RP-938 Import derivatives config file after snapshot import, to ensur…

…e worker initialisation will be complete

reporting-engine-worker/src/main/java/org/ihtsdo/termserver/scripting/reports/InactivationImpactAssessment.java

@@ -1,6 +1,5 @@
 package org.ihtsdo.termserver.scripting.reports;
 
-import com.google.common.base.Charsets;
 import com.google.common.io.Files;
 import com.google.common.util.concurrent.AtomicLongMap;
 import org.ihtsdo.otf.exception.TermServerScriptException;
@@ -10,23 +9,16 @@
 import org.ihtsdo.termserver.scripting.TermServerScript;
 import org.ihtsdo.termserver.scripting.client.TermServerClient;
 import org.ihtsdo.termserver.scripting.dao.ResourceDataLoader;
-import org.ihtsdo.termserver.scripting.domain.AssociationEntry;
-import org.ihtsdo.termserver.scripting.domain.CodeSystem;
-import org.ihtsdo.termserver.scripting.domain.Concept;
-import org.ihtsdo.termserver.scripting.domain.Relationship;
-import org.ihtsdo.termserver.scripting.domain.Template;
+import org.ihtsdo.termserver.scripting.domain.*;
 import org.ihtsdo.termserver.scripting.domain.mrcm.MRCMAttributeDomain;
 import org.ihtsdo.termserver.scripting.reports.qi.AllKnownTemplates;
 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.scheduler.domain.JobParameter.Type;
-import org.snomed.otf.script.dao.ReportSheetManager;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
+import java.io.*;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -43,14 +35,12 @@ public class InactivationImpactAssessment extends AllKnownTemplates implements R
 
  private static final Logger LOGGER = LoggerFactory.getLogger(InactivationImpactAssessment.class);
 
- static public String REFSET_ECL = "(< 446609009 |Simple type reference set| OR < 900000000000496009 |Simple map type reference set|) MINUS 900000000000497000 |CTV3 simple map reference set (foundation metadata concept)|";
- private static String CONCEPT_INACTIVATIONS = "Concepts to inactivate";
- private static String INCLUDE_INFERRED = "Include Inferred Relationships";
+ public static final String REFSET_ECL = "(< 446609009 |Simple type reference set| OR < 900000000000496009 |Simple map type reference set|) MINUS 900000000000497000 |CTV3 simple map reference set (foundation metadata concept)|";
+ private static final String CONCEPT_INACTIVATIONS = "Concepts to inactivate";
+ private static final String INCLUDE_INFERRED = "Include Inferred Relationships";
  private Collection<Concept> referenceSets;
- private List<Concept> emptyReferenceSets;
- private List<Concept> outOfScopeReferenceSets;
  private AtomicLongMap<Concept> refsetSummary = AtomicLongMap.create();
- private static int CHUNK_SIZE = 200;
+ private static final int CHUNK_SIZE = 200;
  private boolean includeInferred = false;
  private String selectionCriteria;
  private boolean isECL = false;
@@ -78,14 +68,13 @@ public void init(JobRun run) throws TermServerScriptException {
  }
 
  getArchiveManager().setPopulateReleasedFlag(true);
- importDerivativeLocations();
- ReportSheetManager.targetFolderId = "1F-KrAwXrXbKj5r-HBLM0qI5hTzv-JgnU"; //Ad-hoc reports
  super.init(run);
  }
 
  @Override
  public void postInit() throws TermServerScriptException {
  referenceSets = findConcepts(REFSET_ECL);
+ importDerivativeLocations();
  removeEmptyNoScopeAndDerivativeRefsets();
  LOGGER.info ("Recovered {} simple reference sets and maps", referenceSets.size());
 
@@ -120,13 +109,13 @@ public void postInit() throws TermServerScriptException {
  }
 
  includeInferred = jobRun.getParameters().getMandatoryBoolean(INCLUDE_INFERRED);
- super.postInit(tabNames, columnHeadings, false);
+ super.postInit(GFOLDER_ADHOC_REPORTS, tabNames, columnHeadings, false);
  }
 
  private void removeEmptyNoScopeAndDerivativeRefsets() throws TermServerScriptException {
  LOGGER.info("Checking local refsets for emptiness, out of scope and derivative refsets");
- emptyReferenceSets = new ArrayList<>();
- outOfScopeReferenceSets = new ArrayList<>();
+ List<Concept> emptyReferenceSets = new ArrayList<>();
+ List<Concept> outOfScopeReferenceSets = new ArrayList<>();
  List<Concept> derivativeRefsets = new ArrayList<>();
  for (Concept refset : referenceSets) {
  if (!inScope(refset)) {
@@ -140,7 +129,11 @@ private void removeEmptyNoScopeAndDerivativeRefsets() throws TermServerScriptExc
  } else {
  refsetSummary.put(refset, 0);
  }
- try { Thread.sleep(1 * 1000); } catch (Exception e) {}
+ try {
+ Thread.sleep(1 * 1000L);
+ } catch (Exception e) {
+ //still need to work out what to do with interrupted sleeps
+ }
  }
  referenceSets.removeAll(emptyReferenceSets);
  referenceSets.removeAll(derivativeRefsets);
@@ -247,22 +240,23 @@ private void reportRefsetInactivationsAgainstEcl(Concept refset, EclCache eclCac
  private void reportRefsetInactivationsAgainstEnumeratedList(Concept refset, EclCache eclCache) throws TermServerScriptException {
  int conceptsProcessed = 0;
  do {
- String subsetList = "";
- for (int i = 0; i < CHUNK_SIZE && conceptsProcessed < inactivatingConceptIds.size(); i++) {
+ StringBuilder subsetList = new StringBuilder();
+ for (int i = 0; i < CHUNK_SIZE && conceptsProcessed < inactivatingConceptIds.size(); i++, conceptsProcessed++) {
  if (i > 0) {
- subsetList += " OR ";
+ subsetList.append(" OR ");
  }
- subsetList += inactivatingConceptIds.get(conceptsProcessed);
- conceptsProcessed++;
+ subsetList.append(inactivatingConceptIds.get(conceptsProcessed));
  }
  String ecl = "^" + refset.getId() + " AND ( " + subsetList + " )";
  String detail = "As per branch " + eclCache.getBranch() + " on " + eclCache.getServer();
  for (Concept c : eclCache.findConcepts(ecl)) {
  report(c, "active in refset", refset.getPreferredSynonym(), detail);
  }
  try {
- Thread.sleep(1 * 200);
- } catch (Exception e) {}
+ Thread.sleep(1 * 200L);
+ } catch (Exception e) {
+ //still need to work out what to do with interrupted sleeps
+ }
  } while (conceptsProcessed < inactivatingConceptIds.size());
  }
 
@@ -316,9 +310,9 @@ private String getBranchForCodeSystem(TermServerClient tsClient, DerivativeLocat
  private void checkHighVolumeUsage() throws TermServerScriptException {
  LOGGER.debug ("Checking {} inactivating concepts against High Usage SCTIDs", inactivatingConceptIds.size());
  String fileName = "resources/HighVolumeSCTIDs.txt";
- LOGGER.debug ("Loading " + fileName );
+ LOGGER.debug ("Loading {}", fileName );
  try {
- List<String> lines = Files.readLines(new File(fileName), Charsets.UTF_8);
+ List<String> lines = Files.readLines(new File(fileName), StandardCharsets.UTF_8);
  for (String line : lines) {
  String id = line.split(TAB)[0];
  if (inactivatingConceptIds.contains(id)) {