private ArrayList<Integer> getCoreChildren(int concept_id, I_IntSet allowed_status, I_Path path)
throws Exception {
// TODO replace with passed in config...
I_ConfigAceFrame config = Terms.get().getActiveAceFrameConfig();
ArrayList<Integer> ret = new ArrayList<Integer>();
final I_TermFactory tf = Terms.get();
I_GetConceptData c = tf.getConcept(concept_id);
I_IntSet isa_rels = tf.newIntSet();
isa_rels.add(SNOMED.Concept.IS_A.localize().getNid());
isa_rels.add(ArchitectonicAuxiliary.Concept.IS_A_REL.localize().getNid());
for (I_GetConceptData d :
c.getDestRelOrigins(
allowed_status,
isa_rels,
null,
config.getPrecedence(),
config.getConflictResolutionStrategy())) {
ret.add(d.getConceptId());
}
Collections.sort(
ret,
new Comparator<Integer>() {
public int compare(Integer obj1, Integer obj2) {
try {
String s1 = tf.getConcept(obj1).getInitialText();
String s2 = tf.getConcept(obj2).getInitialText();
return s1.compareTo(s2);
} catch (Exception e) {
}
return obj1.compareTo(obj2);
}
});
return ret;
}
public I_GetConceptData getConceptSafe(I_TermFactory termFactory, Collection<UUID> concepts)
throws Exception {
if (termFactory.hasId(concepts)) {
return termFactory.getConcept(concepts);
}
return null;
}
private I_IntSet getActiveStatus() throws Exception {
final I_TermFactory tf = Terms.get();
I_IntSet ret = tf.newIntSet();
for (Integer s :
getCoreDescendants(ArchitectonicAuxiliary.Concept.ACTIVE.localize().getNid(), null, null)) {
ret.add(s);
}
return ret;
}
public void execute() throws MojoExecutionException, MojoFailureException {
I_TermFactory termFactory = Terms.get();
try {
FindComponents find = new FindComponents();
termFactory.iterateConcepts(find);
find.getTextWriter().close();
find.getHtmlWriter().close();
} catch (Exception e) {
throw new MojoExecutionException(e.getLocalizedMessage(), e);
}
}
public Condition evaluate(I_EncodeBusinessProcess process, I_Work worker)
throws TaskFailedException {
try {
I_TermFactory tf = Terms.get();
I_Path editPath = tf.getPath(editPathEntry.ids);
I_ConfigAceFrame frameConfig = tf.getActiveAceFrameConfig();
Set<I_Path> editSet = frameConfig.getEditingPathSet();
editSet.clear();
frameConfig.addEditingPath(editPath);
frameConfig.fireUpdateHierarchyView();
return Condition.CONTINUE;
} catch (IllegalArgumentException e) {
throw new TaskFailedException(e);
} catch (IOException e) {
throw new TaskFailedException(e);
} catch (TerminologyException e) {
throw new TaskFailedException(e);
}
}
/** Start this monitor. Batch processing has commenced. */
public void start() throws Exception {
I_TermFactory termFactory = Terms.get();
activity =
termFactory.newActivityPanel(
false, termFactory.getActiveAceFrameConfig(), description, true);
activity.setProgressInfoUpper(description);
activity.setProgressInfoLower("Commencing...");
activity.setMaximum((int) totalEvents);
activity.setValue(0);
activity.setIndeterminate(false);
timer = new BatchReportingThread(this, reportCycleMs, activity);
if (showMessagePanel) {
addMessagePanel();
}
addFinishedButton();
timer.activity.getViewPanel(false).validate();
timer.start();
}
public PositionSetReadOnly getPositions(I_TermFactory termFactory) throws Exception {
/*
* I_ConfigAceFrame activeProfile = termFactory.getActiveAceFrameConfig();
* Set<I_Path> editingPaths = activeProfile.getEditingPathSet();
* Set<I_Position> allPositions = new HashSet<I_Position>();
* for (I_Path path : editingPaths) {
* allPositions.add(termFactory.newPosition(path, Integer.MAX_VALUE));
* for (I_Position position : path.getOrigins()) {
* addOriginPositions(termFactory, position, allPositions);
* }
* }
* return new PositionSetReadOnly(allPositions);
*/
return termFactory.getActiveAceFrameConfig().getViewPositionSetReadOnly();
}
public void processConcept(I_GetConceptData concept) throws Exception {
// get origins
I_Path architectonicPath =
termFactory.getPath(ArchitectonicAuxiliary.Concept.ARCHITECTONIC_BRANCH.getUids());
I_Position latestOnArchitectonicPath =
termFactory.newPosition(architectonicPath, Integer.MAX_VALUE);
origins.add(latestOnArchitectonicPath);
Set<I_Position> branchPositions = new HashSet<I_Position>();
// TODO replace with passed in config...
I_ConfigAceFrame config = Terms.get().getActiveAceFrameConfig();
// get all the concepts/paths/positions for the specified branches
if (branches == null) {
branchPositions = null;
} else {
for (ConceptDescriptor branch : branches) {
I_GetConceptData currentConcept = branch.getVerifiedConcept();
I_Path currentPath = termFactory.getPath(currentConcept.getUids());
I_Position currentPosition = termFactory.newPosition(currentPath, Integer.MAX_VALUE);
branchPositions.add(currentPosition);
}
}
// get latest IS-A relationships
I_IntSet isARel = termFactory.newIntSet();
isARel.add(
termFactory.getConcept(ArchitectonicAuxiliary.Concept.IS_A_REL.getUids()).getConceptId());
List<? extends I_RelTuple> results =
concept.getDestRelTuples(
null,
isARel,
new PositionSetReadOnly(branchPositions),
config.getPrecedence(),
config.getConflictResolutionStrategy());
if (results.size() > count) {
String message = "Concept: " + concept + " has > 20 children.";
getLog().info(message);
htmlWriter.append(message);
htmlWriter.append("<br>");
textWriter.append(concept.getUids().toString());
textWriter.newLine();
}
termFactory.addUncommitted(concept);
}
private void listRefset() throws Exception {
// TODO replace with passed in config...
I_ConfigAceFrame config = Terms.get().getActiveAceFrameConfig();
getLog().info("refset list");
list_file.getParentFile().mkdirs();
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(this.list_file)));
final I_TermFactory tf = Terms.get();
if (this.path_uuid != null) {
this.path = tf.getPath(Arrays.asList(UUID.fromString(this.path_uuid)));
}
// I_IntSet allowed_status = tf.newIntSet();
// allowed_status.add(ArchitectonicAuxiliary.Concept.CURRENT.localize().getNid());
refset_con = tf.getConcept(Arrays.asList(UUID.fromString(this.refset_con_uuid)));
out.println("<html>");
out.println("<head>");
out.println("<style type=\"text/css\">");
out.println("BODY {font:10pt sans-serif}");
out.println("TABLE {font:10pt sans-serif; border-collapse:collapse}");
out.println("TD {border: 1px solid; padding:5px}");
out.println("</style>");
out.println("</head>");
out.println("<body>");
out.println("<h2>");
out.println("Refset Report");
out.println("</h2>");
out.println("<p>");
out.println(
escapeString(
DateFormat.getDateTimeInstance(DateFormat.LONG, DateFormat.LONG).format(new Date())));
ArrayList<Integer> refsets =
getCoreDescendants(refset_con.getConceptId(), getActiveStatus(), this.path);
if (this.sort_by_name) {
Collections.sort(
refsets,
new Comparator<Integer>() {
public int compare(Integer obj1, Integer obj2) {
try {
String s1 = tf.getConcept(obj1).getInitialText();
String s2 = tf.getConcept(obj2).getInitialText();
return s1.compareTo(s2);
} catch (Exception e) {
}
return obj1.compareTo(obj2);
}
});
}
for (Integer con_id : refsets) {
I_GetConceptData con = tf.getConcept(con_id);
out.println("<h3>");
out.println(escapeString(con.getInitialText()));
out.println("</h3>");
out.println("<table border=\"1\">");
for (UUID id : con.getUids()) {
out.println("<tr>");
out.println("<td>");
out.println("ID");
out.println("<td>");
out.println(escapeString(String.valueOf(id)));
}
for (String r :
Arrays.asList(
"dd413e49-c124-3b05-8c25-0da5922379d3",
"7a981930-621f-3935-b26c-47f54413a59d",
"41fbef7f-7210-3288-97cb-c860dfc90601",
"f60922c9-cb3d-3099-8960-1097d2c5afdc")) {
I_GetConceptData r_con = tf.getConcept(Arrays.asList(UUID.fromString(r)));
if (r_con != null) {
boolean found = false;
String head = r_con.getInitialText().replace(" rel", "");
I_IntSet r_set = tf.newIntSet();
r_set.add(r_con.getConceptId());
for (I_GetConceptData val_con :
con.getSourceRelTargets(
getActiveStatus(),
r_set,
null,
config.getPrecedence(),
config.getConflictResolutionStrategy())) {
// for (int val_id : getRelationship(con.getConceptId(),
// r_con.getConceptId(), null, Integer.MAX_VALUE)) {
// I_GetConceptData val_con = tf.getConcept(val_id);
if (val_con != null) {
found = true;
out.println("<tr>");
out.println("<td>");
out.println(escapeString(head));
out.println("<td>");
out.println(escapeString(val_con.getInitialText()));
}
}
if (!found) {
out.println("<tr>");
out.println("<td>");
out.println(escapeString(head));
out.println("<td>");
}
}
}
// comments rel "ff1b55d3-2b7b-382c-ae42-eceffcc47c71"
// promotion rel "9a801240-b3b0-3475-8a7b-07111d3ff564"
for (String r :
Arrays.asList(
"ff1b55d3-2b7b-382c-ae42-eceffcc47c71", "9a801240-b3b0-3475-8a7b-07111d3ff564")) {
I_GetConceptData r_con = tf.getConcept(Arrays.asList(UUID.fromString(r)));
if (r_con != null) {
boolean found = false;
String head = r_con.getInitialText().replace(" rel", "");
I_IntSet r_set = tf.newIntSet();
r_set.add(r_con.getConceptId());
for (I_GetConceptData val_con :
con.getSourceRelTargets(
getActiveStatus(),
r_set,
null,
config.getPrecedence(),
config.getConflictResolutionStrategy())) {
if (val_con != null) {
found = true;
out.println("<tr>");
out.println("<td>");
out.println(escapeString(head));
out.println("<td>");
// out.println(val_con.getInitialText());
//
for (I_ExtendByRef mem : tf.getRefsetExtensionMembers(val_con.getConceptId())) {
I_GetConceptData mem_con = tf.getConcept(mem.getComponentId());
I_ExtendByRefPart p = mem.getMutableParts().get(0);
if (p instanceof I_ExtendByRefPartStr) {
I_ExtendByRefPartStr pccs = (I_ExtendByRefPartStr) p;
out.println("<tr>");
out.println("<td>");
out.println("<td>");
out.println(escapeString(pccs.getStringValue()));
} else {
getLog().info("Wrong type: " + p.getClass() + " " + mem_con.getInitialText());
}
}
//
}
}
if (!found) {
out.println("<tr>");
out.println("<td>");
out.println(escapeString(head));
out.println("<td>");
}
}
}
out.println("</table>");
}
out.println("</body>");
out.println("</html>");
out.close();
// make a copy of the report file, in Maven's site folder
site_output_file.getParentFile().mkdirs();
copy(list_file, site_output_file);
}
public Condition evaluate(I_EncodeBusinessProcess process, I_Work worker)
throws TaskFailedException {
try {
I_ConfigAceFrame config =
(I_ConfigAceFrame) worker.readAttachement(WorkerAttachmentKeys.ACE_FRAME_CONFIG.name());
I_TermFactory tf = Terms.get();
I_ConfigAceFrame workingProfile = (I_ConfigAceFrame) process.getProperty(profilePropName);
if (workingProfile == null) {
workingProfile =
(I_ConfigAceFrame) worker.readAttachement(WorkerAttachmentKeys.ACE_FRAME_CONFIG.name());
}
Object conceptObj = process.getProperty(activeConceptPropName);
I_GetConceptData concept = AceTaskUtil.getConceptFromObject(conceptObj);
List<? extends I_ConceptAttributeTuple> attrTupels =
concept.getConceptAttributeTuples(
workingProfile.getAllowedStatus(), workingProfile.getViewPositionSetReadOnly(),
workingProfile.getPrecedence(), workingProfile.getConflictResolutionStrategy());
I_IntSet pathSet = Terms.get().newIntSet();
ArrayList<UniversalAcePosition> positionList = new ArrayList<UniversalAcePosition>();
for (I_ConceptAttributeTuple t : attrTupels) {
positionList.add(
new UniversalAcePosition(
tf.getUids(t.getPathId()), tf.convertToThickVersion(t.getVersion())));
pathSet.add(t.getPathId());
}
ArrayList<String> addressList = new ArrayList<String>();
I_IntList inboxDescTypeList = Terms.get().newIntList();
inboxDescTypeList.add(ArchitectonicAuxiliary.Concept.USER_INBOX.localize().getNid());
for (int pathId : pathSet.getSetValues()) {
I_GetConceptData pathConcept = Terms.get().getConcept(pathId);
I_DescriptionTuple inboxDesc = pathConcept.getDescTuple(inboxDescTypeList, config);
if (inboxDesc == null) {
worker.getLogger().info("Cannot find inbox for: " + pathConcept.getInitialText());
worker.getLogger().info(" inboxDescTypeList: " + inboxDescTypeList.getListArray());
for (I_DescriptionVersioned desc : pathConcept.getDescriptions()) {
for (I_DescriptionTuple tuple : desc.getTuples()) {
worker.getLogger().info(" desc tuple: " + tuple);
}
}
} else {
addressList.add(inboxDesc.getText());
}
}
process.setProperty(addressListPropName, addressList);
process.setProperty(positionListPropName, positionList);
worker.getLogger().info("Selected status values have these positions: " + positionList);
worker.getLogger().info("Got addresses from status values: " + addressList);
return Condition.CONTINUE;
} catch (IllegalArgumentException e) {
throw new TaskFailedException(e);
} catch (IllegalAccessException e) {
throw new TaskFailedException(e);
} catch (InvocationTargetException e) {
throw new TaskFailedException(e);
} catch (IntrospectionException e) {
throw new TaskFailedException(e);
} catch (IOException e) {
throw new TaskFailedException(e);
} catch (TerminologyException e) {
throw new TaskFailedException(e);
}
}