use of org.geotoolkit.wps.xml.v200.Reference in project xtext-core by eclipse.
the class Bug311337TestLanguageSemanticSequencer method sequence.
@Override
public void sequence(ISerializationContext context, EObject semanticObject) {
EPackage epackage = semanticObject.eClass().getEPackage();
ParserRule rule = context.getParserRule();
Action action = context.getAssignedAction();
Set<Parameter> parameters = context.getEnabledBooleanParameters();
if (epackage == Bug311337Package.eINSTANCE)
switch(semanticObject.eClass().getClassifierID()) {
case Bug311337Package.CHILD:
sequence_Child(context, (Child) semanticObject);
return;
case Bug311337Package.DEFINITION:
sequence_Definition(context, (Definition) semanticObject);
return;
case Bug311337Package.MODEL:
sequence_Model(context, (Model) semanticObject);
return;
case Bug311337Package.NESTED_REF:
sequence_Reference(context, (NestedRef) semanticObject);
return;
case Bug311337Package.REFERENCE:
sequence_Reference(context, (Reference) semanticObject);
return;
}
if (errorAcceptor != null)
errorAcceptor.accept(diagnosticProvider.createInvalidContextOrTypeDiagnostic(semanticObject, context));
}
use of org.geotoolkit.wps.xml.v200.Reference in project xtext-core by eclipse.
the class NestedRefImpl method basicSetLeft.
/**
* <!-- begin-user-doc -->
* <!-- end-user-doc -->
* @generated
*/
public NotificationChain basicSetLeft(Reference newLeft, NotificationChain msgs) {
Reference oldLeft = left;
left = newLeft;
if (eNotificationRequired()) {
ENotificationImpl notification = new ENotificationImpl(this, Notification.SET, Bug311337Package.NESTED_REF__LEFT, oldLeft, newLeft);
if (msgs == null)
msgs = notification;
else
msgs.add(notification);
}
return msgs;
}
use of org.geotoolkit.wps.xml.v200.Reference in project dishevelled by heuermh.
the class AssemblyModel method traversalsFor.
/**
* Create and return a list of path traversals for the specified path.
*
* @param path path, must not be null
* @return a list of path traversals for the specified path
*/
static List<Traversal> traversalsFor(final Path path) {
checkNotNull(path);
int size = path.getSegments().size();
List<Traversal> traversals = new ArrayList<Traversal>(size);
Reference source = null;
Reference target = null;
String overlap = null;
Map<String, Annotation> emptyAnnotations = Collections.emptyMap();
for (int i = 0; i < size; i++) {
target = path.getSegments().get(i);
if (i > 0) {
overlap = (path.getOverlaps() != null && path.getOverlaps().size() > i) ? path.getOverlaps().get(i - 1) : null;
}
if (source != null) {
Traversal traversal = new Traversal(path.getName(), i - 1, source, target, overlap, emptyAnnotations);
traversals.add(traversal);
}
source = target;
}
return traversals;
}
use of org.geotoolkit.wps.xml.v200.Reference in project dishevelled by heuermh.
the class ImportGfa1Task method run.
@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 1.0 format");
final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
final ListMultimap<String, Traversal> traversalsByPathName = ArrayListMultimap.create();
taskMonitor.setStatusMessage("Reading segments from file ...");
try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
// stream segments, building cache
stream(readable, new Gfa1Adapter() {
@Override
protected boolean segment(final Segment segment) {
segmentsById.put(segment.getId(), segment);
return true;
}
});
}
taskMonitor.setStatusMessage("Finding reverse orientation references ...");
final List<Path> paths = new ArrayList<Path>();
final List<Link> links = new ArrayList<Link>();
try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
// stream paths and links, looking for reverse orientation references
stream(readable, new Gfa1Adapter() {
private void putIfAbsent(final Reference reference) {
Segment segment = segmentsById.get(reference.getId());
if (segment == null) {
throw new RuntimeException("could not find segment by id " + reference.getId());
}
if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
}
}
@Override
protected boolean path(final Path path) {
for (Reference reference : path.getSegments()) {
putIfAbsent(reference);
}
if (loadPaths) {
paths.add(path);
}
return true;
}
@Override
protected boolean link(final Link link) {
putIfAbsent(link.getSource());
putIfAbsent(link.getTarget());
links.add(link);
return true;
}
@Override
protected boolean traversal(final Traversal traversal) {
traversalsByPathName.put(traversal.getPathName(), traversal);
return true;
}
});
}
logger.info("read {} segments, {} links, {} paths, and {} traversals from {}", new Object[] { segmentsById.size(), links.size(), paths.size(), traversalsByPathName.size(), inputFile });
segmentsById.clear();
taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
final CyNetwork network = applicationManager.getCurrentNetwork();
final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
String id = c.getRowKey();
Orientation orientation = c.getColumnKey();
Segment segment = c.getValue();
String name = id + (orientation.isForward() ? "+" : "-");
if (!nodes.containsKey(name)) {
CyNode node = network.addNode();
CyTable nodeTable = network.getDefaultNodeTable();
CyRow nodeRow = nodeTable.getRow(node.getSUID());
Integer length = segment.getLengthOpt().orElse(null);
Integer readCount = segment.getReadCountOpt().orElse(null);
Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
Integer kmerCount = segment.getKmerCountOpt().orElse(null);
String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
String sequenceUri = segment.getSequenceUriOpt().orElse(null);
setValue(nodeTable, nodeRow, "name", String.class, name);
setValue(nodeTable, nodeRow, "length", Integer.class, length);
setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
// default display length to length
Integer displayLength = length;
String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
if (sequence != null) {
Integer sequenceLength = sequence.length();
String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
Integer displaySequenceLength = displaySequence.length();
if (loadSequences) {
setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
}
setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
// override display length with sequence length if necessary
if (length == null || length != sequenceLength) {
displayLength = sequenceLength;
}
}
StringBuilder sb = new StringBuilder();
sb.append(name);
if (displayLength != null) {
sb.append(" ");
sb.append(displayLength);
sb.append(" bp");
}
String displayName = sb.toString();
if (readCount != null) {
sb.append(" ");
sb.append(readCount);
sb.append(" reads");
}
if (fragmentCount != null) {
sb.append(" ");
sb.append(fragmentCount);
sb.append(" fragments");
}
if (kmerCount != null) {
sb.append(" ");
sb.append(kmerCount);
sb.append(" kmers");
}
String displayLabel = sb.toString();
setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
nodes.put(name, node);
}
}
logger.info("converted segments and orientation to " + nodes.size() + " nodes");
segmentsByOrientation.clear();
taskMonitor.setStatusMessage("Building Cytoscape edges from links ...");
for (Link link : links) {
String sourceId = link.getSource().getId();
String sourceOrientation = link.getSource().isForwardOrientation() ? "+" : "-";
String targetId = link.getTarget().getId();
String targetOrientation = link.getTarget().isForwardOrientation() ? "+" : "-";
CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
CyNode targetNode = nodes.get(targetId + targetOrientation);
CyEdge edge = network.addEdge(sourceNode, targetNode, true);
CyTable edgeTable = network.getDefaultEdgeTable();
CyRow edgeRow = edgeTable.getRow(edge.getSUID());
setValue(edgeTable, edgeRow, "id", String.class, link.getIdOpt().orElse(null));
setValue(edgeTable, edgeRow, "type", String.class, "edge");
setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
setValue(edgeTable, edgeRow, "overlap", String.class, link.getOverlapOpt().orElse(null));
setValue(edgeTable, edgeRow, "readCount", Integer.class, link.getReadCountOpt().orElse(null));
setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, link.getFragmentCountOpt().orElse(null));
setValue(edgeTable, edgeRow, "kmerCount", Integer.class, link.getKmerCountOpt().orElse(null));
setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, link.getMappingQualityOpt().orElse(null));
setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, link.getMismatchCountOpt().orElse(null));
}
logger.info("converted links to " + links.size() + " edges");
nodes.clear();
links.clear();
// pass paths to AssemblyApp if requested
if (loadPaths && !paths.isEmpty()) {
taskMonitor.setStatusMessage("Loading paths in path view ...");
assemblyModel.setInputFileName(inputFile.toString());
assemblyModel.setPaths(paths, traversalsByPathName);
}
}
use of org.geotoolkit.wps.xml.v200.Reference in project molgenis-emx2 by molgenis.
the class SqlColumnRefBackExecutor method createTriggerForRef.
private static void createTriggerForRef(DSLContext jooq, Column column, boolean isUpdateTrigger) {
// check if any refBack array has non-existing pkey
// remove refs from other table if not any more in refBack array
// update refs from other table to new identifier ( automatic via cascade , nothing to
// do here)
// add refs from other table if new in refBack array
String schemaName = column.getTable().getSchema().getName();
String triggerName = refBackUpdateTriggerName(column) + (isUpdateTrigger ? "_UPDATE" : "_INSERT");
List<Reference> columns = column.getReferences();
// begin
String sql = "CREATE FUNCTION {0}() RETURNS trigger AS $BODY$ " + "\nDECLARE my_row RECORD;" + "\nBEGIN";
// add check if the refs actually exist
sql += "\n\t-- raise error for first refColumn value that does not in refTable key values " + "\n\tFOR my_row IN SELECT {1} FROM newtab EXCEPT (SELECT {2} FROM {3}) LOOP" + "\n\t\tRAISE EXCEPTION USING ERRCODE='23503', " + "\n\t\tMESSAGE = 'insert on table '||{4}||' violates foreign key constraint for refback column(s)'," + "\n\t\tDETAIL = 'Key ('||{5}||')=('|| {6} ||') is not present in table '||{7}||', column '||{8};" + "\n\tEND LOOP;";
// in case of update, we should also remove the references not in the 'old'
if (isUpdateTrigger) {
sql += "\n\t-- remove ref to 'oldtable'.key if not anymore in refarray" + "\n\tFOR my_row IN SELECT {13},{1} FROM oldtab EXCEPT (SELECT {13},{1} FROM newtab) LOOP" + "\n\t\tUPDATE {3} set {9} WHERE {12};" + "\n\tEND LOOP;";
sql += "\n\t-- set to ref to 'newtable'.key if in refBack values list" + "\n\tFOR my_row IN SELECT {13},{1} FROM newtab EXCEPT (SELECT {13},{1} FROM oldtab) LOOP" + "\n\t\tUPDATE {3} set {11} WHERE {12};" + "\n\tEND LOOP;";
} else {
// in case of insert
sql += "\n\t-- set to ref to 'newtable'.key if in refBack values list" + "\n\tFOR my_row IN SELECT {13},{1} FROM newtab LOOP" + "\n\t\tUPDATE {3} set {11} WHERE {12};" + "\n\tEND LOOP;";
}
// end
sql += "\n\tRETURN NEW;" + "\nEND; $BODY$ LANGUAGE plpgsql;";
RowCountQuery q = jooq.query(sql, // 0 function name
name(schemaName, triggerName), // 1 selection of unnested inputs
keyword(columns.stream().map(r -> "unnest(" + name(r.getName()) + ") as " + name(r.getName())).collect(Collectors.joining(","))), // 2 foreign key column names refBack refers to
keyword(columns.stream().map(r -> name(r.getRefTo()).toString()).collect(Collectors.joining(","))), // 3 refTable
table(name(schemaName, column.getRefTableName())), // 4 inline string of table for debug message
inline(column.getTable().getTableName()), // 5 inline columns
keyword(columns.stream().map(r -> inline(r.getName()).toString()).collect(Collectors.joining("||','||"))), // 6 concat of the error column values
keyword(columns.stream().map(r -> "COALESCE(my_row." + name(r.getRefTo()).toString() + ",'NULL')").collect(Collectors.joining("||','||"))), // 7 inline refTable
inline(column.getRefTable().getTableName()), // 8 inline toColumns
keyword(columns.stream().map(r -> inline(r.getRefTo()).toString()).collect(Collectors.joining("||','||"))), // 9 set refBack to null
keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getName()) + "=NULL").collect(Collectors.joining(","))), // 10 where references old key and not new key
keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getName()) + "=OLD." + name(r.getRefTo())).collect(Collectors.joining(" AND "))), // 11 set to point to this.key(s)
keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getName()) + "=my_row." + name(r.getRefTo())).collect(Collectors.joining(","))), // 12 where reftable.key=refback
keyword(columns.stream().map(r -> name(r.getRefTo()) + "=my_row." + name(r.getName())).collect(Collectors.joining(" AND "))), // 13 keys of this table
keyword(column.getRefBackColumn().getReferences().stream().map(r -> name(r.getRefTo()).toString()).collect(Collectors.joining(","))), // 14 where this keys
keyword(column.getRefBackColumn().getReferences().stream().map(Reference::getRefTo).map(s -> name(s) + "=NEW." + name(s)).collect(Collectors.joining(" AND "))));
// System.out.println("sql: " + q.getSQL());
q.execute();
String trigger = isUpdateTrigger ? "CREATE TRIGGER {0} " + "\n\tAFTER UPDATE ON {2}" + "\n\tREFERENCING NEW TABLE AS newtab OLD TABLE AS oldtab" + "\n\tEXECUTE PROCEDURE {3}()" : "CREATE TRIGGER {0} " + "\n\tAFTER INSERT ON {2}" + "\n\tREFERENCING NEW TABLE AS newtab" + "\n\tEXECUTE PROCEDURE {3}()";
jooq.execute(trigger, // 0 name of the trigger
name(triggerName), // 1 the columns of the refBack that should be set to trigger the trigger
keyword(columns.stream().map(r -> name(r.getName()).toString()).collect(Collectors.joining(","))), // name of the table
name(schemaName, column.getTable().getTableName()), // reference to the trigger function
name(schemaName, triggerName));
}
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