Examples with Activity org.sbolstandard.core2.Activity used on opensource projects

Example 6 with Activity

use of org.sbolstandard.core2.Activity in project kie-wb-common by kiegroup.

the class Bpmn2JsonUnmarshaller method setCatchEventsInfo.

public void setCatchEventsInfo(FlowElementsContainer container, Definitions def, List<Signal> toAddSignals, Set<Error> toAddErrors, Set<Escalation> toAddEscalations, Set<Message> toAddMessages, Set<ItemDefinition> toAddItemDefinitions) {
    List<FlowElement> flowElements = container.getFlowElements();
    for (FlowElement fe : flowElements) {
        if (fe instanceof CatchEvent) {
            if (((CatchEvent) fe).getEventDefinitions().size() > 0) {
                EventDefinition ed = ((CatchEvent) fe).getEventDefinitions().get(0);
                if (ed instanceof SignalEventDefinition) {
                    SignalEventDefinition sed = (SignalEventDefinition) ed;
                    if (sed.getSignalRef() != null && sed.getSignalRef().length() > 0) {
                        String signalRef = sed.getSignalRef();
                        boolean shouldAddSignal = true;
                        List<RootElement> rootElements = def.getRootElements();
                        for (RootElement re : rootElements) {
                            if (re instanceof Signal) {
                                if (((Signal) re).getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (toAddSignals != null) {
                            for (Signal s : toAddSignals) {
                                if (s.getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (shouldAddSignal) {
                            Signal signal = Bpmn2Factory.eINSTANCE.createSignal();
                            signal.setName(signalRef);
                            toAddSignals.add(signal);
                        }
                    }
                } else if (ed instanceof ErrorEventDefinition) {
                    String errorCode = null;
                    String errorId = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("erefname")) {
                            errorId = (String) entry.getValue();
                            errorCode = (String) entry.getValue();
                        }
                    }
                    Error err = this._errors.get(errorCode);
                    if (err == null) {
                        err = Bpmn2Factory.eINSTANCE.createError();
                        err.setId(errorId);
                        err.setErrorCode(errorCode);
                        this._errors.put(errorCode, err);
                    }
                    toAddErrors.add(err);
                    ((ErrorEventDefinition) ed).setErrorRef(err);
                } else if (ed instanceof EscalationEventDefinition) {
                    String escalationCode = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("esccode")) {
                            escalationCode = (String) entry.getValue();
                            break;
                        }
                    }
                    Escalation escalation = this._escalations.get(escalationCode);
                    if (escalation == null) {
                        escalation = Bpmn2Factory.eINSTANCE.createEscalation();
                        escalation.setEscalationCode(escalationCode);
                        this._escalations.put(escalationCode, escalation);
                    }
                    toAddEscalations.add(escalation);
                    ((EscalationEventDefinition) ed).setEscalationRef(escalation);
                } else if (ed instanceof MessageEventDefinition) {
                    ((MessageEventDefinition) ed).setMessageRef(extractMessage(ed, toAddMessages, toAddItemDefinitions));
                } else if (ed instanceof CompensateEventDefinition) {
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("actrefname")) {
                            String activityNameRef = (String) entry.getValue();
                            // we have to iterate again through all flow elements
                            // in order to find our activity name
                            List<RootElement> re = def.getRootElements();
                            for (RootElement r : re) {
                                if (r instanceof Process) {
                                    Process p = (Process) r;
                                    List<FlowElement> fes = p.getFlowElements();
                                    for (FlowElement f : fes) {
                                        if (f instanceof Activity && ((Activity) f).getName().equals(activityNameRef)) {
                                            ((CompensateEventDefinition) ed).setActivityRef((Activity) f);
                                            ((Activity) f).setIsForCompensation(true);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
        } else if (fe instanceof FlowElementsContainer) {
            setCatchEventsInfo((FlowElementsContainer) fe, def, toAddSignals, toAddErrors, toAddEscalations, toAddMessages, toAddItemDefinitions);
        }
    }
}

Example 7 with Activity

use of org.sbolstandard.core2.Activity in project kie-wb-common by kiegroup.

the class Bpmn2JsonUnmarshaller method setCatchEventsInfoForLanes.

public void setCatchEventsInfoForLanes(Lane lane, Definitions def, List<Signal> toAddSignals, Set<Error> toAddErrors, Set<Escalation> toAddEscalations, Set<Message> toAddMessages, Set<ItemDefinition> toAddItemDefinitions) {
    List<FlowNode> laneFlowNodes = lane.getFlowNodeRefs();
    for (FlowElement fe : laneFlowNodes) {
        if (fe instanceof CatchEvent) {
            if (((CatchEvent) fe).getEventDefinitions().size() > 0) {
                EventDefinition ed = ((CatchEvent) fe).getEventDefinitions().get(0);
                if (ed instanceof SignalEventDefinition) {
                    SignalEventDefinition sed = (SignalEventDefinition) ed;
                    if (sed.getSignalRef() != null && sed.getSignalRef().length() > 0) {
                        String signalRef = sed.getSignalRef();
                        boolean shouldAddSignal = true;
                        List<RootElement> rootElements = def.getRootElements();
                        for (RootElement re : rootElements) {
                            if (re instanceof Signal) {
                                if (((Signal) re).getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (toAddSignals != null) {
                            for (Signal s : toAddSignals) {
                                if (s.getName().equals(signalRef)) {
                                    shouldAddSignal = false;
                                    break;
                                }
                            }
                        }
                        if (shouldAddSignal) {
                            Signal signal = Bpmn2Factory.eINSTANCE.createSignal();
                            signal.setName(signalRef);
                            toAddSignals.add(signal);
                        }
                    }
                } else if (ed instanceof ErrorEventDefinition) {
                    String errorCode = null;
                    String errorId = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("erefname")) {
                            errorId = (String) entry.getValue();
                            errorCode = (String) entry.getValue();
                        }
                    }
                    Error err = this._errors.get(errorCode);
                    if (err == null) {
                        err = Bpmn2Factory.eINSTANCE.createError();
                        err.setId(errorId);
                        err.setErrorCode(errorCode);
                        this._errors.put(errorCode, err);
                    }
                    toAddErrors.add(err);
                    ((ErrorEventDefinition) ed).setErrorRef(err);
                } else if (ed instanceof EscalationEventDefinition) {
                    String escalationCode = null;
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("esccode")) {
                            escalationCode = (String) entry.getValue();
                            break;
                        }
                    }
                    Escalation escalation = this._escalations.get(escalationCode);
                    if (escalation == null) {
                        escalation = Bpmn2Factory.eINSTANCE.createEscalation();
                        escalation.setEscalationCode(escalationCode);
                        this._escalations.put(escalationCode, escalation);
                    }
                    toAddEscalations.add(escalation);
                    ((EscalationEventDefinition) ed).setEscalationRef(escalation);
                } else if (ed instanceof MessageEventDefinition) {
                    ((MessageEventDefinition) ed).setMessageRef(extractMessage(ed, toAddMessages, toAddItemDefinitions));
                } else if (ed instanceof CompensateEventDefinition) {
                    Iterator<FeatureMap.Entry> iter = ed.getAnyAttribute().iterator();
                    while (iter.hasNext()) {
                        FeatureMap.Entry entry = iter.next();
                        if (entry.getEStructuralFeature().getName().equals("actrefname")) {
                            String activityNameRef = (String) entry.getValue();
                            // we have to iterate again through all flow elements
                            // in order to find our activity name
                            List<RootElement> re = def.getRootElements();
                            for (RootElement r : re) {
                                if (r instanceof Process) {
                                    Process p = (Process) r;
                                    List<FlowElement> fes = p.getFlowElements();
                                    for (FlowElement f : fes) {
                                        if (f instanceof Activity && ((Activity) f).getName().equals(activityNameRef)) {
                                            ((CompensateEventDefinition) ed).setActivityRef((Activity) f);
                                            ((Activity) f).setIsForCompensation(true);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
        } else if (fe instanceof FlowElementsContainer) {
            setCatchEventsInfo((FlowElementsContainer) fe, def, toAddSignals, toAddErrors, toAddEscalations, toAddMessages, toAddItemDefinitions);
        }
    }
}

Example 8 with Activity

use of org.sbolstandard.core2.Activity in project libSBOLj by SynBioDex.

the class Provenance_SpecifyBuildOperations method specifyJoinOperation.

/**
 * specifies a join operation, which joins two linear DNA constructs
 *
 * NOTE! at this point, we do not specify any further information
 * about how to execute the join operation!
 *
 * @throws Exception
 */
public static void specifyJoinOperation() throws Exception {
    // instantiate a document
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(BUILD_PREFIX);
    // the first linear DNA construct
    ComponentDefinition cdPart1 = document.createComponentDefinition("dna_part_1", LINEAR_DOUBLE_STRANDED_DNA);
    cdPart1.setName("dna_part_1");
    // the second linear DNA construct
    ComponentDefinition cdPart2 = document.createComponentDefinition("dna_part_2", LINEAR_DOUBLE_STRANDED_DNA);
    cdPart2.setName("dna_part_2");
    // Create the generic top level entity for the join operation
    Activity joinOperation = document.createActivity("join_" + cdPart1.getName() + "_with_" + cdPart2.getName());
    joinOperation.setName("join(" + cdPart1.getName() + ", " + cdPart2.getName() + ")");
    // specify the "inputs" to the join operation
    joinOperation.createUsage("dna_part_1", cdPart1.getIdentity()).addRole(UPSTREAM);
    joinOperation.createUsage("dna_part_2", cdPart2.getIdentity()).addRole(DOWNSTREAM);
    // specify the "output" of the join operation
    ComponentDefinition cdJoinedPart = document.createComponentDefinition("joined_dna_part", LINEAR_DOUBLE_STRANDED_DNA);
    cdJoinedPart.setName("joined_dna_part");
    cdJoinedPart.addWasGeneratedBy(joinOperation.getIdentity());
    // serialize the document to a file
    SBOLWriter.write(document, System.out);
}

Example 9 with Activity

use of org.sbolstandard.core2.Activity in project libSBOLj by SynBioDex.

the class Provenance_SpecifyBuildOperations method specifyAmplifyOperation.

/**
 * specifies the amplify operation, which amplifies a linear DNA construct using
 * 5' and 3' primers
 *
 * @throws Exception
 */
public static void specifyAmplifyOperation() throws Exception {
    // instantiate a document
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(BUILD_PREFIX);
    // the linear DNA construct
    ComponentDefinition dnaConstruct = document.createComponentDefinition("dna_construct", LINEAR_SINGLE_STRANDED_DNA);
    dnaConstruct.setName("dna_construct");
    // the 5' primer for amplification
    ComponentDefinition fivePrimer = document.createComponentDefinition("five_primer", FORWARD_PRIMER);
    fivePrimer.setName("five_primer");
    // the 3' primer for amplification
    ComponentDefinition threePrimer = document.createComponentDefinition("three_primer", REVERSE_PRIMER);
    threePrimer.setName("three_primer");
    // Create the generic top level entity for the amplify operation
    Activity amplifyOperation = document.createActivity("amplify_" + dnaConstruct.getName() + "_with_" + fivePrimer.getName() + "_and_" + threePrimer.getName());
    amplifyOperation.setName("amplify(" + dnaConstruct.getName() + ", " + fivePrimer.getName() + ", " + threePrimer.getName() + ")");
    // create the qualifiedUsage annotation to describe the inputs of the amplification operation
    // -- the amplicon
    Usage usageDNAConstruct = amplifyOperation.createUsage("dna_construct", dnaConstruct.getIdentity());
    usageDNAConstruct.addRole(URI.create("http://sbols.org/v2#source"));
    usageDNAConstruct.addRole(PCR_PRODUCT);
    // -- the forward primer
    Usage usageFwdPrimer = amplifyOperation.createUsage("forward_primer", fivePrimer.getIdentity());
    usageFwdPrimer.addRole(FORWARD_PRIMER);
    usageFwdPrimer.addRole(FORWARD_PRIMER);
    // -- the reverse primer
    Usage usageRevPrimer = amplifyOperation.createUsage("reverse_primer", threePrimer.getIdentity());
    usageRevPrimer.addRole(REVERSE_PRIMER);
    usageRevPrimer.addRole(REVERSE_PRIMER);
    // the result of the amplification operation
    ComponentDefinition amplified_construct = document.createComponentDefinition("my_amplified_dna", AMPLIFIED_CONSTRUCT);
    amplified_construct.setName("my_amplified_dna");
    amplified_construct.addWasGeneratedBy(amplifyOperation.getIdentity());
    // serialize the document to a file
    SBOLWriter.write(document, System.out);
}

Example 10 with Activity

use of org.sbolstandard.core2.Activity in project libSBOLj by SynBioDex.

the class Provenance_StrainDerivation method main.

public static void main(String[] args) throws Exception {
    NamespaceBinding myAppNs = NamespaceBinding("http://myapp.com/", "myapp");
    SBOLDocument document = new SBOLDocument();
    document.addNamespace(URI.create(myAppNs.getNamespaceURI()), myAppNs.getPrefix());
    document.setDefaultURIprefix(myAppNs.getNamespaceURI());
    ComponentDefinition b168 = getCds(document, "bsubtilis168", "Bacillus subtilis 168");
    ComponentDefinition b3610 = getCds(document, "bsubtilisncimb3610", "Bacillus subtilis NCIMB 3610");
    b168.addWasDerivedFrom(b3610.getIdentity());
    // Create the agent definition to represent X-ray
    Agent agent = document.createAgent("x_ray");
    agent.setName("X-ray");
    // Create the generic top level entity for the X-ray mutagenesis activity
    Activity activity = document.createActivity("xraymutagenesis");
    activity.setName("X-ray mutagenesis");
    // Create the qualifiedUsage annotation to describe the use of the parent strain
    activity.createUsage("usage", b3610.getIdentity()).addRole(URI.create("http://sbols.org/v2#source"));
    // Create the qualifiedAssociation annotation to describe the use of the agent used in the activity
    activity.createAssociation("association", agent.getIdentity()).addRole(myAppNs.namespacedUri("mutagen"));
    b168.addWasGeneratedBy(activity.getIdentity());
    SBOLWriter.write(document, System.out);
}