use of com.google.api.ads.admanager.axis.v202111.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);
}
}
}
use of com.google.api.ads.admanager.axis.v202111.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);
}
}
}
use of com.google.api.ads.admanager.axis.v202111.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);
}
use of com.google.api.ads.admanager.axis.v202111.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);
}
use of com.google.api.ads.admanager.axis.v202111.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);
}
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