
-groovy.compiler.level=40
+groovy.compiler.level=25

common/plugins/eu.esdihumboldt.hale.common.align.tgraph/.settings/org.eclipse.jdt.groovy.core.prefs

@@ -1,2 +1,2 @@
 eclipse.preferences.version=1
-groovy.compiler.level=40
+groovy.compiler.level=25

common/plugins/eu.esdihumboldt.hale.common.cache.test/META-INF/MANIFEST.MF

@@ -7,3 +7,4 @@ Fragment-Host: eu.esdihumboldt.hale.common.cache;bundle-version="2.5.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: data harmonisation panel
 Automatic-Module-Name: eu.esdihumboldt.hale.common.cache.test
+Import-Package: org.junit

common/plugins/eu.esdihumboldt.hale.common.core/src/eu/esdihumboldt/hale/common/core/io/HaleIO.java

@@ -209,15 +209,28 @@ public static List<IContentType> findContentTypesFor(Collection<IContentType> ty
 
 		List<IContentType> results = new ArrayList<IContentType>();
 
+		IContentType highestScoreMatch = null;
+		long highestScore = 0;
+
 		if (filename != null && !filename.isEmpty()) {
 			// test file extension
 			String lowerFile = filename.toLowerCase();
+
 			for (IContentType type : types) {
 				String[] extensions = type.getFileSpecs(IContentType.FILE_EXTENSION_SPEC);
 				boolean match = false;
 				for (int i = 0; i < extensions.length && !match; i++) {
 					if (lowerFile.endsWith("." + extensions[i].toLowerCase())) {
 						match = true;
+
+						// determine score based on how many dots are contained
+						// in the extension (e.g. `gml.gz` has a score of 1 and
+						// is considered a match with a high score)
+						long extensionScore = extensions[i].chars().filter(ch -> ch == '.').count();
+						if (extensionScore > highestScore) {
+							highestScoreMatch = type;
+							highestScore = extensionScore;
+						}
 					}
 				}
 				if (match) {
@@ -226,6 +239,13 @@ public static List<IContentType> findContentTypesFor(Collection<IContentType> ty
 			}
 		}
 
+		if (results.size() > 1 && highestScoreMatch != null) {
+			// if there are multiple results based on extension, use the
+			// available match with the highest score.
+			results.clear();
+			results.add(highestScoreMatch);
+		}
+
 		if ((results.isEmpty() || results.size() > 1) && in != null) {
 			// remember previous results
 			List<IContentType> extensionResults = null;
@@ -322,9 +342,7 @@ public boolean acceptCollection(
 	/**
 	 * Find an I/O provider factory
 	 * 
-	 * @param
-	 * 			<P>
-	 *            the provider interface type
+	 * @param <P> the provider interface type
 	 * 
 	 * @param providerType the provider type, usually an interface
 	 * @param contentType the content type the provider must match, may be
@@ -366,9 +384,7 @@ public static <P extends IOProvider> IOProviderDescriptor findIOProviderFactory(
 	/**
 	 * Creates an I/O provider instance
 	 * 
-	 * @param
-	 * 			<P>
-	 *            the provider interface type
+	 * @param <P> the provider interface type
 	 * 
 	 * @param providerType the provider type, usually an interface
 	 * @param contentType the content type the provider must match, may be
@@ -399,9 +415,7 @@ public static <P extends IOProvider> P createIOProvider(Class<P> providerType,
 	/**
 	 * Find the content type for the given input
 	 * 
-	 * @param
-	 * 			<P>
-	 *            the provider interface type
+	 * @param <P> the provider interface type
 	 * 
 	 * @param providerType the provider type, usually an interface
 	 * @param in the input supplier to use for testing, may be <code>null</code>
@@ -435,9 +449,7 @@ public static <P extends IOProvider> IContentType findContentType(Class<P> provi
 	/**
 	 * Find an I/O provider instance for the given input
 	 * 
-	 * @param
-	 * 			<P>
-	 *            the provider interface type
+	 * @param <P> the provider interface type
 	 * 
 	 * @param providerType the provider type, usually an interface
 	 * @param in the input supplier to use for testing, may be <code>null</code>

ext/ageobw/eu.esdihumboldt.hale.app.bgis.ade/.settings/org.eclipse.jdt.groovy.core.prefs

@@ -1,2 +1,3 @@
 eclipse.preferences.version=1
-groovy.compiler.level=40
+groovy.compiler.level=25
+groovy.script.filters=**/*.dsld,y,**/*.gradle,n

ext/xslt/eu.esdihumboldt.hale.io.xslt.test/.settings/org.eclipse.jdt.groovy.core.prefs

@@ -1,2 +1,2 @@
 eclipse.preferences.version=1
-groovy.compiler.level=40
+groovy.compiler.level=25

ext/xslt/eu.esdihumboldt.hale.io.xslt/.settings/org.eclipse.jdt.groovy.core.prefs

@@ -1,2 +1,2 @@
 eclipse.preferences.version=1
-groovy.compiler.level=40
+groovy.compiler.level=25

io/plugins/eu.esdihumboldt.hale.io.json.test/META-INF/MANIFEST.MF

@@ -14,12 +14,16 @@ Require-Bundle: eu.esdihumboldt.hale.io.json;bundle-version="2.9.0",
  eu.esdihumboldt.cst.functions.geometric;bundle-version="4.2.0",
  org.locationtech.jts.jts-core;bundle-version="1.16.0",
  org.junit;bundle-version="4.13.0",
- eu.esdihumboldt.hale.common.align.groovy;bundle-version="2.9.0"
+ eu.esdihumboldt.hale.common.align.groovy;bundle-version="2.9.0",
+ com.fasterxml.jackson.core.jackson-core;bundle-version="2.13.4",
+ com.fasterxml.jackson.core.jackson-databind;bundle-version="2.13.4"
 Import-Package: de.fhg.igd.slf4jplus,
  eu.esdihumboldt.hale.common.instance.groovy,
  eu.esdihumboldt.hale.common.instance.model,
+ eu.esdihumboldt.util.io,
  eu.esdihumboldt.util.xml,
  net.jcip.annotations,
+ org.assertj.core.api;version="3.22.0",
  org.hamcrest.core;version="1.3.0",
  org.slf4j;version="1.7.2"
 Automatic-Module-Name: eu.esdihumboldt.hale.io.json.test

io/plugins/eu.esdihumboldt.hale.io.json.test/src/eu/esdihumboldt/hale/io/json/test/InstanceToJsonTest.groovy

@@ -24,7 +24,7 @@ import eu.esdihumboldt.hale.common.core.report.SimpleLog
 import eu.esdihumboldt.hale.common.instance.groovy.InstanceBuilder
 import eu.esdihumboldt.hale.common.schema.groovy.SchemaBuilder
 import eu.esdihumboldt.hale.common.schema.model.Schema
-import eu.esdihumboldt.hale.io.json.writer.InstanceToJson
+import eu.esdihumboldt.hale.io.json.internal.InstanceToJson
 import groovy.json.JsonSlurper
 
 class InstanceToJsonTest {