Skip to content

Commit

Permalink
Merge branch 'master' into feature_test
Browse files Browse the repository at this point in the history
  • Loading branch information
@tylerperyea
tylerperyea authored Aug 6, 2024
2 parents 7a6ba66 + 3af210c commit 06a1d0f
Show file tree
Hide file tree
Showing 11 changed files with 616 additions and 29 deletions.
4 changes: 2 additions & 2 deletions gsrs-module-substance-example/pom.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
84 changes: 84 additions & 0 deletions gsrs-module-substance-example/salt_data_public.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
InChI Key SMILES Occurrences
VEXZGXHMUGYJMC-UHFFFAOYSA-N Cl 7206
FKNQFGJONOIPTF-UHFFFAOYSA-N [Na+] 3488
XLYOFNOQVPJJNP-UHFFFAOYSA-N O 1608
NPYPAHLBTDXSSS-UHFFFAOYSA-N [K+] 811
XLYOFNOQVPJJNP-UHFFFAOYSA-M [OH-] 791
CPELXLSAUQHCOX-UHFFFAOYSA-N Br 645
BHPQYMZQTOCNFJ-UHFFFAOYSA-N [Ca+2] 526
QAOWNCQODCNURD-UHFFFAOYSA-N OS(=O)(=O)O 510
AFVFQIVMOAPDHO-UHFFFAOYSA-N CS(=O)(=O)O 350
XMBWDFGMSWQBCA-UHFFFAOYSA-N I 326
JLVVSXFLKOJNIY-UHFFFAOYSA-N [Mg+2] 316
QGZKDVFQNNGYKY-UHFFFAOYSA-N N 300
QTBSBXVTEAMEQO-UHFFFAOYSA-N CC(=O)O 280
GPRLSGONYQIRFK-UHFFFAOYSA-N [H+] 277
REDXJYDRNCIFBQ-UHFFFAOYSA-N [Al+3] 270
VZCYOOQTPOCHFL-UPHRSURJSA-N OC(=O)/C=C\C(O)=O 259
PTFCDOFLOPIGGS-UHFFFAOYSA-N [Zn+2] 241
VEXZGXHMUGYJMC-UHFFFAOYSA-M [Cl-] 240
FEWJPZIEWOKRBE-JCYAYHJZSA-N [C@@H]([C@H](C(=O)O)O)(C(=O)O)O 214
NBIIXXVUZAFLBC-UHFFFAOYSA-N OP(=O)(O)O 212
JPVYNHNXODAKFH-UHFFFAOYSA-N [Cu+2] 172
VZCYOOQTPOCHFL-OWOJBTEDSA-N OC(=O)/C=C/C(O)=O 164
KRKNYBCHXYNGOX-UHFFFAOYSA-N C(C(=O)O)C(CC(=O)O)(C(=O)O)O 162
VTLYFUHAOXGGBS-UHFFFAOYSA-N [Fe+3] 139
HBBGRARXTFLTSG-UHFFFAOYSA-N [Li+] 139
JZMJDSHXVKJFKW-UHFFFAOYSA-M COS(=O)(=O)[O-] 126
CWYNVVGOOAEACU-UHFFFAOYSA-N [Fe+2] 124
QAOWNCQODCNURD-UHFFFAOYSA-L O=S(=O)([O-])[O-] 120
JOXIMZWYDAKGHI-UHFFFAOYSA-N Cc1ccc(cc1)S(=O)(=O)O 116
QTBSBXVTEAMEQO-UHFFFAOYSA-M CC(=O)[O-] 110
KDYFGRWQOYBRFD-UHFFFAOYSA-N C(CC(=O)O)C(=O)O 99
MUBZPKHOEPUJKR-UHFFFAOYSA-N C(=O)(C(=O)O)O 98
NHNBFGGVMKEFGY-UHFFFAOYSA-N [N+](=O)([O-])[O-] 97
XDFCIPNJCBUZJN-UHFFFAOYSA-N [Ba+2] 95
KRHYYFGTRYWZRS-UHFFFAOYSA-N F 90
WAEMQWOKJMHJLA-UHFFFAOYSA-N [Mn+2] 85
GSEJCLTVZPLZKY-UHFFFAOYSA-N C(CO)N(CCO)CCO 80
GRYLNZFGIOXLOG-UHFFFAOYSA-N [N+](=O)(O)[O-] 77
AHKZTVQIVOEVFO-UHFFFAOYSA-N [O-2] 72
BVKZGUZCCUSVTD-UHFFFAOYSA-L C(=O)([O-])[O-] 71
LELOWRISYMNNSU-UHFFFAOYSA-N C#N 70
XMBWDFGMSWQBCA-UHFFFAOYSA-M [I-] 69
QGZKDVFQNNGYKY-UHFFFAOYSA-O [NH4+] 65
XLJKHNWPARRRJB-UHFFFAOYSA-N [Co+2] 64
FOIXSVOLVBLSDH-UHFFFAOYSA-N [Ag+] 63
CPELXLSAUQHCOX-UHFFFAOYSA-M [Br-] 63
KRKNYBCHXYNGOX-UHFFFAOYSA-K C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O 62
JDIBGQFKXXXXPN-UHFFFAOYSA-N [Bi+3] 61
KDXKERNSBIXSRK-YFKPBYRVSA-N C(CCN)C[C@@H](C(=O)O)N 59
BFGKITSFLPAWGI-UHFFFAOYSA-N [Cr+3] 59
RVPVRDXYQKGNMQ-UHFFFAOYSA-N [Pb+2] 59
HRGDZIGMBDGFTC-UHFFFAOYSA-N [Pt+2] 59
PWYYWQHXAPXYMF-UHFFFAOYSA-N [Sr+2] 58
HZAXFHJVJLSVMW-UHFFFAOYSA-N C(CO)N 57
JVTAAEKCZFNVCJ-UHFFFAOYSA-N CC(C(=O)O)O 57
ZBCBWPMODOFKDW-UHFFFAOYSA-N C(CO)NCCO 56
ODKSFYDXXFIFQN-BYPYZUCNSA-N C(C[C@@H](C(=O)O)N)CNC(=N)N 54
MBBZMMPHUWSWHV-BDVNFPICSA-N CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O 52
GBNDTYKAOXLLID-UHFFFAOYSA-N [Zr+4] 51
YGSDEFSMJLZEOE-UHFFFAOYSA-N c1ccc(c(c1)C(=O)O)O 51
SRSXLGNVWSONIS-UHFFFAOYSA-N c1ccc(cc1)S(=O)(=O)O 49
QAOWNCQODCNURD-UHFFFAOYSA-M OS(=O)(=O)[O-] 46
WLJNZVDCPSBLRP-UHFFFAOYSA-N c1ccc2c(c1)cc(c(c2Cc3c4ccccc4cc(c3O)C(=O)O)O)C(=O)O 46
WPYMKLBDIGXBTP-UHFFFAOYSA-N c1ccc(cc1)C(=O)O 45
WLZRMCYVCSSEQC-UHFFFAOYSA-N [Cd+2] 43
LENZDBCJOHFCAS-UHFFFAOYSA-N C(C(CO)(CO)N)O 41
LCKIEQZJEYYRIY-UHFFFAOYSA-N [Ti+4] 39
BQPIGGFYSBELGY-UHFFFAOYSA-N [Hg+2] 39
NBIIXXVUZAFLBC-UHFFFAOYSA-K O=P([O-])([O-])[O-] 39
MUBZPKHOEPUJKR-UHFFFAOYSA-L C(=O)(C(=O)[O-])[O-] 39
GLUUGHFHXGJENI-UHFFFAOYSA-N C1CNCCN1 39
VEQPNABPJHWNSG-UHFFFAOYSA-N [Ni+2] 38
RJOJUSXNYCILHH-UHFFFAOYSA-N [Gd+3] 38
RWSOTUBLDIXVET-UHFFFAOYSA-M [SH-] 37
DTQVDTLACAAQTR-UHFFFAOYSA-N C(=O)(C(F)(F)F)O 37
JOXIMZWYDAKGHI-UHFFFAOYSA-M Cc1ccc(cc1)S(=O)(=O)[O-] 35
XQTIWNLDFPPCIU-UHFFFAOYSA-N [Ce+3] 34
CRBHXDCYXIISFC-UHFFFAOYSA-N C[N+](C)(C)CC[O-] 33
KIWBPDUYBMNFTB-UHFFFAOYSA-M CCOS(=O)(=O)[O-] 33
JAWGVVJVYSANRY-UHFFFAOYSA-N [Co+3] 32
ZMZDMBWJUHKJPS-UHFFFAOYSA-N C(#N)S 32
RGHNJXZEOKUKBD-SQOUGZDYSA-N C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O 31
CKLJMWTZIZZHCS-REOHCLBHSA-L C([C@@H](C(=O)[O-])N)C(=O)[O-] 31
84 changes: 84 additions & 0 deletions gsrs-module-substance-example/src/main/resources/salt_data_public.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
InChI Key SMILES Occurrences
VEXZGXHMUGYJMC-UHFFFAOYSA-N Cl 7206
FKNQFGJONOIPTF-UHFFFAOYSA-N [Na+] 3488
XLYOFNOQVPJJNP-UHFFFAOYSA-N O 1608
NPYPAHLBTDXSSS-UHFFFAOYSA-N [K+] 811
XLYOFNOQVPJJNP-UHFFFAOYSA-M [OH-] 791
CPELXLSAUQHCOX-UHFFFAOYSA-N Br 645
BHPQYMZQTOCNFJ-UHFFFAOYSA-N [Ca+2] 526
QAOWNCQODCNURD-UHFFFAOYSA-N OS(=O)(=O)O 510
AFVFQIVMOAPDHO-UHFFFAOYSA-N CS(=O)(=O)O 350
XMBWDFGMSWQBCA-UHFFFAOYSA-N I 326
JLVVSXFLKOJNIY-UHFFFAOYSA-N [Mg+2] 316
QGZKDVFQNNGYKY-UHFFFAOYSA-N N 300
QTBSBXVTEAMEQO-UHFFFAOYSA-N CC(=O)O 280
GPRLSGONYQIRFK-UHFFFAOYSA-N [H+] 277
REDXJYDRNCIFBQ-UHFFFAOYSA-N [Al+3] 270
VZCYOOQTPOCHFL-UPHRSURJSA-N OC(=O)/C=C\C(O)=O 259
PTFCDOFLOPIGGS-UHFFFAOYSA-N [Zn+2] 241
VEXZGXHMUGYJMC-UHFFFAOYSA-M [Cl-] 240
FEWJPZIEWOKRBE-JCYAYHJZSA-N [C@@H]([C@H](C(=O)O)O)(C(=O)O)O 214
NBIIXXVUZAFLBC-UHFFFAOYSA-N OP(=O)(O)O 212
JPVYNHNXODAKFH-UHFFFAOYSA-N [Cu+2] 172
VZCYOOQTPOCHFL-OWOJBTEDSA-N OC(=O)/C=C/C(O)=O 164
KRKNYBCHXYNGOX-UHFFFAOYSA-N C(C(=O)O)C(CC(=O)O)(C(=O)O)O 162
VTLYFUHAOXGGBS-UHFFFAOYSA-N [Fe+3] 139
HBBGRARXTFLTSG-UHFFFAOYSA-N [Li+] 139
JZMJDSHXVKJFKW-UHFFFAOYSA-M COS(=O)(=O)[O-] 126
CWYNVVGOOAEACU-UHFFFAOYSA-N [Fe+2] 124
QAOWNCQODCNURD-UHFFFAOYSA-L O=S(=O)([O-])[O-] 120
JOXIMZWYDAKGHI-UHFFFAOYSA-N Cc1ccc(cc1)S(=O)(=O)O 116
QTBSBXVTEAMEQO-UHFFFAOYSA-M CC(=O)[O-] 110
KDYFGRWQOYBRFD-UHFFFAOYSA-N C(CC(=O)O)C(=O)O 99
MUBZPKHOEPUJKR-UHFFFAOYSA-N C(=O)(C(=O)O)O 98
NHNBFGGVMKEFGY-UHFFFAOYSA-N [N+](=O)([O-])[O-] 97
XDFCIPNJCBUZJN-UHFFFAOYSA-N [Ba+2] 95
KRHYYFGTRYWZRS-UHFFFAOYSA-N F 90
WAEMQWOKJMHJLA-UHFFFAOYSA-N [Mn+2] 85
GSEJCLTVZPLZKY-UHFFFAOYSA-N C(CO)N(CCO)CCO 80
GRYLNZFGIOXLOG-UHFFFAOYSA-N [N+](=O)(O)[O-] 77
AHKZTVQIVOEVFO-UHFFFAOYSA-N [O-2] 72
BVKZGUZCCUSVTD-UHFFFAOYSA-L C(=O)([O-])[O-] 71
LELOWRISYMNNSU-UHFFFAOYSA-N C#N 70
XMBWDFGMSWQBCA-UHFFFAOYSA-M [I-] 69
QGZKDVFQNNGYKY-UHFFFAOYSA-O [NH4+] 65
XLJKHNWPARRRJB-UHFFFAOYSA-N [Co+2] 64
FOIXSVOLVBLSDH-UHFFFAOYSA-N [Ag+] 63
CPELXLSAUQHCOX-UHFFFAOYSA-M [Br-] 63
KRKNYBCHXYNGOX-UHFFFAOYSA-K C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O 62
JDIBGQFKXXXXPN-UHFFFAOYSA-N [Bi+3] 61
KDXKERNSBIXSRK-YFKPBYRVSA-N C(CCN)C[C@@H](C(=O)O)N 59
BFGKITSFLPAWGI-UHFFFAOYSA-N [Cr+3] 59
RVPVRDXYQKGNMQ-UHFFFAOYSA-N [Pb+2] 59
HRGDZIGMBDGFTC-UHFFFAOYSA-N [Pt+2] 59
PWYYWQHXAPXYMF-UHFFFAOYSA-N [Sr+2] 58
HZAXFHJVJLSVMW-UHFFFAOYSA-N C(CO)N 57
JVTAAEKCZFNVCJ-UHFFFAOYSA-N CC(C(=O)O)O 57
ZBCBWPMODOFKDW-UHFFFAOYSA-N C(CO)NCCO 56
ODKSFYDXXFIFQN-BYPYZUCNSA-N C(C[C@@H](C(=O)O)N)CNC(=N)N 54
MBBZMMPHUWSWHV-BDVNFPICSA-N CNC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O 52
GBNDTYKAOXLLID-UHFFFAOYSA-N [Zr+4] 51
YGSDEFSMJLZEOE-UHFFFAOYSA-N c1ccc(c(c1)C(=O)O)O 51
SRSXLGNVWSONIS-UHFFFAOYSA-N c1ccc(cc1)S(=O)(=O)O 49
QAOWNCQODCNURD-UHFFFAOYSA-M OS(=O)(=O)[O-] 46
WLJNZVDCPSBLRP-UHFFFAOYSA-N c1ccc2c(c1)cc(c(c2Cc3c4ccccc4cc(c3O)C(=O)O)O)C(=O)O 46
WPYMKLBDIGXBTP-UHFFFAOYSA-N c1ccc(cc1)C(=O)O 45
WLZRMCYVCSSEQC-UHFFFAOYSA-N [Cd+2] 43
LENZDBCJOHFCAS-UHFFFAOYSA-N C(C(CO)(CO)N)O 41
LCKIEQZJEYYRIY-UHFFFAOYSA-N [Ti+4] 39
BQPIGGFYSBELGY-UHFFFAOYSA-N [Hg+2] 39
NBIIXXVUZAFLBC-UHFFFAOYSA-K O=P([O-])([O-])[O-] 39
MUBZPKHOEPUJKR-UHFFFAOYSA-L C(=O)(C(=O)[O-])[O-] 39
GLUUGHFHXGJENI-UHFFFAOYSA-N C1CNCCN1 39
VEQPNABPJHWNSG-UHFFFAOYSA-N [Ni+2] 38
RJOJUSXNYCILHH-UHFFFAOYSA-N [Gd+3] 38
RWSOTUBLDIXVET-UHFFFAOYSA-M [SH-] 37
DTQVDTLACAAQTR-UHFFFAOYSA-N C(=O)(C(F)(F)F)O 37
JOXIMZWYDAKGHI-UHFFFAOYSA-M Cc1ccc(cc1)S(=O)(=O)[O-] 35
XQTIWNLDFPPCIU-UHFFFAOYSA-N [Ce+3] 34
CRBHXDCYXIISFC-UHFFFAOYSA-N C[N+](C)(C)CC[O-] 33
KIWBPDUYBMNFTB-UHFFFAOYSA-M CCOS(=O)(=O)[O-] 33
JAWGVVJVYSANRY-UHFFFAOYSA-N [Co+3] 32
ZMZDMBWJUHKJPS-UHFFFAOYSA-N C(#N)S 32
RGHNJXZEOKUKBD-SQOUGZDYSA-N C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)O 31
CKLJMWTZIZZHCS-REOHCLBHSA-L C([C@@H](C(=O)[O-])N)C(=O)[O-] 31
59 changes: 59 additions & 0 deletions gsrs-module-substance-example/src/test/java/example/chem/SaltRemovalTest.java
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
package example.chem;

import example.GsrsModuleSubstanceApplication;
import gov.nih.ncats.molwitch.Chemical;

import gsrs.module.substance.utils.ChemicalUtils;
import gsrs.substances.tests.AbstractSubstanceJpaFullStackEntityTest;
import lombok.extern.slf4j.Slf4j;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.security.test.context.support.WithMockUser;

import java.io.*;
import java.util.stream.Stream;

@Slf4j
@SpringBootTest(classes = GsrsModuleSubstanceApplication.class)
@WithMockUser(username = "admin", roles = "Admin")
class SaltRemovalTest extends AbstractSubstanceJpaFullStackEntityTest {

@Autowired
private ChemicalUtils chemicalUtils;

@Test
void testRemoveSalts() throws IOException {

String inputSmiles = "C[C@H]1[C@@]2([H])CC[C@@]3([H])[C@]4([H])CC=C5C[C@H](CC[C@]5(C)[C@@]4([H])CC[C@]23CN1C)N(C)C.Br.Br";
Chemical chemical = Chemical.parseMol(inputSmiles);
double massBefore = chemical.getMass();
Chemical cleaned = chemicalUtils.stripSalts(chemical);
double massAfter = cleaned.getMass();
log.warn("formula before: {}; after: {}", chemical.getFormula(), cleaned.getFormula());
Assertions.assertTrue(massAfter < massBefore, String.format("formula before: %s; after: %s", chemical.getFormula(), cleaned.getFormula()));
}

@ParameterizedTest
@MethodSource("inputData")
void testSaltRemoval(String smiles, int atomCountChange) throws IOException {
Chemical chemical = Chemical.parseMol(smiles);
Chemical cleaned = chemicalUtils.stripSalts(chemical);
Assertions.assertEquals(atomCountChange, (chemical.getAtomCount() - cleaned.getAtomCount()),
String.format("formula before: %s; after: %s", chemical.getFormula(), cleaned.getFormula()));
}

private static Stream<Arguments> inputData() {
return Stream.of(
Arguments.of("C[C@H]1[C@@]2([H])CC[C@@]3([H])[C@]4([H])CC=C5C[C@H](CC[C@]5(C)[C@@]4([H])CC[C@]23CN1C)N(C)C.Br.Br", 2),
Arguments.of("CCC1C(Cc2cncn2C)COC1=O.Cl", 1),
Arguments.of("c1cc(ccc1C(=C2C=CC(=O)C=C2)c3ccc(cc3)[O-])[O-].[Na+].[Na+]", 2),
Arguments.of("[F-][Ti+4]([F-])([F-])([F-])([F-])[F-].[Li+].[Li+]", 2),
Arguments.of("Cc1c(CCN2CCC(=C(c3ccc(cc3)F)c4ccc(cc4)F)CC2)c(=O)n5ccsc5n1.[C@@H]([C@H](C(=O)O)O)(C(=O)O)O", 10)
);
}
}
25 changes: 16 additions & 9 deletions gsrs-module-substance-example/src/test/java/example/structureSearch/FlexSearchTest.java
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
package example.structureSearch;

import example.GsrsModuleSubstanceApplication;
import gov.nih.ncats.molwitch.Chemical;
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.module.substance.utils.ChemicalUtils;
import gsrs.springUtils.AutowireHelper;
import gsrs.startertests.TestGsrsValidatorFactory;
import gsrs.startertests.TestIndexValueMakerFactory;
Expand Down Expand Up @@ -59,6 +61,9 @@ public class FlexSearchTest extends AbstractSubstanceJpaFullStackEntityTest {
@Autowired
private SubstanceLegacySearchService searchService;

@Autowired
private ChemicalUtils chemicalUtils;

private String fileName = "testdumps/tartrate_set.gsrs";

private boolean loadedData = false;
Expand Down Expand Up @@ -107,7 +112,7 @@ public void generateFlexSearchQuery() throws Exception {
AutowireHelper.getInstance().autowireAndProxy(controller);
log.trace("created and wired controller");

String hash= controller.makeFlexSearchMoietyClauses(structureStd, false) + ")";
String hash= controller.makeFlexSearchMoietyClauses(structureStd) + ")";
log.trace("search hash: {}", hash);
assertTrue(hash.contains("root_moieties_properties_STEREO_INSENSITIVE_HASH"));
}
Expand All @@ -134,9 +139,9 @@ public void generateFlexPlusSearchQuery() throws Exception {
AutowireHelper.getInstance().autowireAndProxy(controller);
log.trace("created and wired controller");

String hash= controller.makeFlexSearchMoietyClauses(structureStd, true) + ")";
String hash= controller.makeFlexSearchMoietyClauses(structureStd) + ")";
log.trace("search hash: {}", hash);
assertTrue(hash.contains("root_moieties_properties_EXACT_HASH"));
assertTrue(hash.contains("root_moieties_properties_STEREO_INSENSITIVE_HASH"));
}

@Test
Expand All @@ -155,11 +160,10 @@ public void runFlexSearchQueryTartaric() throws Exception {
.build()
.instrument()
.getStructure();
String sins= structureStd.getStereoInsensitiveHash();
SubstanceController controller = new SubstanceController();
AutowireHelper.getInstance().autowireAndProxy(controller);

String hash= controller.makeFlexSearch(structureStd, false);
String hash= controller.makeFlexSearch(structureStd);
log.trace("search hash: {}", hash);
SearchRequest request = new SearchRequest.Builder()
.kind(Substance.class)
Expand All @@ -177,7 +181,6 @@ public void runFlexSearchQueryTartaric() throws Exception {
@WithMockUser(value = "admin", roles = "Admin")
public void runFlexSearchQuerySodiumTartrate() throws Exception {
String molfileSource = "molfiles/sodium_tartrate.mol";

File molfile = new ClassPathResource(molfileSource).getFile();
Structure structureStd = structureProcessor.taskFor(Files.readString(molfile.toPath()))
.standardize(true)
Expand All @@ -187,7 +190,7 @@ public void runFlexSearchQuerySodiumTartrate() throws Exception {
SubstanceController controller = new SubstanceController();
AutowireHelper.getInstance().autowireAndProxy(controller);

String hash = controller.makeFlexSearch(structureStd, false);
String hash = controller.makeFlexSearch(structureStd);
log.trace("search hash: {}", hash);
SearchRequest request = new SearchRequest.Builder()
.kind(Substance.class)
Expand All @@ -210,10 +213,14 @@ public void runFlexPlusSearchQuerySodiumTartrate() throws Exception {
.build()
.instrument()
.getStructure();
Chemical cleanedChemical = chemicalUtils.stripSalts(structureStd.toChemical());
Structure cleanedStructure = new Structure();
cleanedStructure.molfile = cleanedChemical.toMol();

SubstanceController controller = new SubstanceController();
AutowireHelper.getInstance().autowireAndProxy(controller);

String hash = controller.makeFlexSearch(structureStd,true);
String hash = controller.makeFlexSearch(cleanedStructure);
log.trace("search hash: {}", hash);
SearchRequest request = new SearchRequest.Builder()
.kind(Substance.class)
Expand All @@ -223,7 +230,7 @@ public void runFlexPlusSearchQuerySodiumTartrate() throws Exception {
log.trace("search results: (total: {})", substances.size());
substances.forEach(s-> log.trace("ID {} - {}", s.uuid, s.getName()));

int expectedNumber = 1;
int expectedNumber = 7;
assertEquals(expectedNumber, substances.size());
}

Expand Down
1 change: 1 addition & 0 deletions gsrs-module-substance-example/src/test/resources/application-test.conf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -586,3 +586,4 @@ gsrs.importAdapterFactories.substances =
}
]

gsrs.substance.structures.saltFilePath=salt_data_public.tsv
15 changes: 15 additions & 0 deletions ...e-substances-core/src/main/java/gsrs/module/substance/StructureHandlingConfiguration.java
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
package gsrs.module.substance;

import lombok.Data;
import lombok.extern.slf4j.Slf4j;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.context.annotation.Configuration;

@Configuration
@ConfigurationProperties("gsrs.substance.structures")
@Data
@Slf4j
public class StructureHandlingConfiguration {

private String saltFilePath;
}
5 changes: 4 additions & 1 deletion ...odule-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import gsrs.module.substance.standardizer.NameStandardizerConfiguration;
import gsrs.module.substance.standardizer.StructureStandardizerConfiguration;
import gsrs.module.substance.standardizer.SubstanceSynchronizer;
import gsrs.module.substance.utils.ChemicalUtils;
import gsrs.module.substance.utils.MolWeightCalculatorProperties;
import gsrs.module.substance.utils.SubstanceMatchViewGenerator;
import gsrs.module.substance.utils.SubstanceResultListRecordGenerator;
Expand Down Expand Up @@ -61,7 +62,9 @@
ImportMetadataLegacySearchService.class,
SubstanceFieldNameDecoratorConfiguration.class,
SubstanceSynchronizer.class,
StructureProcessorConfiguration.class
StructureProcessorConfiguration.class,
StructureHandlingConfiguration.class,
ChemicalUtils.class
})
public class SubstanceCoreConfiguration {

Expand Down
Loading

0 comments on commit 06a1d0f

Please sign in to comment.