updated neo4j driver from version 1.7.2 to 4.4.5

Author: tdudgeon

docker-compose.yml

@@ -31,7 +31,7 @@ services:
   # curl $FRAGNET_SERVER/fragnet-search/rest/v2/search/suppliers
   # curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/molecule/OC(Cn1ccnn1)C1CC1"
   # curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/neighbourhood/OC(Cn1ccnn1)C1CC1?hac=3&rac=1&hops=2"
-  # curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/availability/OC(Cn1ccnn1)C1CC1"
+  # curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/availability/CCC(%3DO)CS(%3DO)(%3DO)c1ccccc1C"
   # curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/expand/OC(Cn1ccnn1)C1CC1?hacMin=5&hacMax=10&racMin=3&racMax=3&hops=2"
   # curl --data-binary "@fragnet-search/src/test/data/expand.smi" -H "Content-Type: chemical/x-daylight-smiles" "$FRAGNET_SERVER/fragnet-search/rest/v2/search/expand-multi?hacMin=5&hacMax=5&racMin=2&racMax=2&hops=2"
   # curl "$FRAGNET_SERVER/fragnet-search/rest/v2/search/fragments/OC(Cn1ccnn1)C1CC1"

fragnet-search/build.gradle

@@ -70,7 +70,7 @@ dependencies {
         compile files("../lib/rdkit/org.RDKit.jar")
     }
 
-    compile 'org.neo4j.driver:neo4j-java-driver:1.7.2'
+    compile 'org.neo4j.driver:neo4j-java-driver:4.4.5'
 
     providedCompile 'javax.servlet:javax.servlet-api:3.0.1'
 

fragnet-search/src/main/java/org/squonk/fragnet/search/FragmentUtils.java

@@ -15,10 +15,10 @@
  */
 package org.squonk.fragnet.search;
 
-import org.neo4j.driver.v1.types.MapAccessor;
-import org.neo4j.driver.v1.types.Node;
-import org.neo4j.driver.v1.types.Path;
-import org.neo4j.driver.v1.types.Relationship;
+import org.neo4j.driver.types.MapAccessor;
+import org.neo4j.driver.types.Node;
+import org.neo4j.driver.types.Path;
+import org.neo4j.driver.types.Relationship;
 import org.squonk.fragnet.Constants;
 import org.squonk.fragnet.search.model.v1.MoleculeEdge;
 import org.squonk.fragnet.search.model.v1.MoleculeNode;

fragnet-search/src/main/java/org/squonk/fragnet/search/model/v1/FragmentGraph.java

@@ -22,9 +22,9 @@
 import org.RDKit.ExplicitBitVect;
 import org.RDKit.RWMol;
 import org.RDKit.SparseIntVectu32;
-import org.neo4j.driver.v1.types.Node;
-import org.neo4j.driver.v1.types.Path;
-import org.neo4j.driver.v1.types.Relationship;
+import org.neo4j.driver.types.Node;
+import org.neo4j.driver.types.Path;
+import org.neo4j.driver.types.Relationship;
 import org.squonk.fragnet.chem.Calculator;
 import org.squonk.fragnet.search.FragmentUtils;
 

fragnet-search/src/main/java/org/squonk/fragnet/search/model/v1/NeighbourhoodGraph.java

@@ -17,9 +17,9 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
-import org.neo4j.driver.v1.types.Node;
-import org.neo4j.driver.v1.types.Path;
-import org.neo4j.driver.v1.types.Relationship;
+import org.neo4j.driver.types.Node;
+import org.neo4j.driver.types.Path;
+import org.neo4j.driver.types.Relationship;
 import org.squonk.fragnet.search.FragmentUtils;
 
 import java.util.*;

fragnet-search/src/main/java/org/squonk/fragnet/search/model/v2/ExpansionResults.java

@@ -18,8 +18,8 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
-import org.neo4j.driver.v1.types.Node;
-import org.neo4j.driver.v1.types.Path;
+import org.neo4j.driver.types.Node;
+import org.neo4j.driver.types.Path;
 import org.squonk.fragnet.Constants;
 import org.squonk.fragnet.search.FragmentUtils;
 

fragnet-search/src/main/java/org/squonk/fragnet/search/model/v2/FragmentGraph.java

@@ -22,9 +22,9 @@
 import org.RDKit.ExplicitBitVect;
 import org.RDKit.RWMol;
 import org.RDKit.SparseIntVectu32;
-import org.neo4j.driver.v1.types.Node;
-import org.neo4j.driver.v1.types.Path;
-import org.neo4j.driver.v1.types.Relationship;
+import org.neo4j.driver.types.Node;
+import org.neo4j.driver.types.Path;
+import org.neo4j.driver.types.Relationship;
 import org.squonk.fragnet.chem.Calculator;
 import org.squonk.fragnet.search.FragmentUtils;
 

fragnet-search/src/main/java/org/squonk/fragnet/search/model/v2/NeighbourhoodGraph.java

@@ -21,9 +21,9 @@
 import org.RDKit.RDKFuncs;
 import org.RDKit.ROMol_Vect;
 import org.RDKit.RWMol;
-import org.neo4j.driver.v1.types.Node;
-import org.neo4j.driver.v1.types.Path;
-import org.neo4j.driver.v1.types.Relationship;
+import org.neo4j.driver.types.Node;
+import org.neo4j.driver.types.Path;
+import org.neo4j.driver.types.Relationship;
 import org.squonk.fragnet.Constants;
 import org.squonk.fragnet.chem.TransformClassifierUtils;
 import org.squonk.fragnet.search.FragmentUtils;

fragnet-search/src/main/java/org/squonk/fragnet/search/queries/AbstractQuery.java

@@ -1,6 +1,6 @@
 package org.squonk.fragnet.search.queries;
 
-import org.neo4j.driver.v1.Session;
+import org.neo4j.driver.Session;
 
 import java.util.logging.Logger;
 

fragnet-search/src/main/java/org/squonk/fragnet/search/queries/v1/Query.java

@@ -17,8 +17,8 @@
 
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.neo4j.driver.v1.*;
-import org.neo4j.driver.v1.types.Path;
+import org.neo4j.driver.*;
+import org.neo4j.driver.types.Path;
 import org.squonk.fragnet.Constants;
 import org.squonk.fragnet.chem.Calculator;
 import org.squonk.fragnet.chem.MolStandardize;
@@ -34,7 +34,7 @@
 import java.util.concurrent.TimeUnit;
 import java.util.logging.Logger;
 
-import static org.neo4j.driver.v1.Values.parameters;
+import static org.neo4j.driver.Values.parameters;
 
 /**
  * v1 API NeighbourhoodQuery for fragment network neighbours
@@ -72,7 +72,7 @@ public NeighbourhoodGraph executeNeighbourhoodQuery(@NotNull String smiles, Inte
 
         NeighbourhoodGraph graph = getSession().writeTransaction((tx) -> {
             LOG.info("Executing NeighbourhoodQuery: " + qandp.getQuery());
-            StatementResult result = tx.run(qandp.getQuery(), parameters(qandp.getParams().toArray()));
+            Result result = tx.run(qandp.getQuery(), parameters(qandp.getParams().toArray()));
             return handleResult(result, stdSmiles);
         });
         return graph;
@@ -117,7 +117,7 @@ private QueryAndParams generateCypherQuery(String stdSmiles, Integer hops, Integ
         return new QueryAndParams(q, params);
     }
 
-    protected NeighbourhoodGraph handleResult(@NotNull StatementResult result, @NotNull String querySmiles) {
+    protected NeighbourhoodGraph handleResult(@NotNull Result result, @NotNull String querySmiles) {
 
         NeighbourhoodGraph graph = new NeighbourhoodGraph(querySmiles);
         long t0 = new Date().getTime();
@@ -131,9 +131,9 @@ protected NeighbourhoodGraph handleResult(@NotNull StatementResult result, @NotN
             });
         });
         long t1 = new Date().getTime();
-        graph.setQuery(result.summary().statement().text());
-        graph.setParameters(result.summary().statement().parameters().asMap());
-        graph.setResultAvailableAfter(result.summary().resultAvailableAfter(TimeUnit.MILLISECONDS));
+        graph.setQuery(result.consume().query().text());
+        graph.setParameters(result.consume().query().parameters().asMap());
+        graph.setResultAvailableAfter(result.consume().resultAvailableAfter(TimeUnit.MILLISECONDS));
         graph.setProcessingTime(t1 - t0);
 
         LOG.info(String.format("Results built. %s nodes, %s edges", graph.numNodes(), graph.numEdges()));