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Example 1 with Reference

use of org.dishevelled.bio.assembly.gfa2.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));
}
Also used : ParserRule(org.eclipse.xtext.ParserRule) NestedRef(org.eclipse.xtext.linking.lazy.bug311337.NestedRef) Action(org.eclipse.xtext.Action) Reference(org.eclipse.xtext.linking.lazy.bug311337.Reference) Definition(org.eclipse.xtext.linking.lazy.bug311337.Definition) Model(org.eclipse.xtext.linking.lazy.bug311337.Model) Parameter(org.eclipse.xtext.Parameter) Child(org.eclipse.xtext.linking.lazy.bug311337.Child) EPackage(org.eclipse.emf.ecore.EPackage)

Example 2 with Reference

use of org.dishevelled.bio.assembly.gfa2.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;
}
Also used : Reference(org.eclipse.xtext.linking.lazy.bug311337.Reference) ENotificationImpl(org.eclipse.emf.ecore.impl.ENotificationImpl)

Example 3 with Reference

use of org.dishevelled.bio.assembly.gfa2.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;
}
Also used : Reference(org.dishevelled.bio.assembly.gfa1.Reference) ArrayList(java.util.ArrayList) Traversal(org.dishevelled.bio.assembly.gfa1.Traversal) Annotation(org.dishevelled.bio.annotation.Annotation)

Example 4 with Reference

use of org.dishevelled.bio.assembly.gfa2.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);
    }
}
Also used : HashMap(java.util.HashMap) ArrayList(java.util.ArrayList) Traversal(org.dishevelled.bio.assembly.gfa1.Traversal) CyNetwork(org.cytoscape.model.CyNetwork) CyRow(org.cytoscape.model.CyRow) Segment(org.dishevelled.bio.assembly.gfa1.Segment) CyTable(org.cytoscape.model.CyTable) FileReader(java.io.FileReader) CyNode(org.cytoscape.model.CyNode) Path(org.dishevelled.bio.assembly.gfa1.Path) HashBasedTable(com.google.common.collect.HashBasedTable) CyTable(org.cytoscape.model.CyTable) Table(com.google.common.collect.Table) Reference(org.dishevelled.bio.assembly.gfa1.Reference) Orientation(org.dishevelled.bio.assembly.gfa1.Orientation) CyEdge(org.cytoscape.model.CyEdge) BufferedReader(java.io.BufferedReader) Gfa1Adapter(org.dishevelled.bio.assembly.gfa1.Gfa1Adapter) Link(org.dishevelled.bio.assembly.gfa1.Link)

Example 5 with Reference

use of org.dishevelled.bio.assembly.gfa2.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));
}
Also used : Column(org.molgenis.emx2.Column) SqlColumnExecutor.validateColumn(org.molgenis.emx2.sql.SqlColumnExecutor.validateColumn) DataAccessException(org.jooq.exception.DataAccessException) List(java.util.List) DSL(org.jooq.impl.DSL) MolgenisException(org.molgenis.emx2.MolgenisException) Reference(org.molgenis.emx2.Reference) RowCountQuery(org.jooq.RowCountQuery) DSLContext(org.jooq.DSLContext) Collectors(java.util.stream.Collectors) RowCountQuery(org.jooq.RowCountQuery) Reference(org.molgenis.emx2.Reference)

Aggregations

BufferedReader (java.io.BufferedReader)4 ArrayList (java.util.ArrayList)4 Reference (org.dishevelled.bio.assembly.gfa1.Reference)4 Traversal (org.dishevelled.bio.assembly.gfa1.Traversal)4 Path (org.dishevelled.bio.assembly.gfa1.Path)3 HashBasedTable (com.google.common.collect.HashBasedTable)2 Table (com.google.common.collect.Table)2 FileReader (java.io.FileReader)2 PrintWriter (java.io.PrintWriter)2 HashMap (java.util.HashMap)2 List (java.util.List)2 Collectors (java.util.stream.Collectors)2 CyEdge (org.cytoscape.model.CyEdge)2 CyNetwork (org.cytoscape.model.CyNetwork)2 CyNode (org.cytoscape.model.CyNode)2 CyRow (org.cytoscape.model.CyRow)2 CyTable (org.cytoscape.model.CyTable)2 Gfa1Listener (org.dishevelled.bio.assembly.gfa1.Gfa1Listener)2 Gfa1Record (org.dishevelled.bio.assembly.gfa1.Gfa1Record)2 CommandLineParseException (org.dishevelled.commandline.CommandLineParseException)2