RP-880 New report for Swiss character ß TO SS

reporting-engine-worker/src/main/java/org/ihtsdo/termserver/job/Application.java

@@ -30,8 +30,6 @@
 @EnableJms
 public class Application {
 
- private static final Logger LOGGER = LoggerFactory.getLogger(Application.class);
-
  static TermServerScript job;
 
  @Bean

reporting-engine-worker/src/main/java/org/ihtsdo/termserver/job/JobManager.java

@@ -1,6 +1,5 @@
 package org.ihtsdo.termserver.job;
 
-import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 
 import jakarta.annotation.PostConstruct;

reporting-engine-worker/src/main/java/org/ihtsdo/termserver/scripting/fixes/CharacterConversionFixUp.java

@@ -0,0 +1,128 @@
+package org.ihtsdo.termserver.scripting.fixes;
+
+import java.io.IOException;
+import java.util.*;
+
+import org.ihtsdo.otf.rest.client.terminologyserver.pojo.Component;
+import org.ihtsdo.otf.rest.client.terminologyserver.pojo.Task;
+import org.ihtsdo.otf.exception.TermServerScriptException;
+import org.ihtsdo.termserver.scripting.ReportClass;
+import org.ihtsdo.termserver.scripting.domain.*;
+import org.ihtsdo.termserver.scripting.util.SnomedUtils;
+import org.snomed.otf.scheduler.domain.*;
+import org.snomed.otf.scheduler.domain.Job.ProductionStatus;
+import org.snomed.otf.script.dao.ReportSheetManager;
+
+
+public class CharacterConversionFixUp extends BatchFix implements ScriptConstants, ReportClass {
+
+ enum KnownCharacterConversions { ß_TO_SS };
+
+ private static final String CHARACTER_CONVERSION = "Character Conversion";
+ private String match;
+ private String replace;
+ private KnownCharacterConversions currentConversionType;
+
+ protected CharacterConversionFixUp() {
+ super(null);
+ }
+
+ protected CharacterConversionFixUp(BatchFix clone) {
+ super(clone);
+ }
+
+ public static void main(String[] args) throws TermServerScriptException, IOException, InterruptedException {
+ CharacterConversionFixUp fix = new CharacterConversionFixUp(null);
+ try {
+ fix.selfDetermining = true;
+ fix.populateEditPanel = false;
+ fix.getArchiveManager().setRunIntegrityChecks(false);
+ fix.init(args);
+ //Recover the current project state from TS (or local cached archive) to allow quick searching of all concepts
+ fix.loadProjectSnapshot(false); //Load all descriptions
+ fix.postInit();
+ fix.processFile();
+ } finally {
+ fix.finish();
+ }
+ }
+
+ @Override
+ public Job getJob() {
+ JobParameters params = new JobParameters()
+ .add(CHARACTER_CONVERSION).withType(JobParameter.Type.DROPDOWN).withValues(KnownCharacterConversions.ß_TO_SS.name()).withMandatory()
+ .add(DRY_RUN).withType(JobParameter.Type.BOOLEAN).withDefaultValue(true).withMandatory()
+ .build();
+ return new Job()
+ .withCategory(new JobCategory(JobType.REPORT, JobCategory.DEVOPS))
+ .withName("Character Conversion Fix-up")
+ .withDescription("This report creates a single task which replaces descriptions containing the selected ")
+ .withProductionStatus(ProductionStatus.PROD_READY)
+ .withTag(MS)
+ .withParameters(params)
+ .build();
+ }
+
+ @Override
+ protected void preInit() throws TermServerScriptException {
+ ReportSheetManager.targetFolderId="1MDEvSDJ1EW2Piy2AfaO1UIEPAGhGbG4j"; //User Initiated Batch Updates
+ populateEditPanel = true;
+ populateTaskDescription = true;
+ selfDetermining = true;
+ classifyTasks = false;
+
+ JobRun jobRun = getJobRun();
+ dryRun = jobRun.getParamBoolean(DRY_RUN);
+ taskSize = Integer.MAX_VALUE;
+ String characterConversionStr = jobRun.getMandatoryParamValue(CHARACTER_CONVERSION);
+ currentConversionType = KnownCharacterConversions.valueOf(characterConversionStr);
+ if (currentConversionType == KnownCharacterConversions.ß_TO_SS) {
+ match = "ß";
+ replace = "ss";
+ } else {
+ throw new TermServerScriptException("Unknown Character Conversion specified: " + characterConversionStr);
+ }
+ }
+
+ @Override
+ public int doFix(Task t, Concept concept, String info) throws TermServerScriptException {
+ Concept loadedConcept = loadConcept(concept, t.getBranchPath());
+ int changesMade = replaceTerms(t, loadedConcept);
+ if (changesMade > 0) {
+ updateConcept(t, loadedConcept, info);
+ }
+ return changesMade;
+ }
+
+ private int replaceTerms(Task t, Concept c) throws TermServerScriptException {
+ int changesMade = 0;
+ for (Description d : c.getDescriptions(ActiveState.ACTIVE)) {
+ if (inScope(d) && d.getTerm().contains(match)) {
+ String newTerm = d.getTerm().replace(match, replace);
+ replaceDescription(t, c, d, newTerm, InactivationIndicator.NONCONFORMANCE_TO_EDITORIAL_POLICY, false, "");
+ changesMade++;
+ }
+ }
+ return changesMade;
+ }
+
+ protected List<Component> identifyComponentsToProcess() throws TermServerScriptException {
+
+ List<Concept> allPotential = SnomedUtils.sort(gl.getAllConcepts());
+ Set<Concept> allAffected = new TreeSet<Concept>(); //We want to process in the same order each time, in case we restart and skip some.
+ List<DescriptionType> descTypes = new ArrayList<>();
+ descTypes.add(DescriptionType.FSN);
+ descTypes.add(DescriptionType.SYNONYM);
+ info("Identifying concepts to process");
+ for (Concept c : allPotential) {
+ for (Description d : c.getDescriptions(ActiveState.ACTIVE, descTypes)) {
+ if (inScope(d) && d.getTerm().contains(match)) {
+ allAffected.add(c);
+ break;
+ }
+ }
+ }
+ info ("Identified " + allAffected.size() + " concepts to process");
+ return new ArrayList<Component>(allAffected);
+ }
+}