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ARTIF-683 corrected field types in Ontology, allowing Hibernate to fu…
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…lly serialize/deserialize
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@brmeyer
brmeyer committed Jun 8, 2015
1 parent d254c06 commit ed02665
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Showing 13 changed files with 66 additions and 63 deletions.
2 changes: 1 addition & 1 deletion atom/src/main/java/org/artificer/atom/mappers/OntologyToRdfMapper.java
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Expand Up @@ -57,7 +57,7 @@ public void map(ArtificerOntology ontology, RDF rdf) {
rdfClass.setComment(oclass.getComment());
if (oclass.getParent() != null) {
SubClassOf subclass = new SubClassOf();
subclass.setResource(oclass.getParent().getUri().toString());
subclass.setResource(oclass.getParent().getUri());
rdfClass.setSubClassOf(subclass);
}
rdf.getClazz().add(rdfClass);
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3 changes: 1 addition & 2 deletions atom/src/main/java/org/artificer/atom/mappers/RdfToOntologyMapper.java
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Expand Up @@ -23,7 +23,6 @@
import org.w3._2002._07.owl_.Ontology;

import javax.xml.namespace.QName;
import java.net.URI;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
Expand Down Expand Up @@ -85,7 +84,7 @@ public void map(RDF rdf, ArtificerOntology ontology) throws Exception {
oclass.setLabel(rdfClass.getLabel());
oclass.setComment(rdfClass.getComment());
String uri = base + "#" + rdfClass.getID(); //$NON-NLS-1$
oclass.setUri(new URI(uri));
oclass.setUri(uri);
Object[] classData = new Object[] {
oclass, rdfClass.getSubClassOf() != null ? rdfClass.getSubClassOf().getResource() : null
};
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25 changes: 12 additions & 13 deletions common/src/main/java/org/artificer/common/ontology/ArtificerOntology.java
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Expand Up @@ -22,10 +22,11 @@
import javax.persistence.Id;
import javax.persistence.Lob;
import javax.persistence.OneToMany;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import javax.persistence.Transient;
import java.io.Serializable;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
Expand Down Expand Up @@ -139,6 +140,13 @@ public List<ArtificerOntologyClass> getRootClasses() {
return rootClasses;
}

/**
* @param rootClasses the rootClasses to set
*/
public void setRootClasses(List<ArtificerOntologyClass> rootClasses) {
this.rootClasses = rootClasses;
}

@Transient
public List<ArtificerOntologyClass> getAllClasses() {
List<ArtificerOntologyClass> allClasses = new ArrayList<ArtificerOntologyClass>();
Expand All @@ -158,13 +166,6 @@ private void addAllClasses(List<ArtificerOntologyClass> allClasses, List<Artific
}
}

/**
* @param rootClasses the rootClasses to set
*/
public void setRootClasses(List<ArtificerOntologyClass> rootClasses) {
this.rootClasses = rootClasses;
}

/**
* Creates a new class within this ontology.
* @param id
Expand All @@ -173,11 +174,7 @@ public ArtificerOntologyClass createClass(String id) {
ArtificerOntologyClass c = new ArtificerOntologyClass();
c.setId(id);
String uri = this.getBase() + "#" + id; //$NON-NLS-1$
try {
c.setUri(new URI(uri));
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
c.setUri(uri);
return c;
}

Expand Down Expand Up @@ -242,6 +239,7 @@ public void setCreatedBy(String createdBy) {
/**
* @return the createdOn
*/
@Temporal(TemporalType.DATE)
public Date getCreatedOn() {
return createdOn;
}
Expand Down Expand Up @@ -270,6 +268,7 @@ public void setLastModifiedBy(String lastModifiedBy) {
/**
* @return the lastModifiedOn
*/
@Temporal(TemporalType.DATE)
public Date getLastModifiedOn() {
return lastModifiedOn;
}
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16 changes: 9 additions & 7 deletions common/src/main/java/org/artificer/common/ontology/ArtificerOntologyClass.java
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Expand Up @@ -12,6 +12,7 @@
import javax.persistence.OneToMany;
import java.io.Serializable;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
Expand All @@ -28,7 +29,7 @@ public class ArtificerOntologyClass implements Serializable {
private String id;
private String label;
private String comment;
private URI uri;
private String uri;
private ArtificerOntology root;
private ArtificerOntologyClass parent;
private List<ArtificerOntologyClass> children = new ArrayList<ArtificerOntologyClass>();
Expand All @@ -44,6 +45,7 @@ public void setSurrogateId(long surrogateId) {
this.surrogateId = surrogateId;
}

// Note: Cannot be @Id! Not guaranteed to be set by clients.
public String getId() {
return id;
}
Expand Down Expand Up @@ -78,7 +80,7 @@ public ArtificerOntologyClass findClass(String id) {
* @param uri
*/
public ArtificerOntologyClass findClass(URI uri) {
if (this.uri.equals(uri)) {
if (this.uri.equals(uri.toString())) {
return this;
} else {
for (ArtificerOntologyClass c : this.children) {
Expand Down Expand Up @@ -158,26 +160,26 @@ public void setChildren(List<ArtificerOntologyClass> children) {
/**
* @return the uri
*/
public URI getUri() {
public String getUri() {
return uri;
}

/**
* @param uri the uri to set
*/
public void setUri(URI uri) {
public void setUri(String uri) {
this.uri = uri;
}

/**
* Normalize the hierarchy into a list of ArtificerOntologyClasses. The returned list of
* ArtificerOntologyClasses will contain this class and all ancestors.
*/
public Set<URI> normalize() {
Set<URI> uris = new HashSet<URI>();
public Set<URI> normalize() throws URISyntaxException {
Set<URI> uris = new HashSet<>();
ArtificerOntologyClass current = this;
while (current != null) {
uris.add(current.getUri());
uris.add(new URI(current.getUri()));
current = current.getParent();
}
return uris;
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6 changes: 3 additions & 3 deletions distro/assembly/src/main/resources/ROOT/ddl/db2.sql
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Expand Up @@ -76,11 +76,11 @@
base varchar(255),
comment clob,
createdBy varchar(255),
createdOn timestamp,
createdOn date,
id varchar(255),
label varchar(255),
lastModifiedBy varchar(255),
lastModifiedOn timestamp,
lastModifiedOn date,
uuid char(36),
primary key (surrogateId)
);
Expand All @@ -90,7 +90,7 @@
comment clob,
id varchar(255),
label varchar(255),
uri varchar(255) for bit data,
uri varchar(255),
parent_surrogateId bigint,
root_surrogateId bigint,
primary key (surrogateId)
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6 changes: 3 additions & 3 deletions distro/assembly/src/main/resources/ROOT/ddl/h2.sql
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Expand Up @@ -76,11 +76,11 @@
base varchar(255),
comment clob,
createdBy varchar(255),
createdOn timestamp,
createdOn date,
id varchar(255),
label varchar(255),
lastModifiedBy varchar(255),
lastModifiedOn timestamp,
lastModifiedOn date,
uuid char(36),
primary key (surrogateId)
);
Expand All @@ -90,7 +90,7 @@
comment clob,
id varchar(255),
label varchar(255),
uri binary(255),
uri varchar(255),
parent_surrogateId bigint,
root_surrogateId bigint,
primary key (surrogateId)
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6 changes: 3 additions & 3 deletions distro/assembly/src/main/resources/ROOT/ddl/mssql2012.sql
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Expand Up @@ -76,11 +76,11 @@
base varchar(255),
comment varchar(MAX),
createdBy varchar(255),
createdOn datetime2,
createdOn date,
id varchar(255),
label varchar(255),
lastModifiedBy varchar(255),
lastModifiedOn datetime2,
lastModifiedOn date,
uuid char(36),
primary key (surrogateId)
);
Expand All @@ -90,7 +90,7 @@
comment varchar(MAX),
id varchar(255),
label varchar(255),
uri varbinary(255),
uri varchar(255),
parent_surrogateId bigint,
root_surrogateId bigint,
primary key (surrogateId)
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6 changes: 3 additions & 3 deletions distro/assembly/src/main/resources/ROOT/ddl/mysql5.sql
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Expand Up @@ -76,11 +76,11 @@
base varchar(255),
comment longtext,
createdBy varchar(255),
createdOn datetime,
createdOn date,
id varchar(255),
label varchar(255),
lastModifiedBy varchar(255),
lastModifiedOn datetime,
lastModifiedOn date,
uuid char(36),
primary key (surrogateId)
);
Expand All @@ -90,7 +90,7 @@
comment longtext,
id varchar(255),
label varchar(255),
uri tinyblob,
uri varchar(255),
parent_surrogateId bigint,
root_surrogateId bigint,
primary key (surrogateId)
Expand Down
6 changes: 3 additions & 3 deletions distro/assembly/src/main/resources/ROOT/ddl/oracle10.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,11 @@
base varchar2(255 char),
comment clob,
createdBy varchar2(255 char),
createdOn timestamp,
createdOn date,
id varchar2(255 char),
label varchar2(255 char),
lastModifiedBy varchar2(255 char),
lastModifiedOn timestamp,
lastModifiedOn date,
uuid char(36),
primary key (surrogateId)
);
Expand All @@ -90,7 +90,7 @@
comment clob,
id varchar2(255 char),
label varchar2(255 char),
uri raw(255),
uri varchar2(255 char),
parent_surrogateId number(19,0),
root_surrogateId number(19,0),
primary key (surrogateId)
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6 changes: 3 additions & 3 deletions distro/assembly/src/main/resources/ROOT/ddl/postgres9.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,11 @@
base varchar(255),
comment text,
createdBy varchar(255),
createdOn timestamp,
createdOn date,
id varchar(255),
label varchar(255),
lastModifiedBy varchar(255),
lastModifiedOn timestamp,
lastModifiedOn date,
uuid char(36),
primary key (surrogateId)
);
Expand All @@ -90,7 +90,7 @@
comment text,
id varchar(255),
label varchar(255),
uri bytea,
uri varchar(255),
parent_surrogateId int8,
root_surrogateId int8,
primary key (surrogateId)
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39 changes: 21 additions & 18 deletions repository/src/main/java/org/artificer/repository/AbstractPersistenceManager.java
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Expand Up @@ -34,33 +34,36 @@ public abstract class AbstractPersistenceManager implements PersistenceManager,

@Override
public URI resolve(String classifiedBy) throws ArtificerException {
URI classifiedUri = null;
try {
classifiedUri = new URI(classifiedBy);
} catch (URISyntaxException e) {
throw ArtificerUserException.invalidClassifiedBy(classifiedBy);
}
Collection<ArtificerOntology> ontologies = getOntologies();
for (ArtificerOntology ontology : ontologies) {
ArtificerOntologyClass sclass = ontology.findClass(classifiedBy);
if (sclass == null) {
sclass = ontology.findClass(classifiedUri);
}
if (sclass != null) {
return sclass.getUri();
URI classifiedUri = new URI(classifiedBy);
Collection<ArtificerOntology> ontologies = getOntologies();
for (ArtificerOntology ontology : ontologies) {
ArtificerOntologyClass sclass = ontology.findClass(classifiedBy);
if (sclass == null) {
sclass = ontology.findClass(classifiedUri);
}
if (sclass != null) {
return new URI(sclass.getUri());
}
}
} catch (URISyntaxException e) {
// fall through
}
throw ArtificerUserException.invalidClassifiedBy(classifiedBy);
}

@Override
public Collection<URI> normalize(URI classification) throws ArtificerException {
List<ArtificerOntology> ontologies = getOntologies();
for (ArtificerOntology ontology : ontologies) {
ArtificerOntologyClass sclass = ontology.findClass(classification);
if (sclass != null) {
return sclass.normalize();
try {
List<ArtificerOntology> ontologies = getOntologies();
for (ArtificerOntology ontology : ontologies) {
ArtificerOntologyClass sclass = ontology.findClass(classification);
if (sclass != null) {
return sclass.normalize();
}
}
} catch (URISyntaxException e) {
// fall through
}
throw ArtificerUserException.invalidClassifiedBy(classification.toString());
}
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2 changes: 1 addition & 1 deletion ...itory/test/src/test/java/org/artificer/repository/test/ClassificationPersistenceTest.java
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Expand Up @@ -45,7 +45,7 @@ public void testPersistClassifications() throws Exception {
Document document = new Document();
document.setName(artifactFileName);
document.setArtifactType(BaseArtifactEnum.DOCUMENT);
document.getClassifiedBy().add(ontology.findClass("China").getUri().toString());
document.getClassifiedBy().add(ontology.findClass("China").getUri());

BaseArtifactType artifact = persistenceManager.persistArtifact(document, new ArtifactContent(artifactFileName, contentStream));
Assert.assertNotNull(artifact);
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6 changes: 3 additions & 3 deletions repository/test/src/test/java/org/artificer/repository/test/OntologyPersistenceTest.java
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Expand Up @@ -114,9 +114,9 @@ public void testPersistOntology_Full() throws Exception {
Assert.assertEquals(0, actualJapan.getChildren().size());

Set<URI> expectedJapanNormalized = new HashSet<>();
expectedJapanNormalized.add(actualWorld.getUri());
expectedJapanNormalized.add(actualAsia.getUri());
expectedJapanNormalized.add(actualJapan.getUri());
expectedJapanNormalized.add(new URI(actualWorld.getUri()));
expectedJapanNormalized.add(new URI(actualAsia.getUri()));
expectedJapanNormalized.add(new URI(actualJapan.getUri()));
Assert.assertEquals(expectedJapanNormalized, actualJapan.normalize());
}

Expand Down

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