From 37b3208fe8664396af3c34fc08ff48c7474de1f5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Jun 2017 14:03:53 +0200
Subject: [PATCH] export to xml improved (additional field data added)
---
.../annotation/RestAnnotationParser.java | 96 ++++++++++++++++---
.../annotation/RestAnnotationParserTest.java | 12 ++-
2 files changed, 93 insertions(+), 15 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index a1ab11fc4a..ccec089ae5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.annotation;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -21,6 +22,8 @@ import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -100,25 +103,90 @@ public class RestAnnotationParser extends XmlParser {
* @return note string with structural information about element
*/
public String createAnnotationString(Element element) {
- String symbol = element.getSymbol();
- if (symbol == null) {
- symbol = "";
- }
- String name = element.getFullName();
- if (name == null) {
- name = "";
- }
+ return createAnnotationString(element, false);
+ }
+
+ /**
+ * Creates note string with structural information about element.
+ *
+ * @param element
+ * element for which notes are created
+ * @param forceFullInfo
+ * when true annotation string will contain information about empty
+ * fields
+ * @return note string with structural information about element
+ */
+ public String createAnnotationString(Element element, boolean forceFullInfo) {
+ Set<MiriamData> data = element.getMiriamData();
StringBuilder sb = new StringBuilder();
- sb.append(NoteField.SYMBOL.getCommonName() + ": " + symbol + "\n");
- sb.append(NoteField.NAME.getCommonName() + ": " + name + "\n");
- // descrfiption will be in the string anyways so we don't need to repeat it
- sb.append(NoteField.DESCRIPTION.getCommonName() + ": \n");
- sb.append(NoteField.PREVIOUS_SYMBOLS.getCommonName() + ": " + StringUtils.join(element.getFormerSymbols(), ", ") + "\n");
- sb.append(NoteField.SYNONYMS.getCommonName() + ": " + StringUtils.join(element.getSynonyms(), ", ") + "\n");
+ sb.append(createEntry(NoteField.SYMBOL, element.getSymbol(), forceFullInfo));
+ sb.append(createEntry(NoteField.NAME, element.getFullName(), forceFullInfo));
+ sb.append(createEntry(NoteField.PREVIOUS_SYMBOLS, element.getFormerSymbols(), forceFullInfo));
+ sb.append(createEntry(NoteField.SYNONYMS, element.getSynonyms(), forceFullInfo));
+ sb.append(createEntry(NoteField.HGNC, filterMiriam(data, MiriamType.HGNC), forceFullInfo));
+ sb.append(createEntry(NoteField.ENTREZ, filterMiriam(data, MiriamType.ENTREZ), forceFullInfo));
+ sb.append(createEntry(NoteField.REFSEQ, filterMiriam(data, MiriamType.REFSEQ), forceFullInfo));
+ sb.append(createEntry(NoteField.REACTOME, filterMiriam(data, MiriamType.REACTOME), forceFullInfo));
+ sb.append(createEntry(NoteField.PUBMED, filterMiriam(data, MiriamType.PUBMED), forceFullInfo));
+ sb.append(createEntry(NoteField.KEGG_GENES, filterMiriam(data, MiriamType.KEGG_GENES), forceFullInfo));
+ sb.append(createEntry(NoteField.PANTHER, filterMiriam(data, MiriamType.PANTHER), forceFullInfo));
+ sb.append(createEntry(NoteField.DESCRIPTION, null, forceFullInfo));
+ sb.append(createEntry(NoteField.ABBREVIATION, element.getAbbreviation(), forceFullInfo));
+ sb.append(createEntry(NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY, element.getSemanticZoomLevelVisibility(), forceFullInfo));
+ sb.append(createEntry(NoteField.CHARGED_FORMULA, element.getFormula(), forceFullInfo));
+ if (element instanceof Species) {
+ sb.append(createEntry(NoteField.CHARGE, ((Species) element).getCharge(), forceFullInfo));
+ }
+
sb.append("\n");
return sb.toString();
}
+ private List<MiriamData> filterMiriam(Collection<MiriamData> miriamDataSet, MiriamType type) {
+ List<MiriamData> result = new ArrayList<>();
+ for (MiriamData miriamData : miriamDataSet) {
+ if (miriamData.getDataType().equals(type)) {
+ result.add(miriamData);
+ }
+ }
+ return result;
+ }
+
+ private String createEntry(NoteField type, Object value, boolean forceFullInfo) {
+ if (value == null) {
+ if (forceFullInfo) {
+ return type.getCommonName() + ": \n";
+ } else {
+ return "";
+ }
+ } else if (value instanceof String) {
+ return type.getCommonName() + ": " + value + "\n";
+ } else if (value instanceof Integer) {
+ return type.getCommonName() + ": " + value + "\n";
+ } else if (value instanceof Collection) {
+ Collection<?> collection = (Collection) value;
+ if (collection.size() > 0 || forceFullInfo) {
+ String result = "";
+ for (Object object : collection) {
+ if (!result.equals("")) {
+ result = result + ", ";
+ }
+ if (object instanceof MiriamData) {
+ result += ((MiriamData) object).getResource();
+ } else {
+ result += object;
+ }
+
+ }
+ return type.getCommonName() + ": " + result + "\n";
+ } else {
+ return "";
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + value.getClass());
+ }
+ }
+
/**
* Returns value for the type of the structurized annotation. Structurized
* annotation is in format:
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index f8ab6d2d44..6cca1af6e5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -22,6 +22,7 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -286,10 +287,19 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
GenericProtein element = new GenericProtein("id");
element.addFormerSymbol(former1);
element.addFormerSymbol(former2);
- String str = rap.createAnnotationString(element);
+ element.setCharge(1);
+ String str = rap.createAnnotationString(element, true);
+ logger.debug(str);
assertTrue(str.contains(former1));
assertTrue(str.contains(former2));
+ for (NoteField field : NoteField.values()) {
+ if (field.getClazz().isAssignableFrom(element.getClass()) || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
+ assertTrue("Export string doesn't contain info about: " + field.getCommonName(), str.indexOf(field.getCommonName()) >= 0);
+ }
+
+ }
+
} catch (Exception e) {
e.printStackTrace();
throw e;
--
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