gCubeSystem
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metadata-profile-discovery
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Refactored and added method 'toMetadataFormat'

This commit is contained in:
Francesco Mangiacrapa 2020-09-30 14:10:09 +02:00
parent e0671579da
commit a6d91a4b7d
9 changed files with 119 additions and 46 deletions
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12
.classpath
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@ -6,7 +6,17 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" path="src/main/resources"/>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="test" value="true"/>

2
.settings/org.eclipse.core.resources.prefs
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@ -1,4 +1,6 @@
eclipse.preferences.version=1
encoding//src/main/java=UTF-8
encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
encoding//src/test/resources=UTF-8
encoding/<project>=UTF-8

4
README.md
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@ -2,9 +2,9 @@
The metadata-profile-discovery library is able to build java objects parsing the 'gCube Metadata Profiles' models:
- defined in the contexts (scopes) of the D4Science Infrastructure;
* defined in the contexts (scopes) of the D4Science Infrastructure;
- passed as an input stream;
* passed as an input stream;
## Built With

4
src/main/java/org/gcube/common/metadataprofilediscovery/DataCatalogueMetadataDiscovery.java → src/main/java/org/gcube/common/metadataprofilediscovery/MetadataProfileDiscovery.java
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@ -11,13 +11,13 @@ import org.gcube.common.metadataprofilediscovery.jaxb.NamespaceCategory;
/**
* The Interface DataCatalogueMetadataDiscovery.
* The Interface MetadataProfileDiscovery.
*
* @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
*
* Sep 30, 2020
*/
public interface DataCatalogueMetadataDiscovery {
public interface MetadataProfileDiscovery {
/**
* Gets the list of metadata types.

111
src/main/java/org/gcube/common/metadataprofilediscovery/DataCalogueMetadataFormatReader.java → src/main/java/org/gcube/common/metadataprofilediscovery/MetadataProfileReader.java
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@ -13,6 +13,9 @@ import java.util.Map;
import java.util.stream.Collectors;
import javax.xml.XMLConstants;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
@ -37,12 +40,17 @@ import org.w3c.dom.Document;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
/**
* The Class DataCalogueMetadataReader.
* The Class MetadataProfileReader.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it Jun 8, 2016
* @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
*
* Sep 30, 2020
*/
public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDiscovery {
public class MetadataProfileReader implements MetadataProfileDiscovery {
public static final String URL_OF_GCDCMETADATAPROFILEV3_XSD = "https://wiki.gcube-system.org/images_gcube/e/e8/Gcdcmetadataprofilev3.xsd";
private static String SCHEMA_FILENAME = "Gdcmetadataprofilev3.xsd";
@ -53,15 +61,24 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
private String profileSchema = null;
private static Logger logger = LoggerFactory.getLogger(DataCalogueMetadataFormatReader.class);
private String grMetadataProfileSecondaryType;
private static Logger logger = LoggerFactory.getLogger(MetadataProfileReader.class);
/**
* Instantiates a new data calogue metadata format reader.
* Instantiates a new metadata profile reader.
*
* @param grMetadataProfileSecondaryType the SecondaryType that must be used to discover the "gCube Metadata Profiles" from Information System
* @throws Exception the exception
*/
public DataCalogueMetadataFormatReader() throws Exception {
public MetadataProfileReader(String grMetadataProfileSecondaryType) throws Exception {
if(grMetadataProfileSecondaryType==null || grMetadataProfileSecondaryType.isEmpty())
throw new NullPointerException("Invalid input parameter");
this.grMetadataProfileSecondaryType = grMetadataProfileSecondaryType;
String scopeString = ScopeProvider.instance.get();
logger.debug("Read scope " + scopeString + " from ScopeProvider");
@ -70,28 +87,32 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
scope = new ScopeBean(scopeString);
readNamespaces();
readMetadaFormats();
readMetadataFormats();
}
/**
* Read metada formats.
*
* @throws Exception the exception
*/
private void readMetadaFormats() throws Exception {
medataFormatDiscovery = new MetadataFormatDiscovery(scope);
logger.info("MedataFormatDiscovery has retrieved: " + medataFormatDiscovery.getMetadataProfiles().size()
+ " metadata type/s");
logger.debug("filling cache for MedataFormat");
hashMetadataFormats = new HashMap<String, MetadataFormat>(medataFormatDiscovery.getMetadataProfiles().size());
for (MetadataProfile mT : medataFormatDiscovery.getMetadataProfiles()) {
if (mT == null)
continue;
MetadataFormatReader reader = new MetadataFormatReader(scope, mT.getId());
hashMetadataFormats.put(mT.getId(), reader.getMetadataFormat());
logger.debug("MetadataType id: " + mT.getId() + " cached as: " + reader.getMetadataFormat());
private void readMetadataFormats() throws Exception {
//reading from Generic Resource for Secondary Type
if(grMetadataProfileSecondaryType!=null) {
medataFormatDiscovery = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType);
logger.info("MedataFormatDiscovery has retrieved: " + medataFormatDiscovery.getMetadataProfiles().size()
+ " metadata type/s");
logger.debug("filling cache for MedataFormat");
hashMetadataFormats = new HashMap<String, MetadataFormat>(medataFormatDiscovery.getMetadataProfiles().size());
for (MetadataProfile mT : medataFormatDiscovery.getMetadataProfiles()) {
if (mT == null)
continue;
MetadataFormatReader reader = new MetadataFormatReader(scope, mT.getId());
hashMetadataFormats.put(mT.getId(), reader.getMetadataFormat());
logger.debug("MetadataType id: " + mT.getId() + " cached as: " + reader.getMetadataFormat());
}
}
}
@ -120,7 +141,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
* @return the profile schema string
*/
public static String getProfileSchemaString() {
InputStream inputStream = DataCalogueMetadataFormatReader.getProfileSchemaInputStream();
InputStream inputStream = MetadataProfileReader.getProfileSchemaInputStream();
return new BufferedReader(new InputStreamReader(inputStream)).lines().collect(Collectors.joining("\n"));
}
@ -130,7 +151,15 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
* @return the profile schema input stream
*/
public static InputStream getProfileSchemaInputStream() {
return DataCalogueMetadataFormatReader.class.getResourceAsStream(SCHEMA_FILENAME);
try {
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.info("Returning local resource: "+SCHEMA_FILENAME);
return MetadataProfileReader.class.getResourceAsStream(SCHEMA_FILENAME);
}
/**
@ -139,7 +168,15 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
* @return the profile schema URL
*/
public static URL getProfileSchemaURL() {
return DataCalogueMetadataFormatReader.class.getResource(SCHEMA_FILENAME);
try {
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.info("Returning local URL of: "+SCHEMA_FILENAME);
return MetadataProfileReader.class.getResource(SCHEMA_FILENAME);
}
/**
@ -198,7 +235,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
public List<MetadataProfile> getListOfMetadataProfiles() throws Exception {
if (medataFormatDiscovery == null)
readMetadaFormats();
readMetadataFormats();
return medataFormatDiscovery.getMetadataProfiles();
}
@ -252,7 +289,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
*/
public String getProfileSchema() {
if (profileSchema == null) {
profileSchema = DataCalogueMetadataFormatReader.getProfileSchemaString();
profileSchema = MetadataProfileReader.getProfileSchemaString();
}
return profileSchema;
@ -271,5 +308,23 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
DOMSource source = new DOMSource(doc);
validateAgainstXSD(source, getProfileSchemaURL());
}
/**
* 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 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);
}
}

19
src/main/java/org/gcube/common/metadataprofilediscovery/reader/MetadataFormatDiscovery.java
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@ -28,28 +28,30 @@ import org.xml.sax.InputSource;
/**
* The Class MedataFormatDiscovery.
* The Class MetadataFormatDiscovery.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jun 8, 2016
* @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
*
* Sep 30, 2020
*/
public class MetadataFormatDiscovery {
private static Logger logger = LoggerFactory.getLogger(MetadataFormatDiscovery.class);
public static final String DATA_CATALOGUE_METADATA_SECONDARY_TYPE = "DataCatalogueMetadata";
private String secondaryType;
private ScopeBean scope;
private List<MetadataProfile> metadataProfiles;
/**
* Instantiates a new medata format reader.
* Instantiates a new metadata format discovery.
*
* @param scope - the scope to be searched
* @param scope the scope
* @param secondaryType the secondary type
* @throws Exception the exception
*/
public MetadataFormatDiscovery(ScopeBean scope) throws Exception {
public MetadataFormatDiscovery(ScopeBean scope, String secondaryType) throws Exception {
this.scope = scope;
this.secondaryType = DATA_CATALOGUE_METADATA_SECONDARY_TYPE;
this.secondaryType = secondaryType;
this.metadataProfiles = readMetadataProfilesFromInfrastrucure();
}
@ -115,6 +117,7 @@ public class MetadataFormatDiscovery {
/**
* Gets the metadata type from resource.
*
* @param doc the doc
* @param helper the helper
* @return the metadata type from resource
* @throws MetadataProfileNotFoundException the application profile not found exception

1
src/test/.gitignore vendored Normal file
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@ -0,0 +1 @@
/resources/

7
src/test/java/org/gcube/common/metadataprofilediscovery/TestDataCatalogueMetadataFormatReader.java
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@ -28,12 +28,13 @@ public class TestDataCatalogueMetadataFormatReader {
/**
* Test.
*/
// @Test
@Test
public void test() {
try {
String scopeString = "/gcube/devsec/devVRE";
String grMetadataProfileSecondaryType = "DataCatalogueMetadata";
ScopeProvider.instance.set(scopeString);
DataCalogueMetadataFormatReader reader = new DataCalogueMetadataFormatReader();
MetadataProfileReader reader = new MetadataProfileReader(grMetadataProfileSecondaryType);
int i = 0;
List<NamespaceCategory> categs = reader.getListOfNamespaceCategories();
@ -63,7 +64,7 @@ public class TestDataCatalogueMetadataFormatReader {
// @Test
public void validateAgainstProfileSchema() throws Exception {
InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(PROFILE_EXAMPLE_FILENAME);
DataCalogueMetadataFormatReader.validateProfile(inputStream);
MetadataProfileReader.validateProfile(inputStream);
}
}

5
src/test/java/org/gcube/common/metadataprofilediscovery/TestMetadataFormatDiscovery.java
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@ -21,15 +21,16 @@ public class TestMetadataFormatDiscovery {
/**
* Test.
*/
// @Test
@Test
public void test() {
String scopeString = "/gcube/devsec/devVRE";
String grMetadataProfileSecondaryType = "DataCatalogueMetadata";
final ScopeBean scope = new ScopeBean(scopeString);
MetadataFormatDiscovery reader;
try {
ScopeProvider.instance.set(scopeString);
reader = new MetadataFormatDiscovery(scope);
reader = new MetadataFormatDiscovery(scope, grMetadataProfileSecondaryType);
//System.out.println(reader.getMetadataProfiles());
for (MetadataProfile metaProfile : reader.getMetadataProfiles()) {