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Merge branch '0.9.2'
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@eduramiba
eduramiba committed Nov 18, 2017
2 parents 2b9a7c8 + 56f48cd commit 5a789b1
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Showing 14 changed files with 7,707 additions and 32 deletions.
17 changes: 13 additions & 4 deletions modules/ExportPlugin/src/main/java/org/gephi/io/exporter/plugin/ExporterGraphML.java
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Original file line number Diff line number Diff line change
Expand Up @@ -444,10 +444,19 @@ private Element createEdge(Document document, Edge e, Graph graph) throws Except
Element weightE = createEdgeWeight(document, e, graph);
edgeE.appendChild(weightE);

if (e.isDirected() && !graph.isDirected()) {
edgeE.setAttribute("type", "directed");
} else if (!e.isDirected() && graph.isDirected()) {
edgeE.setAttribute("type", "undirected");
boolean directedEdgeDefault = graph.isDirected() || graph.isMixed();
if (e.isDirected() && !directedEdgeDefault) {
edgeE.setAttribute("directed", "true");
} else if (!e.isDirected() && directedEdgeDefault) {
edgeE.setAttribute("directed", "false");
}

if (e.getTypeLabel() != null) {
//Edge labels not retained on graphml export https://github.com/gephi/gephi/issues/1516
String typeLabel = e.getTypeLabel().toString().trim();
if (!typeLabel.isEmpty()) {
edgeE.setAttribute("label", typeLabel);
}
}

//Attribute values
Expand Down
2 changes: 1 addition & 1 deletion modules/ExportPlugin/src/main/nbm/manifest.mf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Manifest-Version: 1.0
AutoUpdate-Essential-Module: true
OpenIDE-Module-Localizing-Bundle: org/gephi/io/exporter/plugin/Bundle.properties
OpenIDE-Module-Specification-Version: ${gephi.modules.specification.version}
OpenIDE-Module-Specification-Version: 0.9.2.1
OpenIDE-Module-Display-Category: Plugin
OpenIDE-Module-Name: Export Plugin
32 changes: 21 additions & 11 deletions modules/ImportAPI/src/main/java/org/gephi/io/importer/impl/ImportContainerImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -333,6 +333,16 @@ public void addEdge(EdgeDraft edgeDraft) {
edgeMap.put(edgeDraft.getId(), index);
}

private void removeNode(NodeDraftImpl node) {
String id = node.getId();
if (!nodeMap.containsKey(id)) {
return;
}

int index = nodeMap.removeInt(id);
nodeList.set(index, null);
}

@Override
public void removeEdge(EdgeDraft edgeDraft) {
checkElementDraftImpl(edgeDraft);
Expand All @@ -343,6 +353,8 @@ public void removeEdge(EdgeDraft edgeDraft) {
if (!edgeMap.containsKey(id)) {
return;
}

boolean directed = edgeDraftImpl.getDirection() == EdgeDirection.DIRECTED;

if (edgeDraftImpl.getDirection() != null) {
//UnCounting
Expand All @@ -361,12 +373,12 @@ public void removeEdge(EdgeDraft edgeDraft) {
}

int edgeType = getEdgeType(edgeDraftImpl.getType());
long sourceTargetLong = getLongId(edgeDraftImpl);
long sourceTargetLong = getLongId(edgeDraftImpl.getSource(), edgeDraftImpl.getTarget(), directed);
ensureLongSetArraySize(edgeType);
Long2ObjectMap<int[]> edgeTypeSet = edgeTypeSets[edgeType];

//Get index
int index = edgeMap.remove(id);
int index = edgeMap.removeInt(id);

//Update edgeType set
int[] edges = edgeTypeSet.remove(sourceTargetLong);
Expand Down Expand Up @@ -727,14 +739,14 @@ public void closeLoader() {
if (directedEdgesCount > 0 && edgeDefault.equals(EdgeDirectionDefault.UNDIRECTED)) {
//Force undirected
for (EdgeDraftImpl edge : edgeList.toArray(new EdgeDraftImpl[0])) {
if (edge != null && edge.getDirection().equals(EdgeDirection.DIRECTED)) {
final boolean notAlreadyRemoved = edge != null
&& edgeMap.containsKey(edge.getId());

if (notAlreadyRemoved && edge.getDirection().equals(EdgeDirection.DIRECTED)) {
EdgeDraftImpl opposite = getOpposite(edge);
if (opposite != null) {
int oppositeIndex = edgeMap.getInt(opposite.getId());
mergeDirectedEdges(opposite, edge);

edgeMap.removeInt(opposite.getId());
edgeList.set(oppositeIndex, null);
removeEdge(opposite);
}
}
}
Expand All @@ -745,14 +757,12 @@ public void closeLoader() {
if (!allowAutoNode()) {
for (NodeDraftImpl node : nodeList) {
if (node != null && node.isCreatedAuto()) {
int index = nodeMap.removeInt(node.getId());
nodeList.set(index, null);
removeNode(node);
}
}
for (EdgeDraftImpl edge : edgeList) {
if (edge != null && (edge.getSource().isCreatedAuto() || edge.getTarget().isCreatedAuto())) {
int index = edgeMap.remove(edge.getId());
edgeList.set(index, null);
removeEdge(edge);
}
}
}
Expand Down
31 changes: 18 additions & 13 deletions modules/ImportPlugin/src/main/java/org/gephi/io/importer/plugin/file/ImporterGraphML.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ public class ImporterGraphML implements FileImporter, LongTask {
private static final String EDGE_SOURCE = "source";
private static final String EDGE_TARGET = "target";
private static final String EDGE_DIRECTED = "directed";
private static final String EDGE_TYPE = "label";
private static final String ATTRIBUTE = "key";
private static final String ATTRIBUTE_ID = "id";
private static final String ATTRIBUTE_TITLE = "attr.name";
Expand Down Expand Up @@ -130,9 +131,6 @@ public ImporterGraphML() {
properties.addEdgePropertyAssociation(EdgeProperties.G, "g");
properties.addEdgePropertyAssociation(EdgeProperties.B, "b");
properties.addEdgePropertyAssociation(EdgeProperties.COLOR, "color");

nodePropertiesAttributes.put("d3", NodeProperties.LABEL);// Default node label used by yEd from yworks.com.
edgePropertiesAttributes.put("d7", EdgeProperties.LABEL);// Default edge label used by yEd from yworks.com.
}

@Override
Expand Down Expand Up @@ -197,7 +195,7 @@ private void readGraph(XMLStreamReader reader) throws Exception {
for (int i = 0; i < reader.getAttributeCount(); i++) {
String attName = reader.getAttributeName(i).getLocalPart();
if (GRAPH_DEFAULT_EDGETYPE.equalsIgnoreCase(attName)) {
defaultEdgeType = reader.getAttributeValue(i);
defaultEdgeType = reader.getAttributeValue(i).trim();
} else if (GRAPH_ID.equalsIgnoreCase(attName)) {
id = reader.getAttributeValue(i);
}
Expand Down Expand Up @@ -279,7 +277,7 @@ private void readNodeAttValue(XMLStreamReader reader, NodeDraft node) throws Exc
for (int i = 0; i < reader.getAttributeCount(); i++) {
String attName = reader.getAttributeName(i).getLocalPart();
if (ATTVALUE_FOR.equalsIgnoreCase(attName)) {
fore = reader.getAttributeValue(i);
fore = reader.getAttributeValue(i).trim();
}
}

Expand Down Expand Up @@ -374,6 +372,7 @@ private void readEdge(XMLStreamReader reader) throws Exception {
String source = "";
String target = "";
String directed = "";
String type = null;

//Attributes
for (int i = 0; i < reader.getAttributeCount(); i++) {
Expand All @@ -386,6 +385,8 @@ private void readEdge(XMLStreamReader reader) throws Exception {
id = reader.getAttributeValue(i);
} else if (EDGE_DIRECTED.equalsIgnoreCase(attName)) {
directed = reader.getAttributeValue(i);
} else if (EDGE_TYPE.equalsIgnoreCase(attName)) {
type = reader.getAttributeValue(i).trim();
}
}

Expand All @@ -401,6 +402,10 @@ private void readEdge(XMLStreamReader reader) throws Exception {
NodeDraft nodeTarget = container.getNode(target);
edge.setSource(nodeSource);
edge.setTarget(nodeTarget);
if (type != null && !type.isEmpty()) {
//Edge labels not retained on graphml export https://github.com/gephi/gephi/issues/1516
edge.setType(type);
}

//Type
if (!directed.isEmpty()) {
Expand All @@ -418,9 +423,9 @@ private void readEdge(XMLStreamReader reader) throws Exception {

boolean end = false;
while (reader.hasNext() && !end) {
int type = reader.next();
int elemType = reader.next();

switch (type) {
switch (elemType) {
case XMLStreamReader.START_ELEMENT:
if (ATTVALUE.equalsIgnoreCase(xmlReader.getLocalName())) {
readEdgeAttValue(reader, edge);
Expand All @@ -444,7 +449,7 @@ private void readEdgeAttValue(XMLStreamReader reader, EdgeDraft edge) throws Exc
for (int i = 0; i < reader.getAttributeCount(); i++) {
String attName = reader.getAttributeName(i).getLocalPart();
if (ATTVALUE_FOR.equalsIgnoreCase(attName)) {
fore = reader.getAttributeValue(i);
fore = reader.getAttributeValue(i).trim();
}
}

Expand Down Expand Up @@ -533,13 +538,13 @@ private void readAttribute(XMLStreamReader reader) throws Exception {
for (int i = 0; i < reader.getAttributeCount(); i++) {
String attName = reader.getAttributeName(i).getLocalPart();
if (ATTRIBUTE_ID.equalsIgnoreCase(attName)) {
id = reader.getAttributeValue(i);
id = reader.getAttributeValue(i).trim();
} else if (ATTRIBUTE_TYPE.equalsIgnoreCase(attName)) {
type = reader.getAttributeValue(i);
type = reader.getAttributeValue(i).trim();
} else if (ATTRIBUTE_TITLE.equalsIgnoreCase(attName)) {
title = reader.getAttributeValue(i);
title = reader.getAttributeValue(i).trim();
} else if (ATTRIBUTE_FOR.equalsIgnoreCase(attName)) {
forStr = reader.getAttributeValue(i);
forStr = reader.getAttributeValue(i).trim();
}
}

Expand All @@ -565,7 +570,7 @@ private void readAttribute(XMLStreamReader reader) throws Exception {
property = true;
}
}

if (property) {
return;
}
Expand Down
17 changes: 17 additions & 0 deletions ...tPlugin/src/main/java/org/gephi/io/importer/plugin/file/spreadsheet/SpreadsheetUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ Development and Distribution License("CDDL") (collectively, the
import org.gephi.io.importer.api.Issue;
import org.gephi.io.importer.api.Report;
import org.gephi.io.importer.plugin.file.spreadsheet.sheet.SheetParser;
import org.gephi.utils.CharsetToolkit;
import org.openide.util.NbBundle;

/**
Expand Down Expand Up @@ -127,8 +128,24 @@ public static CSVParser configureCSVParser(File file, Character fieldSeparator,
csvFormat = csvFormat.withHeader((String[]) null).withSkipHeaderRecord(false);
}

boolean hasBOM = false;
try (FileInputStream is = new FileInputStream(file)) {
CharsetToolkit charsetToolkit = new CharsetToolkit(is);
hasBOM = charsetToolkit.hasUTF8Bom() || charsetToolkit.hasUTF16BEBom() || charsetToolkit.hasUTF16LEBom();
} catch (IOException e) {
//NOOP
}

FileInputStream fileInputStream = new FileInputStream(file);
InputStreamReader is = new InputStreamReader(fileInputStream, charset);
if (hasBOM) {
try {
is.read();
} catch (IOException e) {
// should never happen, as a file with no content
// but with a BOM has at least one char
}
}
return new CSVParser(is, csvFormat);
}
}
57 changes: 56 additions & 1 deletion modules/ImportPlugin/src/test/java/org/gephi/io/importer/plugin/file/SpreadsheetNGTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ Development and Distribution License("CDDL") (collectively, the
import org.gephi.graph.api.types.IntervalSet;
import org.gephi.io.exporter.plugin.ExporterSpreadsheet;
import org.gephi.io.importer.api.Container;
import org.gephi.io.importer.api.EdgeDirectionDefault;
import org.gephi.io.importer.api.EdgeMergeStrategy;
import org.gephi.io.importer.api.ImportController;
import org.gephi.io.importer.plugin.file.spreadsheet.ImporterSpreadsheetCSV;
Expand Down Expand Up @@ -343,7 +344,7 @@ public void testEdgesTableWithTimeset_Interval() throws FileNotFoundException, I

@Test
public void testEdgesTableDynamicWeightsMerged() throws FileNotFoundException, IOException {
File file = FileUtil.archiveOrDirForURL(SpreadsheetNGTest.class.getResource("/org/gephi/io/importer/plugin/file/spreadsheet/edgest_table_dynamic_weights.csv"));
File file = FileUtil.archiveOrDirForURL(SpreadsheetNGTest.class.getResource("/org/gephi/io/importer/plugin/file/spreadsheet/edges_table_dynamic_weights.csv"));

ImporterSpreadsheetCSV importer = new ImporterSpreadsheetCSV();

Expand Down Expand Up @@ -491,6 +492,60 @@ public void testUTF8Chars() throws FileNotFoundException, IOException {

checkNodesSpreadsheet();
}

@Test
public void testUTF8CharsWithBOM() throws FileNotFoundException, IOException {
File file = FileUtil.archiveOrDirForURL(SpreadsheetNGTest.class.getResource("/org/gephi/io/importer/plugin/file/spreadsheet/test_utf8_chars_with_bom.csv"));

ImporterSpreadsheetCSV importer = new ImporterSpreadsheetCSV();

importer.setFile(file);

Assert.assertEquals(importer.getMode(), Mode.NODES_TABLE);
Assert.assertEquals(importer.getCharset().name(), "UTF-8");

Container container = importController.importFile(
file, importer
);
Assert.assertNotNull(container);

importController.process(container, new DefaultProcessor(), workspace);

checkNodesSpreadsheet();
}

@Test
public void testEdgesTableOppositeForceUndirected_Merged() throws FileNotFoundException, IOException {
File file = FileUtil.archiveOrDirForURL(SpreadsheetNGTest.class.getResource("/org/gephi/io/importer/plugin/file/spreadsheet/edges_table_opposite_force_undirected_merged.csv"));

Container container = importController.importFile(file);
Assert.assertNotNull(container);

//Force undirected:
container.getLoader().setEdgeDefault(EdgeDirectionDefault.UNDIRECTED);
container.getLoader().setEdgesMergeStrategy(EdgeMergeStrategy.SUM);

importController.process(container, new DefaultProcessor(), workspace);

checkEdgesSpreadsheet();
}

@Test
public void testEdgesTableOppositeForceUndirected_Issue1848() throws FileNotFoundException, IOException {
//https://github.com/gephi/gephi/issues/1848
File file = FileUtil.archiveOrDirForURL(SpreadsheetNGTest.class.getResource("/org/gephi/io/importer/plugin/file/spreadsheet/edges_table_opposite_force_undirected_issue_1848.csv"));

Container container = importController.importFile(file);
Assert.assertNotNull(container);

//Force undirected:
container.getLoader().setEdgeDefault(EdgeDirectionDefault.UNDIRECTED);
container.getLoader().setEdgesMergeStrategy(EdgeMergeStrategy.SUM);

importController.process(container, new DefaultProcessor(), workspace);

checkEdgesSpreadsheet();
}

private void checkEdgesSpreadsheet() throws IOException {
checkEdgesSpreadsheet(true);
Expand Down
0 ...eadsheet/edgest_table_dynamic_weights.csv → ...readsheet/edges_table_dynamic_weights.csv
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