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Commit 59ddae65 authored by Piotr Gawron's avatar Piotr Gawron
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Merge branch '238-data-overlay-with-miriam-ids' into 'master' 

Resolve "data overlay with miriam ids"

Closes #238

See merge request piotr.gawron/minerva!195
parents d9654bd5 8628ce0e
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1 merge request!195Resolve "data overlay with miriam ids"
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model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+ 9
− 27
View file @ 59ddae65
......@@ -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)) {
......
model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+ 79
− 8
View file @ 59ddae65
......@@ -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;
}
}
}
model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+ 15
− 74
View file @ 59ddae65
......@@ -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;
}
}
model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+ 124
− 129
View file @ 59ddae65
......@@ -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;
}
}
}
rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
+ 14
− 13
View file @ 59ddae65
......@@ -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<>();
......
service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+ 4
− 8
View file @ 59ddae65
......@@ -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)) {
......
service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+ 16
− 16
View file @ 59ddae65
......@@ -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) {
......
service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+ 5
− 5
View file @ 59ddae65
......@@ -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) {
......
service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+ 2
− 2
View file @ 59ddae65
......@@ -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");
......
service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+ 6
− 5
View file @ 59ddae65
......@@ -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());
}
}
......
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