diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index f6ff490e8d5364c39a14b0a0afe6d6c468e4be1f..bda5fc3e6191d9ff22e3140cced9ad3e2439d081 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -4,8 +4,10 @@ import java.awt.Color;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import org.apache.log4j.Logger;
@@ -134,20 +136,9 @@ public class ColorModelCommand extends ModelCommand {
return false;
}
- if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
- if (reaction.getMiriamData().contains(md)) {
- return true;
- }
- }
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().equals("")) {
-
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (reaction.getMiriamData().contains(md)) {
- return true;
- }
+ for (MiriamData md : schema.getMiriamData()) {
+ if (!reaction.getMiriamData().contains(md)) {
+ return false;
}
}
@@ -234,21 +225,11 @@ public class ColorModelCommand extends ModelCommand {
return false;
}
}
- if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
+ for (MiriamData md : schema.getMiriamData()) {
if (!element.getMiriamData().contains(md)) {
return false;
}
}
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().equals("")) {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (!element.getMiriamData().contains(md)) {
- return false;
- }
- }
- }
if (schema.getCompartments().size() > 0) {
boolean found = false;
@@ -310,9 +291,10 @@ public class ColorModelCommand extends ModelCommand {
List<Model> models = new ArrayList<>();
models.add(getModel());
models.addAll(getModel().getSubmodels());
+
for (Model model : models) {
- for (ColorSchema schema : schemas) {
- for (BioEntity element : model.getBioEntities()) {
+ for (BioEntity element : model.getBioEntities()) {
+ for (ColorSchema schema : schemas) {
if (match(element, schema)) {
if (result.get(element) != null
&& !colorExtractor.getNormalizedColor(result.get(element)).equals(Color.WHITE)) {
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index d240a93b7c25239f27c96d0db283afb02c1a5e30..4f6be19fe04c2a0c97e866f15a4a5b9adca02104 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.commands;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.awt.Color;
@@ -17,6 +18,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -86,15 +88,15 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/coloring_model.xml", true);
Collection<ColorSchema> schemas = new ArrayList<>();
ColorSchema schema = new GenericColorSchema();
- schema.setGeneralIdentifier("HGNC:11138");
+ schema.addMiriamData(new MiriamData(MiriamType.HGNC,"11138"));
schema.setValue(1.0);
schemas.add(schema);
schema = new GenericColorSchema();
- schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
+ schema.addMiriamData(new MiriamData(MiriamType.CHEBI,"CHEBI:15377"));
schema.setValue(1.0);
schemas.add(schema);
schema = new GenericColorSchema();
- schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
+ schema.addMiriamData(new MiriamData(MiriamType.CHEBI,"CHEBI:15376"));
schema.setValue(1.0);
schemas.add(schema);
@@ -187,11 +189,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Reaction re3 = model.getReactionByReactionId("re3");
Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
ColorSchema schema = new GenericColorSchema();
- Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
- List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
- identifiers.add(pair);
-
- schema.setIdentifierColumns(identifiers);
+ schema.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
schema.setValue(-1.0);
schemas.add(schema);
@@ -363,6 +361,51 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
+ @Test
+ public void testReactionMatchWithProteinMiriamData() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL,"SNCA"));
+
+ Reaction reaction = new Reaction();
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertFalse(factory.match(reaction, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testReactionMatchWithMiriamData() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED,"1234"));
+
+ Reaction reaction = new Reaction();
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(reaction, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
@Test
public void testReactionColoringWithModelNotMatching() throws Exception {
try {
@@ -495,4 +538,32 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
}
+ @Test
+ public void testGetModifiedElements() throws Exception {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ Model model = new ModelFullIndexed(null);
+ model.addReaction(reaction);
+
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED,"1234"));
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+ assertNotNull(factory.getModifiedElements().get(reaction));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index a8628a834534bf6818b6746332309f05188f12d2..53174c04f409b6e235df02fa07fa216f3a7c14fc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -4,11 +4,12 @@ import java.awt.Color;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
-import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
@@ -78,14 +79,9 @@ public abstract class ColorSchema implements Serializable {
private Color color = null;
/**
- * General identifier that identifies the element.
+ * Set of identifiers that filter the elements.
*/
- private String generalIdentifier = null;
-
- /**
- * List of specific identifiers that filter the elements.
- */
- private List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
+ private Set<MiriamData> miriamData = new HashSet<>();
/**
* Number of elements matched by this entry.
@@ -118,25 +114,11 @@ public abstract class ColorSchema implements Serializable {
this.addTypes(original.getTypes());
this.setValue(original.getValue());
this.setColor(original.getColor());
- this.setGeneralIdentifier(original.getGeneralIdentifier());
- this.addIdentifierColumns(original.getIdentifierColumns());
+ this.miriamData.addAll(original.getMiriamData());
this.setMatches(original.getMatches());
this.setDescription(original.getDescription());
}
- /**
- * Adds identifiers to {@link #identifierColumns} list.
- *
- * @param identifierColumnsList
- * list of pairs defining type of identifier and the identifier value
- */
- public void addIdentifierColumns(List<Pair<MiriamType, String>> identifierColumnsList) {
- for (Pair<MiriamType, String> pair : identifierColumnsList) {
- addIdentifierColumn(pair);
- }
-
- }
-
/**
* Adds class types to {@link #types} list.
*
@@ -200,16 +182,8 @@ public abstract class ColorSchema implements Serializable {
if (color != null) {
result.append(color + ",");
}
- if (generalIdentifier != null) {
- result.append(generalIdentifier + ",");
- }
- if (types.size() > 0) {
- result.append("(");
- for (Pair<MiriamType, String> pair : identifierColumns) {
- result.append(pair.getLeft() + "-" + pair.getRight() + ",");
- }
- result.append("),");
- }
+ result.append(miriamData + ",");
+
result.append(matches + "]");
return result.toString();
}
@@ -303,40 +277,6 @@ public abstract class ColorSchema implements Serializable {
this.color = color;
}
- /**
- * @return the generalIdentifier
- * @see #generalIdentifier
- */
- public String getGeneralIdentifier() {
- return generalIdentifier;
- }
-
- /**
- * @param generalIdentifier
- * the generalIdentifier to set
- * @see #generalIdentifier
- */
- public void setGeneralIdentifier(String generalIdentifier) {
- this.generalIdentifier = generalIdentifier;
- }
-
- /**
- * @return the identifierColumns
- * @see #identifierColumns
- */
- public List<Pair<MiriamType, String>> getIdentifierColumns() {
- return identifierColumns;
- }
-
- /**
- * @param identifierColumns
- * the identifierColumns to set
- * @see #identifierColumns
- */
- public void setIdentifierColumns(List<Pair<MiriamType, String>> identifierColumns) {
- this.identifierColumns = identifierColumns;
- }
-
/**
* @return the matches
* @see #matches
@@ -355,14 +295,11 @@ public abstract class ColorSchema implements Serializable {
}
/**
- * Adds identifier to {@link #identifierColumns} list.
+ * Adds identifier to {@link #miriamData} set.
*
- * @param pair
- * pair defining type of identifier and the identifier value
*/
- public void addIdentifierColumn(Pair<MiriamType, String> pair) {
- identifierColumns.add(pair);
-
+ public void addMiriamData(MiriamData md) {
+ miriamData.add(md);
}
/**
@@ -459,4 +396,8 @@ public abstract class ColorSchema implements Serializable {
this.elementId = elementId;
}
+ public Set<MiriamData> getMiriamData() {
+ return miriamData;
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
index 717ca331c5d130f0881272b2d6b2f3b0a3ab6b83..1f58992fcfdaf9ef9cb9b0816e6549df11461738 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
@@ -12,6 +12,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
@@ -19,134 +20,128 @@ import lcsb.mapviewer.model.map.species.Species;
public class ColorSchemaTest {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSetGetters() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<String> compartments = new ArrayList<>();
- List<Class<? extends Element>> types = new ArrayList<>();
- String name = "S";
- String generalIdentifier = "id";
- List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
- int matches = 79;
- Double lineWidth = 5.89;
- String reactionIdentifier = "re id";
- Boolean reverseReaction = true;
-
- cs.setName(name);
- assertEquals(name, cs.getName());
-
- cs.setCompartments(compartments);
- assertEquals(compartments, cs.getCompartments());
-
- cs.setTypes(types);
- assertEquals(types, cs.getTypes());
-
- cs.setGeneralIdentifier(generalIdentifier);
- assertEquals(generalIdentifier, cs.getGeneralIdentifier());
-
- cs.setIdentifierColumns(identifierColumns);
- assertEquals(identifierColumns, cs.getIdentifierColumns());
-
- cs.setMatches(matches);
- assertEquals(matches, cs.getMatches());
-
- cs.setLineWidth(lineWidth);
- assertEquals(lineWidth, cs.getLineWidth());
-
- cs.setElementId(reactionIdentifier);
- assertEquals(reactionIdentifier, cs.getElementId());
-
- cs.setReverseReaction(reverseReaction);
- assertEquals(reverseReaction, cs.getReverseReaction());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- assertNotNull(cs.toString());
- cs.setName("gene name");
- cs.addCompartment("A");
- cs.addType(Species.class);
- cs.setValue(1.2);
- cs.setColor(Color.BLACK);
- cs.setGeneralIdentifier("a");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "X"));
- assertNotNull(cs.toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCompartments() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- cs.addCompartments(new String[] { "a", "b" });
- assertEquals(2, cs.getCompartments().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCompartments2() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<String> compartments = new ArrayList<>();
- compartments.add("a");
- compartments.add("b");
- cs.addCompartments(compartments);
- assertEquals(2, cs.getCompartments().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddIdentifgierColumns() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<Pair<MiriamType, String>> compartments = new ArrayList<>();
- compartments.add(new Pair<MiriamType, String>(MiriamType.CAS, "x"));
- cs.addIdentifierColumns(compartments);
- assertEquals(1, cs.getIdentifierColumns().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddTypes() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<Class<? extends Element>> compartments = new ArrayList<>();
- compartments.add(Species.class);
- compartments.add(Protein.class);
- cs.addTypes(compartments);
- assertEquals(2, cs.getTypes().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSetGetters() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ List<String> compartments = new ArrayList<>();
+ List<Class<? extends Element>> types = new ArrayList<>();
+ String name = "S";
+ int matches = 79;
+ Double lineWidth = 5.89;
+ String reactionIdentifier = "re id";
+ Boolean reverseReaction = true;
+
+ cs.setName(name);
+ assertEquals(name, cs.getName());
+
+ cs.setCompartments(compartments);
+ assertEquals(compartments, cs.getCompartments());
+
+ cs.setTypes(types);
+ assertEquals(types, cs.getTypes());
+
+ cs.setMatches(matches);
+ assertEquals(matches, cs.getMatches());
+
+ cs.setLineWidth(lineWidth);
+ assertEquals(lineWidth, cs.getLineWidth());
+
+ cs.setElementId(reactionIdentifier);
+ assertEquals(reactionIdentifier, cs.getElementId());
+
+ cs.setReverseReaction(reverseReaction);
+ assertEquals(reverseReaction, cs.getReverseReaction());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ assertNotNull(cs.toString());
+ cs.setName("gene name");
+ cs.addCompartment("A");
+ cs.addType(Species.class);
+ cs.setValue(1.2);
+ cs.setColor(Color.BLACK);
+ cs.addMiriamData(new MiriamData(MiriamType.CAS, "X"));
+ assertNotNull(cs.toString());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCompartments() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ cs.addCompartments(new String[] { "a", "b" });
+ assertEquals(2, cs.getCompartments().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCompartments2() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ List<String> compartments = new ArrayList<>();
+ compartments.add("a");
+ compartments.add("b");
+ cs.addCompartments(compartments);
+ assertEquals(2, cs.getCompartments().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddIdentifgierColumns() throws Exception {
+ try {
+ MiriamData generalIdentifier = new MiriamData();
+ ColorSchema cs = new GenericColorSchema();
+ List<Pair<MiriamType, String>> compartments = new ArrayList<>();
+ compartments.add(new Pair<MiriamType, String>(MiriamType.CAS, "x"));
+ cs.addMiriamData(generalIdentifier);
+
+ assertEquals(1, cs.getMiriamData().size());
+ assertEquals(generalIdentifier, cs.getMiriamData().iterator().next());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddTypes() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ List<Class<? extends Element>> compartments = new ArrayList<>();
+ compartments.add(Species.class);
+ compartments.add(Protein.class);
+ cs.addTypes(compartments);
+ assertEquals(2, cs.getTypes().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
index 7e9ca40a76fc9c562bd22f607d5a79f71536adf3..90a1431e5107de641f887a6a65b91c59e2abc7a9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
@@ -18,6 +18,7 @@ import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.google.gson.Gson;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -30,30 +31,30 @@ public abstract class BaseController {
@ExceptionHandler({ Exception.class })
public ResponseEntity<Object> handleException(Exception e, WebRequest request) {
if (e instanceof lcsb.mapviewer.services.SecurityException) {
- return new ResponseEntity<Object>("{\"error\" : \"Access denied.\",\"reason\":\"" + e.getMessage() + "\"}",
- new HttpHeaders(), HttpStatus.FORBIDDEN);
+ return createErrorResponse("Access denied.", e.getMessage(), new HttpHeaders(), HttpStatus.FORBIDDEN);
} else if (e instanceof ObjectNotFoundException) {
- return new ResponseEntity<Object>("{\"error\" : \"Object not found.\",\"reason\":\"" + e.getMessage() + "\"}",
- new HttpHeaders(), HttpStatus.NOT_FOUND);
+ return createErrorResponse("Object not found.", e.getMessage(), new HttpHeaders(), HttpStatus.NOT_FOUND);
} else if (e instanceof ObjectExistsException) {
- return new ResponseEntity<Object>(
- "{\"error\" : \"Object already exists.\",\"reason\":\"" + e.getMessage() + "\"}", new HttpHeaders(),
- HttpStatus.CONFLICT);
+ return createErrorResponse("Object already exists.", e.getMessage(), new HttpHeaders(), HttpStatus.CONFLICT);
} else if (e instanceof QueryException) {
logger.error(e, e);
- return new ResponseEntity<Object>("{\"error\" : \"Query server error.\",\"reason\":\"" + e.getMessage() + "\"}",
- new HttpHeaders(), HttpStatus.BAD_REQUEST);
+ return createErrorResponse("Query server error.", e.getMessage(), new HttpHeaders(), HttpStatus.BAD_REQUEST);
} else if (e instanceof ServletRequestBindingException && e.getMessage().indexOf(Configuration.AUTH_TOKEN) >= 0) {
- return new ResponseEntity<Object>("{\"error\" : \"Access denied.\",\"reason\":\"" + e.getMessage() + "\"}",
- new HttpHeaders(), HttpStatus.FORBIDDEN);
+ return createErrorResponse("Access denied.", e.getMessage(), new HttpHeaders(), HttpStatus.FORBIDDEN);
} else {
logger.error(e, e);
- return new ResponseEntity<Object>(
- "{\"error\" : \"Internal server error.\",\"reason\":\"" + e.getMessage() + "\"}", new HttpHeaders(),
+ return createErrorResponse("Internal server error.", e.getMessage(), new HttpHeaders(),
HttpStatus.INTERNAL_SERVER_ERROR);
}
}
+ private ResponseEntity<Object> createErrorResponse(String errorMessage, String error, HttpHeaders httpHeaders,
+ HttpStatus status) {
+
+ return new ResponseEntity<Object>(
+ "{\"error\" : \"" + errorMessage + "\",\"reason\":" + new Gson().toJson(error) + "}", httpHeaders, status);
+ }
+
public Map<String, Object> parseBody(String body) throws IOException, JsonParseException, JsonMappingException {
if (body == null || body.isEmpty()) {
return new HashMap<>();
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 990e348f5e63bef38210c4760b3baaa0ba4876d5..be6946bd40ca608b4e58c715dee66555863aeca0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -807,10 +807,8 @@ public class LayoutService implements ILayoutService {
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().trim().equals("")) {
- sb.append(pair.getLeft().getCommonName() + ": " + pair.getRight() + ", ");
- }
+ for (MiriamData md : schema.getMiriamData()) {
+ sb.append(md.getDataType().getCommonName() + ": " + md.getResource() + ", ");
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
@@ -864,10 +862,8 @@ public class LayoutService implements ILayoutService {
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().trim().equals("")) {
- sb.append(pair.getLeft().getCommonName() + ": " + pair.getRight() + ", ");
- }
+ for (MiriamData md : schema.getMiriamData()) {
+ sb.append(md.getDataType().getCommonName() + ": " + md.getResource() + ", ");
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.ELEMENT_IDENTIFIER)) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index e2a41ccbe2666f1c9667ee54c84ea19f1c3b04a0..624927757ad13fdfeaf903dbf2ec635a08bc84b6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -194,6 +194,7 @@ public class ColorSchemaReader {
line = br.readLine();
while (line != null) {
lineIndex++;
+ String errorPrefix = "[Line " + lineIndex + "]\t";
if (!line.trim().equals("")) {
String[] values = line.split("\t", -1);
if (values.length != columns.length) {
@@ -224,12 +225,7 @@ public class ColorSchemaReader {
schema.setColor(colorParser.parse(values[colorColumn]));
}
if (identifierColumn != null && !values[identifierColumn].equals("")) {
- if (mc.isValidIdentifier(values[identifierColumn])) {
- schema.setGeneralIdentifier(values[identifierColumn]);
- } else {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "] Invalid identifier: " + values[identifierColumn]);
- }
+ processGeneralIdentifier(values[identifierColumn], schema, errorPrefix);
}
if (descriptionColumn != null) {
schema.setDescription(values[descriptionColumn]);
@@ -303,6 +299,15 @@ public class ColorSchemaReader {
return mergeSchemas(result);
}
+ private void processGeneralIdentifier(String string, ColorSchema schema, String errorPrefix)
+ throws InvalidColorSchemaException {
+ if (mc.isValidIdentifier(string)) {
+ schema.addMiriamData(MiriamType.getMiriamDataFromIdentifier(string));
+ } else {
+ throw new InvalidColorSchemaException(errorPrefix + " Invalid identifier: " + string);
+ }
+ }
+
/**
* Sets proper value of identifier to {@link ColorSchema} from cell content.
*
@@ -315,7 +320,7 @@ public class ColorSchemaReader {
*/
private void processIdentifier(String content, MiriamType type, ColorSchema schema) {
if (!content.isEmpty()) {
- schema.addIdentifierColumn(new Pair<MiriamType, String>(type, content));
+ schema.addMiriamData(new MiriamData(type, content));
}
}
@@ -487,9 +492,8 @@ public class ColorSchemaReader {
if (nameColumn == null && identifierColumn == null && customIdentifiers.size() == 0
&& elementIdentifierColumn == null) {
- throw new InvalidColorSchemaException(
- "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle() + ","
- + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
+ throw new InvalidColorSchemaException("One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle()
+ + "," + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
}
if (valueColumn == null && colorColumn == null) {
@@ -552,11 +556,7 @@ public class ColorSchemaReader {
schema.setReverseReaction("true".equalsIgnoreCase(values[reverseReactionColumn]));
}
if (identifierColumn != null && !values[identifierColumn].equals("")) {
- if (mc.isValidIdentifier(values[identifierColumn])) {
- schema.setGeneralIdentifier(values[identifierColumn]);
- } else {
- throw new InvalidColorSchemaException(errorPrefix + "Invalid identifier: " + values[identifierColumn]);
- }
+ processGeneralIdentifier(values[identifierColumn], schema, errorPrefix);
}
for (Pair<MiriamType, Integer> pair : customIdentifiers) {
processIdentifier(values[pair.getRight()], pair.getLeft(), schema);
@@ -738,7 +738,7 @@ public class ColorSchemaReader {
if (schema.getCompartments().size() > 0) {
result.add(ColorSchemaColumn.COMPARTMENT);
}
- if (schema.getGeneralIdentifier() != null || schema.getIdentifierColumns().size() > 0) {
+ if (schema.getMiriamData().size() > 0) {
result.add(ColorSchemaColumn.IDENTIFIER);
}
if (schema.getLineWidth() != null) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index 12a4f24bb406354047ab855482414801d0382d42..c3df7132575a1a2f33e52008b816fc3bd9fa8dd0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -12,7 +12,6 @@ import java.util.Map;
import java.util.Set;
import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.ss.usermodel.Cell;
@@ -28,6 +27,7 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -257,7 +257,7 @@ public class ColorSchemaXlsxReader {
MiriamConnector miriamConnector = new MiriamConnector();
String value = cell.getStringCellValue().trim();
if (miriamConnector.isValidIdentifier(value)) {
- schema.setGeneralIdentifier(value);
+ schema.addMiriamData(MiriamType.getMiriamDataFromIdentifier(value));
} else {
throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
}
@@ -266,7 +266,7 @@ public class ColorSchemaXlsxReader {
for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
cell = row.getCell(pair.getRight());
if (cell != null) {
- schema.addIdentifierColumn(new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
+ schema.addMiriamData(new MiriamData(pair.getLeft(), cell.getStringCellValue()));
}
}
@@ -275,7 +275,7 @@ public class ColorSchemaXlsxReader {
throw new InvalidColorSchemaException("Value or Color is needed not both");
}
- if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
+ if (schema.getName() == null && schema.getMiriamData().size() == 0 && foundCustomIdentifiers.size() == 0
&& schema.getElementId() == null) {
throw new InvalidColorSchemaException(
"One of these columns values is obligatory: name, identifier, reactionIdentifier");
@@ -316,7 +316,7 @@ public class ColorSchemaXlsxReader {
if (schema.getCompartments().size() > 0) {
result.add(ColorSchemaColumn.COMPARTMENT);
}
- if (schema.getGeneralIdentifier() != null || schema.getIdentifierColumns().size() > 0) {
+ if (schema.getMiriamData().size() > 0) {
result.add(ColorSchemaColumn.IDENTIFIER);
}
if (schema.getLineWidth() != null) {
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 1bf9bb3ab450e8e7dc75f0548927a9c75e6ee994..ef9c4ddf5b15398aa01a758f4edef551940791f9 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -66,7 +66,7 @@ public class LayoutServiceTest2 {
ColorSchema cs = new GenericColorSchema();
cs.setColor(Color.CYAN);
cs.addCompartment("BLA");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+ cs.addMiriamData(new MiriamData(MiriamType.CAS, "CAS_ID"));
cs.setLineWidth(3.3);
cs.setMatches(2);
cs.setName("UUU");
@@ -105,7 +105,7 @@ public class LayoutServiceTest2 {
GeneVariationColorSchema cs = new GeneVariationColorSchema();
cs.setColor(Color.CYAN);
cs.addCompartment("BLA");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+ cs.addMiriamData(new MiriamData(MiriamType.CAS, "CAS_ID"));
cs.setLineWidth(3.3);
cs.setMatches(2);
cs.setName("UUU");
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index d5cc32a2086bfb208dbd47976bbdb6caf77021cc..671877a0c7cd18f503fa40b0c2a658686c104857 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -26,6 +26,7 @@ import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
@@ -322,9 +323,9 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schemaWithIdentifiers.txt");
for (ColorSchema colorSchema : schemas) {
- for (Pair<MiriamType, String> pair : colorSchema.getIdentifierColumns()) {
- assertNotNull(pair.getRight());
- assertFalse(pair.getRight().isEmpty());
+ for (MiriamData md: colorSchema.getMiriamData()) {
+ assertNotNull(md.getResource());
+ assertFalse(md.getResource().isEmpty());
}
}
@@ -341,8 +342,8 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schemaIdWithoutName.txt");
for (ColorSchema colorSchema : schemas) {
- for (Pair<MiriamType, String> pair : colorSchema.getIdentifierColumns()) {
- assertFalse(pair.getRight().isEmpty());
+ for (MiriamData md: colorSchema.getMiriamData()) {
+ assertFalse(md.getResource().isEmpty());
assertNull(colorSchema.getName());
}
}