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gcubedatacatalogue-metadata-discovery
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Working on #8267 

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/gcubedatacatalogue-metadata-discovery@147200 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Francesco Mangiacrapa 2017-04-26 16:18:32 +00:00
parent 83d0640800
commit 05972d72c3
18 changed files with 591 additions and 153 deletions
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19
NamespacesCatalogueCategories.xml Normal file
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@ -0,0 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<namespaces xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="NamespacesCatalogueCategories.xsd">
<namespace id="contact">
<name>Contact</name>
<title>Contact Title</title>
<description>This section is about Contact(s)</description>
</namespace>
<namespace id="developer_information">
<name>Developer</name>
<title>Developer Information</title>
<description>This section is about Developer(s)</description>
</namespace>
<namespace id="extra_information">
<name>Extra Information</name>
<title>Extras</title>
<description>This section is about Extra(s)</description>
</namespace>
</namespaces>

19
NamespacesCatalogueCategories.xsd Normal file
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@ -0,0 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="namespaces">
<xs:complexType>
<xs:sequence>
<xs:element name="namespace" minOccurs="1" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
<xs:element type="xs:string" name="name" minOccurs="1" maxOccurs="1"/>
<xs:element type="xs:string" name="title" minOccurs="1" maxOccurs="1"/>
<xs:element type="xs:string" name="description" minOccurs="0" maxOccurs="1"/>
</xs:sequence>
<xs:attribute type="xs:ID" name="id" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>

4
distro/changelog.xml
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@ -1,7 +1,9 @@
<ReleaseNotes>
<Changeset
component="org.gcube.data-catalogue.gcubedatacatalogue-metadata-discovery.3-0-0"
date="2017-03-21">
date="2017-04-26">
<Change>[Task #8267] Medatada Discovery Library: definition of namespaces and metadata fields must be separated
</Change>
<Change>[Task #7616] Porting library to Metadata Profile model v3.0
</Change>
</Changeset>

69
src/main/java/org/gcube/datacatalogue/metadatadiscovery/DataCalogueMetadataFormatReader.java
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@ -1,5 +1,6 @@
package org.gcube.datacatalogue.metadatadiscovery;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@ -8,8 +9,10 @@ import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.scope.impl.ScopeBean;
import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategory;
import org.gcube.datacatalogue.metadatadiscovery.reader.MetadataFormatDiscovery;
import org.gcube.datacatalogue.metadatadiscovery.reader.MetadataFormatReader;
import org.gcube.datacatalogue.metadatadiscovery.reader.NamespaceCategoryReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -24,8 +27,9 @@ import org.slf4j.LoggerFactory;
public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDiscovery{
private MetadataFormatDiscovery medataFormatDiscovery;
private final ScopeBean scope;
private Map<String, MetadataFormat> hash = new HashMap<String, MetadataFormat>();
private ScopeBean scope;
private Map<String, MetadataFormat> hashMetadataFormats = new HashMap<String, MetadataFormat>();
private List<NamespaceCategory> namespaceCategories = new ArrayList<NamespaceCategory>();
private static Logger logger = LoggerFactory.getLogger(DataCalogueMetadataFormatReader.class);
@ -37,12 +41,24 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
public DataCalogueMetadataFormatReader() throws Exception {
String scopeString = ScopeProvider.instance.get();
logger.debug("DataCalogueMetadataFormatReader read scope "+scopeString +" from ScopeProvider");
logger.debug("Read scope "+scopeString +" from ScopeProvider");
if(scopeString==null || scopeString.isEmpty())
throw new Exception("Please set a valid scope into ScopeProvider");
scope = new ScopeBean(scopeString);
//readMetadaFormats();
readNamespaces();
}
/**
* 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");
@ -51,18 +67,25 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
continue;
MetadataFormatReader reader = new MetadataFormatReader(scope, mT.getId());
hash.put(mT.getId(), reader.getMetadataFormat());
hashMetadataFormats.put(mT.getId(), reader.getMetadataFormat());
logger.debug("MetadataType id: "+mT.getId() +" cached as: "+reader.getMetadataFormat());
}
}
/* (non-Javadoc)
* @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getListOfMetadataTypes()
*/
@Override
public List<MetadataProfile> getListOfMetadataProfiles() throws Exception {
return medataFormatDiscovery.getMetadataProfiles();
/**
* Read namespaces.
*/
private void readNamespaces() {
try{
if(namespaceCategories == null || namespaceCategories.isEmpty()){
NamespaceCategoryReader rd = new NamespaceCategoryReader(scope, NamespaceCategoryReader.NamespacesCatalogueCategoriesResourceID());
namespaceCategories.addAll(rd.getNamespaces().getNamespaceCategories());
}
}catch(Exception e){
logger.debug("An error occurred during read namespaces for categories: ", e);
}
}
/* (non-Javadoc)
@ -74,7 +97,7 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
if(profile==null)
throw new Exception("Input "+ MetadataProfile.class.getSimpleName() + " is null");
MetadataFormat format = hash.get(profile.getId());
MetadataFormat format = hashMetadataFormats.get(profile.getId());
if(format!=null)
return format;
@ -82,4 +105,28 @@ public class DataCalogueMetadataFormatReader implements DataCatalogueMetadataDis
return reader.getMetadataFormat();
}
/* (non-Javadoc)
* @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getListOfMetadataTypes()
*/
@Override
public List<MetadataProfile> getListOfMetadataProfiles() throws Exception {
if(medataFormatDiscovery==null)
readMetadaFormats();
return medataFormatDiscovery.getMetadataProfiles();
}
/* (non-Javadoc)
* @see org.gcube.datacatalogue.metadatadiscovery.DataCatalogueMetadataDiscovery#getListOfNamespaceCategories()
*/
@Override
public List<NamespaceCategory> getListOfNamespaceCategories() throws Exception {
if(namespaceCategories == null)
readNamespaces();
return namespaceCategories;
}
}

11
src/main/java/org/gcube/datacatalogue/metadatadiscovery/DataCatalogueMetadataDiscovery.java
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@ -7,6 +7,7 @@ import java.util.List;
import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategory;
@ -29,6 +30,16 @@ public interface DataCatalogueMetadataDiscovery {
List<MetadataProfile> getListOfMetadataProfiles() throws Exception;
/**
* Gets the list of namespace categories.
*
* @return the list of namespace categories
* @throws Exception the exception
*/
List<NamespaceCategory> getListOfNamespaceCategories() throws Exception;
/**
* Gets the metadata format for metadata type.
*

10
src/main/java/org/gcube/datacatalogue/metadatadiscovery/MetadataNamespace.java → src/main/java/org/gcube/datacatalogue/metadatadiscovery/Namespace.java
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@ -3,13 +3,17 @@
*/
package org.gcube.datacatalogue.metadatadiscovery;
/**
* The Interface Namespace.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Mar 23, 2017
* Apr 26, 2017
*/
public interface MetadataNamespace {
public interface Namespace {
public static final String Separator = ":";
public String id = null;
public String name = null;
public String title = null;
public String description = "";
}

8
src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/MetadataField.java
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@ -13,7 +13,7 @@ import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import org.gcube.datacatalogue.metadatadiscovery.MetadataNamespace;
import org.gcube.datacatalogue.metadatadiscovery.Namespace;
import org.gcube.datacatalogue.metadatadiscovery.adapter.DataTypeAdapter;
@ -115,7 +115,7 @@ public class MetadataField implements Serializable{
*/
private void setNamespaceFieldToCategoryRef() {
this.namespaceFieldToCategoryReference = LOCAL_NAME_CATEGORYREF+MetadataNamespace.Separator+categoryRef;
this.namespaceFieldToCategoryReference = LOCAL_NAME_CATEGORYREF+Namespace.Separator+categoryRef;
}
@ -146,7 +146,7 @@ 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#LOCAL_NAME_CATEGORYREF} {@link MetadataNamespace#Separator}} fieldName;
* If the Metadata Field belongs to a category returns the qualified name: {@link MetadataField#LOCAL_NAME_CATEGORYREF} {@link Namespace#Separator}} fieldName;
* Otherwise returns the fieldName
*
* @return the category q name
@ -154,7 +154,7 @@ public class MetadataField implements Serializable{
public String getCategoryFieldQName(){
initNamespaceFieldToCategoryReference();
return namespaceFieldToCategoryReference==null?fieldName:namespaceFieldToCategoryReference+MetadataNamespace.Separator+fieldName;
return namespaceFieldToCategoryReference==null?fieldName:namespaceFieldToCategoryReference+Namespace.Separator+fieldName;
}

55
src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/MetadataFormat.java
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@ -31,25 +31,22 @@ public class MetadataFormat implements Serializable{
*/
private static final long serialVersionUID = -5881074882343424963L;
public static final String LOCAL_NAME_METADATA_TYPE = "metadatatype";
public static final String LOCAL_NAME_METADATA_TYPE = "type";
public static final String LOCAL_NAME_METADATA_FORMAT = "metadataformat";
/**
* Instantiates a new metadata format.
*/
public MetadataFormat() {
}
@XmlElement(name = "metadatacategory")
private List<MetadataCategory> metadataCategories;
@XmlElement(name = "metadatafield")
private List<MetadataField> metadataFields;
@XmlAttribute(name = LOCAL_NAME_METADATA_TYPE, required=true)
private String metadataType = "";
private String type = "";
@XmlTransient
private String metadataSource = null;
@ -65,25 +62,27 @@ public class MetadataFormat implements Serializable{
return metadataFields;
}
/**
* Gets the metadata type.
*
* @return the metadataType
*/
public String getMetadataType() {
return metadataType;
/**
* Gets the type.
*
* @return the type
*/
public String getType() {
return type;
}
/**
* Gets the metadata categories.
* Sets the type.
*
* @return the metadataCategories
* @param type the type to set
*/
public List<MetadataCategory> getMetadataCategories() {
public void setType(String type) {
return metadataCategories;
this.type = type;
}
/**
@ -122,18 +121,6 @@ public class MetadataFormat implements Serializable{
/**
* Adds the category.
*
* @param metadataCategory the metadata category
*/
public void addCategory(MetadataCategory metadataCategory){
if(this.metadataCategories==null)
this.metadataCategories = new ArrayList<MetadataCategory>();
this.metadataCategories.add(metadataCategory);
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@ -141,12 +128,12 @@ public class MetadataFormat implements Serializable{
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("MetadataFormat [metadataCategories=");
builder.append(metadataCategories);
builder.append(", metadataFields=");
builder.append("MetadataFormat [metadataFields=");
builder.append(metadataFields);
builder.append(", metadataType=");
builder.append(metadataType);
builder.append(", type=");
builder.append(type);
builder.append(", metadataSource=");
builder.append(metadataSource);
builder.append("]");
return builder.toString();
}

80
src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/NamespaceCategories.java Normal file
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@ -0,0 +1,80 @@
/**
*
*/
package org.gcube.datacatalogue.metadatadiscovery.bean.jaxb;
import java.util.List;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
/**
* The Class NamespaceCategories.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Apr 26, 2017
*/
@XmlRootElement(name="namespaces")
@XmlAccessorType(XmlAccessType.FIELD)
public class NamespaceCategories {
@XmlElement(name = "namespace")
private List<NamespaceCategory> namespaceCategories;
/**
* Instantiates a new namespace categories.
*/
public NamespaceCategories() {
}
/**
* @param namespaceCategories
*/
public NamespaceCategories(List<NamespaceCategory> namespaceCategories) {
this.namespaceCategories = namespaceCategories;
}
/**
* @return the namespaceCategories
*/
public List<NamespaceCategory> getNamespaceCategories() {
return namespaceCategories;
}
/**
* @param namespaceCategories the namespaceCategories to set
*/
public void setNamespaceCategories(List<NamespaceCategory> namespaceCategories) {
this.namespaceCategories = namespaceCategories;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("NamespaceCategories [namespaceCategories=");
builder.append(namespaceCategories);
builder.append("]");
return builder.toString();
}
}

97
src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/MetadataCategory.java → src/main/java/org/gcube/datacatalogue/metadatadiscovery/bean/jaxb/NamespaceCategory.java
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@ -10,73 +10,72 @@ import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlTransient;
import org.gcube.datacatalogue.metadatadiscovery.MetadataNamespace;
import org.gcube.datacatalogue.metadatadiscovery.Namespace;
/**
* The Class MetadataCategory.
* The Class Namespace.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Mar 21, 2017
* Apr 26, 2017
*/
@XmlRootElement(name = "metadatacategory")
@XmlRootElement(name = "namespace")
@XmlAccessorType (XmlAccessType.FIELD)
public class MetadataCategory implements Serializable{
public class NamespaceCategory implements Namespace, Serializable{
/**
*
*/
private static final String NAME_ELEMENT_METADATACATEGORY = "metadatacategory";
/**
*
*/
private static final long serialVersionUID = -7282676787740920115L;
/** The Constant serialVersionUID. */
private static final long serialVersionUID = -1632300992065668875L;
@XmlAttribute(required = true)
private String id = null;
@XmlElement(required = true)
private String title = "";
private String name = null;
private String description = null;
@XmlElement(required = true)
private String title = null;
@XmlTransient
private String namespaceCategory = NAME_ELEMENT_METADATACATEGORY;
private String description = "";
/**
* Instantiates a new metadata category.
* Instantiates a new namespace category.
*/
public MetadataCategory() {
public NamespaceCategory() {
}
/**
* Instantiates a new metadata category.
*
* @param id the id
* @param title the title
*/
public MetadataCategory(String id, String title) {
super();
setId(id);
this.title = title;
}
/**
* Instantiates a new metadata category.
* Instantiates a new namespace category.
*
* @param id the id
* @param name the name
* @param title the title
* @param description the description
*/
public MetadataCategory(String id, String title, String description) {
public NamespaceCategory(String id, String name, String title) {
super();
this.id = id;
this.name = name;
this.title = title;
}
/**
* Instantiates a new namespace category.
*
* @param id the id
* @param name the name
* @param title the title
* @param description the description
*/
public NamespaceCategory(String id, String name, String title, String description) {
super();
this.id = id;
this.name = name;
this.title = title;
this.description = description;
}
@ -126,14 +125,12 @@ public class MetadataCategory implements Serializable{
/**
* Gets the category qualifier name. The QName is a unique name to identify the category.
* It is the identifier: {@link MetadataCategory#namespaceCategory} + {@link MetadataNamespace#Separator} + {@link MetadataCategory#id}
*
* @return the category q name
* Gets the namespace category qualifier name. The QName is a unique name to identify the category. It corresponds to {@link NamespaceCategory#id}
* @return the namespace category q name
*/
public String getCategoryQName(){
public String getNamespaceCategoryQName(){
return namespaceCategory+MetadataNamespace.Separator+id;
return id;
}
@ -159,16 +156,6 @@ public class MetadataCategory implements Serializable{
}
/**
* Gets the namespace category.
*
* @return the namespace category
*/
public String getNamespaceCategory() {
return namespaceCategory;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
@ -177,18 +164,16 @@ public class MetadataCategory implements Serializable{
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("MetadataCategory [id=");
builder.append("NamespaceCategory [id=");
builder.append(id);
builder.append(", name=");
builder.append(name);
builder.append(", title=");
builder.append(title);
builder.append(", description=");
builder.append(description);
builder.append(", namespaceCategory=");
builder.append(namespaceCategory);
builder.append("]");
return builder.toString();
}
}

17
src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/MetadataFormatDiscovery.java
View File

@ -78,7 +78,7 @@ public class MetadataFormatDiscovery {
// ScopeProvider.instance.set(scopeString);
logger.info("Using scope from ScopeProvider: "+scopeString);
String queryString = getGcubeGenericQueryString(secondaryType);
String queryString = QueryForResourceUtil.getGcubeGenericQueryStringForSecondaryType(secondaryType);
logger.trace("queryString: " +queryString);
Query q = new QueryBox(queryString);
@ -121,11 +121,9 @@ public class MetadataFormatDiscovery {
*/
private MetadataProfile getMetadataProfileFromResource(Document doc, XPathHelper helper) throws MetadataProfileNotFoundException{
try {
MetadataProfile metadataProfile = new MetadataProfile();
List<String> id = helper.evaluate("/Resource/ID/text()");
if(id==null || id.isEmpty())
@ -167,19 +165,6 @@ public class MetadataFormatDiscovery {
}
/**
* Gets the gcube generic query string.
*
* @param secondaryType the secondary type
* @return the gcube generic query string
*/
public synchronized String getGcubeGenericQueryString(String secondaryType){
return "for $profile in collection('/db/Profiles/GenericResource')//Resource" +
" where $profile/Profile/SecondaryType/string() eq '"+secondaryType+"'" +
" return $profile";
}
/**
* Gets the secondary type.
*

22
src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/MetadataFormatReader.java
View File

@ -49,7 +49,7 @@ public class MetadataFormatReader {
public MetadataFormatReader(ScopeBean scope, String resourceID) throws Exception {
this.scope = scope;
this.resourceID = resourceID;
this.metadataFormat = getMetadataFormatByID(resourceID);
this.metadataFormat = getMetadataFormatByResourceID(resourceID);
}
@ -61,8 +61,8 @@ public class MetadataFormatReader {
* @return the metadata format by id
* @throws Exception the exception
*/
private MetadataFormat getMetadataFormatByID(String resourceID) throws Exception {
logger.trace("Getting MedataFormat with resourceID: "+resourceID);
private MetadataFormat getMetadataFormatByResourceID(String resourceID) throws Exception {
logger.trace("Getting MedataFormat for resourceID: "+resourceID);
if(this.scope==null)
throw new Exception("Scope is null");
@ -76,7 +76,7 @@ public class MetadataFormatReader {
logger.info("Using scope from ScopeProvider: "+scopeString);
String queryString = getQuesryStringForGenericResourceById(resourceID);
String queryString = QueryForResourceUtil.queryForGenericResourceById(resourceID);
logger.trace("queryString: " +queryString);
Query q = new QueryBox(queryString);
@ -163,7 +163,7 @@ public class MetadataFormatReader {
InputStream stream = new ByteArrayInputStream(metadataFormatSource.get(0).getBytes());
MetadataFormat mtdf = (MetadataFormat) jaxbUnmarshaller.unmarshal(stream);
logger.debug("returning metadata format with medata type: "+mtdf.getMetadataType());
logger.debug("returning metadata format with medata type: "+mtdf.getType());
return mtdf;
@ -221,18 +221,6 @@ public class MetadataFormatReader {
}
/**
* Gets the quesry string for generic resource by id.
*
* @param resourceId the resource id
* @return the quesry string for generic resource by id
*/
public synchronized String getQuesryStringForGenericResourceById(String resourceId){
return String.format("declare namespace ic = 'http://gcube-system.org/namespaces/informationsystem/registry'; " +
"for $resource in collection('/db/Profiles')//Document/Data/ic:Profile/Resource " +
"where ($resource/ID/text() eq '%s') return $resource", resourceId);
}
/**

204
src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/NamespaceCategoryReader.java Normal file
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@ -0,0 +1,204 @@
/**
*
*/
package org.gcube.datacatalogue.metadatadiscovery.reader;
import static org.gcube.resources.discovery.icclient.ICFactory.client;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringReader;
import java.util.List;
import java.util.Properties;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.gcube.common.resources.gcore.utils.XPathHelper;
import org.gcube.common.scope.impl.ScopeBean;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategories;
import org.gcube.resources.discovery.client.api.DiscoveryClient;
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.Node;
import org.xml.sax.InputSource;
/**
* The Class NamespaceCategoryReader.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Apr 26, 2017
*/
public class NamespaceCategoryReader {
/**
*
*/
public static final String NAMESPACES_CATALOGUE_CATEGORIES_PROPERTIES = "NamespacesCatalogueCategories.properties";
private static Logger logger = LoggerFactory.getLogger(NamespaceCategoryReader.class);
private ScopeBean scope;
private String resourceID;
private NamespaceCategories namespaces;
/**
* Instantiates a new medata format reader.
*
* @param scope the scope
* @param resourceID the resource id
* @throws Exception the exception
*/
public NamespaceCategoryReader(ScopeBean scope, String resourceID) throws Exception {
this.scope = scope;
this.resourceID = resourceID;
if(resourceID == null || resourceID.isEmpty())
throw new Exception("Please, specify a valid ResourceID in the property file: "+NAMESPACES_CATALOGUE_CATEGORIES_PROPERTIES);
readNamespaceCategoryByResourceID();
}
/**
* Gets the metadata format by id.
*
* @return the metadata format by id
* @throws Exception the exception
*/
private void readNamespaceCategoryByResourceID() throws Exception {
logger.trace("Getting Namespace Category for resourceID: "+resourceID);
if(this.scope==null)
throw new Exception("Scope is null");
String scopeString = this.scope.toString();
logger.trace("read scope: "+scopeString);
namespaces = new NamespaceCategories();
try {
logger.info("Using scope from ScopeProvider: "+scopeString);
String queryString = QueryForResourceUtil.queryForGenericResourceById(resourceID);
logger.trace("queryString: " +queryString);
Query q = new QueryBox(queryString);
DiscoveryClient<String> client = client();
List<String> appProfile = client.submit(q);
if (appProfile == null || appProfile.size() == 0)
throw new MetadataProfileNotFoundException("Your resourceID "+resourceID+" is not registered in the infrastructure, the scope is "+scopeString);
else {
String theResource = null;
try{
theResource = appProfile.get(0);
// logger.trace("Resource with resourceID "+resourceID+" matched "+theResource);
logger.debug("Resource (Namespaces Catalogue Categories) within resourceID "+resourceID+" found");
DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Node node = docBuilder.parse(new InputSource(new StringReader(theResource))).getDocumentElement();
XPathHelper helper = new XPathHelper(node);
// List<MetadataField> fields = getMetadataFieldsFromResource(helper);
// mf.setMetadataFields(fields);
logger.debug("Unmarshalling it..");
readNamespaceCategoryFromResource(helper);
}catch(Exception e){
logger.error("Error while parsing Resource "+theResource+" from the infrastructure, the scope is "+scopeString,e);
}
}
} catch (Exception e) {
logger.error("Error while trying to fetch resourceID "+resourceID+" from the infrastructure, the scope is "+scopeString,e);
throw new Exception("Error while trying to fetch resourceID "+resourceID+" from the infrastructure, the scope is "+scopeString, e);
} finally{
// ScopeProvider.instance.reset();
}
}
/**
* Read namespace category from resource.
*
* @param helper the helper
* @throws Exception the exception
*/
private void readNamespaceCategoryFromResource(XPathHelper helper) throws Exception{
try {
List<String> namespaceSources = helper.evaluate("/Resource/Profile/Body/namespaces");
JAXBContext jaxbContext = JAXBContext.newInstance(NamespaceCategories.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
if(namespaceSources==null || namespaceSources.size()==0){
throw new Exception("Resource does not contain <namespaces> <namespace>...</namespace> </namespaces> in the body");
}
InputStream stream = new ByteArrayInputStream(namespaceSources.get(0).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);
}
}
/**
* Namespaces catalogue categories resource id.
*
* @return the string
* @throws PropertyFileNotFoundException the property file not found exception
*/
public static String NamespacesCatalogueCategoriesResourceID() throws PropertyFileNotFoundException {
Properties prop = new Properties();
try {
InputStream in = NamespaceCategoryReader.class.getResourceAsStream(NAMESPACES_CATALOGUE_CATEGORIES_PROPERTIES);
// load a properties file
prop.load(in);
return prop.getProperty("RESOURCE_ID");
} catch (IOException e) {
logger.error("An error occurred on read property file "+NAMESPACES_CATALOGUE_CATEGORIES_PROPERTIES, e);
throw new PropertyFileNotFoundException("An error occurred on read property file "+NAMESPACES_CATALOGUE_CATEGORIES_PROPERTIES+": "+e);
}
}
/**
* Gets the namespaces.
*
* @return the namespaces
*/
public NamespaceCategories getNamespaces() {
return namespaces;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("NamespaceCategoryReader [scope=");
builder.append(scope);
builder.append(", resourceID=");
builder.append(resourceID);
builder.append(", namespaces=");
builder.append(namespaces);
builder.append("]");
return builder.toString();
}
}

10
src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/NamespacesCatalogueCategories.properties Normal file
View File

@ -0,0 +1,10 @@
# Property files
#
# author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
# created 04/2017
#
# Generic resource id of "Namespaces Calogue Categories"
#
#
RESOURCE_ID = cdc52c27-6d7b-4d55-b4cd-314d7cc2e224

8
src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/PropertyFileNotFoundException.java Normal file
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@ -0,0 +1,8 @@
package org.gcube.datacatalogue.metadatadiscovery.reader;
@SuppressWarnings("serial")
public class PropertyFileNotFoundException extends Exception {
public PropertyFileNotFoundException(String message) {
super(message);
}
}

44
src/main/java/org/gcube/datacatalogue/metadatadiscovery/reader/QueryForResourceUtil.java Normal file
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@ -0,0 +1,44 @@
/**
*
*/
package org.gcube.datacatalogue.metadatadiscovery.reader;
/**
* The Class QueryForResourceUtil.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Apr 26, 2017
*/
public class QueryForResourceUtil {
/**
* Query for generic resource by id. Returns a query string to get a generic resource by input resource id
*
* @param resourceId the resource id
* @return the string
*/
public static synchronized String queryForGenericResourceById(String resourceId){
return String.format("declare namespace ic = 'http://gcube-system.org/namespaces/informationsystem/registry'; " +
"for $resource in collection('/db/Profiles')//Document/Data/ic:Profile/Resource " +
"where ($resource/ID/text() eq '%s') return $resource", resourceId);
}
/**
* Gets the gcube generic query string for secondary type.
*
* @param secondaryType the secondary type
* @return the gcube generic query string for secondary type
*/
public static synchronized String getGcubeGenericQueryStringForSecondaryType(String secondaryType){
return "for $profile in collection('/db/Profiles/GenericResource')//Resource" +
" where $profile/Profile/SecondaryType/string() eq '"+secondaryType+"'" +
" return $profile";
}
}

24
src/test/java/org/gcube/datacatalogue/metadatadiscovery/TestDataCatalogueMetadataFormatReader.java
View File

@ -3,9 +3,10 @@
*/
package org.gcube.datacatalogue.metadatadiscovery;
import java.util.List;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.datacatalogue.metadatadiscovery.bean.MetadataProfile;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategory;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -31,15 +32,22 @@ public class TestDataCatalogueMetadataFormatReader {
ScopeProvider.instance.set(scopeString);
DataCalogueMetadataFormatReader reader = new DataCalogueMetadataFormatReader();
int i = 0;
for (MetadataProfile mt : reader.getListOfMetadataProfiles()) {
if(mt==null)
continue;
MetadataFormat metadataFormat = reader.getMetadataFormatForMetadataProfile(mt);
logger.trace("\n\n "+ ++i +".) Metadata source: "+metadataFormat.getMetadataSource().substring(0, 100));
List<NamespaceCategory> categs = reader.getListOfNamespaceCategories();
for (NamespaceCategory namespaceCategory : categs) {
logger.trace("\n\n "+ ++i +".) Category: "+namespaceCategory);
}
i = 0;
// for (MetadataProfile mt : reader.getListOfMetadataProfiles()) {
//
// if(mt==null)
// continue;
//
// MetadataFormat metadataFormat = reader.getMetadataFormatForMetadataProfile(mt);
// logger.trace("\n\n "+ ++i +".) Metadata source: "+metadataFormat.getMetadataSource().substring(0, 100));
// }
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();

43
src/test/java/org/gcube/datacatalogue/metadatadiscovery/TestJaxbMetadataMarshUnmarsh.java
View File

@ -11,9 +11,10 @@ import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataCategory;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataField;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.MetadataFormat;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategories;
import org.gcube.datacatalogue.metadatadiscovery.bean.jaxb.NamespaceCategory;
import org.junit.Test;
@ -28,7 +29,8 @@ public class TestJaxbMetadataMarshUnmarsh {
static MetadataField ckanMetadata;
static MetadataFormat metadatas;
static String tmpFileXML = "." + File.separator + "CkanMetadatas.xml";
private ArrayList<MetadataCategory> ckanCategories;
static String tmpCategoriesXML = "." + File.separator + "NamespacesCatalogueCategories.xml";
private ArrayList<NamespaceCategory> ckanCategories;
public static int MAX_CATEGORIES = 3;
/**
@ -93,7 +95,8 @@ public class TestJaxbMetadataMarshUnmarsh {
try {
//marshalingExample();
unMarshalingExample();
//unMarshalingExample();
unMarshalingCategories();
}
catch (JAXBException e) {
// TODO Auto-generated catch block
@ -159,6 +162,40 @@ public class TestJaxbMetadataMarshUnmarsh {
}
/**
* Un marshaling example.
*
* @throws JAXBException the JAXB exception
*/
private static void unMarshalingCategories() throws JAXBException
{
JAXBContext jaxbContext = JAXBContext.newInstance(NamespaceCategories.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
//We had written this file in marshalling example
NamespaceCategories mtds = (NamespaceCategories) jaxbUnmarshaller.unmarshal(new File(tmpCategoriesXML));
System.out.println("NamespaceCategories: ");
System.out.println(mtds);
// System.out.println("Metadata Categories");
// if(mtds.getMetadataCategories()!=null){
// for (MetadataCategory cat : mtds.getMetadataCategories()) {
// System.out.println(cat);
// System.out.println(cat.getCategoryQName());
// }
// }
System.out.println("\nCategories: ");
for (NamespaceCategory category : mtds.getNamespaceCategories()) {
System.out.println(category);
// System.out.println(field.getGrouping());
// System.out.println(field.getTagging());
}
}
public static void main(String[] args) {
//System.out.println(DataType.valueOf("aa"));