diff --git a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java index 848b67c35..20e7a209d 100644 --- a/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java +++ b/gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java @@ -3,18 +3,29 @@ import com.fasterxml.jackson.databind.ObjectMapper; import gsrs.module.substance.definitional.ChemicalSubstanceDefinitionalElementImpl; import gsrs.module.substance.definitional.DefinitionalElement; +import gsrs.module.substance.definitional.MixtureDefinitionalElementImpl; +import gsrs.module.substance.definitional.StructurallyDiverseDefinitionalElementImpl; +import gsrs.springUtils.AutowireHelper; import gsrs.substances.tests.AbstractSubstanceJpaEntityTest; import ix.core.chem.StructureProcessor; import ix.core.models.Structure; import ix.ginas.modelBuilders.ChemicalSubstanceBuilder; -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; import org.junit.jupiter.api.Test; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.core.io.ClassPathResource; + +import java.io.File; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; +@Slf4j public class DefHashCalcTest extends AbstractSubstanceJpaEntityTest { @Autowired @@ -85,4 +96,123 @@ public void testOpticalInDefinitionalHashCalcPos() throws Exception { definitionalElements.forEach(de-> System.out.printf("key: %s = %s\n", de.getKey(), de.getValue())); Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(opticalActivityKey))); } + + @Test + public void testPropertiesInDefinitionalHashMixtures() throws Exception { + String propertyElementName = "properties.HYDROPHILLIC-LIPOPHILLIC BALANCE (HLB).value"; + File mixtureFile = new ClassPathResource("testJSON/SURFHOPe C-1811_mixture.json").getFile(); + MixtureSubstanceBuilder builder = SubstanceBuilder.from(mixtureFile); + MixtureSubstance mixtureSubstance = builder.build(); + MixtureDefinitionalElementImpl definitionalElement = new MixtureDefinitionalElementImpl(); + AutowireHelper.getInstance().autowireAndProxy(definitionalElement); + + List definitionalElements = new ArrayList<>(); + definitionalElement.computeDefinitionalElements(mixtureSubstance, definitionalElements::add); + definitionalElements.forEach(de-> log.trace("key: {} = {}", de.getKey(), de.getValue())); + Assertions.assertTrue(definitionalElements.stream().anyMatch(de->de.getKey().equals(propertyElementName))); + } + + @Test + public void testPropertiesInDefinitionalHashStrDiv() throws Exception { + String propertyElementNameDefining = "properties.DEGREE OF REACTION.value"; + String propertyElementNameNotDefining = "properties.ABSORBING POWER.value"; + File strDivSubFile = new ClassPathResource("testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json").getFile(); + StructurallyDiverseSubstanceBuilder builder = SubstanceBuilder.from(strDivSubFile); + StructurallyDiverseSubstance structurallyDiverseSubstance = builder.build(); + StructurallyDiverseDefinitionalElementImpl definitionalElement = new StructurallyDiverseDefinitionalElementImpl(); + AutowireHelper.getInstance().autowireAndProxy(definitionalElement); + + List definitionalElements = new ArrayList<>(); + definitionalElement.computeDefinitionalElements(structurallyDiverseSubstance, definitionalElements::add); + definitionalElements.forEach(de-> log.trace("key: {} = {}", de.getKey(), de.getValue())); + Assertions.assertEquals(1, definitionalElements.stream().filter(de->de.getKey().equals(propertyElementNameDefining)).count()); + Assertions.assertEquals(0, definitionalElements.stream().filter(de->de.getKey().equals(propertyElementNameNotDefining)).count()); + } + + @Test + public void testTwoChemicalsNoDefPropertiesEqual() throws Exception { + String opticalActivityKey="structure.properties.opticalActivity"; + String structureJson = "{\n" + + " \"opticalActivity\": \"UNSPECIFIED\",\n" + + " \"molfile\": \"\\n ACCLDraw07282209012D\\n\\n 5 4 0 0 0 0 0 0 0 0999 V2000\\n 10.5000 -8.5938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.5229 -8.0032 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0\\n 11.5229 -6.8217 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.5460 -8.5939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.5692 -8.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0 0 0 0\\n 2 3 1 0 0 0 0\\n 2 4 1 0 0 0 0\\n 4 5 1 0 0 0 0\\nM END\",\n" + + " \"stereoCenters\": 1,\n" + + " \"definedStereo\": 0,\n" + + " \"ezCenters\": 0,\n" + + " \"charge\": 0,\n" + + " \"mwt\": 92.56726,\n" + + " \"count\": 1,\n" + + " \"stereochemistry\": \"RACEMIC\"\n" + + "}\n" + + ""; + ObjectMapper om = new ObjectMapper(); + Structure rawStructure = om.readValue(structureJson, Structure.class); + Structure instrumentedStructure =structureProcessor.instrument(rawStructure.toChemical(), true); + GinasChemicalStructure ginasChemicalStructure = new GinasChemicalStructure(instrumentedStructure); + + ChemicalSubstanceBuilder builder = new ChemicalSubstanceBuilder(); + ChemicalSubstance chem =builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl(); + List definitionalElements = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add); + + ChemicalSubstance chem2 = builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + List definitionalElements2 = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem2, definitionalElements2::add); + Assertions.assertArrayEquals(definitionalElements.toArray(), definitionalElements2.toArray()); + } + + @Test + public void testTwoChemicalsDefPropertiesNotEqual() throws Exception { + String opticalActivityKey="structure.properties.opticalActivity"; + String structureJson = "{\n" + + " \"opticalActivity\": \"UNSPECIFIED\",\n" + + " \"molfile\": \"\\n ACCLDraw07282209012D\\n\\n 5 4 0 0 0 0 0 0 0 0999 V2000\\n 10.5000 -8.5938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 11.5229 -8.0032 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0\\n 11.5229 -6.8217 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\\n 12.5460 -8.5939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 13.5692 -8.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0 0 0 0\\n 2 3 1 0 0 0 0\\n 2 4 1 0 0 0 0\\n 4 5 1 0 0 0 0\\nM END\",\n" + + " \"stereoCenters\": 1,\n" + + " \"definedStereo\": 0,\n" + + " \"ezCenters\": 0,\n" + + " \"charge\": 0,\n" + + " \"mwt\": 92.56726,\n" + + " \"count\": 1,\n" + + " \"stereochemistry\": \"RACEMIC\"\n" + + "}\n" + + ""; + ObjectMapper om = new ObjectMapper(); + Structure rawStructure = om.readValue(structureJson, Structure.class); + Structure instrumentedStructure =structureProcessor.instrument(rawStructure.toChemical(), true); + GinasChemicalStructure ginasChemicalStructure = new GinasChemicalStructure(instrumentedStructure); + + ChemicalSubstanceBuilder builder = new ChemicalSubstanceBuilder(); + ChemicalSubstance chem =builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + ChemicalSubstanceDefinitionalElementImpl defHashCalculator = new ChemicalSubstanceDefinitionalElementImpl(); + List definitionalElements = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add); + + ChemicalSubstance chem2 = builder + .setStructure(ginasChemicalStructure) + .addName("2-chlorobutane") + .build(); + Property definingBoilingPoint = new Property(); + definingBoilingPoint.setName("Boiling Point"); + definingBoilingPoint.setType("Physical"); + Amount bpAmout = new Amount(); + bpAmout.average = 70d; + bpAmout.units = "degrees C"; + + definingBoilingPoint.setValue(bpAmout); + definingBoilingPoint.setDefining(true); + chem2.properties.add(definingBoilingPoint); + + List definitionalElements2 = new ArrayList<>(); + defHashCalculator.computeDefinitionalElements(chem2, definitionalElements::add); + Assertions.assertFalse(Arrays.equals(definitionalElements.toArray(), definitionalElements2.toArray())); + } } diff --git a/gsrs-module-substance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json b/gsrs-module-substance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json new file mode 100644 index 000000000..4c7fa6f30 --- /dev/null +++ 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+ ], + "access": [], + "languages": [ + "en" + ], + "type": "cn", + "name": "Sucrose sequipalmitostearate (HLB 11)" + }, + { + "references": [ + "6bc5629f-4183-6271-4c9f-7dc9b38165f9" + ], + "access": [], + "languages": [ + "en" + ], + "type": "cn", + "name": "Surfhope SE Cosme C-1811", + "displayName": false + } + ], + "codes": [ + { + "references": [ + "755dd19f-ee8b-8153-6554-6846415a133a" + ], + "access": [], + "code": "25168-73-4", + "type": "GENERIC (FAMILY)", + "codeSystem": "CAS" + } + ], + "notes": [], + "properties": [ + { + "value": { + "average": "11", + "type": "EXACT" + }, + "references": [ + "6bc5629f-4183-6271-4c9f-7dc9b38165f9" + ], + "access": [], + "name": "HYDROPHILLIC-LIPOPHILLIC BALANCE (HLB)", + "propertyType": "PHYSICAL", + "defining": true + } + ], + "relationships": [], + "references": [ + { + "tags": [], + "access": [], + "docType": "STN (SCIFINDER)", + "citation": "STN", + "publicDomain": true, + "uuid": "755dd19f-ee8b-8153-6554-6846415a133a" + }, + { + "tags": [], + "access": [], + "docType": "MANUFACTURER PRODUCT DESCRIPTION", + "url": "https://www.pharmacompass.com/pAssets/pdf/edqm/application/JRS-Pharma-LLP-edqm-application-1457952389.pdf", + "citation": "https://www.pharmacompass.com/pAssets/pdf/edqm/application/JRS-Pharma-LLP-edqm-application-1457952389.pdf", + "publicDomain": true, + "uuid": "6bc5629f-4183-6271-4c9f-7dc9b38165f9" + }, + { + "deprecated": false, + "uuid": "9a03fb0b-f473-0e4c-47e4-5f5f91748eb1", + "citation": "SRS", + "docType": "SRS", + "publicDomain": true, + "tags": [ + "PUBLIC_DOMAIN_RELEASE" + ], + "access": [] + } + ], + "tags": [], + "mixture": { + "deprecated": false, + "uuid": "ff244317-9e59-3b8f-548e-3f4b9fe94161", + "components": [ + { + "deprecated": false, + "uuid": "915c7458-30d1-f6e1-acbb-0dffdc1a44ad", + "type": "MUST_BE_PRESENT", + "substance": { + "deprecated": false, + "uuid": "a56a9250-17ed-61fc-5c18-e0c34e556398", + "refPname": "SUCROSE, 6-STEARATE", + "refuuid": "6eefb92b-e55d-4e27-8730-5880a236ca4f", + "substanceClass": "reference", + "approvalID": "114S1GA41U", + "linkingID": "114S1GA41U", + "name": "SUCROSE, 6-STEARATE", + "references": [], + "access": [] + }, + "references": [], + "access": [] + }, + { + "deprecated": false, + "uuid": "7c40417f-e68a-b952-dd39-3e9a3e383cc0", + "type": "MUST_BE_PRESENT", + "substance": { + "deprecated": false, + "uuid": "1b087160-2ab6-887f-2b8a-20a46089c6cb", + "refPname": "SUCROSE, 6'-STEARATE", + "refuuid": "efded1a3-de59-4642-b74b-79fc2a65005f", + "substanceClass": "reference", + "approvalID": "J7MT237SNW", + "linkingID": "J7MT237SNW", + "name": "SUCROSE, 6'-STEARATE", + "references": [], + "access": [] + }, + "references": [], + "access": [] + }, + { + "deprecated": false, + "uuid": "da434958-79f6-c2bf-81b4-1a050289c324", + "type": "MUST_BE_PRESENT", + "substance": { + "deprecated": false, + "uuid": "0a558e0c-3b5f-2e3e-c3e0-ce76b0139294", + "refPname": "SUCROSE, 1-STEARATE", + "refuuid": "a8db9c64-9fca-4cec-80d4-5daa7111ff03", + "substanceClass": "reference", + "approvalID": "58RP7JU52K", + "linkingID": "58RP7JU52K", + "name": "SUCROSE, 1-STEARATE", + "references": [], + "access": [] + }, + "references": [], + "access": [] + } + ], + "references": [ + "9a03fb0b-f473-0e4c-47e4-5f5f91748eb1" + ], + "access": [] + }, + "_approvalIDDisplay": "274KW0O50M", + "access": [], + "_self": "https://gsrs.preprod.fda.gov/api/v1/substances(91c883d0-b404-4252-8c50-6896e7df0bfb)?view=full", + "modifications": { + "agentModifications": [], + "structuralModifications": [], + "physicalModifications": [] + } +} \ No newline at end of file diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java index e3f9afed6..db3aae180 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java @@ -27,6 +27,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); ChemicalSubstance chemicalSubstance = (ChemicalSubstance) s; Structure structure = chemicalSubstance.getStructure(); if(structure==null){ diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java index 3151dd876..24cc1aa6e 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java @@ -30,7 +30,8 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { - log.trace("performAddition of mixture substance"); + log.trace("computeDefinitionalElements of mixture substance"); + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); MixtureSubstance mixtureSubstance = (MixtureSubstance)s; Mixture mix = mixtureSubstance.mixture; if (mix != null && !mix.components.isEmpty()) { diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java index aa7b52650..8f1a9e9d4 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java @@ -15,6 +15,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); String primaryName = ""; for(Name name : ((Substance)s).getAllNames()) { if( name.displayName ){ diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java index ca46ca3aa..550eebbd2 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java @@ -29,6 +29,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object substance, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(substance, consumer); NucleicAcidSubstance nucleicAcidSubstance = (NucleicAcidSubstance) substance; if(nucleicAcidSubstance.nucleicAcid ==null || nucleicAcidSubstance.nucleicAcid.subunits ==null){ return; @@ -75,10 +76,8 @@ public void computeDefinitionalElements(Object substance, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); PolymerSubstance polymerSubstance = (PolymerSubstance)s; Polymer polymer = polymerSubstance.polymer; @@ -105,30 +106,6 @@ public void computeDefinitionalElements(Object s, Consumer } - if (polymerSubstance.properties != null) { - for (Property property : polymerSubstance.properties) { - if (property.isDefining() && property.getValue() != null) { - String defElementName = String.format("properties.%s.value", - property.getName()); - DefinitionalElement propertyValueDefElement = - DefinitionalElement.of(defElementName, property.getValue().toString(), 2); - consumer.accept(propertyValueDefElement); - log.debug("added def element for property " + defElementName); - for (Parameter parameter : property.getParameters()) { - defElementName = String.format("properties.%s.parameters.%s.value", - property.getName(), parameter.getName()); - if (parameter.getValue() != null) { - DefinitionalElement propertyParamValueDefElement = - DefinitionalElement.of(defElementName, - parameter.getValue().toString(), 2); - consumer.accept(propertyParamValueDefElement); - log.debug("added def element for property parameter " + defElementName); - } - } - } - } - } - } } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java index e6b328eca..902424b54 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/ProteinSubstanceDefinitionalElementImpl.java @@ -54,7 +54,7 @@ private List canonicalizeSites(List oldSites, Map @Override public void computeDefinitionalElements(Object substance, Consumer consumer) { - + DefinitionalElementImplementation.super.computeDefinitionalElements(substance, consumer); ProteinSubstance proteinSubstance = (ProteinSubstance)substance; //this implementation is different than the version in GSRS 2.x in that //the old version made a copy of the ProteinSubstance to reorder the subunits and all corresponding Sites diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java index 45bae0ed9..aa6a00b4c 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/SSG1DefinitionalElementImpl.java @@ -27,6 +27,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); SpecifiedSubstanceGroup1Substance ssg1 = (SpecifiedSubstanceGroup1Substance) s; if(ssg1.specifiedSubstance.constituents != null) { @@ -63,29 +64,5 @@ public void computeDefinitionalElements(Object s, Consumer definitionalElementFactory.addDefinitionalElementsFor(ssg1.modifications, consumer); } - - if( ssg1.properties != null ) { - for(Property property : ssg1.properties) { - if(property.isDefining() && property.getValue() != null) { - String defElementName = String.format("properties.%s.value", - property.getName()); - DefinitionalElement propertyValueDefElement = - DefinitionalElement.of(defElementName, property.getValue().toString(), 2); - consumer.accept(propertyValueDefElement); - log.debug("added def element for property " + defElementName); - for(Parameter parameter : property.getParameters()) { - defElementName = String.format("properties.%s.parameters.%s.value", - property.getName(), parameter.getName()); - if( parameter.getValue() != null) { - DefinitionalElement propertyParamValueDefElement = - DefinitionalElement.of(defElementName, - parameter.getValue().toString(), 2); - consumer.accept(propertyParamValueDefElement); - log.debug("added def element for property parameter " + defElementName); - } - } - } - } - } } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java index 8775b0988..24850347d 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/definitional/StructurallyDiverseDefinitionalElementImpl.java @@ -6,6 +6,7 @@ import ix.ginas.models.v1.Parameter; import ix.ginas.models.v1.Property; import ix.ginas.models.v1.StructurallyDiverseSubstance; +import ix.ginas.models.v1.Substance; import lombok.extern.slf4j.Slf4j; import org.springframework.beans.factory.annotation.Autowired; @@ -31,6 +32,7 @@ public boolean supports(Object s) { @Override public void computeDefinitionalElements(Object s, Consumer consumer) { + DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer); StructurallyDiverseSubstance substance = (StructurallyDiverseSubstance) s; /* @@ -162,29 +164,5 @@ public void computeDefinitionalElements(Object s, Consumer log.trace("adding infraspecificName"); consumer.accept(infraspecificNameElement); } - - if( substance.properties != null ) { - for(Property property : substance.properties) { - if(property.isDefining() && property.getValue() != null) { - String defElementName = String.format("properties.%s.value", - property.getName()); - DefinitionalElement propertyValueDefElement = - DefinitionalElement.of(defElementName, property.getValue().toString(), 2); - consumer.accept(propertyValueDefElement); - log.trace("added def element for property " + defElementName); - for(Parameter parameter : property.getParameters()) { - defElementName = String.format("properties.%s.parameters.%s.value", - property.getName(), parameter.getName()); - if( parameter.getValue() != null) { - DefinitionalElement propertyParamValueDefElement = - DefinitionalElement.of(defElementName, - parameter.getValue().toString(), 2); - consumer.accept(propertyParamValueDefElement); - log.trace("added def element for property parameter " + defElementName); - } - } - } - } - } } } diff --git a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java index 2887fc80c..f9a5f913a 100644 --- a/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java +++ b/gsrs-module-substances-core/src/main/java/gsrs/module/substance/services/DefinitionalElementImplementation.java @@ -1,12 +1,47 @@ package gsrs.module.substance.services; import gsrs.module.substance.definitional.DefinitionalElement; +import ix.ginas.models.v1.Parameter; +import ix.ginas.models.v1.Property; +import ix.ginas.models.v1.Substance; import java.util.function.Consumer; +import java.util.logging.Logger; public interface DefinitionalElementImplementation { boolean supports(Object s); - void computeDefinitionalElements(Object s, Consumer consumer); + default void computeDefinitionalElements(Object s, Consumer consumer) { + if (s instanceof Substance) { + Logger log= Logger.getLogger(this.getClass().getName()); + addPropertiesToDefHash((Substance) s, consumer, Logger.getLogger(getClass().getName())); + } + } + + default void addPropertiesToDefHash(Substance substance, Consumer consumer, Logger logger) { + if( substance.properties != null ) { + for(Property property : substance.properties) { + if(property.isDefining() && property.getValue() != null) { + String defElementName = String.format("properties.%s.value", + property.getName()); + DefinitionalElement propertyValueDefElement = + DefinitionalElement.of(defElementName, property.getValue().toString(), 2); + consumer.accept(propertyValueDefElement); + logger.fine("added def element for property " + defElementName); + for(Parameter parameter : property.getParameters()) { + defElementName = String.format("properties.%s.parameters.%s.value", + property.getName(), parameter.getName()); + if( parameter.getValue() != null) { + DefinitionalElement propertyParamValueDefElement = + DefinitionalElement.of(defElementName, + parameter.getValue().toString(), 2); + consumer.accept(propertyParamValueDefElement); + logger.fine("added def element for property parameter " + defElementName); + } + } + } + } + } + } }