imporved tests setup

Author: tdudgeon

fragnet-search/build.gradle

@@ -26,6 +26,15 @@ plugins {
 
 description = 'Fragment network search'
 
+// To run the tests you must setup RDBASE to point to a valid RDKit build that includes
+// The Java wrappers. To do this follow the "Building from Source" instructions found here:
+// http://rdkit.org/docs/Install.html#building-from-source
+// Just do a build - don't do a `make install` and then set the RDBASE environment variable
+// to the top level directory for that checkout.
+// You do not need to do this to build the code, just to test it. If RDBASE is not defined a locally provided
+// org.RDKit.jar is user to allow compilation.
+// If the RDBASE environment variable is not defined the tests that require RDKit functionality are ignored.
+
 String RDBASE = System.getenv('RDBASE') ?: ''
 String RDKitJarFile = RDBASE + '/Code/JavaWrappers/gmwrapper/org.RDKit.jar'
 boolean RDKitJava = RDBASE && file(RDKitJarFile).exists()
@@ -82,7 +91,7 @@ tomcat {
 }
 
 task createNeoContainer(type: DockerCreateContainer) {
-    targetImageId 'informaticsmatters/fragnet-test:3.5-xchem-v1-build-2'
+    targetImageId 'informaticsmatters/fragnet-test:3.5.25-xchem-combi-sample-2021-02'
     portBindings = ['7474:7474','7687:7687']
     envVars = ['NEO4J_dbms_memory_pagecache_size': '2g',
                'NEO4J_dbms_memory_heap_initial__size': '2g',
@@ -104,11 +113,10 @@ task stopNeoContainer(type: DockerStopContainer) {
 
 test {
     environment = [
-            // TODO - fix the hard coded RDBASE setup.
-            'NEO4J_PASSWORD':'test123',
-            'NEO4J_SERVER':'localhost',
-            'LD_LIBRARY_PATH':'/home/timbo/github/rdkit/rdkit_2020_03/Code/JavaWrappers/gmwrapper:/usr/x86_64-linux-gnu',
-            'RDBASE':'/home/timbo/github/rdkit/rdkit_2020_03'
+            'NEO4J_PASSWORD': 'test123',
+            'NEO4J_SERVER': 'localhost',
+            'LD_LIBRARY_PATH': RDBASE + '/build/Code/JavaWrappers/gmwrapper:/usr/x86_64-linux-gnu',
+            'RDBASE': RDBASE
     ]
 //    beforeTest { descriptor ->
 //        logger.lifecycle("Running test: " + descriptor)
@@ -126,7 +134,7 @@ task buildDockerFile(type: Dockerfile) {
     ]
 
     destFile = project.file('build/Dockerfile')
-    from "informaticsmatters/rdkit-tomcat-debian:Release_2020_09"
+    from "informaticsmatters/rdkit-tomcat-debian:latest"
     label(['maintainer': 'Tim Dudgeon "[email protected]"'])
 
     // include the keycloak adapters

fragnet-search/src/test/groovy/org/squonk/fragnet/chem/MolStandardizeSpec.groovy

@@ -17,16 +17,16 @@ package org.squonk.fragnet.chem
 
 import org.RDKit.RDKFuncs
 import org.RDKit.RWMol
-
+import spock.lang.IgnoreIf
 import spock.lang.Specification
 
+@IgnoreIf({!env.RDBASE})
 class MolStandardizeSpec extends Specification {
 
     static {
         Runtime.getRuntime().loadLibrary0(groovy.lang.GroovyClassLoader.class, "GraphMolWrap")
     }
 
-
     void "rdkit version"() {
 
         when:

fragnet-search/src/test/groovy/org/squonk/fragnet/chem/TransformClassifierSpec.groovy

@@ -19,8 +19,10 @@ import org.RDKit.RWMol
 import org.squonk.fragnet.search.model.v2.GroupingType
 import org.squonk.fragnet.search.model.v2.MolTransform
 import org.squonk.fragnet.search.model.v2.TransformData
+import spock.lang.IgnoreIf
 import spock.lang.Specification
 
+@IgnoreIf({!env.RDBASE})
 class TransformClassifierSpec extends Specification {
 
     static {

fragnet-search/src/test/groovy/org/squonk/fragnet/search/queries/v2/AvailabilityQuerySpec.groovy

@@ -18,17 +18,18 @@ package org.squonk.fragnet.search.queries.v2
 import org.neo4j.driver.v1.Session
 import org.squonk.fragnet.AbstractGraphDBSpec
 import org.squonk.fragnet.search.model.v2.Availability
+import spock.lang.IgnoreIf
 
+@IgnoreIf({!env.RDBASE})
 class AvailabilityQuerySpec extends AbstractGraphDBSpec {
 
-
     void "simple search"() {
 
         Session session = graphDB.getSession()
         AvailabilityQuery query = new AvailabilityQuery(session)
 
         when:
-        Availability a = query.getAvailability("CCOc1ccccc1CN1CCC(O)CC1")
+        Availability a = query.getAvailability("N#Cc1cccc(N(CC(=O)O)C2CC2)n1")
         println "Found ${a.items.size()} items"
 
         then:

fragnet-search/src/test/groovy/org/squonk/fragnet/search/queries/v2/ExpansionQuerySpec.groovy

@@ -18,7 +18,9 @@ package org.squonk.fragnet.search.queries.v2
 import org.neo4j.driver.v1.Session
 import org.squonk.fragnet.AbstractGraphDBSpec
 import org.squonk.fragnet.search.model.v2.ExpansionResults
+import spock.lang.IgnoreIf
 
+@IgnoreIf({!env.RDBASE})
 class ExpansionQuerySpec extends AbstractGraphDBSpec {
 
     static {
@@ -30,7 +32,7 @@ class ExpansionQuerySpec extends AbstractGraphDBSpec {
         ExpansionQuery query = new ExpansionQuery(session, null)
 
         when:
-        ExpansionResults results = query.executeQuery("CCOc1ccccc1CN1CCC(O)CC1", "chemical/x-daylight-smiles",
+        ExpansionResults results = query.executeQuery("Cc1cc(Cl)c(C(=O)CN)s1", "chemical/x-daylight-smiles",
                 1, 10, 10, 3, 3, null)
         println "Found ${results.getSize()} items"
 

fragnet-search/src/test/groovy/org/squonk/fragnet/search/queries/v2/HitExpanderSpec.groovy

@@ -19,7 +19,9 @@ import org.neo4j.driver.v1.Session
 import org.squonk.fragnet.AbstractGraphDBSpec
 import org.squonk.fragnet.Constants
 import org.squonk.fragnet.search.model.v2.ConvertedSmilesMols
+import spock.lang.IgnoreIf
 
+@IgnoreIf({!env.RDBASE})
 class HitExpanderSpec extends AbstractGraphDBSpec {
 
     static {

fragnet-search/src/test/groovy/org/squonk/fragnet/search/queries/v2/SimpleNeighbourhoodQuerySpec.groovy

@@ -20,34 +20,23 @@ import org.squonk.fragnet.AbstractGraphDBSpec
 import org.squonk.fragnet.search.model.v2.NeighbourhoodGraph
 import org.squonk.fragnet.service.GraphDB
 import spock.lang.Ignore
+import spock.lang.IgnoreIf
 
+@IgnoreIf({!env.RDBASE})
 class SimpleNeighbourhoodQuerySpec extends AbstractGraphDBSpec {
 
     static {
         Runtime.getRuntime().loadLibrary0(groovy.lang.GroovyClassLoader.class, "GraphMolWrap")
     }
 
-    @Ignore
-    void "4-hydroxy-biphenyl-1-hop"() {
-        GraphDB db = new GraphDB()
-        Session session = db.getSession()
-
-        when:
-        NeighbourhoodQuery query = new NeighbourhoodQuery(session, [:])
-        NeighbourhoodGraph result = query.executeNeighbourhoodQuery('Oc1ccc(-c2ccccc2)cc1', 1, 3, 1, null, 10)
-        print "Results: $result.nodeCount"
-
-        then:
-        result.nodeCount > 0
-    }
 
     void "1-hop neighbourhood query"() {
         GraphDB db = new GraphDB()
         Session session = db.getSession()
 
         when:
         NeighbourhoodQuery query = new NeighbourhoodQuery(session, [:])
-        NeighbourhoodGraph result = query.executeNeighbourhoodQuery('CCOc1ccccc1CN1CCC(O)CC1', 1, 3, 1, null, 10)
+        NeighbourhoodGraph result = query.executeNeighbourhoodQuery('Brc1cnc(N2CCCC2)nc1', 1, 3, 1, null, 10)
         print "Results: $result.nodeCount"
 
         then: