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added defining properties to def hash for mixtures. #370

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merged 4 commits into from
Oct 11, 2024
Merged

added defining properties to def hash for mixtures. #370

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1c42017
added defining properties to def hash for mixtures.
ChemMitch Sep 23, 2024
23e8900
cleaned up polymers and SSG1 and additional unit test
ChemMitch Sep 23, 2024
20135c5
Merge branch 'master' into mixture_props_in_def_hash
ChemMitch Oct 10, 2024
0dff42f
added consideration of properties (marked defining) within definition…
ChemMitch Oct 11, 2024
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134 changes: 132 additions & 2 deletions gsrs-module-substance-example/src/test/java/example/chem/DefHashCalcTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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<DefinitionalElement> 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<DefinitionalElement> 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<DefinitionalElement> definitionalElements = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem, definitionalElements::add);

ChemicalSubstance chem2 = builder
.setStructure(ginasChemicalStructure)
.addName("2-chlorobutane")
.build();
List<DefinitionalElement> 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<DefinitionalElement> 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<DefinitionalElement> definitionalElements2 = new ArrayList<>();
defHashCalculator.computeDefinitionalElements(chem2, definitionalElements::add);
Assertions.assertFalse(Arrays.equals(definitionalElements.toArray(), definitionalElements2.toArray()));
}
}
1 change: 1 addition & 0 deletions ...tance-example/src/test/resources/testJSON/28927b6a-6b0d-4733-a1a4-b2b38a569daa_props.json
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195 changes: 195 additions & 0 deletions gsrs-module-substance-example/src/test/resources/testJSON/SURFHOPe C-1811_mixture.json
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@@ -0,0 +1,195 @@
{
"deprecated": false,
"definitionType": "PRIMARY",
"definitionLevel": "COMPLETE",
"substanceClass": "mixture",
"status": "pending",
"names": [
{
"references": [
"9a03fb0b-f473-0e4c-47e4-5f5f91748eb1"
],
"access": [],
"languages": [
"en"
],
"type": "cn",
"name": "Sucrose stearate (HLB 11)",
"displayName": true,
"nameOrgs": [
{
"nameOrg": "BAN"
}
]
},
{
"references": [
"6bc5629f-4183-6271-4c9f-7dc9b38165f9"
],
"access": [],
"languages": [
"en"
],
"type": "cn",
"name": "SURFHOPe C-1811",
"displayName": false
},
{
"references": [
"9a03fb0b-f473-0e4c-47e4-5f5f91748eb1"
],
"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": []
}
}
1 change: 1 addition & 0 deletions ...ain/java/gsrs/module/substance/definitional/ChemicalSubstanceDefinitionalElementImpl.java
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Expand Up @@ -27,6 +27,7 @@ public boolean supports(Object s) {

@Override
public void computeDefinitionalElements(Object s, Consumer<DefinitionalElement> consumer) {
DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer);
ChemicalSubstance chemicalSubstance = (ChemicalSubstance) s;
Structure structure = chemicalSubstance.getStructure();
if(structure==null){
Expand Down
3 changes: 2 additions & 1 deletion ...core/src/main/java/gsrs/module/substance/definitional/MixtureDefinitionalElementImpl.java
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Expand Up @@ -30,7 +30,8 @@ public boolean supports(Object s) {

@Override
public void computeDefinitionalElements(Object s, Consumer<DefinitionalElement> 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()) {
Expand Down
1 change: 1 addition & 0 deletions ...rs/module/substance/definitional/NonSubstanceConceptDefintionalElementImplementation.java
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Expand Up @@ -15,6 +15,7 @@ public boolean supports(Object s) {

@Override
public void computeDefinitionalElements(Object s, Consumer<DefinitionalElement> consumer) {
DefinitionalElementImplementation.super.computeDefinitionalElements(s, consumer);
String primaryName = "";
for(Name name : ((Substance)s).getAllNames()) {
if( name.displayName ){
Expand Down
3 changes: 1 addition & 2 deletions .../src/main/java/gsrs/module/substance/definitional/NucleicAcidDefinitionalElementImpl.java
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Expand Up @@ -29,6 +29,7 @@ public boolean supports(Object s) {

@Override
public void computeDefinitionalElements(Object substance, Consumer<DefinitionalElement> consumer) {
DefinitionalElementImplementation.super.computeDefinitionalElements(substance, consumer);
NucleicAcidSubstance nucleicAcidSubstance = (NucleicAcidSubstance) substance;
if(nucleicAcidSubstance.nucleicAcid ==null || nucleicAcidSubstance.nucleicAcid.subunits ==null){
return;
Expand Down Expand Up @@ -75,10 +76,8 @@ public void computeDefinitionalElements(Object substance, Consumer<DefinitionalE
}
}


if( nucleicAcidSubstance.modifications != null ){
definitionalElementFactory.addDefinitionalElementsFor(nucleicAcidSubstance.modifications, consumer);
}

}
}
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