#44 Implemented as rest/v2/search/fragments endpoint

tdudgeon · tdudgeon · commit 63049b5fafaf · 2021-08-27T09:19:09.000+01:00
diff --git a/fragnet-search/README.md b/fragnet-search/README.md
@@ -588,6 +588,34 @@ hit as well as various information about the query. Example output (part of data
 }
 ```
   
+### Fragments search
+
+This search returns all the child fragments (recursive) of a molecule. The input is the same as the Molecule search,
+comprising a single molecule in SMILES or Molfile format.
+
+If that molecule is not found your get a 404 response. If it is found you get a 200 response containing a list of child 
+fragments in JSON format.
+
+Typical execution looks like this:
+```
+curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/fragments/OC(Cn1ccnn1)C1CC1"
+```
+
+The response would look like this:
+```
+[
+  "[Xe]C1CC1",
+  "C1CC1",
+  "c1c[nH]nn1",
+  "CC(O)[Xe]",
+  "[Xe]C1CC1.[Xe]n1ccnn1",
+  "OC(C[Xe])C1CC1",
+  "[Xe]n1ccnn1",
+  "OC([Xe])Cn1ccnn1",
+  "OC([Xe])C[Xe]",
+  "OCC[Xe]"
+]
+```
 
 ## Authentication
 
diff --git a/fragnet-search/src/main/java/org/squonk/fragnet/search/queries/v2/FragmentQuery.java b/fragnet-search/src/main/java/org/squonk/fragnet/search/queries/v2/FragmentQuery.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright (c) 2021 Informatics Matters Ltd.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.squonk.fragnet.search.queries.v2;
+
+import org.neo4j.driver.v1.Record;
+import org.neo4j.driver.v1.Session;
+import org.neo4j.driver.v1.StatementResult;
+import org.neo4j.driver.v1.Value;
+import org.neo4j.driver.v1.types.Relationship;
+import org.squonk.fragnet.chem.MolStandardize;
+import org.squonk.fragnet.search.queries.AbstractQuery;
+
+import javax.validation.constraints.NotNull;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.logging.Logger;
+
+import static org.neo4j.driver.v1.Values.parameters;
+
+public class FragmentQuery extends AbstractQuery {
+
+    private static final Logger LOG = Logger.getLogger(FragmentQuery.class.getName());
+
+    public FragmentQuery(Session session) {
+        super(session);
+
+    }
+
+    private final String SYNTHON_QUERY = "MATCH (fa:F2 {smiles: $smiles})-[e:FRAG*]->(f:F2) RETURN e";
+
+    @Override
+    protected String getQueryTemplate() {
+        return SYNTHON_QUERY;
+    }
+
+    public List<String> execute(@NotNull String mol, @NotNull String mimeType) {
+
+        // standardize the mol. It can be in smiles or molfile formats
+        String stdSmiles = MolStandardize.prepareNonisoMol(mol, mimeType);
+
+        HashSet<String> values = getSession().writeTransaction((tx) -> {
+            LOG.fine("Executing MoleculeQuery: " + SYNTHON_QUERY);
+            StatementResult result = tx.run(SYNTHON_QUERY, parameters(new Object[]{"smiles", stdSmiles}));
+            HashSet<String> smiles = new HashSet<>();
+            while (result.hasNext()) {
+                Record rec = result.next();
+                Value val = rec.get(0);
+                List<Object> edges = val.asList();
+                for (Object o : edges) {
+                    Relationship rel = (Relationship)o;
+                    String label = rel.get("label").asString();
+                    String[] tokens = label.split("\\|");
+                    LOG.fine("Label: " + label + " Tokens: " + tokens[1] + " " + tokens[4]);
+                    smiles.add(tokens[1]);
+                    smiles.add(tokens[4]);
+                }
+            }
+            return smiles;
+        });
+
+        return new ArrayList(values);
+    }
+}
diff --git a/fragnet-search/src/main/java/org/squonk/fragnet/service/v2/FragnetSearchRouteBuilder.java b/fragnet-search/src/main/java/org/squonk/fragnet/service/v2/FragnetSearchRouteBuilder.java
@@ -59,6 +59,11 @@ public class FragnetSearchRouteBuilder extends AbstractFragnetSearchRouteBuilder
             .help("Total number of molecule search requests")
             .register();
 
+    private final Counter fragmentSearchRequestsTotal = Counter.build()
+            .name("requests_fragment_total")
+            .help("Total number of fragment search requests")
+            .register();
+
     private final Counter neighbourhoodSearchRequestsTotal = Counter.build()
             .name("requests_neighbourhood_total")
             .help("Total number of neighbourhood search requests")
@@ -84,6 +89,11 @@ public class FragnetSearchRouteBuilder extends AbstractFragnetSearchRouteBuilder
             .help("Total duration of molecule Neo4j cypher query")
             .register();
 
+    private final Counter fragmentSearchNeo4jSearchDuration = Counter.build()
+            .name("duration_fragment_neo4j_ns")
+            .help("Total duration of fragment Neo4j cypher query")
+            .register();
+
     private final Counter neighbourhoodSearchNeo4jSearchDuration = Counter.build()
             .name("duration_neighbourhood_neo4j_ns")
             .help("Total duration of neighbourhood Neo4j cypher query")
@@ -104,6 +114,16 @@ public class FragnetSearchRouteBuilder extends AbstractFragnetSearchRouteBuilder
             .help("Total number of molecule search misses")
             .register();
 
+    private final Counter fragmentSearchMissesTotal = Counter.build()
+            .name("results_fragment_misses_molecules")
+            .help("Total number of fragment search misses")
+            .register();
+
+    private final Counter fragmentSearchMoleculesTotal = Counter.build()
+            .name("results_fragments_molecules")
+            .help("Total number of fragment search fragments")
+            .register();
+
     private final Counter neighbourhoodSearchHitsTotal = Counter.build()
             .name("results_neighbourhood_hits_molecules")
             .help("Total number of molecules found for neighbourhood search")
@@ -191,7 +211,7 @@ public void configure() throws Exception {
                     executeMoleculeQuery(exch);
                 })
                 .endRest()
-                .post("molecule/").description("Molecule search")
+                .post("molecule").description("Molecule search")
                 .bindingMode(RestBindingMode.off)
                 .param().name("molfile").type(RestParamType.body).description("Molfile query").endParam()
                 .produces("application/json")
@@ -201,6 +221,27 @@ public void configure() throws Exception {
                 })
                 .marshal().json(JsonLibrary.Jackson)
                 .endRest()
+                // Is this molecule part of the fragment network
+                // example:
+                // curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/molecule/OC(Cn1ccnn1)C1CC1"
+                .get("fragments/{smiles}").description("Find fragments of a molecule")
+                .param().name("smiles").type(RestParamType.path).description("SMILES query").endParam()
+                .produces("application/json")
+                .route()
+                .process((Exchange exch) -> {
+                    executeFragmentQuery(exch);
+                })
+                .endRest()
+                .post("fragments").description("MFind fragments of a molecule")
+                .bindingMode(RestBindingMode.off)
+                .param().name("molfile").type(RestParamType.body).description("Molfile query").endParam()
+                .produces("application/json")
+                .route()
+                .process((Exchange exch) -> {
+                    executeFragmentQuery(exch);
+                })
+                .marshal().json(JsonLibrary.Jackson)
+                .endRest()
                 // example:
                 // curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/neighbourhood/c1ccc%28Nc2nc3ccccc3o2%29cc1?hac=3&rac=1&hops=2&calcs=LOGP,SIM_RDKIT_TANIMOTO"
                 .get("neighbourhood/{smiles}").description("Neighbourhood search")
@@ -568,6 +609,23 @@ void executeExpansionMultiQuery(Exchange exch) {
         }
     }
 
+    private String[] fetchSmilesOrMolfile(Message message) {
+        String queryMol = null;
+        String mimeType = message.getHeader(Exchange.CONTENT_TYPE, String.class);
+        LOG.info("mime-type is " + mimeType);
+        if (mimeType == null) {
+            mimeType = Constants.MIME_TYPE_SMILES;
+        }
+        if (Constants.MIME_TYPE_SMILES.equals(mimeType)) {
+            queryMol = message.getHeader("smiles", String.class);
+        } else if (Constants.MIME_TYPE_MOLFILE.equals(mimeType)) {
+            queryMol = message.getBody(String.class);
+        } else {
+            throw new IllegalStateException("Only support SMILES using GET or molfile using POST");
+        }
+        return new String[] {queryMol, mimeType};
+    }
+
     void executeMoleculeQuery(Exchange exch) {
 
         LOG.info("Executing executeMoleculeQuery");
@@ -580,19 +638,9 @@ void executeMoleculeQuery(Exchange exch) {
         String username = getUsername(exch);
 
         try {
-            String queryMol = null;
-            String mimeType = message.getHeader(Exchange.CONTENT_TYPE, String.class);
-            LOG.info("mime-type is " + mimeType);
-            if (mimeType == null) {
-                mimeType = Constants.MIME_TYPE_SMILES;
-            }
-            if (Constants.MIME_TYPE_SMILES.equals(mimeType)) {
-                queryMol = message.getHeader("smiles", String.class);
-            } else if (Constants.MIME_TYPE_MOLFILE.equals(mimeType)) {
-                queryMol = message.getBody(String.class);
-            } else {
-                throw new IllegalStateException("Only support SMILES using GET or molfile using POST");
-            }
+            String[] data = fetchSmilesOrMolfile(message);
+            String queryMol = data[0];
+            String mimeType = data[1];
 
             if (queryMol == null || queryMol.isEmpty()) {
                 throw new IllegalArgumentException("Query molecule must be specified");
@@ -630,6 +678,59 @@ void executeMoleculeQuery(Exchange exch) {
         }
     }
 
+    void executeFragmentQuery(Exchange exch) {
+        LOG.info("Executing executeMoleculeQuery");
+
+        fragmentSearchRequestsTotal.inc();
+
+        Message message = exch.getIn();
+
+        long t0 = System.nanoTime();
+        String username = getUsername(exch);
+
+        try {
+            String[] data = fetchSmilesOrMolfile(message);
+            String queryMol = data[0];
+            String mimeType = data[1];
+
+            if (queryMol == null || queryMol.isEmpty()) {
+                throw new IllegalArgumentException("Query molecule must be specified");
+            }
+
+            List<String> smiles;
+            try (Session session = graphdb.getSession()) {
+                // execute the query
+                FragmentQuery query = new FragmentQuery(session);
+
+                long n0 = System.nanoTime();
+                smiles = query.execute(queryMol, mimeType);
+                long n1 = System.nanoTime();
+                fragmentSearchNeo4jSearchDuration.inc((double) (n1 - n0));
+                if (smiles == null || smiles.isEmpty()) {
+                    fragmentSearchMissesTotal.inc(1.0d);
+                    // throw 404
+                    message.setBody("{\"error\": \"MoleculeQuery Failed\",\"message\": \"Molecule not found\"}");
+                    message.setHeader(Exchange.HTTP_RESPONSE_CODE, 404);
+                } else {
+                    int size = smiles.size();
+                    fragmentSearchMoleculesTotal.inc((double)size);
+                    LOG.info(size + " fragments found");
+                    message.setBody(smiles);
+                    message.setHeader(Exchange.HTTP_RESPONSE_CODE, 200);
+                }
+            }
+
+        } catch (Exception ex) {
+            LOG.log(Level.SEVERE, "MoleculeQuery Failed", ex);
+            neighbourhoodSearchErrorsTotal.inc();
+            message.setBody("{\"error\": \"MoleculeQuery Failed\",\"message\":\"" + ex.getLocalizedMessage() + "\"}");
+            message.setHeader(Exchange.HTTP_RESPONSE_CODE, 500);
+
+            long t1 = System.nanoTime();
+            writeErrorToQueryLog(username, "MoleculeQuery", t1 - t0, ex.getLocalizedMessage());
+        }
+    }
+
     void executeNeighbourhoodQuery(Exchange exch) {
 
         neighbourhoodSearchRequestsTotal.inc();
