Please do not merge Enhanced flex search

gsrs-module-substance-example/pom.xml

@@ -31,8 +31,8 @@
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-compiler-plugin</artifactId>
             <configuration>
-                <source>8</source>
-                <target>8</target>
+                <source>11</source>
+                <target>11</target>
             </configuration>
         </plugin>
         <!-- Uncomment this for maven public release deployment

gsrs-module-substance-example/src/test/java/example/structureSearch/FlexSearchTest.java

@@ -0,0 +1,198 @@
+package example.structureSearch;
+
+import example.GsrsModuleSubstanceApplication;
+import gsrs.legacy.structureIndexer.StructureIndexerService;
+import gsrs.module.substance.controllers.SubstanceController;
+import gsrs.module.substance.controllers.SubstanceLegacySearchService;
+import gsrs.module.substance.indexers.SubstanceDefinitionalHashIndexer;
+import gsrs.springUtils.AutowireHelper;
+import gsrs.startertests.TestGsrsValidatorFactory;
+import gsrs.startertests.TestIndexValueMakerFactory;
+import gsrs.substances.tests.AbstractSubstanceJpaFullStackEntityTest;
+import gsrs.validator.DefaultValidatorConfig;
+import gsrs.validator.ValidatorConfig;
+import ix.core.chem.StructureProcessor;
+import ix.core.models.Structure;
+import ix.core.search.SearchRequest;
+import ix.core.search.SearchResult;
+import ix.core.util.EntityUtils;
+import ix.ginas.modelBuilders.ChemicalSubstanceBuilder;
+import ix.ginas.models.v1.ChemicalSubstance;
+import ix.ginas.models.v1.Substance;
+import ix.ginas.utils.validation.validators.ChemicalValidator;
+import lombok.extern.slf4j.Slf4j;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.security.test.context.support.WithMockUser;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.List;
+import java.util.UUID;
+import java.util.stream.Collectors;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@SpringBootTest(classes = GsrsModuleSubstanceApplication.class)
+@WithMockUser(username = "admin", roles = "Admin")
+@Slf4j
+public class FlexSearchTest extends AbstractSubstanceJpaFullStackEntityTest {
+
+    @Autowired
+    StructureProcessor structureProcessor;
+
+    @Autowired
+    private TestIndexValueMakerFactory testIndexValueMakerFactory;
+
+    @Autowired
+    private TestGsrsValidatorFactory factory;
+
+    @Autowired
+    private StructureIndexerService indexer;
+
+    @Autowired
+    private SubstanceLegacySearchService searchService;
+
+    private String fileName = "testdumps/tartrate_set.gsrs";
+
+    private boolean loadedData = false;
+
+    @BeforeEach
+    public void clearIndexers() throws IOException {
+        if( !loadedData) {
+            log.trace("starting to load data");
+            SubstanceDefinitionalHashIndexer hashIndexer = new SubstanceDefinitionalHashIndexer();
+            AutowireHelper.getInstance().autowire(hashIndexer);
+            testIndexValueMakerFactory.addIndexValueMaker(hashIndexer);
+            {
+                ValidatorConfig config = new DefaultValidatorConfig();
+                config.setValidatorClass(ChemicalValidator.class);
+                config.setNewObjClass(ChemicalSubstance.class);
+                factory.addValidator("substances", config);
+            }
+
+            File dataFile = new ClassPathResource(fileName).getFile();
+            Assertions.assertTrue(dataFile.exists());
+            loadGsrsFile(dataFile);
+            loadedData = true;
+            log.info("loaded data");
+        }
+    }
+
+    @Test
+    @WithMockUser(value = "admin", roles = "Admin")
+    public void generateFlexSearchQuery() throws Exception {
+        String structure = "C(C(C(=O)O)O)(C(=O)O)O";
+        UUID uuid = UUID.randomUUID();
+        ChemicalSubstance substance= new ChemicalSubstanceBuilder()
+                    .setStructureWithDefaultReference(structure)
+                    .addName("Tartaric acid")
+                    .setUUID(uuid)
+                    .build();
+
+        log.trace("created query substance");
+        Structure structureStd = structureProcessor.taskFor(substance.getStructure().molfile)
+                .standardize(true)
+                .build()
+                .instrument()
+                .getStructure();
+        log.trace("created structureStd");
+        SubstanceController controller = new SubstanceController();
+        AutowireHelper.getInstance().autowireAndProxy(controller);
+        log.trace("created and wired controller");
+
+        String hash=  controller.makeFlexSearchMoietyClauses(structureStd) + ")";
+        log.trace("search hash: {}", hash);
+        assertTrue(hash.contains("root_moieties_properties_STEREO_INSENSITIVE_HASH"));
+    }
+
+    @Test
+    @WithMockUser(value = "admin", roles = "Admin")
+    public void runFlexSearchQueryTartaric() throws Exception {
+        String structure = "C(C(C(=O)O)O)(C(=O)O)O";
+        UUID uuid = UUID.randomUUID();
+        ChemicalSubstance substance= new ChemicalSubstanceBuilder()
+                .setStructureWithDefaultReference(structure)
+                .addName("Tartaric acid")
+                .setUUID(uuid)
+                .build();
+
+        Structure structureStd = structureProcessor.taskFor(substance.getStructure().molfile)
+                .standardize(true)
+                .build()
+                .instrument()
+                .getStructure();
+        String sins= structureStd.getStereoInsensitiveHash();
+        SubstanceController controller = new SubstanceController();
+        AutowireHelper.getInstance().autowireAndProxy(controller);
+
+        String hash=  controller.makeFlexSearch(structureStd);
+        log.trace("search hash: {}", hash);
+        SearchRequest request = new SearchRequest.Builder()
+                .kind(Substance.class)
+                .query(hash)
+                .build();
+        List<Substance> substances = getSearchList(request);
+        log.trace("Flex search hits:");
+        substances.forEach(s-> log.trace("ID {} - {}", s.uuid, s.getName()));
+
+        int expectedNumber = 7;
+        assertEquals(expectedNumber, substances.size());
+    }
+
+    @Test
+    @WithMockUser(value = "admin", roles = "Admin")
+    public void runFlexSearchQuerySodiumTartrate() throws Exception {
+        String structureSmiles = "C(C(C(=O)[O-])O)(C(=O)O)O.[Na+]";
+        String molfileSource = "molfiles/sodium_tartrate.mol";
+
+        File molfile = new ClassPathResource(molfileSource).getFile();
+        UUID uuid = UUID.randomUUID();
+
+        Structure structureStd = structureProcessor.taskFor(Files.readString(molfile.toPath()))
+                .standardize(true)
+                .build()
+                .instrument()
+                .getStructure();
+        String sins= structureStd.getStereoInsensitiveHash();
+        SubstanceController controller = new SubstanceController();
+        AutowireHelper.getInstance().autowireAndProxy(controller);
+
+        String hash=  controller.makeFlexSearch(structureStd);
+        log.trace("search hash: {}", hash);
+        SearchRequest request = new SearchRequest.Builder()
+                .kind(Substance.class)
+                .query(hash)
+                .build();
+        List<Substance> substances = getSearchList(request);
+        substances.forEach(s-> log.trace("ID {} - {}", s.uuid, s.getName()));
+
+        int expectedNumber = 3;
+        assertEquals(expectedNumber, substances.size());
+    }
+
+    private List<Substance> getSearchList(SearchRequest sr) {
+        TransactionTemplate transactionSearch = new TransactionTemplate(transactionManager);
+        List<Substance> substances = transactionSearch.execute(ts -> {
+            try {
+                SearchResult sresult = searchService.search(sr.getQuery(), sr.getOptions());
+                List<Substance> first = sresult.getMatches();
+                return first.stream()
+                        //force fetching
+                        .peek(ss -> EntityUtils.EntityWrapper.of(ss).toInternalJson())
+                        .collect(Collectors.toList());
+            } catch (Exception e) {
+                throw new RuntimeException(e);
+
+            }
+        });
+        return substances;
+    }
+
+}

gsrs-module-substance-example/src/test/resources/application-test.conf

@@ -7,7 +7,6 @@ substance.renderer.configPath=substances-default-renderer.json
 
 approval_id_code_system="UNII from FDA"
 logging.level.root=error
-logging.level.example.imports=trace
 #logging.level.example.imports=trace
 #logging.level.gsrs.imports=trace
 #logging.level.example.substance.processor=trace
@@ -41,11 +40,13 @@ logging.level.ix.core.EntityFetcher=OFF
 
 #for travis CI
 #logging.level.root=OFF
-#logging.level.gsrs.module.substance.scrubbers=trace
-#logging.level.example.exports.scrubbers=trace
+logging.level.gsrs.module.substance.scrubbers=trace
+logging.level.example.exports.scrubbers=trace
 
+logging.level.gsrs.module.substance.controllers=TRACE
 logging.level.ix.core.chem=TRACE
 logging.level.example.chem=TRACE
+logging.level.example.structureSearch=TRACE
 
 spring.jpa.database-platform=org.hibernate.dialect.H2Dialect
 spring.jpa.defer-datasource-initialization=true

gsrs-module-substance-example/src/test/resources/molfiles/sodium_tartrate.mol

@@ -0,0 +1,26 @@
+
+   JSDraw203202416202D
+
+ 11  9  0  0  0  0              0 V2000
+   19.1884   -8.0856    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   20.5396   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   20.5396   -5.7460    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   21.8917   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.8917   -9.6460    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   23.2437   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.2437   -5.7460    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   24.5956   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   24.5956   -9.6460    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+   25.9468   -7.3064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   28.5476   -7.6960    0.0000 Na  0  3  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  2  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  4  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  6  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+  8 10  2  0  0  0  0
+M  CHG  2   9  -1  11   1
+M  END

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java

@@ -31,8 +31,6 @@
 import org.freehep.graphicsio.svg.SVGGraphics2D;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.DependsOn;
-import org.springframework.core.env.ConfigurableEnvironment;
-import org.springframework.core.env.Environment;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.hateoas.server.ExposesResourceFor;
 import org.springframework.http.HttpHeaders;
@@ -742,8 +740,9 @@ public Object structureSearchGet(
             hash = "root_structure_properties_EXACT_HASH:" + structure.getExactHash();
         }else if(sanitizedRequest.getType() == SubstanceStructureSearchService.StructureSearchType.FLEX){
             //note we purposefully don't have the lucene path so it finds moieties and polymers etc
-            String sins=structure.getStereoInsensitiveHash();
-            hash= "( root_structure_properties_STEREO_INSENSITIVE_HASH:" + sins + " OR " + "root_moieties_properties_STEREO_INSENSITIVE_HASH:" + sins + " )";
+            hash= makeFlexSearch(structure);
+            log.trace("search hash: {}", hash);
+                    //"root_moieties_properties_STEREO_INSENSITIVE_HASH:" + sins + " )";
         }
 
         if(hash !=null){
@@ -1871,5 +1870,38 @@ public List<Text> getHardcodedConfigsBackup() throws JsonProcessingException {
         return items;
     }
 
-}
+    public String makeFlexSearch(Structure structure) {
+        String sins=structure.getStereoInsensitiveHash();
+        return "( root_structure_properties_STEREO_INSENSITIVE_HASH:\"" + sins + "\" OR " + makeFlexSearchMoietyClauses(structure) + ")";
+    }
+
+    public String makeFlexSearchMoietyClauses(Structure structure) {
 
+        List<Structure> moieties = new ArrayList<>();
+        try {
+            structureProcessor.taskFor(structure.molfile)
+                    .components(moieties)
+                    .standardize(false)
+                    .build()
+                    .instrument()
+                    .getStructure();
+            log.trace(" created {} moieties", moieties.size());
+            String moietySearchString= moieties.stream()
+                    .map(m->{
+                        StringBuilder sb = new StringBuilder();
+                        sb.append("root_moieties_properties_STEREO_INSENSITIVE_HASH:\"");
+                        sb.append(m.getStereoInsensitiveHash());
+                        sb.append("\"");
+                        return sb.toString();
+                    })
+                    .collect(Collectors.joining(" AND "));
+            if( moieties.size() > 1) {
+                moietySearchString = "(" + moietySearchString + ")";
+            }
+            return moietySearchString;
+        } catch (Exception e) {
+            log.error("Error constructing query: ", e);
+            throw new RuntimeException(e);
+        }
+    }
+}