gCubeSystem
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metadata-profile-discovery
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Merge pull request 'task_22890' (!1) from task_22890 into master 

Reviewed-on: #1
This commit is contained in:
Francesco Mangiacrapa 2022-11-14 15:10:08 +01:00
parent e0d5c00e5f 4851d5558b
commit c66fa56a85
16 changed files with 517 additions and 115 deletions
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2
.classpath
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@ -32,7 +32,7 @@
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
<attributes>
<attribute name="maven.pomderived" value="true"/>
<attribute name="owner.project.facets" value="java"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>

6
.settings/org.eclipse.jdt.core.prefs
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@ -3,12 +3,14 @@ org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.7
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.7
org.eclipse.jdt.core.compiler.source=1.8

1
.settings/org.eclipse.wst.common.component Normal file
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@ -0,0 +1 @@
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId"/>

2
.settings/org.eclipse.wst.common.project.facet.core.xml
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@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<faceted-project>
<installed facet="java" version="1.7"/>
<installed facet="jst.utility" version="1.0"/>
<installed facet="java" version="1.8"/>
</faceted-project>

2
.settings/org.eclipse.wst.validation.prefs Normal file
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@ -0,0 +1,2 @@
disabled=06target
eclipse.preferences.version=1

11
CHANGELOG.md
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@ -4,8 +4,17 @@
All notable changes to this project will be documented in this file.
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [v1.1.0-SNAPSHOT] - 2022-11-09
#### Enhancement
- [#22890] Extend the MetadataDiscovery logic
- [#23537] Introduce the fieldId in the gCube Metadata Profile
- Moved to maven-portal-bom 3.6.4
- [#24110] Added dependency required for building with JDK_11
## [v1.0.0] - 2020-09-30
#### First release
[#19880] Create the library metadata-profile-discovery
- [#19880] Create the library metadata-profile-discovery

33
pom.xml
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@ -12,7 +12,7 @@
<groupId>org.gcube.common</groupId>
<artifactId>metadata-profile-discovery</artifactId>
<version>1.0.0</version>
<version>1.1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>The Metadata Profile discovery library</name>
<description>The metadata-profile-discovery library is able to build java objects parsing the 'gCube Metadata Profiles' models:
@ -43,7 +43,7 @@
<dependency>
<groupId>org.gcube.distribution</groupId>
<artifactId>maven-portal-bom</artifactId>
<version>3.6.0</version>
<version>3.7.0-SNAPSHOT</version>
<type>pom</type>
<scope>import</scope>
</dependency>
@ -54,7 +54,7 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<!-- GWT needs at least java 1.6 -->
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
<dependencies>
@ -99,6 +99,21 @@
<scope>provided</scope>
</dependency>
<!-- REQUIRED FOR JDK_11 -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.0</version>
<scope>provided</scope>
</dependency>
<!-- END REQUIRED FOR JDK_11 -->
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<!-- JUNIT -->
<dependency>
<groupId>junit</groupId>
@ -108,12 +123,12 @@
</dependency>
<!-- Required to log on tests -->
<!-- <dependency> -->
<!-- <groupId>ch.qos.logback</groupId> -->
<!-- <artifactId>logback-classic</artifactId> -->
<!-- <version>1.0.13</version> -->
<!-- <scope>test</scope> -->
<!-- </dependency> -->
<!-- <dependency> -->
<!-- <groupId>ch.qos.logback</groupId> -->
<!-- <artifactId>logback-classic</artifactId> -->
<!-- <version>1.0.13</version> -->
<!-- <scope>test</scope> -->
<!-- </dependency> -->
</dependencies>

158
src/main/java/org/gcube/common/metadataprofilediscovery/MetadataProfileReader.java
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@ -28,10 +28,10 @@ import javax.xml.validation.Validator;
import org.gcube.common.metadataprofilediscovery.bean.MetadataProfile;
import org.gcube.common.metadataprofilediscovery.jaxb.MetadataFormat;
import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategories;
import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategory;
import org.gcube.common.metadataprofilediscovery.reader.MetadataFormatDiscovery;
import org.gcube.common.metadataprofilediscovery.reader.MetadataFormatReader;
import org.gcube.common.metadataprofilediscovery.reader.NamespaceCategoryReader;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.scope.impl.ScopeBean;
import org.slf4j.Logger;
@ -40,13 +40,12 @@ import org.w3c.dom.Document;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
/**
* The Class MetadataProfileReader.
*
* @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
* @author Francesco Mangiacrapa at ISTI-CNR francesco.mangiacrapa@isti.cnr.it
*
* Sep 30, 2020
* Mar 1, 2022
*/
public class MetadataProfileReader implements MetadataProfileDiscovery {
@ -63,22 +62,61 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
private String grMetadataProfileSecondaryType;
private String grMetadataProfileResourceName;
private static Logger logger = LoggerFactory.getLogger(MetadataProfileReader.class);
/**
* Instantiates a new metadata profile reader.
*
* @param grMetadataProfileSecondaryType the SecondaryType that must be used to discover the "gCube Metadata Profiles" from Information System
* @param grMetadataProfileSecondaryType the SecondaryType that must be used to
* discover the "gCube Metadata Profiles"
* from Information System
* @throws Exception the exception
*/
public MetadataProfileReader(String grMetadataProfileSecondaryType) throws Exception {
if(grMetadataProfileSecondaryType==null || grMetadataProfileSecondaryType.isEmpty())
throw new NullPointerException("Invalid input parameter");
if (grMetadataProfileSecondaryType == null || grMetadataProfileSecondaryType.isEmpty())
throw new NullPointerException("Invalid input parameter: grMetadataProfileSecondaryType");
this.grMetadataProfileSecondaryType = grMetadataProfileSecondaryType;
readNamespacesAndProfiles();
}
/**
* Instantiates a new metadata profile reader.
*
* @param grMetadataProfileSecondaryType the gr metadata profile secondary type
* @param resourceName the resource name
*
* the SecondaryType and the ResourceName
* that must be used to discover the
* "gCube Metadata Profiles" from
* Information System
* @throws Exception the exception
*/
public MetadataProfileReader(String grMetadataProfileSecondaryType, String resourceName) throws Exception {
if (grMetadataProfileSecondaryType == null || grMetadataProfileSecondaryType.isEmpty())
throw new NullPointerException("Invalid input parameter: grMetadataProfileSecondaryType");
if (resourceName == null || resourceName.isEmpty())
throw new NullPointerException("Invalid input parameter: resourceName");
this.grMetadataProfileSecondaryType = grMetadataProfileSecondaryType;
this.grMetadataProfileResourceName = resourceName;
readNamespacesAndProfiles();
}
/**
* Read namespaces and profiles.
*
* @throws Exception the exception
*/
private void readNamespacesAndProfiles() throws Exception {
String scopeString = ScopeProvider.instance.get();
logger.debug("Read scope " + scopeString + " from ScopeProvider");
@ -86,20 +124,22 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
throw new Exception("Please set a valid scope into ScopeProvider");
scope = new ScopeBean(scopeString);
readNamespaces();
readMetadataFormats();
}
/**
* Read metada formats.
*
* @throws Exception the exception
*/
private void readMetadataFormats() throws Exception {
//reading from Generic Resource for Secondary Type passed in input
medataFormatDiscovery = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType);
// reading from Generic Resource for Secondary Type and Resource Name passed in
// input
medataFormatDiscovery = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType,
grMetadataProfileResourceName);
logger.info("MedataFormatDiscovery has retrieved: " + medataFormatDiscovery.getMetadataProfiles().size()
+ " metadata type/s");
@ -113,12 +153,13 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
hashMetadataFormats.put(mT.getId(), reader.getMetadataFormat());
logger.debug("MetadataType id: " + mT.getId() + " cached as: " + reader.getMetadataFormat());
}
}
/**
* Read namespaces.
* @throws Exception
*
* @throws Exception the exception
*/
private void readNamespaces() throws Exception {
@ -128,11 +169,11 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
if (namespaceCategories == null)
namespaceCategories = new ArrayList<NamespaceCategory>();
NamespaceCategoryReader rd = new NamespaceCategoryReader(scope);
namespaceCategories.addAll(rd.getNamespaces().getNamespaceCategories());
NamespaceCategories ncCache = NamespaceCategoriesCache.loadNamespaces(scope.toString());
namespaceCategories.addAll(ncCache.getNamespaceCategories());
}
} catch (Exception e) {
logger.debug("An error occurred during read namespaces for categories: ", e);
logger.warn("An error occurred during read namespaces for categories: ", e);
throw e;
}
}
@ -154,13 +195,13 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
*/
public static InputStream getProfileSchemaInputStream() {
try {
logger.info("Trying to return the URL resource: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
logger.info("Trying to return the URL resource: " + URL_OF_GCDCMETADATAPROFILEV3_XSD);
return new URL(URL_OF_GCDCMETADATAPROFILEV3_XSD).openStream();
} catch (Exception e) {
logger.warn("Error on reading the URL: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
logger.warn("Error on reading the URL: " + URL_OF_GCDCMETADATAPROFILEV3_XSD);
}
logger.info("Returning local resource: "+SCHEMA_FILENAME);
logger.info("Returning local resource: " + SCHEMA_FILENAME);
return MetadataProfileReader.class.getResourceAsStream(SCHEMA_FILENAME);
}
@ -171,13 +212,13 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
*/
public static URL getProfileSchemaURL() {
try {
logger.info("Trying to return the URL object: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
logger.info("Trying to return the URL object: " + URL_OF_GCDCMETADATAPROFILEV3_XSD);
return new URL(URL_OF_GCDCMETADATAPROFILEV3_XSD);
} catch (Exception e) {
logger.warn("Error on reading the URL: "+URL_OF_GCDCMETADATAPROFILEV3_XSD);
logger.warn("Error on reading the URL: " + URL_OF_GCDCMETADATAPROFILEV3_XSD);
}
logger.info("Returning local URL of: "+SCHEMA_FILENAME);
logger.info("Returning local URL of: " + SCHEMA_FILENAME);
return MetadataProfileReader.class.getResource(SCHEMA_FILENAME);
}
@ -206,6 +247,13 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
validateAgainstXSD(new StreamSource(xml), getProfileSchemaURL());
}
/**
* Gets the metadata format for metadata profile.
*
* @param profile the profile
* @return the metadata format for metadata profile
* @throws Exception the exception
*/
/*
* (non-Javadoc)
*
@ -227,6 +275,12 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
return reader.getMetadataFormat();
}
/**
* Gets the list of metadata profiles.
*
* @return the list of metadata profiles
* @throws Exception the exception
*/
/*
* (non-Javadoc)
*
@ -242,6 +296,12 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
return medataFormatDiscovery.getMetadataProfiles();
}
/**
* Gets the list of namespace categories.
*
* @return the list of namespace categories
* @throws Exception the exception
*/
/*
* (non-Javadoc)
*
@ -257,6 +317,9 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
return namespaceCategories;
}
/**
* Reset metadata profile.
*/
/*
* (non-Javadoc)
*
@ -270,6 +333,9 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
hashMetadataFormats = null;
}
/**
* Reset namespace categories.
*/
/*
* (non-Javadoc)
*
@ -282,6 +348,11 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
namespaceCategories = null;
}
/**
* Gets the profile schema.
*
* @return the profile schema
*/
/*
* (non-Javadoc)
*
@ -297,6 +368,15 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
}
/**
* Validate profile.
*
* @param xmlProfile the xml profile
* @throws ParserConfigurationException the parser configuration exception
* @throws SAXException the SAX exception
* @throws IOException Signals that an I/O exception has
* occurred.
*/
/*
* (non-Javadoc)
*
@ -310,23 +390,23 @@ public class MetadataProfileReader implements MetadataProfileDiscovery {
DOMSource source = new DOMSource(doc);
validateAgainstXSD(source, getProfileSchemaURL());
}
/**
* Utility method to get a metadata format from a "gCube Metadata Profiles" model (XML-based)
* Utility method to get a metadata format from a "gCube Metadata Profiles"
* model (XML-based).
*
* @param metadataProfileStream the metadata profile stream
* @return the metadata format
* @throws JAXBException the JAXB exception
*/
public static MetadataFormat toMetadataFormat(InputStream metadataProfileStream) throws JAXBException{
if(metadataProfileStream==null)
public static MetadataFormat toMetadataFormat(InputStream metadataProfileStream) throws JAXBException {
if (metadataProfileStream == null)
throw new NullPointerException("Invalid input parameter");
JAXBContext jaxbContext = JAXBContext.newInstance(MetadataFormat.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
return (MetadataFormat) jaxbUnmarshaller.unmarshal(metadataProfileStream);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
return (MetadataFormat) jaxbUnmarshaller.unmarshal(metadataProfileStream);
}
}

145
src/main/java/org/gcube/common/metadataprofilediscovery/NamespaceCategoriesCache.java Normal file
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@ -0,0 +1,145 @@
/**
*
*/
package org.gcube.common.metadataprofilediscovery;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.TimeUnit;
import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategories;
import org.gcube.common.metadataprofilediscovery.reader.NamespaceCategoryReader;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.scope.impl.ScopeBean;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.cache.CacheBuilder;
import com.google.common.cache.CacheLoader;
import com.google.common.cache.LoadingCache;
import com.google.common.cache.RemovalListener;
import com.google.common.cache.RemovalNotification;
/**
* The Class NamespaceCategoriesCache.
*
* @author Francesco Mangiacrapa at ISTI-CNR francesco.mangiacrapa@isti.cnr.it
*
* Mar 3, 2022
*/
public class NamespaceCategoriesCache {
private static Logger LOG = LoggerFactory.getLogger(NamespaceCategoriesCache.class);
private static LoadingCache<String, NamespaceCategories> namespaces;
static {
CacheLoader<String, NamespaceCategories> loader = new CacheLoader<String, NamespaceCategories>() {
@Override
public NamespaceCategories load(String scope) throws Exception {
LOG.info("Loading the NamespaceCategories cache for scope: {}", scope);
NamespaceCategories namespacesCat = loadNamespaces(scope);
if (namespacesCat != null)
LOG.info("Returning {} for the scope name: {}", NamespaceCategories.class.getSimpleName(), scope);
else {
LOG.info("No NamespaceCategories obj for scope {}", scope);
}
return namespacesCat;
}
};
RemovalListener<String, NamespaceCategories> removalListener = new RemovalListener<String, NamespaceCategories>() {
@Override
public void onRemoval(RemovalNotification<String, NamespaceCategories> arg0) {
LOG.debug("cache expired");
}
};
namespaces = CacheBuilder.newBuilder().maximumSize(300).expireAfterWrite(30, TimeUnit.MINUTES)
.removalListener(removalListener).build(loader);
}
/**
* Populate the cache.
*
* @param scope the scope
*/
private static void populateTheCache(ScopeBean scope) {
String origScope = null;
String instScope = scope.toString();
try {
origScope = ScopeProvider.instance.get();
// Populating the cache by using the detachedres-library
ScopeProvider.instance.set(scope.toString());
LOG.info("Trying to populate the Namespaces cache in the scope: "+instScope);
NamespaceCategoryReader rd = new NamespaceCategoryReader(scope);
namespaces.put(instScope, rd.getNamespaces());
} catch (Exception e) {
// SILENT
} finally {
if (origScope != null && !origScope.equals(scope.toString())) {
// Setting original scope
ScopeProvider.instance.set(scope.toString());
}
}
}
/**
* Gets the VRE obj for input VRE name.
*
* @param scope the scope
* @return the vre
* @throws ExecutionException the execution exception
*/
public static NamespaceCategories get(String scope) throws ExecutionException {
try {
return namespaces.get(scope);
} catch (Exception e) {
LOG.info("Error on getting NamespaceCategories obj for scope {}. Is the key {} not found in the cache?",
scope, namespaces);
throw e;
}
}
/**
* Load VRE obj for VRE name.
*
* @param scope the scope
* @return the vre
*/
protected static NamespaceCategories loadNamespaces(String scope) {
NamespaceCategories namespacesCategories = namespaces.getIfPresent(scope);
// THIS CHECK SHOULD NOT BE NEEDED
if (namespacesCategories == null) {
LOG.info("loading Catalogue Namespaces for scope: {}",scope);
ScopeBean scopeB = new ScopeBean(scope);
populateTheCache(scopeB);
namespacesCategories = namespaces.getIfPresent(scope);
LOG.info("NamespaceCategories populated correclty with scope: {}",scope);
}else {
LOG.info("NamespaceCategories cache already populated with scope: {}, returning cached NamespaceCategories",scope);
}
return namespacesCategories;
}
/**
* Gets the cache.
*
* @return the cache
*/
public LoadingCache<String, NamespaceCategories> getCache() {
return namespaces;
}
}

92
src/main/java/org/gcube/common/metadataprofilediscovery/jaxb/MetadataField.java
View File

@ -15,17 +15,16 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import org.gcube.common.metadataprofilediscovery.Namespace;
import org.gcube.common.metadataprofilediscovery.adapter.DataTypeAdapter;
/**
* The Class MetadataField.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jun 8, 2016
* @author Francesco Mangiacrapa at ISTI-CNR francesco.mangiacrapa@isti.cnr.it
*
* Jun 20, 2022
*/
@XmlRootElement(name="metadatafield")
@XmlRootElement(name = "metadatafield")
@XmlAccessorType(XmlAccessType.FIELD)
public class MetadataField implements Serializable{
public class MetadataField implements Serializable {
/**
*
@ -37,22 +36,27 @@ public class MetadataField implements Serializable{
*/
private static final long serialVersionUID = 5935573474465015727L;
@XmlAttribute(name=LOCAL_NAME_CATEGORYREF)
private String categoryRef = null; //ITS VALUE IS A CATEGORY-ID
@XmlAttribute(name = LOCAL_NAME_CATEGORYREF)
private String categoryRef = null; // ITS VALUE IS A CATEGORY-ID
// optional Field used as fieldName in the (result) Document. If it absent, the
// mandatory fieldName is used
private String fieldId = null;
@XmlElement(required = true)
private String fieldName;
@XmlElement(required = true)
@XmlElement(required = true)
private Boolean mandatory = false;
@XmlElement(name = "maxOccurs")
@XmlElement(name = "maxOccurs")
private String maxOccurs;
// private Boolean isBoolean = false;
@XmlJavaTypeAdapter(DataTypeAdapter.class)
@XmlJavaTypeAdapter(DataTypeAdapter.class)
private DataType dataType = DataType.String;
private String defaultValue;
private String note;
//It's the list of eligible values;
// It's the list of eligible values;
@XmlElement(name = "vocabulary")
private MetadataVocabulary vocabulary;
@ -84,12 +88,11 @@ public class MetadataField implements Serializable{
this.mandatory = mandatory;
}
/**
* Instantiates a new metadata field.
*
* @param fieldName the field name
* @param mandatory the mandatory
* @param fieldName the field name
* @param mandatory the mandatory
* @param categoryID the category id
*/
public MetadataField(String fieldName, Boolean mandatory, String categoryID) {
@ -110,7 +113,6 @@ public class MetadataField implements Serializable{
return categoryRef;
}
/**
* Sets the category ref to category id.
*
@ -124,17 +126,37 @@ public class MetadataField implements Serializable{
/**
* Gets the category field qualified name.
*
* If the Metadata Field belongs to a category, returns the qualified name: {@link MetadataField#categoryRef} {@link Namespace#Separator}} fieldName;
* If the Metadata Field belongs to a category, returns the qualified name:
* {@link MetadataField#categoryRef} {@link Namespace#Separator}} fieldName;
* Otherwise returns the fieldName
*
* @return the category q name
*/
public String getCategoryFieldQName(){
public String getCategoryFieldQName() {
return categoryRef==null?fieldName:categoryRef+Namespace.Separator+fieldName;
return categoryRef == null ? fieldName : categoryRef + Namespace.Separator + fieldName;
}
/**
* Gets the field id.
*
* @return the field id
*/
public String getFieldId() {
return fieldId;
}
/**
* Sets the field id. Optional Field used as fieldName in the (result) Document.
* (e.g. JSON Document { fieldId: [data entry value]} If it absent, the
* mandatory fieldName is used
*
* @param fieldId the new field id
*/
public void setFieldId(String fieldId) {
this.fieldId = fieldId;
}
/**
* Gets the field name.
@ -146,7 +168,6 @@ public class MetadataField implements Serializable{
return fieldName;
}
/**
* Gets the mandatory.
*
@ -157,7 +178,6 @@ public class MetadataField implements Serializable{
return mandatory;
}
/**
* Gets the data type.
*
@ -168,7 +188,6 @@ public class MetadataField implements Serializable{
return dataType;
}
/**
* Gets the max occurs.
*
@ -179,8 +198,9 @@ public class MetadataField implements Serializable{
return maxOccurs;
}
/**
* Sets the max occurs.
*
* @param maxOccurs the maxOccurs to set
*/
public void setMaxOccurs(String maxOccurs) {
@ -198,7 +218,6 @@ public class MetadataField implements Serializable{
return defaultValue;
}
/**
* Gets the note.
*
@ -209,7 +228,6 @@ public class MetadataField implements Serializable{
return note;
}
/**
* Gets the vocabulary.
*
@ -220,7 +238,6 @@ public class MetadataField implements Serializable{
return vocabulary;
}
/**
* Gets the validator.
*
@ -231,7 +248,6 @@ public class MetadataField implements Serializable{
return validator;
}
/**
* Gets the tagging.
*
@ -242,7 +258,6 @@ public class MetadataField implements Serializable{
return tagging;
}
/**
* Gets the grouping.
*
@ -253,7 +268,6 @@ public class MetadataField implements Serializable{
return grouping;
}
/**
* Sets the field name.
*
@ -264,7 +278,6 @@ public class MetadataField implements Serializable{
this.fieldName = fieldName;
}
/**
* Sets the mandatory.
*
@ -275,7 +288,6 @@ public class MetadataField implements Serializable{
this.mandatory = mandatory;
}
/**
* Sets the data type.
*
@ -286,7 +298,6 @@ public class MetadataField implements Serializable{
this.dataType = dataType;
}
/**
* Sets the default value.
*
@ -297,7 +308,6 @@ public class MetadataField implements Serializable{
this.defaultValue = defaultValue;
}
/**
* Sets the note.
*
@ -308,7 +318,6 @@ public class MetadataField implements Serializable{
this.note = note;
}
/**
* Sets the vocabulary.
*
@ -319,7 +328,6 @@ public class MetadataField implements Serializable{
this.vocabulary = vocabulary;
}
/**
* Sets the validator.
*
@ -330,7 +338,6 @@ public class MetadataField implements Serializable{
this.validator = validator;
}
/**
* Sets the tagging.
*
@ -341,7 +348,6 @@ public class MetadataField implements Serializable{
this.tagging = tagging;
}
/**
* Sets the grouping.
*
@ -352,7 +358,14 @@ public class MetadataField implements Serializable{
this.grouping = grouping;
}
/* (non-Javadoc)
/**
* To string.
*
* @return the string
*/
/*
* (non-Javadoc)
*
* @see java.lang.Object#toString()
*/
@Override
@ -361,6 +374,8 @@ public class MetadataField implements Serializable{
StringBuilder builder = new StringBuilder();
builder.append("MetadataField [categoryRef=");
builder.append(categoryRef);
builder.append(", fieldId=");
builder.append(fieldId);
builder.append(", fieldName=");
builder.append(fieldName);
builder.append(", mandatory=");
@ -385,5 +400,4 @@ public class MetadataField implements Serializable{
return builder.toString();
}
}

12
src/main/java/org/gcube/common/metadataprofilediscovery/reader/MetadataFormatDiscovery.java
View File

@ -40,6 +40,7 @@ public class MetadataFormatDiscovery {
private String secondaryType;
private ScopeBean scope;
private List<MetadataProfile> metadataProfiles;
private String resourceName;
/**
@ -49,9 +50,10 @@ public class MetadataFormatDiscovery {
* @param secondaryType the secondary type
* @throws Exception the exception
*/
public MetadataFormatDiscovery(ScopeBean scope, String secondaryType) throws Exception {
public MetadataFormatDiscovery(ScopeBean scope, String secondaryType, String resourceName) throws Exception {
this.scope = scope;
this.secondaryType = secondaryType;
this.resourceName = resourceName;
this.metadataProfiles = readMetadataProfilesFromInfrastrucure();
}
@ -79,8 +81,12 @@ public class MetadataFormatDiscovery {
// ScopeProvider.instance.set(scopeString);
logger.info("Using scope from ScopeProvider: "+scopeString);
String queryString = QueryForResourceUtil.getGcubeGenericQueryStringForSecondaryType(secondaryType);
String queryString = null;
if(resourceName!=null)
queryString = QueryForResourceUtil.getGcubeGenericQueryStringForSecondaryTypeAndName(resourceName, secondaryType);
else
queryString = QueryForResourceUtil.getGcubeGenericQueryStringForSecondaryType(secondaryType);
logger.trace("queryString: " +queryString);
Query q = new QueryBox(queryString);

75
src/main/java/org/gcube/common/metadataprofilediscovery/reader/NamespaceCategoryReader.java
View File

@ -8,12 +8,21 @@ import static org.gcube.resources.discovery.icclient.ICFactory.client;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.List;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathFactory;
import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategories;
import org.gcube.common.resources.gcore.utils.XPathHelper;
@ -23,7 +32,9 @@ import org.gcube.resources.discovery.client.queries.api.Query;
import org.gcube.resources.discovery.client.queries.impl.QueryBox;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
@ -35,6 +46,8 @@ import org.xml.sax.InputSource;
*/
public class NamespaceCategoryReader {
private static final String PATH_RESOURCE_PROFILE_BODY_NAMESPACES = "/Resource/Profile/Body/namespaces";
private static Logger logger = LoggerFactory.getLogger(NamespaceCategoryReader.class);
private static final String GENERIC_RESOURCE_NAMESPACES_NAME = "Namespaces Catalogue Categories";
@ -89,12 +102,11 @@ public class NamespaceCategoryReader {
String theResource = null;
try{
theResource = appProfile.get(0);
logger.debug("Resource (Namespaces Catalogue Categories) found");
logger.debug("Resource "+GENERIC_RESOURCE_NAMESPACES_NAME+" found");
logger.trace("Resource "+GENERIC_RESOURCE_NAMESPACES_NAME+" is: "+theResource);
DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Node node = docBuilder.parse(new InputSource(new StringReader(theResource))).getDocumentElement();
XPathHelper helper = new XPathHelper(node);
logger.debug("Unmarshalling it..");
readNamespaceCategoryFromResource(helper);
Document xmlDocument = docBuilder.parse(new InputSource(new StringReader(theResource)));
readNamespaceCategoryFromResource(xmlDocument);
}catch(Exception e){
logger.error("Error while parsing Resource "+theResource+" from the infrastructure, the scope is "+scopeString,e);
}
@ -109,6 +121,52 @@ public class NamespaceCategoryReader {
}
}
/**
* Read namespace category from resource.
*
* @param helper the helper
* @throws Exception the exception
*/
private void readNamespaceCategoryFromResource(Document xmlDocument) throws Exception{
try {
XPath xPath = XPathFactory.newInstance().newXPath();
String expression = PATH_RESOURCE_PROFILE_BODY_NAMESPACES;
NodeList nodeList = (NodeList) xPath.compile(expression).evaluate(xmlDocument, XPathConstants.NODESET);
String namespaceSources = getNodeString(nodeList.item(0));
JAXBContext jaxbContext = JAXBContext.newInstance(NamespaceCategories.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
if(namespaceSources==null || namespaceSources.length()==0){
throw new Exception("Resource does not contain <namespaces> <namespace>...</namespace> </namespaces> in the body");
}
logger.debug("Unmarshalling document path "+PATH_RESOURCE_PROFILE_BODY_NAMESPACES +" to "+NamespaceCategories.class.getSimpleName());
InputStream stream = new ByteArrayInputStream(namespaceSources.getBytes());
namespaces = (NamespaceCategories) jaxbUnmarshaller.unmarshal(stream);
}catch(Exception e){
String error = "An error occurred in readNamespaceCategoryFromResource " + e.getMessage();
logger.error("An error occurred in readNamespaceCategoryFromResource ", e);
throw new Exception(error);
}
}
private String getNodeString(Node node) {
try {
StringWriter writer = new StringWriter();
Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.transform(new DOMSource(node), new StreamResult(writer));
String output = writer.toString();
return output;
} catch (TransformerException e) {
e.printStackTrace();
}
return node.getTextContent();
}
/**
* Read namespace category from resource.
@ -119,8 +177,13 @@ public class NamespaceCategoryReader {
private void readNamespaceCategoryFromResource(XPathHelper helper) throws Exception{
try {
if(helper==null) {
logger.warn("**************************\n\nXpathHelper is null!!!!\n\n");
}
List<String> namespaceSources = helper.evaluate("/Resource/Profile/Body/namespaces");
List<String> namespaceSources = helper.evaluate(PATH_RESOURCE_PROFILE_BODY_NAMESPACES);
JAXBContext jaxbContext = JAXBContext.newInstance(NamespaceCategories.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();

6
src/test/java/org/gcube/common/metadataprofilediscovery/TestDataCatalogueMetadataFormatReader.java
View File

@ -29,7 +29,7 @@ public class TestDataCatalogueMetadataFormatReader {
* Test.
* @throws Exception
*/
@Test
//@Test
public void test() throws Exception {
@ -45,7 +45,7 @@ public class TestDataCatalogueMetadataFormatReader {
List<NamespaceCategory> categs = reader.getListOfNamespaceCategories();
for (NamespaceCategory namespaceCategory : categs) {
logger.trace("\n\n "+ ++i +".) Category: "+namespaceCategory);
logger.info("\n\n "+ ++i +".) Category: "+namespaceCategory);
}
i = 0;
@ -55,7 +55,7 @@ public class TestDataCatalogueMetadataFormatReader {
continue;
MetadataFormat metadataFormat = reader.getMetadataFormatForMetadataProfile(mt);
logger.trace("\n\n "+ ++i +".) Metadata source: "+metadataFormat.getMetadataSource().substring(0, 100));
logger.info("\n\n "+ ++i +".) Metadata source: "+metadataFormat.getMetadataSource().substring(0, 100));
}
}

22
src/test/java/org/gcube/common/metadataprofilediscovery/TestMetadataFormatDiscovery.java
View File

@ -4,6 +4,8 @@
package org.gcube.common.metadataprofilediscovery;
import org.gcube.common.metadataprofilediscovery.bean.MetadataProfile;
import org.gcube.common.metadataprofilediscovery.jaxb.MetadataField;
import org.gcube.common.metadataprofilediscovery.jaxb.MetadataFormat;
import org.gcube.common.metadataprofilediscovery.reader.MetadataFormatDiscovery;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.scope.impl.ScopeBean;
@ -25,16 +27,32 @@ public class TestMetadataFormatDiscovery {
String scopeString = "/gcube/devsec/devVRE";
String grMetadataProfileSecondaryType = "DataCatalogueMetadata";
grMetadataProfileSecondaryType = "GeoNaMetadata";
final ScopeBean scope = new ScopeBean(scopeString);
MetadataFormatDiscovery reader;
try {
ScopeProvider.instance.set(scopeString);
reader = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType);
reader = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType, null);
//System.out.println(reader.getMetadataProfiles());
for (MetadataProfile metaProfile : reader.getMetadataProfiles()) {
System.out.println(metaProfile.getId() +", name: "+metaProfile.getName() +", type: "+metaProfile.getMetadataType());
System.out.println("\n\n###" + metaProfile.getId() +", name: "+metaProfile.getName() +", type: "+metaProfile.getMetadataType());
MetadataProfileReader readerProfile = new MetadataProfileReader(grMetadataProfileSecondaryType, metaProfile.getName());
MetadataFormat format = readerProfile.getMetadataFormatForMetadataProfile(metaProfile);
int i = 0;
try {
for (MetadataField field : format.getMetadataFields()) {
System.out.println("\t"+ ++i +") "+field);
}
}catch (Exception e) {
System.err.println("\t## Error occurred reading: " + metaProfile.getId() +", name: "+metaProfile.getName() +", type: "+metaProfile.getMetadataType());
e.printStackTrace();
}
}
} catch (Exception e) {
e.printStackTrace();

17
src/test/java/org/gcube/common/metadataprofilediscovery/TestMetadataFormatReader.java
View File

@ -11,11 +11,9 @@ import org.gcube.common.metadataprofilediscovery.reader.MetadataFormatReader;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.scope.impl.ScopeBean;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jun 8, 2016
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it Jun 8, 2016
*/
public class TestMetadataFormatReader {
@ -23,7 +21,7 @@ public class TestMetadataFormatReader {
public void test() {
String scopeString = "/gcube/devsec/devVRE";
final ScopeBean scope = new ScopeBean(scopeString);
final ScopeBean scope = new ScopeBean(scopeString);
MetadataFormatReader reader;
try {
ScopeProvider.instance.set(scopeString);
@ -33,16 +31,17 @@ public class TestMetadataFormatReader {
e.printStackTrace();
}
}
//@Test
// @Test
public void testReadInputStream() {
String fileNameMeatadataProfile = "HarvestedObject.xml";
try {
InputStream in = ClassLoader.getSystemResourceAsStream(fileNameMeatadataProfile);
//InputStream in = TestMetadataFormatReader.class.getResourceAsStream(fileNameMeatadataProfile);
// InputStream in =
// TestMetadataFormatReader.class.getResourceAsStream(fileNameMeatadataProfile);
MetadataFormat mf = MetadataProfileReader.toMetadataFormat(in);
System.out.println("Source: "+mf.getMetadataSource());
System.out.println("Source: " + mf.getMetadataSource());
for (MetadataField field : mf.getMetadataFields()) {
System.out.println(field);
}

48
src/test/java/org/gcube/common/metadataprofilediscovery/TestMetadataProfileReader.java Normal file
View File

@ -0,0 +1,48 @@
/**
*
*/
package org.gcube.common.metadataprofilediscovery;
import org.gcube.common.metadataprofilediscovery.bean.MetadataProfile;
import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategory;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.scope.impl.ScopeBean;
import org.junit.Test;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it Jun 8, 2016
*/
public class TestMetadataProfileReader {
//@Test
public void test() {
String scopeString = "/gcube/devsec/devVRE";
final ScopeBean scope = new ScopeBean(scopeString);
String[] genericResourceNames = new String[] {"Informazioni_di_progetto","Relazione_di_Scavo"};
for (int i = 0; i < 2; i++) {
MetadataProfileReader reader;
try {
ScopeProvider.instance.set(scope.toString());
reader = new MetadataProfileReader("GeoNaMetadata",genericResourceNames[i]);
int j = 0;
for (MetadataProfile metadataProfile : reader.getListOfMetadataProfiles()) {
System.out.println(j++ + ")" + metadataProfile);
}
j = 0;
for (NamespaceCategory namespaceCategory : reader.getListOfNamespaceCategories()) {
System.out.println(j++ + ")" + namespaceCategory);
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
}