Merge pull request #357 from ncats/feature_test

Feature test

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

@@ -0,0 +1,83 @@
+package example.chem;
+
+import gov.fda.gsrs.ndsri.FeaturizeNitrosamine;
+import gov.nih.ncats.molwitch.Chemical;
+import gsrs.module.substance.utils.FeatureUtils;
+import ix.ginas.models.v1.GinasChemicalStructure;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+@Slf4j
+public class FeatureGenerationTest {
+
+    @Test
+    void testOneMol() throws Exception{
+        String molfileText = IOUtils.toString(
+                this.getClass().getResourceAsStream("/molfiles/1~{H}-quinolin-4-one.mol"),
+                "UTF-8"
+        );
+        GinasChemicalStructure structure = new GinasChemicalStructure();
+        structure.molfile = molfileText;
+        List<Map<String, String>> properties = FeatureUtils.calculateFeatures( structure.toChemical());
+        //properties.get(0).entrySet().forEach(e-> System.out.printf("key: %s = value: %s\n", e.getKey(), e.getValue()));
+        Assertions.assertEquals("5", properties.get(0).get("categoryScore"));
+    }
+
+    @Test
+    void testIVACAFTORType() throws Exception {
+        Chemical c1= Chemical.parse("c1ccc2c(c1)c(=O)cc[nH]2");
+
+        List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
+        assertEquals(1, properties.size());
+        assertEquals("A. Secondary Amine" ,properties.get(0).get("type"));
+        assertEquals("0,1", properties.get(0).get("Alpha-Hydrogens"));
+    }
+
+    @Test
+    void testFostamatibib() throws Exception {
+        Chemical c1= Chemical.parse("O.O.O.O.O.O.[Na+].[Na+].COC1=CC([NH:1]C2=NC=C(F)C(NC3=NC4=C(OC(C)(C)C(=O)N4COP([O-])([O-])=O)C=C3)=N2)=CC(OC)=C1OC");
+
+        List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
+
+        assertEquals(2,properties.size());
+        assertEquals("A. Multiple Secondary Amine", properties.get(0).get("type"));
+        assertEquals("0,0", properties.get(0).get("Alpha-Hydrogens"));
+    }
+
+    @Test
+    public void testIsPiperazine() throws Exception {
+        FeaturizeNitrosamine.GLOBAL_SETTINGS.DO_EXTENDED_FEATURES_TOO=true;
+
+        Chemical c1= Chemical.parse("N1CCNCC1");
+        List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
+
+        assertEquals(2,properties.size());
+        assertEquals("A. Multiple Secondary Amine", properties.get(0).get("type"));
+        assertEquals("2,2", properties.get(0).get("Alpha-Hydrogens"));
+        assertEquals("YES", properties.get(0).get( FeaturizeNitrosamine.FeaturePairRegistry.PIPERAZINE.getFeatureName()));
+    }
+
+    @Test
+    public void testCarboxylicAcidOnSaltDoesNotCount() throws Exception {
+        Chemical c1= Chemical.parse("O[C@H]([C@@H](O)C(O)=O)C(O)=O.COC1=CC=C(C[C@@H](C)[NH:20]C[C@H](O)C2=CC=C(O)C(NC=O)=C2)C=C1");
+        List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
+        assertEquals(1, properties.size());
+        assertEquals("A. Secondary Amine", properties.get(0).get("type"));
+        assertEquals("NO" ,properties.get(0).get(FeaturizeNitrosamine.FeaturePairRegistry.COOH.getFeatureName()));
+    }
+
+    @Test
+    public void testBenzylLikeFeatureShouldNotFindPsuedoAromaticity() throws Exception {
+        Chemical c1= Chemical.parse("C[C@H]([NH:3]C1=C2N=CNC2=NC=N1)C3=CC4=C(C(Cl)=CC=C4)C(=O)N3C5=CC=CC=C5");
+        List<Map<String, String>> properties = FeatureUtils.calculateFeatures( c1);
+        assertEquals(1, properties.size());
+        assertEquals("A. Secondary Amine", properties.get(0).get("type"));
+        assertEquals("NO", properties.get(0).get(FeaturizeNitrosamine.FeaturePairRegistry.ARYL_ALPHA.getFeatureName()));
+    }
+}

gsrs-module-substance-example/src/test/resources/molfiles/1~{H}-quinolin-4-one.mol

@@ -0,0 +1,28 @@
+
+
+
+ 11 12  0  0  0  0  0  0  0  0999 V2000
+    6.9665  -11.7372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.9665  -12.9183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.9436  -13.5088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9207  -12.9183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9207  -11.7372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.9436  -11.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.9436   -9.9655    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+    6.9665   -9.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9893   -9.9655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9893  -11.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.0122  -11.7372    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  6  1  0  0  0  0
+  1 10  1  0  0  0  0
+  2  1  2  0  0  0  0
+  3  2  1  0  0  0  0
+  4  3  2  0  0  0  0
+  5  4  1  0  0  0  0
+  6  5  2  0  0  0  0
+  7  6  1  0  0  0  0
+  8  7  1  0  0  0  0
+  9  8  2  0  0  0  0
+ 10  9  1  0  0  0  0
+ 11 10  2  0  0  0  0
+M  END

gsrs-module-substances-core/pom.xml

@@ -329,5 +329,10 @@
             <artifactId>batik-svg-dom</artifactId>
             <version>1.17</version>
         </dependency>
+        <dependency>
+            <groupId>gov.fda.gsrs</groupId>
+            <artifactId>Featureize-Nitrosamines</artifactId>
+            <version>0.0.2-SNAPSHOT</version>
+        </dependency>
     </dependencies>
 </project>

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

@@ -28,6 +28,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.validation.constraints.NotBlank;
 
+import gsrs.module.substance.utils.FeatureUtils;
 import gsrs.module.substance.utils.ChemicalUtils;
 import org.freehep.graphicsio.svg.SVGGraphics2D;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -38,6 +39,7 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionDefinition;
 import org.springframework.transaction.annotation.Transactional;
@@ -980,6 +982,7 @@ public ResponseEntity<Object> interpretStructure(@NotBlank @RequestBody String m
 
         boolean isQuery="query".equalsIgnoreCase(mode);
 
+        boolean appendFeatures = queryParameters.containsKey("appendNNOFeatures") && queryParameters.get("appendNNOFeatures").equalsIgnoreCase("true");
 
         try {
             String payload = ChemCleaner.getCleanMolfile(mol);
@@ -1019,6 +1022,10 @@ public ResponseEntity<Object> interpretStructure(@NotBlank @RequestBody String m
                 saveTempStructure(struc);
                 node.put("structure", mapper.valueToTree(struc));
                 node.put("moieties", an);
+                if( appendFeatures) {
+                    log.trace("going to append nitrosamine features");
+                    appendFeatureStuff(struc.toChemical(), node);
+                }
             } catch (Exception e) {
                 e.printStackTrace();
             }
@@ -1034,6 +1041,7 @@ public ResponseEntity<Object> interpretStructure(@NotBlank @RequestBody String m
                 e.printStackTrace();
                 log.error("Can't enumerate polymer", e);
             }
+
             return new ResponseEntity<>(node, HttpStatus.OK);
 
         } catch (Exception ex) {
@@ -1044,6 +1052,79 @@ public ResponseEntity<Object> interpretStructure(@NotBlank @RequestBody String m
 
     }
 
+    @PostGsrsRestApiMapping("/interpretFeatures")
+    @PreAuthorize("isAuthenticated()")
+    public ResponseEntity<Object> interpretStructureFeatures(@NotBlank @RequestBody String mol, @RequestParam Map<String, String> queryParameters){
+        String[] standardize = Optional.ofNullable(queryParameters.get("standardize"))
+                .orElse("NONE")
+                .split(",");
+        SimpleStandardizer simpStd=Arrays.stream(standardize)
+                .filter(s->!s.equals("NONE"))
+                .map(val->val.toUpperCase())
+                .map(val->StructureStandardizerPresets.value(val))
+                .filter(v->v.isPresent())
+                .map(v->v.get())
+                .map(std->std.getStandardizer())
+                .reduce(SimpleStandardizer::and).orElse(null);
+
+        String mode = Optional.ofNullable(queryParameters.get("mode"))
+                .orElse("basic");
+
+        boolean isQuery="query".equalsIgnoreCase(mode);
+
+
+        try {
+            String payload = ChemCleaner.getCleanMolfile(mol);
+            List<Structure> moieties = new ArrayList<>();
+            ObjectMapper mapper = EntityFactory.EntityMapper.FULL_ENTITY_MAPPER();
+            ObjectNode node = mapper.createObjectNode();
+            try {
+                Structure struc = structureProcessor.taskFor(payload)
+                        .components(moieties)
+                        .standardize(false)
+                        .query(isQuery)
+                        .build()
+                        .instrument()
+                        .getStructure();
+                // don't standardize!
+                // we should be really use the PersistenceQueue to do this
+                // so that it doesn't block
+                // in fact, it probably shouldn't be saving this at all
+                if (payload.contains("\n") && payload.contains("M  END")) {
+                    struc.molfile = payload;
+                }
+
+                if(simpStd!=null) {
+                    struc.molfile=simpStd.standardize(struc.molfile);
+                }
+
+                ArrayNode an = mapper.createArrayNode();
+                for (Structure m : moieties) {
+                    saveTempStructure(m);
+                    ObjectNode on = mapper.valueToTree(m);
+                    Amount c1 = Moiety.intToAmount(m.count);
+                    JsonNode amt = mapper.valueToTree(c1);
+                    on.set("countAmount", amt);
+                    an.add(on);
+                }
+                //TODO: fill in calculation
+                //saveTempStructure(struc);
+                node.put("structure", mapper.valueToTree(struc));
+                node.put("moieties", an);
+                appendFeatureStuff(struc.toChemical(), node);
+
+            } catch (Exception e) {
+                e.printStackTrace();
+            }
+            return new ResponseEntity<>(node, HttpStatus.OK);
+
+        } catch (Exception ex) {
+            log.error("Can't process payload", ex);
+            return new ResponseEntity<>("Can't process mol payload",
+                    this.getGsrsControllerConfiguration().getHttpStatusFor(HttpStatus.INTERNAL_SERVER_ERROR, queryParameters));
+        }
+
+    }
     public void saveTempStructure(Structure s) {
         if (s.id == null){
             s.id = UUID.randomUUID();
@@ -1931,4 +2012,16 @@ public String makeFlexSearchMoietyClauses(Structure structure) {
         }
     }
 
+    private void appendFeatureStuff(Chemical chemical, ObjectNode topLevelNode ) throws Exception {
+        log.trace("in appendFeatureStuff");
+        ObjectMapper mapper = new ObjectMapper();
+        List<Map<String, String>> featureList = FeatureUtils.calculateFeatures(chemical);
+        ArrayNode featureArrayNode = mapper.createArrayNode();
+        featureList.forEach(features ->{
+            ObjectNode oneSet = mapper.createObjectNode();
+            features.entrySet().forEach(f-> oneSet.put(f.getKey(), f.getValue()));
+            featureArrayNode.add(oneSet);
+        });
+        topLevelNode.put("featureList", featureArrayNode);
+    }
 }

gsrs-module-substances-core/src/main/java/gsrs/module/substance/utils/FeatureUtils.java

@@ -0,0 +1,38 @@
+package gsrs.module.substance.utils;
+
+import gov.nih.ncats.molwitch.Chemical;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import gov.fda.gsrs.ndsri.FeaturizeNitrosamine;
+import gov.fda.gsrs.ndsri.FeaturizeNitrosamine.FeatureJob;
+import gov.fda.gsrs.ndsri.FeaturizeNitrosamine.FeatureResponse;
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class FeatureUtils {
+    public static List<Map<String, String>> calculateFeatures(Chemical chemical) throws Exception{
+        FeatureJob fj;
+        try{
+            fj = FeatureJob.forOneNitrosamine(chemical);
+        } catch (Exception ex) {
+            log.info("forOneNitrosamine failed; using regular constructor");
+            fj = new FeatureJob(chemical);
+        }
+
+        List<FeatureResponse> resp = FeaturizeNitrosamine.fingerprintNitrosamine(fj);
+
+        List<Map<String,String>> maps = new ArrayList<>();
+        resp.forEach(r->{
+            Map<String, String> ret = new HashMap<>();
+            r.getFeatureSet().entrySet().forEach(e-> ret.put(e.getKey(), e.getValue()));
+            ret.put("categoryScore", Integer.toString( r.getCategoryScore()));
+            ret.put("sumOfScores", Integer.toString(r.getSumOfScores()));
+            ret.put("type", r.getType());
+            maps.add(ret);
+        });
+        return maps;
+    }
+}

installExtraJars.cmd

@@ -1,4 +1,4 @@
 mvnw.cmd install:install-file -Dfile=extraJars/applications-api-3.1-SNAPSHOT.jar
 mvnw.cmd install:install-file -Dfile=extraJars/products-api-3.1.1-SNAPSHOT.jar
 mvnw.cmd install:install-file -Dfile=extraJars/clinical-trials-api-3.1.1-SNAPSHOT.jar
-
+mvnw.cmd install:install-file -Dfile=extraJars/Featureize-Nitrosamines-0.0.2-SNAPSHOT.jar

installExtraJars.sh

@@ -1,3 +1,4 @@
 ./mvnw install:install-file -Dfile=extraJars/applications-api-3.1-SNAPSHOT.jar
 ./mvnw install:install-file -Dfile=extraJars/products-api-3.1.1-SNAPSHOT.jar
 ./mvnw install:install-file -Dfile=extraJars/clinical-trials-api-3.1.1-SNAPSHOT.jar
+./mvnw install:install-file -Dfile=extraJars/Featureize-Nitrosamines-0.0.2-SNAPSHOT.jar