protected void addNodes(
Integer graphId, Connection con, ContainerLoader cl, Map<String, Object> graphParam)
throws SQLException {
String urlbaseTmp = (String) graphParam.get("url_base");
final ElementDraft.Factory elementDraftFactory = cl.factory();
final Pattern tagSplitter = Pattern.compile(",");
final String urlbase = urlbaseTmp == null ? "/" : urlbaseTmp;
graphDataSource.populateNodesForGraph(
con,
graphId,
(num, name, tag) -> {
String[] tags = tag != null ? tagSplitter.split(tag) : new String[] {};
NodeDraft nd = elementDraftFactory.newNodeDraft(num.toString());
nd.setLabel(name);
nd.setValue(KEY_URL, urlbase + num);
nd.setValue(KEY_TAG, tags);
cl.addNode(nd);
return true;
});
}
@Override
public Container create(Integer graphId, Map<String, Object> extraParam) {
LOGGER.debug("Gephi: Setup container, nodes and edges.");
Container container = CONTAINER_FACTORY.newContainer();
container.setReport(new Report());
try (Connection con = graphDataSource.getConnection()) {
con.setAutoCommit(false);
Map<String, Object> graphParam = graphDataSource.getGraphByID(con, graphId);
graphParam.putAll(extraParam);
ContainerLoader cl = container.getLoader();
setupDirectedMode(cl, graphParam);
cl.addNodeColumn(KEY_URL, String.class);
cl.addNodeColumn(KEY_TAG, String[].class);
addNodes(graphId, con, cl, graphParam);
addEdges(graphId, con, cl, graphParam);
} catch (SQLException e) {
throw new RuntimeException(e);
}
return container;
}
private void setupDirectedMode(ContainerLoader cl, Map<String, Object> graphParam) {
Integer directed = (Integer) graphParam.get("directed");
if (Integer.valueOf(2).equals(directed)) {
cl.setEdgeDefault(EdgeDirectionDefault.MIXED);
} else if (Integer.valueOf(1).equals(directed)) {
cl.setEdgeDefault(EdgeDirectionDefault.DIRECTED);
} else {
cl.setEdgeDefault(EdgeDirectionDefault.UNDIRECTED);
}
}
protected void addEdges(
Integer graphId, Connection con, ContainerLoader cl, Map<String, Object> graphParam)
throws SQLException {
final ElementDraft.Factory elementDraftFactory = cl.factory();
graphDataSource.populateEdgesForGraph(
con,
graphId,
(num, source, target, val) -> {
EdgeDraft ed = elementDraftFactory.newEdgeDraft(num.toString());
ed.setSource(cl.getNode(source.toString()));
ed.setTarget(cl.getNode(target.toString()));
ed.setWeight(val.floatValue());
cl.addEdge(ed);
return true;
});
}
public void convertToNetwork() throws IOException, InvalidFormatException {
container = MyFileImporter.container;
container.setEdgeDefault(EdgeDefault.UNDIRECTED);
String firstDelimiter;
String secondDelimiter;
firstDelimiter = Utils.getCharacter(MyFileImporter.firstConnectorDelimiter);
secondDelimiter = Utils.getCharacter(MyFileImporter.secondConnectorDelimiter);
boolean oneTypeOfAgent =
MyFileImporter.getFirstConnectedAgent().equals(MyFileImporter.getSecondConnectedAgent());
nbColumnFirstAgent = MyFileImporter.firstConnectedAgentIndex;
nbColumnSecondAgent = MyFileImporter.secondConnectedAgentIndex;
Integer lineCounter = 0;
InputStream inp;
inp = new FileInputStream(fileName);
Workbook wb = WorkbookFactory.create(inp);
Row row;
Sheet sheet = wb.getSheet(sheetName);
int startingRow;
if (MyFileImporter.headersPresent) {
startingRow = 1;
} else {
startingRow = 0;
}
Set<String> linesFirstAgent = new HashSet();
Set<String> linesSecondAgent = new HashSet();
for (int i = startingRow; i <= sheet.getLastRowNum(); i++) {
row = sheet.getRow(i);
if (row == null) {
break;
}
Cell cell = row.getCell(nbColumnFirstAgent);
if (cell == null) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getFirstConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
String firstAgent = row.getCell(nbColumnFirstAgent).getStringCellValue();
if (firstAgent == null || firstAgent.isEmpty()) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getFirstConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
if (MyFileImporter.removeDuplicates) {
boolean newLine = linesFirstAgent.add(firstAgent);
if (!newLine) {
continue;
}
}
String secondAgent = null;
if (!oneTypeOfAgent) {
cell = row.getCell(nbColumnSecondAgent);
if (cell == null) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getFirstConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
secondAgent = row.getCell(nbColumnSecondAgent).getStringCellValue();
if (secondAgent == null || secondAgent.isEmpty()) {
Issue issue =
new Issue(
"problem with line "
+ lineCounter
+ " (empty column "
+ MyFileImporter.getSecondConnectedAgent()
+ "). It was skipped in the conversion",
Issue.Level.WARNING);
MyFileImporter.getStaticReport().logIssue(issue);
continue;
}
if (MyFileImporter.removeDuplicates) {
boolean newLine = linesFirstAgent.add(firstAgent);
if (!newLine) {
continue;
}
}
}
lineCounter++;
String[] firstAgentSplit;
String[] secondAgentSplit;
if (firstDelimiter != null) {
firstAgentSplit = firstAgent.trim().split(firstDelimiter);
} else {
firstAgentSplit = new String[1];
firstAgentSplit[0] = firstAgent;
}
for (String node : firstAgentSplit) {
nodesFirst.add(node.trim());
}
if (!oneTypeOfAgent) {
if (secondDelimiter != null) {
secondAgentSplit = secondAgent.trim().split(secondDelimiter);
} else {
secondAgentSplit = new String[1];
secondAgentSplit[0] = secondAgent;
}
for (String node : secondAgentSplit) {
nodesSecond.add(node.trim());
}
} else {
secondAgentSplit = null;
}
String[] both = ArrayUtils.addAll(firstAgentSplit, secondAgentSplit);
// let's find all connections between all the tags for this picture
Utils usefulTools = new Utils();
List<String> connections = usefulTools.getListOfLinks(both, MyFileImporter.removeSelfLoops);
edges.addAll(connections);
}
NodeDraft node;
AttributeTable atNodes = container.getAttributeModel().getNodeTable();
AttributeColumn acFrequency = atNodes.addColumn("frequency", AttributeType.INT);
AttributeColumn acType = atNodes.addColumn("type", AttributeType.STRING);
for (String n : nodesFirst.elementSet()) {
node = container.factory().newNodeDraft();
node.setId(n);
node.setLabel(n);
node.addAttributeValue(acFrequency, nodesFirst.count(n));
node.addAttributeValue(acType, MyFileImporter.getFirstConnectedAgent());
container.addNode(node);
}
for (String n : nodesSecond.elementSet()) {
node = container.factory().newNodeDraft();
node.setId(n);
node.setLabel(n);
node.addAttributeValue(acFrequency, nodesSecond.count(n));
node.addAttributeValue(acType, MyFileImporter.getSecondConnectedAgent());
container.addNode(node);
}
// loop for edges
Integer idEdge = 0;
EdgeDraft edge;
for (String e : edges.elementSet()) {
System.out.println("edge: " + e);
String sourceNode = e.split("\\|")[0];
String targetNode = e.split("\\|")[1];
if (!MyFileImporter.innerLinksIncluded) {
if ((nodesFirst.contains(sourceNode) & nodesFirst.contains(targetNode))
|| (nodesSecond.contains(sourceNode) & nodesSecond.contains(targetNode))) {
continue;
}
}
edge = container.factory().newEdgeDraft();
idEdge = idEdge + 1;
edge.setSource(container.getNode(sourceNode));
edge.setTarget(container.getNode(targetNode));
edge.setWeight((float) edges.count(e));
edge.setId(String.valueOf(idEdge));
edge.setType(EdgeDraft.EdgeType.UNDIRECTED);
container.addEdge(edge);
}
}