Add search sorting: active, PT word count + alpha.

.gitignore

@@ -1,3 +1,4 @@
 .*
 target
 lucene-index
+test-lucene-index

pom.xml

@@ -10,7 +10,7 @@
  <parent>
  <groupId>org.snomed</groupId>
  <artifactId>snomed-parent-bom</artifactId>
- <version>1.0.9</version>
+ <version>1.0.11-SNAPSHOT</version>
  </parent>
 
  <properties>

src/main/java/org/snomed/snowstormmicro/SnowstormMicroApplication.java

@@ -1,30 +1,19 @@
 package org.snomed.snowstormmicro;
 
-import org.apache.logging.log4j.util.Strings;
-import org.apache.lucene.index.DirectoryReader;
-import org.apache.lucene.search.IndexSearcher;
-import org.apache.lucene.store.NIOFSDirectory;
+import org.hibernate.service.spi.ServiceException;
 import org.ihtsdo.otf.snomedboot.ReleaseImportException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.snomed.snowstormmicro.loading.ImportService;
-import org.snomed.snowstormmicro.service.CodeSystemService;
-import org.snomed.snowstormmicro.service.ValueSetService;
-import org.snomed.snowstormmicro.util.TimerUtil;
+import org.snomed.snowstormmicro.service.AppSetupService;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.CommandLineRunner;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration;
 import org.springframework.boot.autoconfigure.quartz.QuartzAutoConfiguration;
 import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration;
 
-import java.io.File;
 import java.io.IOException;
-import java.util.Arrays;
-import java.util.Set;
-import java.util.stream.Collectors;
 
 @SpringBootApplication(
  exclude = {
@@ -35,38 +24,20 @@
 )
 public class SnowstormMicroApplication implements CommandLineRunner {
 
- @Value("${load}")
- private String loadReleaseArchives;
-
- @Autowired
- private ImportService importService;
-
- @Autowired
- private CodeSystemService codeSystemService;
-
  @Autowired
- private ValueSetService valueSetService;
+ private AppSetupService appSetupService;
 
  private final Logger logger = LoggerFactory.getLogger(getClass());
 
  @Override
- public void run(String... args) throws IOException {
- if (!Strings.isEmpty(loadReleaseArchives)) {
- Set<String> filePaths = Arrays.stream(loadReleaseArchives.split(",")).collect(Collectors.toSet());
- try {
- TimerUtil timer = new TimerUtil("Import");
- importService.importRelease(filePaths);
- timer.finish();
- logger.info("Import complete");
+ public void run(String... args) {
+ try {
+ if (appSetupService.run()) {
  System.exit(0);
- } catch (ReleaseImportException | IOException e) {
- logger.error("Import failed", e);
- System.exit(1);
  }
- } else {
- IndexSearcher indexSearcher = new IndexSearcher(DirectoryReader.open(new NIOFSDirectory(new File("lucene-index").toPath())));
- codeSystemService.setIndexSearcher(indexSearcher);
- valueSetService.setIndexSearcher(indexSearcher);
+ } catch (ServiceException | IOException | ReleaseImportException e) {
+ logger.error(e.getMessage(), e);
+ System.exit(1);
  }
  }
 

src/main/java/org/snomed/snowstormmicro/domain/Concept.java

@@ -7,12 +7,17 @@ public class Concept {
  public static final String DOC_TYPE = "concept";
 
  public interface FieldNames {
-
  String ID = "id";
  String ACTIVE = "active";
+ String ACTIVE_SORT = "active_sort";
  String ANCESTORS = "ancestors";
  String MEMBERSHIP = "membership";
  String TERM = "term";
+ String TERM_STORED = "term_stored";
+ String PT_TERM_LENGTH = "pt_term_score";
+ String PT_WORD_COUNT = "pt_word_count";
+ String PT_STORED = "pt_stored";
+ String PT = "pt";
  }
  private String conceptId;
  private boolean active;
@@ -34,9 +39,10 @@ public Concept(String conceptId, boolean active) {
  }
 
  public String getPT() {
- // TODO: fix
  for (Description description : descriptions) {
- return description.getTerm();
+ if (!description.isFsn() && !description.getPreferredLangRefsets().isEmpty()) {
+ return description.getTerm();
+ }
  }
  return null;
  }

src/main/java/org/snomed/snowstormmicro/domain/Concepts.java

@@ -8,4 +8,6 @@ public class Concepts {
  public static final String IS_A = "116680003";
  public static final String INFERRED_RELATIONSHIP = "900000000000011006";
 
+ public static final String PREFERRED = "900000000000548007";
+ public static final String ACCEPTABLE = "900000000000549004";
 }

src/main/java/org/snomed/snowstormmicro/domain/Description.java

@@ -1,29 +1,26 @@
 package org.snomed.snowstormmicro.domain;
 
-import java.util.HashMap;
-import java.util.Map;
+import java.util.HashSet;
+import java.util.Set;
 
 public class Description {
 
  private String id;
  private String term;
  private String lang;
  private boolean fsn;
- private Map<String, String> acceptability;
+ private Set<String> preferredLangRefsets;
 
  public Description() {
+ preferredLangRefsets = new HashSet<>();
  }
 
  public Description(String id, String languageCode, boolean fsn, String term) {
+ this();
  this.id = id;
  this.lang = languageCode;
  this.fsn = fsn;
  this.term = term;
- acceptability = new HashMap<>();
- }
-
- public Description(String term) {
- this.term = term;
  }
 
  public String getId() {
@@ -54,11 +51,11 @@ public void setFsn(boolean fsn) {
  this.fsn = fsn;
  }
 
- public Map<String, String> getAcceptability() {
- return acceptability;
+ public Set<String> getPreferredLangRefsets() {
+ return preferredLangRefsets;
  }
 
- public void setAcceptability(Map<String, String> acceptability) {
- this.acceptability = acceptability;
+ public void setPreferredLangRefsets(Set<String> preferredLangRefsets) {
+ this.preferredLangRefsets = preferredLangRefsets;
  }
 }

src/main/java/org/snomed/snowstormmicro/fhir/CodeSystemProvider.java

@@ -1,8 +1,12 @@
 package org.snomed.snowstormmicro.fhir;
 
+import ca.uhn.fhir.rest.annotation.IdParam;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.Read;
 import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.IdType;
 import org.snomed.snowstormmicro.service.CodeSystemService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
@@ -18,15 +22,33 @@ public class CodeSystemProvider implements IResourceProvider {
  private CodeSystemService codeSystemService;
 
  @Search
- public List<CodeSystem> findCodeSystems() throws IOException {
+ public List<CodeSystem> findCodeSystems(
+ @OptionalParam(name="id") String id,
+ @OptionalParam(name="url") String url) throws IOException {
  List<CodeSystem> codeSystems = new ArrayList<>();
  org.snomed.snowstormmicro.domain.CodeSystem codeSystem = codeSystemService.getCodeSystem();
  if (codeSystem != null) {
- codeSystems.add(codeSystem.toHapi());
+ CodeSystem hapi = codeSystem.toHapi();
+ if ((id == null || hapi.getId().equals(id)) && (url == null || hapi.getUrl().equals(url))) {
+ codeSystems.add(hapi);
+ }
  }
  return codeSystems;
  }
 
+ @Read()
+ public CodeSystem getCodeSystem(@IdParam IdType id) throws IOException {
+ String idPart = id.getIdPart();
+ org.snomed.snowstormmicro.domain.CodeSystem codeSystem = codeSystemService.getCodeSystem();
+ if (codeSystem != null) {
+ CodeSystem hapi = codeSystem.toHapi();
+ if (hapi.getId().equals(idPart)) {
+ return hapi;
+ }
+ }
+ return null;
+ }
+
  @Override
  public Class<CodeSystem> getResourceType() {
  return CodeSystem.class;

src/main/java/org/snomed/snowstormmicro/fhir/FHIRTerminologyCapabilities.java

@@ -12,11 +12,13 @@
 import java.util.Collections;
 
 @ResourceDef(name="TerminologyCapabilities", profile="http:https://hl7.org/fhir/StructureDefinition/TerminologyCapabilities")
-@ChildOrder(names={"url", "version", "name", "title", "status", "experimental", "date", "publisher", "contact", "description", "useContext", "jurisdiction", "purpose", "copyright", "kind", "software", "implementation", "lockedDate", "codeSystem", "expansion", "codeSearch", "validateCode", "translation", "closure"})
+@ChildOrder(names={"url", "version", "name", "title", "status", "experimental", "date", "publisher", "contact", "description", "useContext",
+ "jurisdiction", "purpose", "copyright", "kind", "software", "implementation", "lockedDate", "codeSystem", "expansion", "codeSearch",
+ "validateCode", "translation", "closure"})
 public class FHIRTerminologyCapabilities extends TerminologyCapabilities implements IBaseConformance {
 
  private static final long serialVersionUID = 1L;
- 
+
  public FHIRTerminologyCapabilities withDefaults() {
  setContact();
  setCodeSystem();

src/main/java/org/snomed/snowstormmicro/fhir/ValueSetProvider.java

@@ -2,6 +2,7 @@
 
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
+import ca.uhn.fhir.rest.annotation.Search;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.OperationOutcome;
@@ -12,6 +13,9 @@
 import org.springframework.stereotype.Component;
 
 import java.io.IOException;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
 
 import static org.snomed.snowstormmicro.fhir.FHIRHelper.exception;
 
@@ -21,6 +25,11 @@ public class ValueSetProvider implements IResourceProvider {
  @Autowired
  private ValueSetService valueSetService;
 
+ @Search
+ public List<ValueSet> search() {
+ return Collections.emptyList();
+ }
+
  @Operation(name = "$expand", idempotent = true)
  public ValueSet expand(
  @OperationParam(name="url") UriType url,

src/main/java/org/snomed/snowstormmicro/loading/ComponentFactoryImpl.java

@@ -6,30 +6,37 @@
 import org.snomed.snowstormmicro.domain.Description;
 
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 
 public class ComponentFactoryImpl extends ImpotentComponentFactory {
 
  private final Map<Long, Concept> conceptMap;
+ private final Map<Long, Description> descriptionSynonymMap;
  private final Concept dummyConcept;
  private Integer maxDate = null;
 
  public ComponentFactoryImpl() {
  conceptMap = new HashMap<>();
+ descriptionSynonymMap = new HashMap<>();
  dummyConcept = new Concept();
  }
 
  @Override
  public void newConceptState(String conceptId, String effectiveTime, String active, String moduleId, String definitionStatusId) {
  conceptMap.put(Long.parseLong(conceptId), new Concept(conceptId, active.equals("1")));
+ collectMaxEffectiveTime(effectiveTime);
  }
 
  @Override
  public void newDescriptionState(String id, String effectiveTime, String active, String moduleId, String conceptId, String languageCode, String typeId, String term, String caseSignificanceId) {
  if (active.equals("1") && (typeId.equals(Concepts.FSN) || typeId.equals(Concepts.SYNONYM))) {
- conceptMap.getOrDefault(Long.parseLong(conceptId), dummyConcept).addDescription(new Description(id, languageCode, typeId.equals(Concepts.FSN), term));
+ Description description = new Description(id, languageCode, typeId.equals(Concepts.FSN), term);
+ conceptMap.getOrDefault(Long.parseLong(conceptId), dummyConcept).addDescription(description);
+ if (typeId.equals(Concepts.SYNONYM)) {
+ descriptionSynonymMap.put(Long.parseLong(id), description);
+ }
  }
+ collectMaxEffectiveTime(effectiveTime);
  }
 
  @Override
@@ -40,6 +47,7 @@ public void newRelationshipState(String id, String effectiveTime, String active,
  conceptMap.getOrDefault(Long.parseLong(sourceId), dummyConcept).addParent(parent);
  }
  }
+ collectMaxEffectiveTime(effectiveTime);
  }
 
  @Override
@@ -48,16 +56,18 @@ public void newReferenceSetMemberState(String[] fieldNames, String id, String ef
  if (fieldNames.length == 0) {
  // Active simple refset member
  conceptMap.getOrDefault(Long.parseLong(referencedComponentId), dummyConcept).addMembership(refsetId);
- } else if (fieldNames.length == 1 && fieldNames[0].equals("acceptabilityId")) {
+ } else if (fieldNames.length == 7 && fieldNames[6].equals("acceptabilityId") && otherValues[0].equals(Concepts.PREFERRED)) {
  // Active lang refset member
- List<Description> descriptions = conceptMap.getOrDefault(Long.parseLong(referencedComponentId), dummyConcept).getDescriptions();
- for (Description description : descriptions) {
- if (description.getId().equals(referencedComponentId)) {
- description.getAcceptability().put(refsetId, otherValues[0]);
- }
+ Description description = descriptionSynonymMap.get(Long.parseLong(referencedComponentId));
+ if (description != null) {
+ description.getPreferredLangRefsets().add(refsetId);
  }
  }
  }
+ collectMaxEffectiveTime(effectiveTime);
+ }
+
+ private void collectMaxEffectiveTime(String effectiveTime) {
  if (maxDate == null || (effectiveTime != null && Integer.parseInt(effectiveTime) > maxDate)) {
  maxDate = Integer.parseInt(effectiveTime);
  }

src/main/java/org/snomed/snowstormmicro/loading/ImportService.java

@@ -9,6 +9,7 @@
 import org.slf4j.LoggerFactory;
 import org.snomed.snowstormmicro.service.CodeSystemService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 import org.springframework.util.FileSystemUtils;
 
@@ -27,6 +28,9 @@ public class ImportService {
  @Autowired
  private CodeSystemService codeSystemService;
 
+ @Value("${index.path}")
+ private String indexPath;
+
  private final Logger logger = LoggerFactory.getLogger(getClass());
 
  private final LoadingProfile loadingProfile = LoadingProfile.light
@@ -45,7 +49,7 @@ public void importRelease(Set<String> releaseArchivePaths) throws IOException, R
  }
 
  ReleaseImporter releaseImporter = new ReleaseImporter();
- File luceneIndex = new File("lucene-index");
+ File luceneIndex = new File(indexPath);
  if (luceneIndex.exists()) {
  logger.info("Deleting existing index directory.");
  FileSystemUtils.deleteRecursively(luceneIndex);