Skip to content

GitLab

Commit 2c649f66 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch '566-merge-rest-api-services-into-main-service-module' into 'master' 

Resolve "Merge REST API services into main service module"

See merge request !1324
parents a5b36a0a 0dcca279
Pipeline #45324 passed with stage
in 19 minutes and 7 seconds
Hide whitespace changes
Inline Side-by-side
CHANGELOG
View file @ 2c649f66
minerva (16.1.0~alpha.0) stable; urgency=medium
* Bug fix: api endpoints were exposed without 'api' prefix
* Bug fix: anonymous user could upload file using API
* Bug fix: when passing JSON in patch/post methods contentType was not
checked
minerva (16.0.0~beta.1) stable; urgency=medium
* Backward incompatibility: layout parameter in minerva url is not supported
anymore
......
CellDesigner-plugin/pom.xml
View file @ 2c649f66
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
......@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<dependency>
......
annotation/pom.xml
View file @ 2c649f66
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
......@@ -18,7 +18,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
......@@ -34,13 +34,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.1</version>
<version>16.1.0~alpha.0</version>
</dependency>
<!-- Log4J2 -->
......
annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
View file @ 2c649f66
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import javax.xml.bind.annotation.XmlRootElement;
......@@ -315,8 +318,15 @@ public class Chemical implements Serializable, TargettingStructure {
}
public void removeTargets(Set<Target> targetsToRemove) {
public void removeTargets(Collection<Target> targetsToRemove) {
this.getTargets().removeAll(targetsToRemove);
}
@Override
public void addTargets(List<? extends Target> projectTargets) {
for (Target target : projectTargets) {
addTarget(target);
}
}
}
annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
View file @ 2c649f66
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
......@@ -9,6 +12,9 @@ import javax.xml.bind.annotation.XmlRootElement;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import lcsb.mapviewer.annotation.data.serializer.DrugSerializer;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.model.map.MiriamData;
......@@ -19,6 +25,7 @@ import lcsb.mapviewer.model.map.MiriamData;
*
*/
@XmlRootElement
@JsonSerialize(using = DrugSerializer.class)
public class Drug implements Serializable, TargettingStructure {
/**
......@@ -285,7 +292,8 @@ public class Drug implements Serializable, TargettingStructure {
* @param targets2
* list of targets to add
*/
public void addTargets(List<Target> targets2) {
@Override
public void addTargets(List<? extends Target> targets2) {
this.targets.addAll(targets2);
}
......@@ -332,4 +340,8 @@ public class Drug implements Serializable, TargettingStructure {
public void addSynonyms(List<String> synonyms) {
this.synonyms.addAll(synonyms);
}
public void removeTargets(Collection<Target> targetsToRemove) {
this.getTargets().removeAll(targetsToRemove);
}
}
\ No newline at end of file
annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
View file @ 2c649f66
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import javax.xml.bind.annotation.XmlRootElement;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import lcsb.mapviewer.annotation.data.serializer.MiRNASerializer;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.model.map.MiriamData;
......@@ -15,6 +21,7 @@ import lcsb.mapviewer.model.map.MiriamData;
*
*/
@XmlRootElement
@JsonSerialize(using = MiRNASerializer.class)
public class MiRNA implements Serializable, TargettingStructure {
/**
......@@ -127,4 +134,14 @@ public class MiRNA implements Serializable, TargettingStructure {
}
@Override
public void removeTargets(Collection<Target> targets) {
this.targets.removeAll(targets);
}
@Override
public void addTargets(List<? extends Target> projectTargets) {
this.targets.addAll(projectTargets);
}
}
annotation/src/main/java/lcsb/mapviewer/annotation/data/ProjectTarget.java 0 → 100644
View file @ 2c649f66
package lcsb.mapviewer.annotation.data;
import java.util.Comparator;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.modelutils.serializer.model.map.MinifiedBioEntitySerializer;
public class ProjectTarget extends Target {
/**
*
*/
private static final long serialVersionUID = 1L;
public static final Comparator<? super ProjectTarget> COMPARATOR = new Comparator<ProjectTarget>() {
@Override
public int compare(ProjectTarget o1, ProjectTarget o2) {
Integer size1 = o1.bioEntities.size();
Integer size2 = o2.bioEntities.size();
if (size1 == size2) {
return new StringComparator().compare(o1.getName(), o2.getName());
}
return -size1.compareTo(size2);
}
};
@JsonSerialize(contentUsing = MinifiedBioEntitySerializer.class)
@JsonProperty("targetElements")
private List<BioEntity> bioEntities;
public ProjectTarget(Target target, List<BioEntity> bioEntities) {
setSource(target.getSource());
setName(target.getName());
setOrganism(target.getOrganism());
setAssociatedDisease(target.getAssociatedDisease());
setGenes(target.getGenes());
addReferences(target.getReferences());
setType(target.getType());
this.bioEntities = bioEntities;
}
public List<BioEntity> getBioEntities() {
return bioEntities;
}
public void setBioEntites(List<BioEntity> bioEntities) {
this.bioEntities = bioEntities;
}
}
annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
View file @ 2c649f66
package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import javax.xml.bind.annotation.XmlElement;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
......@@ -33,33 +38,40 @@ public class Target implements Serializable {
/**
* Database from which target was received.
*/
@JsonIgnore
private MiriamData source;
/**
* Name of the target.
*/
@JsonProperty("name")
private String name;
/**
* Organism in which target is located.
*/
@JsonIgnore
private MiriamData organism;
@JsonIgnore
private MiriamData associatedDisease;
/**
* List of genes located in a target.
*/
@JsonProperty("targetParticipants")
private List<MiriamData> genes = new ArrayList<>();
/**
* List of references describing target.
*/
@JsonProperty("references")
private List<MiriamData> references = new ArrayList<>();
/**
* Type of target.
*/
@JsonIgnore
private TargetType type;
/**
......
annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java
View file @ 2c649f66
package lcsb.mapviewer.annotation.data;
import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.model.map.MiriamData;
......@@ -25,4 +26,8 @@ public interface TargettingStructure {
*/
Collection<Target> getTargets();
void removeTargets(Collection<Target> targets);
void addTargets(List<? extends Target> projectTargets);
}
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/ChemicalSerializer.java 0 → 100644
View file @ 2c649f66
package lcsb.mapviewer.annotation.data.serializer;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.function.Function;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import com.fasterxml.jackson.databind.ser.FilterProvider;
import com.fasterxml.jackson.databind.ser.PropertyFilter;
import lcsb.mapviewer.annotation.data.Chemical;
import lcsb.mapviewer.annotation.data.MeSH;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.modelutils.serializer.CustomExceptFilter;
public class ChemicalSerializer extends JsonSerializer<Chemical> {
private Function<MiriamData, MeSH> getMesh;
public ChemicalSerializer(Function<MiriamData, MeSH> getMesh) {
this.getMesh = getMesh;
}
@Override
public void serialize(final Chemical chemical, final JsonGenerator gen,
final SerializerProvider serializers)
throws IOException {
PropertyFilter filter = null;
FilterProvider provider = serializers.getConfig().getFilterProvider();
if (provider != null) {
filter = provider.findPropertyFilter("chemicalFilter", null);
}
String description = "Mesh term not available";
List<String> synonyms = new ArrayList<>();
MeSH mesh = getMesh.apply(chemical.getChemicalId());
if (mesh != null) {
description = mesh.getDescription();
synonyms = mesh.getSynonyms();
}
gen.writeStartObject();
for (String string : availableColumns()) {
String column = string.toLowerCase();
Object value = null;
switch (column) {
case "id":
case "idobject":
value = chemical.getChemicalId();
break;
case "name":
value = chemical.getChemicalName();
break;
case "references":
List<MiriamData> references = new ArrayList<>();
references.add(chemical.getChemicalId());
if (chemical.getCasID() != null) {
references.add(chemical.getCasID());
}
value = references;
break;
case "directevidencereferences":
value = chemical.getDirectEvidencePublication();
break;
case "description":
value = description;
break;
case "directevidence":
if (chemical.getDirectEvidence() != null) {
value = chemical.getDirectEvidence().getValue();
}
break;
case "synonyms":
value = synonyms;
break;
case "targets":
value = chemical.getTargets();
break;
default:
value = "Unknown column";
break;
}
writeField(gen, string, value, filter);
}
gen.writeEndObject();
}
private void writeField(JsonGenerator gen, String field, Object value, PropertyFilter filter) throws IOException {
if (filter == null ||
(filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
gen.writeObjectField(field, value);
}
}
public static List<String> availableColumns() {
return Arrays.asList("name", "references", "description", "synonyms", "id", "directEvidenceReferences", "directEvidence", "targets");
}
}
\ No newline at end of file
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/DrugSerializer.java 0 → 100644
View file @ 2c649f66
package lcsb.mapviewer.annotation.data.serializer;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import com.fasterxml.jackson.databind.ser.FilterProvider;
import com.fasterxml.jackson.databind.ser.PropertyFilter;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.modelutils.serializer.CustomExceptFilter;
public class DrugSerializer extends JsonSerializer<Drug> {
@Override
public void serialize(final Drug drug, final JsonGenerator gen,
final SerializerProvider serializers)
throws IOException {
PropertyFilter filter = null;
FilterProvider provider = serializers.getConfig().getFilterProvider();
if (provider != null) {
filter = provider.findPropertyFilter("drugFilter", null);
}
gen.writeStartObject();
for (String string : availableColumns()) {
String column = string.toLowerCase();
Object value = null;
if (column.equals("id") || column.equals("idobject")) {
value = drug.getName();
} else if (column.equals("name")) {
value = drug.getName();
} else if (column.equals("references")) {
value = drug.getSources();
} else if (column.equals("description")) {
value = drug.getDescription();
} else if (column.equals("bloodbrainbarrier")) {
value = drug.getBloodBrainBarrier();
} else if (column.equals("brandnames")) {
value = drug.getBrandNames();
} else if (column.equals("synonyms")) {
value = drug.getSynonyms();
} else if (column.equals("targets")) {
value = drug.getTargets();
} else {
value = "Unknown column";
}
writeField(gen, string, value, filter);
}
gen.writeEndObject();
}
private void writeField(JsonGenerator gen, String field, Object value, PropertyFilter filter) throws IOException {
if (filter == null ||
(filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
gen.writeObjectField(field, value);
}
}
public static List<String> availableColumns() {
return Arrays.asList("name", "references", "description", "bloodBrainBarrier", "brandNames", "synonyms", "id", "targets");
}
}
\ No newline at end of file
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/MiRNASerializer.java 0 → 100644
View file @ 2c649f66
package lcsb.mapviewer.annotation.data.serializer;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import com.fasterxml.jackson.databind.ser.FilterProvider;
import com.fasterxml.jackson.databind.ser.PropertyFilter;
import lcsb.mapviewer.annotation.data.MiRNA;
import lcsb.mapviewer.modelutils.serializer.CustomExceptFilter;
public class MiRNASerializer extends JsonSerializer<MiRNA> {
@Override
public void serialize(final MiRNA miRna, final JsonGenerator gen,
final SerializerProvider serializers)
throws IOException {
PropertyFilter filter = null;
FilterProvider provider = serializers.getConfig().getFilterProvider();
if (provider != null) {
filter = provider.findPropertyFilter("miRnaFilter", null);
}
gen.writeStartObject();
for (String string : availableColumns()) {
String column = string.toLowerCase();
Object value = null;
switch (column) {
case "id":
case "idobject":
case "name":
value = miRna.getName();
break;
case "targets":
value = miRna.getTargets();
break;
default:
value = "Unknown column";
break;
}
writeField(gen, string, value, filter);
}
gen.writeEndObject();
}
private void writeField(JsonGenerator gen, String field, Object value, PropertyFilter filter) throws IOException {
if (filter == null ||
(filter instanceof CustomExceptFilter && ((CustomExceptFilter) filter).includeField(field))) {
gen.writeObjectField(field, value);
}
}
public static List<String> availableColumns() {
return Arrays.asList("name", "id", "targets");
}
}
\ No newline at end of file
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/ProjectTargetSerializer.java 0 → 100644
View file @ 2c649f66
package lcsb.mapviewer.annotation.data.serializer;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.JsonSerializer;
import com.fasterxml.jackson.databind.SerializerProvider;
import lcsb.mapviewer.annotation.data.ProjectTarget;