Multiple inchis

gsrs-module-substance-example/pom.xml

@@ -212,7 +212,7 @@
 
         <dependency>
             <groupId>com.h2database</groupId>
-            <artifactId>h2</artifactId>           	
+            <artifactId>h2</artifactId>
         </dependency>
         <dependency>
             <groupId>org.projectlombok</groupId>

gsrs-module-substance-example/src/main/java/example/GsrsModuleSubstanceApplication.java

@@ -10,7 +10,6 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.web.servlet.config.annotation.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
 
 //import org.springframework.cloud.netflix.eureka.EnableEurekaClient;
 

gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java

@@ -10,11 +10,9 @@
 import ix.core.chem.StructureProcessor;
 import ix.core.models.Structure;
 import ix.ginas.modelBuilders.ChemicalSubstanceBuilder;
-import ix.ginas.modelBuilders.SubstanceBuilder;
-import ix.ginas.models.v1.ChemicalSubstance;
-import ix.ginas.models.v1.GinasChemicalStructure;
 import ix.ginas.modelBuilders.MixtureSubstanceBuilder;
 import ix.ginas.modelBuilders.StructurallyDiverseSubstanceBuilder;
+import ix.ginas.modelBuilders.SubstanceBuilder;
 import ix.ginas.models.v1.*;
 import lombok.extern.slf4j.Slf4j;
 import org.junit.jupiter.api.Assertions;

gsrs-module-substance-example/src/test/java/example/substance/FlexAndExactSearchFullStackTest.java

@@ -1,8 +1,5 @@
 package example.substance;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.util.Collection;
@@ -15,6 +12,7 @@
 
 import javax.servlet.http.HttpServletRequest;
 
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.junit.jupiter.api.Test;
 import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -41,6 +39,9 @@
 import ix.core.chem.StructureStandardizer;
 import ix.core.models.Structure;
 import ix.ginas.modelBuilders.SubstanceBuilder;
+
+import static org.junit.jupiter.api.Assertions.*;
+
 @SpringBootTest(classes = GsrsModuleSubstanceApplication.class)
 @ActiveProfiles("test")
 @RecordApplicationEvents
@@ -60,10 +61,6 @@ public class FlexAndExactSearchFullStackTest  extends AbstractSubstanceJpaFullSt
 
     @TestConfiguration
     public static class Configuration{
-//        @Value("${ix.core.structureIndex.atomLimit}")
-//        private int maxNumberOfAtoms = 240;
-//        @Value(value ="${ix.structure-standardizer}")
-//        private Class<? extends AbstractStructureStandardizer> standardizerClass = InchiStandardizer.class;
         @Bean
         public StructureStandardizer getStructureStandardizer() throws InstantiationException, IllegalAccessException, NoSuchMethodException, InvocationTargetException {
             InchiStandardizer istd = new InchiStandardizer();
@@ -262,4 +259,38 @@ public void ensureAFlexSearchForADirectSmilesGetsStandardized() throws Exception
     }
 
 
+    @Test
+    public void ensureSmilesLeadsToReasonableMolfile() throws Exception {
+
+        ObjectMapper om = new ObjectMapper();
+        String smiles = "c1ccc(cc1)P(CCCC#N)(c2ccccc2)c3ccccc3";
+        UUID uuid1 = UUID.randomUUID();
+        new SubstanceBuilder()
+                .asChemical()
+                .setStructureWithDefaultReference(smiles)
+                .addName("triphenyl-Phosphene,(3-cyanopropyl)")
+                .setUUID(uuid1)
+                .buildJsonAnd(this::assertCreatedAPI);
+
+        HttpServletRequest  mockedRequest = Mockito.mock(HttpServletRequest.class);
+        Mockito.when(mockedRequest.getRequestURI()).thenReturn("http://mock");
+        Mockito.when(mockedRequest.getRequestURL()).thenReturn(new StringBuffer("http://mock"));
+
+        LoggingStructureStandardizer lstd=(LoggingStructureStandardizer)standardizer;
+
+        lstd.reset();
+        assertEquals(0,lstd.getStdCallCount());
+
+        ResponseEntity<Object> response= substanceController.interpretStructure(smiles, new HashMap<>());
+        assertTrue(response.getBody() instanceof ObjectNode);
+        ObjectNode baseNode = (ObjectNode)response.getBody();
+        ObjectNode structureNode = (ObjectNode) baseNode.get("structure");
+        String molfile = structureNode.get("molfile").asText();
+        assertNotNull(molfile);
+        Chemical chem = Chemical.parseMol(molfile);
+        assertTrue(chem.bonds().allMatch(b->b.isQueryBond()));
+        System.out.printf("molfile=%s\n", molfile);
+    }
+
+
 }

gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java

@@ -16,6 +16,7 @@
 import gsrs.module.substance.utils.MolWeightCalculatorProperties;
 import gsrs.module.substance.utils.SubstanceMatchViewGenerator;
 import gsrs.module.substance.utils.SubstanceResultListRecordGenerator;
+import gsrs.security.LegacyAuthenticationConfiguration;
 import ix.core.chem.StructureProcessorConfiguration;
 import ix.core.search.bulk.BulkSearchService;
 import ix.core.search.bulk.UserSavedListService;
@@ -64,6 +65,7 @@
         SubstanceSynchronizer.class,
         StructureProcessorConfiguration.class,
         StructureHandlingConfiguration.class,
+        LegacyAuthenticationConfiguration.class,
         ChemicalUtils.class
 })
 public class SubstanceCoreConfiguration {

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

@@ -1,6 +1,7 @@
 package gsrs.module.substance.controllers;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import gsrs.cache.GsrsCache;
 import ix.core.controllers.EntityFactory;
 

gsrs-module-substances-core/src/main/java/gsrs/module/substance/exporters/DefaultSubstanceSpreadsheetExporterFactory.java

@@ -10,6 +10,8 @@
 import ix.core.models.Group;
 import ix.core.models.Structure;
 import ix.core.util.EntityUtils.Key;
+import ix.core.util.pojopointer.extensions.InChIFullRegisteredFunction;
+import ix.core.util.pojopointer.extensions.InChIRegisteredFunction;
 import ix.ginas.exporters.*;
 import ix.ginas.exporters.Spreadsheet.SpreadsheetRow;
 import ix.ginas.models.v1.*;
@@ -20,6 +22,7 @@
 import java.io.IOException;
 import java.io.OutputStream;
 import java.util.*;
+import java.util.function.BiFunction;
 import java.util.stream.Stream;
 
 /**
@@ -208,9 +211,13 @@ public Map<Column, ColumnValueRecipe<Substance>> createColumnRecipes(Parameters
 
     			try {
     				Chemical chem = s.toChemical();
-    				cell.writeString(Inchi.asStdInchi(Chem.RemoveQueryFeaturesForPseudoInChI(chem))
+                    InChIRegisteredFunction functionHolder = new InChIRegisteredFunction();
+                    BiFunction<InChIRegisteredFunction.InChIPath, Structure, Optional<String>> fun = functionHolder.getOperation();
+                    Optional<String> result =fun.apply(new InChIRegisteredFunction.InChIPath(), ((ChemicalSubstance) s).getStructure());
+                    cell.writeString(result.orElse(""));
+    				/*cell.writeString(Inchi.asStdInchi(Chem.RemoveQueryFeaturesForPseudoInChI(chem))
     						.getKey()
-    						.replace("InChIKey=", ""));
+    						.replace("InChIKey=", ""));*/
     			} catch (Exception e) {
 
     			}

gsrs-module-substances-core/src/main/java/ix/core/models/Structure.java

@@ -487,6 +487,7 @@ public String getInChIKeyAndThrow() throws Exception{
     }
 
     @JsonProperty("_inchiKeySet")
+    @JsonIgnore
     @Transient
     public List<String> getInChIKeysAndThrow() {
 
@@ -508,7 +509,6 @@ public List<String> getInChIKeysAndThrow() {
                         return null;
                     }
                 }).filter(i -> i != null)
-                //.collect(Collectors.joining("\\n"));
                 .collect(Collectors.toList());
         }
         catch (Exception ex) {
@@ -518,6 +518,7 @@ public List<String> getInChIKeysAndThrow() {
     }
 
     @JsonProperty("_inchiSet")
+    @JsonIgnore
     @Transient
     public List<String> getInChIsAndThrow() {
 

gsrs-module-substances-spring-boot-starter/pom.xml

@@ -15,7 +15,6 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter</artifactId>
-            <version>2.4.5</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

gsrs-module-substances-tests/src/main/java/gsrs/substances/tests/AbstractSubstanceJpaEntityTestSuperClass.java

@@ -17,6 +17,7 @@
 
 import javax.persistence.EntityManager;
 
+import gsrs.scheduler.GsrsSchedulerTaskPropertiesConfiguration;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.extension.RegisterExtension;
 import org.quartz.Scheduler;
@@ -151,6 +152,13 @@ protected GsrsExportConfiguration mockGsrsExportConfiguration(){
             return mock(GsrsExportConfiguration.class);
         }
 
+        @Bean
+        @ConditionalOnMissingBean
+        @Primary
+        public GsrsSchedulerTaskPropertiesConfiguration getGsrsSchedulerTaskPropertiesConfiguration() {
+            return new GsrsSchedulerTaskPropertiesConfiguration();
+        }
+
     }
 
     static class Initializer implements ApplicationContextInitializer<ConfigurableApplicationContext> {

pom.xml

@@ -12,7 +12,7 @@
         <module>gsrs-module-substances-api</module>
         <module>gsrs-module-substances-dto</module>
         <module>gsrs-module-substances-tests</module>
-	<module>gsrs-ncats-substance-extension</module>
+        <module>gsrs-ncats-substance-extension</module>
         <module>gsrs-module-substances-data-exchange</module>
     </modules>
     <parent>
@@ -32,13 +32,13 @@
     </scm>
     <properties>
         <java.version>1.8</java.version>
-        <spring-cloud.version>Hoxton.SR1</spring-cloud.version>
         <gsrs.version>3.1.2-SNAPSHOT</gsrs.version>
         <gsrs.substance.version>3.1.2-SNAPSHOT</gsrs.substance.version>
+        <spring-cloud.version>Hoxton.SR1</spring-cloud.version>
+        <spring-boot.version>2.4.5</spring-boot.version>
         <gsrs.applications-api.version>3.1.2-SNAPSHOT</gsrs.applications-api.version>
         <gsrs.clinical-trials-api.version>3.1.2-SNAPSHOT</gsrs.clinical-trials-api.version>
         <gsrs.products-api.version>3.1.2-SNAPSHOT</gsrs.products-api.version>
-        <spring-boot.version>2.4.5</spring-boot.version>
         <log4j2.version>2.17.2</log4j2.version>
     </properties>