New Upstream Release - libbeam-java
Ready changes
Summary
Merged new upstream version: 1.3.5 (was: 1.3.3).
Resulting package
Built on 2023-04-09T17:33 (took 16m36s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-releases libbeam-java
Lintian Result
Diff
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..e324d3e
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,36 @@
+name: Build
+on:
+ push:
+ branches:
+ - master
+ pull_request:
+ types: [opened, synchronize, reopened]
+jobs:
+ build:
+ name: Build
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ with:
+ fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
+ - name: Set up JDK 11
+ uses: actions/setup-java@v1
+ with:
+ java-version: 11
+ - name: Cache SonarCloud packages
+ uses: actions/cache@v1
+ with:
+ path: ~/.sonar/cache
+ key: ${{ runner.os }}-sonar
+ restore-keys: ${{ runner.os }}-sonar
+ - name: Cache Maven packages
+ uses: actions/cache@v1
+ with:
+ path: ~/.m2
+ key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
+ restore-keys: ${{ runner.os }}-m2
+ - name: Build and analyze
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
+ SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+ run: mvn -B verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=johnmay_beam -Pcoverage
\ No newline at end of file
diff --git a/core/pom.xml b/core/pom.xml
index 9c04219..3281abc 100644
--- a/core/pom.xml
+++ b/core/pom.xml
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.3</version>
+ <version>1.3.5</version>
</parent>
<modelVersion>4.0.0</modelVersion>
@@ -16,19 +16,16 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
- <artifactId>hamcrest-all</artifactId>
- <version>1.3</version>
+ <artifactId>hamcrest-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
- <artifactId>mockito-all</artifactId>
- <version>1.9.5</version>
+ <artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
diff --git a/core/src/main/java/uk/ac/ebi/beam/GraphBuilder.java b/core/src/main/java/uk/ac/ebi/beam/GraphBuilder.java
index 01448e4..4941e84 100644
--- a/core/src/main/java/uk/ac/ebi/beam/GraphBuilder.java
+++ b/core/src/main/java/uk/ac/ebi/beam/GraphBuilder.java
@@ -304,6 +304,8 @@ public final class GraphBuilder {
Edge eLab = findBondToLabel(g, builder.u);
Edge fLab = findBondToLabel(g, builder.v);
+ if (eLab == null || fLab == null)
+ continue;
// adjust for reference
Configuration.DoubleBond config = builder.c;
diff --git a/core/src/main/java/uk/ac/ebi/beam/Localise.java b/core/src/main/java/uk/ac/ebi/beam/Localise.java
index ac18eae..846e345 100644
--- a/core/src/main/java/uk/ac/ebi/beam/Localise.java
+++ b/core/src/main/java/uk/ac/ebi/beam/Localise.java
@@ -159,8 +159,9 @@ final class Localise {
for (int j = 0; j < d; ++j) {
Edge e = g.edgeAt(v, j);
if (e.bond() == Bond.DOUBLE) {
- if (q == 0 && (a.element() == Element.Nitrogen || (a.element() == Element.Sulfur && deg > 3))
- )
+ if (q == 0 && (a.element() == Element.Nitrogen ||
+ a.element() == Element.Phosphorus ||
+ (a.element() == Element.Sulfur && deg > 3)))
return false;
return true;
}
@@ -258,10 +259,12 @@ final class Localise {
if (hasAdjDirectionalLabels(g, e, cyclic) && !inSmallRing(g, e)) {
other = -1;
+ target = null;
break;
}
if (vExtra > 1 && hasAdditionalCyclicDoubleBond(g, cyclic, u, v)) {
other = -1;
+ target = null;
break;
}
if (other == -1) {
@@ -269,6 +272,7 @@ final class Localise {
target = e;
} else {
other = -2; // found more than one
+ target = null;
}
}
// only one double bond don't check any more
@@ -277,7 +281,7 @@ final class Localise {
}
}
- if (other >= 0) {
+ if (target != null) {
subset.set(u);
subset.set(other);
target.bond(Bond.IMPLICIT);
diff --git a/core/src/main/java/uk/ac/ebi/beam/Parser.java b/core/src/main/java/uk/ac/ebi/beam/Parser.java
index 1cee6ee..3a1a1dd 100644
--- a/core/src/main/java/uk/ac/ebi/beam/Parser.java
+++ b/core/src/main/java/uk/ac/ebi/beam/Parser.java
@@ -386,8 +386,34 @@ final class Parser {
us = insertDbImplicitRef(u, us); // XXX: temp fix
else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
g.addFlags(Graph.HAS_EXT_STRO);
- if ((us = getAlleneCarriers(u)) == null)
- return;
+ if ((us = getAlleneCarriers(u)) == null) {
+ if (strict)
+ throw new InvalidSmilesException("Invalid Allene stereo");
+ else
+ warnings.add("Ignored invalid Allene stereochemistry");
+ return;
+ }
+ } else if (c.type() == Configuration.Type.SquarePlanar &&
+ us.length != 4) {
+ if (strict)
+ throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 4 explicit neighbours");
+ return;
+ } else if (c.type() == Configuration.Type.TrigonalBipyramidal &&
+ us.length != 5) {
+ if (strict)
+ throw new InvalidSmilesException("SquarePlanar without 5 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 5 explicit neighbours");
+ return;
+ } else if (c.type() == Configuration.Type.Octahedral &&
+ us.length != 6) {
+ if (strict)
+ throw new InvalidSmilesException("SquarePlanar without 6 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 6 explicit neighbours");
+ return;
}
g.addTopology(Topology.create(u, us, es, c));
}
@@ -680,7 +706,7 @@ final class Parser {
sb.append(c);
}
g.setTitle(sb.toString());
-
+ return;
case '\n':
case '\r':
return;
diff --git a/core/src/test/java/uk/ac/ebi/beam/AtomCentricDBConfigTest.java b/core/src/test/java/uk/ac/ebi/beam/AtomCentricDBConfigTest.java
index f1c6e9c..eb54b0b 100644
--- a/core/src/test/java/uk/ac/ebi/beam/AtomCentricDBConfigTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/AtomCentricDBConfigTest.java
@@ -77,17 +77,17 @@ public class AtomCentricDBConfigTest {
}
@Test public void difluoroethene() throws InvalidSmilesException {
- GeneratorTest.roundTrip("F[C@H]=[C@H]F");
- GeneratorTest.roundTrip("F[C@@H]=[C@@H]F");
- GeneratorTest.roundTrip("F[C@H]=[C@@H]F");
- GeneratorTest.roundTrip("F[C@@H]=[C@H]F");
+ GeneratorTest.assertRoundTrip("F[C@H]=[C@H]F");
+ GeneratorTest.assertRoundTrip("F[C@@H]=[C@@H]F");
+ GeneratorTest.assertRoundTrip("F[C@H]=[C@@H]F");
+ GeneratorTest.assertRoundTrip("F[C@@H]=[C@H]F");
}
@Test public void difluoroethene_permute() throws InvalidSmilesException {
- GeneratorTest.roundTrip("F[C@H]=[C@H]F",
+ GeneratorTest.assertRoundTrip("F[C@H]=[C@H]F",
new int[]{1, 0, 2, 3},
"[C@@H](F)=[C@H]F");
- GeneratorTest.roundTrip("[C@@H](F)=[C@H]F",
+ GeneratorTest.assertRoundTrip("[C@@H](F)=[C@H]F",
new int[]{1, 0, 2, 3},
"F[C@H]=[C@H]F");
}
diff --git a/core/src/test/java/uk/ac/ebi/beam/ConfigurationTest.java b/core/src/test/java/uk/ac/ebi/beam/ConfigurationTest.java
index 517b137..8fd3235 100644
--- a/core/src/test/java/uk/ac/ebi/beam/ConfigurationTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/ConfigurationTest.java
@@ -131,7 +131,8 @@ public class ConfigurationTest {
}
@Test public void antiClockwise() throws InvalidSmilesException {
- Configuration.read(CharBuffer.fromString("@H"));
+ assertThat(Configuration.read(CharBuffer.fromString("@H")),
+ is(Configuration.ANTI_CLOCKWISE));
}
@Test(expected = InvalidSmilesException.class)
diff --git a/core/src/test/java/uk/ac/ebi/beam/GeneratorTest.java b/core/src/test/java/uk/ac/ebi/beam/GeneratorTest.java
index dc79853..512f82c 100644
--- a/core/src/test/java/uk/ac/ebi/beam/GeneratorTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/GeneratorTest.java
@@ -45,79 +45,79 @@ public class GeneratorTest {
@Test public void implicitHCentre() throws InvalidSmilesException {
- roundTrip("[C@@H](N)(O)C");
+ assertRoundTrip("[C@@H](N)(O)C");
// permutations
- roundTrip("[C@@H](N)(O)C", new int[]{0, 1, 2, 3}, "[C@@H](N)(O)C");
- roundTrip("[C@@H](N)(O)C", new int[]{0, 1, 3, 2}, "[C@H](N)(C)O");
- roundTrip("[C@@H](N)(O)C", new int[]{0, 2, 1, 3}, "[C@H](O)(N)C");
- roundTrip("[C@@H](N)(O)C", new int[]{0, 2, 3, 1}, "[C@@H](C)(N)O");
- roundTrip("[C@@H](N)(O)C", new int[]{0, 3, 1, 2}, "[C@@H](O)(C)N");
- roundTrip("[C@@H](N)(O)C", new int[]{0, 3, 2, 1}, "[C@H](C)(O)N");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{0, 1, 2, 3}, "[C@@H](N)(O)C");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{0, 1, 3, 2}, "[C@H](N)(C)O");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{0, 2, 1, 3}, "[C@H](O)(N)C");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{0, 2, 3, 1}, "[C@@H](C)(N)O");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{0, 3, 1, 2}, "[C@@H](O)(C)N");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{0, 3, 2, 1}, "[C@H](C)(O)N");
- roundTrip("[C@@H](N)(O)C", new int[]{1, 0, 2, 3}, "N[C@H](O)C");
- roundTrip("[C@@H](N)(O)C", new int[]{1, 0, 3, 2}, "N[C@@H](C)O");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{1, 0, 2, 3}, "N[C@H](O)C");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{1, 0, 3, 2}, "N[C@@H](C)O");
- roundTrip("[C@@H](N)(O)C", new int[]{1, 2, 0, 3}, "O[C@@H](N)C");
- roundTrip("[C@@H](N)(O)C", new int[]{1, 3, 0, 2}, "O[C@H](C)N");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{1, 2, 0, 3}, "O[C@@H](N)C");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{1, 3, 0, 2}, "O[C@H](C)N");
- roundTrip("[C@@H](N)(O)C", new int[]{1, 2, 3, 0}, "C[C@H](N)O");
- roundTrip("[C@@H](N)(O)C", new int[]{1, 3, 2, 0}, "C[C@@H](O)N");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{1, 2, 3, 0}, "C[C@H](N)O");
+ assertRoundTrip("[C@@H](N)(O)C", new int[]{1, 3, 2, 0}, "C[C@@H](O)N");
- roundTrip("[C@H](N)(C)O");
+ assertRoundTrip("[C@H](N)(C)O");
- roundTrip("[C@H](N)(C)O", new int[]{0, 1, 2, 3}, "[C@H](N)(C)O");
- roundTrip("[C@H](N)(C)O", new int[]{0, 1, 3, 2}, "[C@@H](N)(O)C");
- roundTrip("[C@H](N)(C)O", new int[]{0, 2, 1, 3}, "[C@@H](C)(N)O");
- roundTrip("[C@H](N)(C)O", new int[]{0, 2, 3, 1}, "[C@H](O)(N)C");
- roundTrip("[C@H](N)(C)O", new int[]{0, 3, 1, 2}, "[C@H](C)(O)N");
- roundTrip("[C@H](N)(C)O", new int[]{0, 3, 2, 1}, "[C@@H](O)(C)N");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{0, 1, 2, 3}, "[C@H](N)(C)O");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{0, 1, 3, 2}, "[C@@H](N)(O)C");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{0, 2, 1, 3}, "[C@@H](C)(N)O");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{0, 2, 3, 1}, "[C@H](O)(N)C");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{0, 3, 1, 2}, "[C@H](C)(O)N");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{0, 3, 2, 1}, "[C@@H](O)(C)N");
- roundTrip("[C@H](N)(C)O", new int[]{1, 0, 2, 3}, "N[C@@H](C)O");
- roundTrip("[C@H](N)(C)O", new int[]{1, 0, 3, 2}, "N[C@H](O)C");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{1, 0, 2, 3}, "N[C@@H](C)O");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{1, 0, 3, 2}, "N[C@H](O)C");
- roundTrip("[C@H](N)(C)O", new int[]{1, 2, 0, 3}, "C[C@H](N)O");
- roundTrip("[C@H](N)(C)O", new int[]{1, 3, 0, 2}, "C[C@@H](O)N");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{1, 2, 0, 3}, "C[C@H](N)O");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{1, 3, 0, 2}, "C[C@@H](O)N");
- roundTrip("[C@H](N)(C)O", new int[]{1, 2, 3, 0}, "O[C@@H](N)C");
- roundTrip("[C@H](N)(C)O", new int[]{1, 3, 2, 0}, "O[C@H](C)N");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{1, 2, 3, 0}, "O[C@@H](N)C");
+ assertRoundTrip("[C@H](N)(C)O", new int[]{1, 3, 2, 0}, "O[C@H](C)N");
- roundTrip("N[C@@H](C)O");
- roundTrip("N[C@@H](C)O");
- roundTrip("N[C@H](O)C");
- roundTrip("O[C@@H](N)C");
- roundTrip("O[C@H](C)N");
- roundTrip("C[C@@H](O)N");
- roundTrip("C[C@H](N)O");
+ assertRoundTrip("N[C@@H](C)O");
+ assertRoundTrip("N[C@@H](C)O");
+ assertRoundTrip("N[C@H](O)C");
+ assertRoundTrip("O[C@@H](N)C");
+ assertRoundTrip("O[C@H](C)N");
+ assertRoundTrip("C[C@@H](O)N");
+ assertRoundTrip("C[C@H](N)O");
}
@Test public void ring_closures1() throws Exception {
- roundTrip("C1=CN=CC2=NC=N[C@@H]21");
+ assertRoundTrip("C1=CN=CC2=NC=N[C@@H]21");
}
@Test public void ring_closures2() throws Exception {
- roundTrip("C1=CN=CC2=NC=N[C@H]21");
+ assertRoundTrip("C1=CN=CC2=NC=N[C@H]21");
}
@Test public void ring_closures3() throws Exception {
- roundTrip("C1=CC(=CC2=NC(=N[C@@H]21)C(F)(F)F)N");
+ assertRoundTrip("C1=CC(=CC2=NC(=N[C@@H]21)C(F)(F)F)N");
}
@Test public void ring_closures4() throws Exception {
- roundTrip("C1=CC(=CC2=NC(=N[C@H]21)C(F)(F)F)N");
+ assertRoundTrip("C1=CC(=CC2=NC(=N[C@H]21)C(F)(F)F)N");
}
@Test public void lowRingNumberOrder() throws InvalidSmilesException {
- roundTrip("C1=CC2=CC=CC=C2C=C1");
+ assertRoundTrip("C1=CC2=CC=CC=C2C=C1");
}
@Test public void multipleRingNumberOrder() throws InvalidSmilesException {
- roundTrip("C1=CC2=C3C4=C5C(C=CC6=C5C7=C(C=C6)C=CC(C=C2)=C37)=CC=C14");
+ assertRoundTrip("C1=CC2=C3C4=C5C(C=CC6=C5C7=C(C=C6)C=CC(C=C2)=C37)=CC=C14");
}
@Test public void highRingNumberOrder() throws InvalidSmilesException {
- roundTrip("C1CC2CCC3=C4C2=C5C1CCC6=C5C7=C8C(C=C9CCC%10CCC%11CCC%12=CC(=C3)C(C%13=C8C9=C%10C%11=C%12%13)=C47)=C6");
+ assertRoundTrip("C1CC2CCC3=C4C2=C5C1CCC6=C5C7=C8C(C=C9CCC%10CCC%11CCC%12=CC(=C3)C(C%13=C8C9=C%10C%11=C%12%13)=C47)=C6");
}
@Test public void bondTypeOnFirstAtom1() throws InvalidSmilesException {
@@ -166,11 +166,11 @@ public class GeneratorTest {
}
@Test public void sodiumChloride() throws InvalidSmilesException {
- roundTrip("[Na+].[Cl-]");
+ assertRoundTrip("[Na+].[Cl-]");
}
@Test public void disconnected() throws InvalidSmilesException {
- roundTrip("CCCC.OOOO.C[CH]C.CNO");
+ assertRoundTrip("CCCC.OOOO.C[CH]C.CNO");
}
@Test public void extendedTetrhedral_al1() throws Exception {
@@ -301,11 +301,11 @@ public class GeneratorTest {
assertThat(g.toSmiles(), is("CC=[C@]=C1OCCCC1"));
}
- static void roundTrip(String smi) throws InvalidSmilesException {
+ static void assertRoundTrip(String smi) throws InvalidSmilesException {
assertThat(Generator.generate(Parser.parse(smi)), is(smi));
}
- static void roundTrip(String smi, int[] p, String res) throws
+ static void assertRoundTrip(String smi, int[] p, String res) throws
InvalidSmilesException {
assertThat(Generator.generate(Parser.parse(smi).permute(p)), is(res));
}
diff --git a/core/src/test/java/uk/ac/ebi/beam/GraphBuilderTest.java b/core/src/test/java/uk/ac/ebi/beam/GraphBuilderTest.java
index f0620c4..e0b3c43 100644
--- a/core/src/test/java/uk/ac/ebi/beam/GraphBuilderTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/GraphBuilderTest.java
@@ -35,6 +35,7 @@ import org.junit.Test;
import java.io.IOException;
import static org.hamcrest.CoreMatchers.is;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static uk.ac.ebi.beam.Configuration.DoubleBond.OPPOSITE;
@@ -212,6 +213,7 @@ public class GraphBuilderTest {
.geometric(7, 6).configure(8, 3, OPPOSITE)
.geometric(3, 4).configure(2, 5, OPPOSITE)
.build();
+ assertNotNull(g); // g builds okay
}
@Test
@@ -301,6 +303,7 @@ public class GraphBuilderTest {
.geometric(8, 9).opposite(4, 10)
.geometric(3, 4).opposite(2, 8)
.build();
+ assertNotNull(g); // builds okay
}
@Test
@@ -337,6 +340,7 @@ public class GraphBuilderTest {
.neighbors(2, 3, 4)
.winding(Configuration.AL1)
.build();
+ assertNotNull(gb.build()); // builds okay
}
@Test
diff --git a/core/src/test/java/uk/ac/ebi/beam/GraphTest.java b/core/src/test/java/uk/ac/ebi/beam/GraphTest.java
index e3bad3d..d118f0d 100644
--- a/core/src/test/java/uk/ac/ebi/beam/GraphTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/GraphTest.java
@@ -220,7 +220,9 @@ public class GraphTest {
@Test public void addUnknownTopology() {
Topology t = Topology.unknown();
Graph g = new Graph(5);
- g.addTopology(t);
+ g.addTopology(t); // don't fail
+ assertThat(g.order(), is(0));
+ assertThat(g.size(), is(0));
}
@Test public void defaultTopology() {
@@ -479,6 +481,7 @@ public class GraphTest {
@Test public void CHEMBL1215012() throws Exception {
Graph g = Graph.fromSmiles("[Na+].[Na+].CC(C)c1c(O)c(O)c(\\C=N\\[C@H]2[C@H]3SC(C)(C)[C@@H](N3C2=O)C(=O)[O-])c4C(=O)C(=C(C)C(=O)c14)C5=C(C)C(=O)c6c(C(C)C)c(O)c(O)c(\\C=N\\[C@H]7[C@H]8SC(C)(C)[C@@H](N8C7=O)C(=O)[O-])c6C5=O CHEMBL1215012");
+ Assert.assertNotNull(g);
}
@Test public void nitgrogenStereochemistry() throws Exception {
@@ -542,4 +545,10 @@ public class GraphTest {
Graph g = Graph.fromSmiles("[CH3:3]1.[CH3:1]C(=[C@@]=[CH:2]1)[CH2:4]C");
Assert.assertThat(g.topologyOf(3).configuration(), is(Configuration.AL2));
}
+
+ @Test public void nofail() throws IOException {
+ Graph g = Graph.fromSmiles("CCCO[P@H]1(OC[C@@H]2[C@@H](O1)[C@@]([C@@H](O2)n3cnc4c3nc(nc4OCC)N)(C)F)O CHEMBL1630021");
+ assertThat(g.toSmiles(),
+ CoreMatchers.is("CCCO[PH]1(OC[C@@H]2[C@@H](O1)[C@@]([C@@H](O2)n3cnc4c3nc(nc4OCC)N)(C)F)O"));
+ }
}
diff --git a/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java b/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
index 963a6e3..a92e791 100644
--- a/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
@@ -385,6 +385,10 @@ public class LocaliseTest {
test("*1ccccc1", "*1=CC=CC=C1");
}
+ @Test public void aromphos() throws Exception {
+ test("O=p1ccccc1", "O=P1=CC=CC=C1");
+ }
+
static void test(String delocalised, String localised) throws Exception {
Graph g = Graph.fromSmiles(delocalised);
Graph h = Localise.localise(g);
diff --git a/core/src/test/java/uk/ac/ebi/beam/ParserTest.java b/core/src/test/java/uk/ac/ebi/beam/ParserTest.java
index d9e6077..3c16959 100644
--- a/core/src/test/java/uk/ac/ebi/beam/ParserTest.java
+++ b/core/src/test/java/uk/ac/ebi/beam/ParserTest.java
@@ -36,9 +36,8 @@ import org.junit.Test;
import java.io.IOException;
import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
/** @author John May */
public class ParserTest {
@@ -96,7 +95,9 @@ public class ParserTest {
}
@Test public void tellurophene() throws InvalidSmilesException {
- Parser.parse("c1cc[te]c1");
+ Graph g = Parser.parse("c1cc[te]c1");
+ assertThat(g.order(), is(5));
+ assertThat(g.size(), is(5));
}
@Test public void mixingAromaticAndKekule() throws InvalidSmilesException {
@@ -142,6 +143,8 @@ public class ParserTest {
@Test
public void hydrogen_strict_okay() throws IOException {
Graph g = Parser.strict("[H][H]");
+ assertNotNull(g);
+ assertThat(g.order(), is(2));
}
@Test public void tellurium() throws IOException {
@@ -157,6 +160,8 @@ public class ParserTest {
@Test public void largeRnum() throws Exception {
Graph g = Parser.parse("C%99CCCC%99");
+ assertThat(g.order(), is(5));
+ assertThat(g.size(), is(5));
}
// not part of spec
@@ -215,7 +220,7 @@ public class ParserTest {
@Test
public void acceptMultipleBonds() throws Exception {
- Parser.parse("C/C=C/C\\C=C/C");
+ assertNotNull(Parser.parse("C/C=C/C\\C=C/C"));
}
@Test
diff --git a/debian/changelog b/debian/changelog
index 38e6a32..6784993 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbeam-java (1.3.5-1) UNRELEASED; urgency=low
+
+ * New upstream release.
+
+ -- Debian Janitor <janitor@jelmer.uk> Sun, 09 Apr 2023 17:18:20 -0000
+
libbeam-java (1.3.3-3) unstable; urgency=medium
* Executing build time tests.
diff --git a/exec/pom.xml b/exec/pom.xml
index 92b111d..8e629a6 100644
--- a/exec/pom.xml
+++ b/exec/pom.xml
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.3</version>
+ <version>1.3.5</version>
</parent>
<modelVersion>4.0.0</modelVersion>
diff --git a/exec/src/main/java/uk/ac/ebi/beam/FunctorCmdLnModule.java b/exec/src/main/java/uk/ac/ebi/beam/FunctorCmdLnModule.java
index eb8dd05..8641bfe 100644
--- a/exec/src/main/java/uk/ac/ebi/beam/FunctorCmdLnModule.java
+++ b/exec/src/main/java/uk/ac/ebi/beam/FunctorCmdLnModule.java
@@ -27,7 +27,7 @@ abstract class FunctorCmdLnModule extends PipingCmdLnModule {
* How much input we process at once, could be adjustable.
*/
final int WORK_UNIT_SIZE = 15000;
- final boolean debug = false;
+ static final boolean DEBUG = false;
FunctorCmdLnModule(String name) {
super(name);
@@ -89,7 +89,6 @@ abstract class FunctorCmdLnModule extends PipingCmdLnModule {
elapsedMilli(tStart)), cnt);
}
} catch (Exception | InternalError e) {
- if (debug) e.printStackTrace();
if (showWarnings) {
report("error, " + e.getMessage() + "\nline:" + escapeForPrintf(line) + "\n");
}
@@ -186,7 +185,7 @@ abstract class FunctorCmdLnModule extends PipingCmdLnModule {
try {
Thread.sleep(ms);
} catch (InterruptedException e) {
- // ignore
+ Thread.currentThread().interrupt();
}
}
@@ -197,10 +196,11 @@ abstract class FunctorCmdLnModule extends PipingCmdLnModule {
private Result getResult(Future<Result> future) {
try {
return future.get();
- } catch (InterruptedException | ExecutionException e) {
+ } catch (InterruptedException e) {
+ Thread.currentThread().interrupt();
+ } catch (ExecutionException e) {
System.err.println(e.getMessage());
- if (debug)
- e.printStackTrace();
+
}
return null;
}
@@ -221,7 +221,7 @@ abstract class FunctorCmdLnModule extends PipingCmdLnModule {
}
return cnt;
} catch (IOException e) {
- e.printStackTrace();
+ System.err.println("IO Error: " + e.getMessage());
}
return 0;
}
@@ -270,7 +270,6 @@ abstract class FunctorCmdLnModule extends PipingCmdLnModule {
} catch (Exception e) {
if (warn) {
report("\nerror, " + e.getMessage() + "\nline:" + escapeForPrintf(lines.get(i)) + "\n");
- if (debug) e.printStackTrace();
}
lines.set(i, null);
}
diff --git a/exec/src/main/java/uk/ac/ebi/beam/PipingCmdLnModule.java b/exec/src/main/java/uk/ac/ebi/beam/PipingCmdLnModule.java
index f199228..ac3bbaf 100644
--- a/exec/src/main/java/uk/ac/ebi/beam/PipingCmdLnModule.java
+++ b/exec/src/main/java/uk/ac/ebi/beam/PipingCmdLnModule.java
@@ -68,7 +68,7 @@ public abstract class PipingCmdLnModule implements CmdLnModule {
try {
process(args);
} catch (IOException e) {
- e.printStackTrace();
+ System.err.println("Execution error: " + e.getMessage());
}
}
@@ -81,25 +81,24 @@ public abstract class PipingCmdLnModule implements CmdLnModule {
final File fin = nonopt.size() > 0 ? new File(nonopt.get(0).toString())
: null;
- InputStream in = fin == null ? System.in : new CountingInputStream(fin);
- OutputStream out = nonopt.size() < 2 ? System.out
- : new FileOutputStream(nonopt.get(1).toString());
-
+ try (InputStream in = fin == null ? System.in : new CountingInputStream(fin);
+ OutputStream out = nonopt.size() < 2 ? System.out : new FileOutputStream(nonopt.get(1).toString());
+ BufferedWriter bwtr = new BufferedWriter(new OutputStreamWriter(out, UTF_8));
+ BufferedReader brdr = new BufferedReader(new InputStreamReader(in, UTF_8))) {
- InputCounter nonFileCounter = new InputCounter() {
- @Override public long count() {
- return 0;
- }
+ InputCounter nonFileCounter = new InputCounter() {
+ @Override public long count() {
+ return 0;
+ }
- @Override public long total() {
- return -1;
- }
- };
- InputCounter inputCounter = fin == null ? nonFileCounter
- : (CountingInputStream) in;
+ @Override public long total() {
+ return -1;
+ }
+ };
+ InputCounter inputCounter = fin == null
+ ? nonFileCounter
+ : (CountingInputStream) in;
- try (BufferedWriter bwtr = new BufferedWriter(new OutputStreamWriter(out, UTF_8));
- BufferedReader brdr = new BufferedReader(new InputStreamReader(in, UTF_8))) {
process(brdr, bwtr, inputCounter, optset);
}
}
diff --git a/func/pom.xml b/func/pom.xml
index 670e5b4..2925c0b 100644
--- a/func/pom.xml
+++ b/func/pom.xml
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.3</version>
+ <version>1.3.5</version>
</parent>
<modelVersion>4.0.0</modelVersion>
@@ -16,13 +16,11 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
- <artifactId>mockito-all</artifactId>
- <version>1.9.5</version>
+ <artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
diff --git a/func/src/main/java/uk/ac/ebi/beam/Functions.java b/func/src/main/java/uk/ac/ebi/beam/Functions.java
index 7052351..0feb2fe 100644
--- a/func/src/main/java/uk/ac/ebi/beam/Functions.java
+++ b/func/src/main/java/uk/ac/ebi/beam/Functions.java
@@ -32,6 +32,8 @@ public final class Functions {
private static final AddDirectionalLabels adl = new AddDirectionalLabels();
+ private static Random rand = new Random();
+
/// non-instantiable
private Functions() {
}
@@ -164,14 +166,28 @@ public final class Functions {
return g;
}
- private static int[] random(int n) {
+ /**
+ * Generate a random permutation.
+ * @param n size of the permutation
+ * @param rnd random number generator
+ * @return the permutation
+ */
+ private static int[] random(int n, Random rnd) {
int[] p = ident(n);
- Random rnd = new Random();
for (int i = n; i > 1; i--)
swap(p, i - 1, rnd.nextInt(i));
return p;
}
+ /**
+ * Generate a random permutation using a shared RNG instance. The method is synchronized
+ * @param n size of the permutation
+ * @return the permutation
+ */
+ private synchronized static int[] random(int n) {
+ return random(n, rand);
+ }
+
private static int[] reverse(int n) {
int[] p = new int[n];
for (int i = 0; i < n; i++)
diff --git a/func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java b/func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java
index 8b53630..625f5a6 100644
--- a/func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java
+++ b/func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java
@@ -179,6 +179,8 @@ final class NormaliseDirectionalLabels
}
private void flip(Edge first, int u, BitSet dbAtoms) {
+ if (first == null)
+ return;
if (ordering[first.other(u)] < ordering[u]) {
if (first.bond(u) == Bond.UP)
invertExistingDirectionalLabels(g,
diff --git a/pom.xml b/pom.xml
index e114646..cf4517e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,7 +7,7 @@
<description>SMILES parsing and generation library for cheminformatics</description>
<url>http://www.github.com/johnmay/beam/</url>
<packaging>pom</packaging>
- <version>1.3.3</version>
+ <version>1.3.5</version>
<modules>
<module>core</module>
<module>func</module>
@@ -34,6 +34,8 @@
</distributionManagement>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <sonar.organization>johnmay</sonar.organization>
+ <sonar.host.url>https://sonarcloud.io</sonar.host.url>
</properties>
<licenses>
<license>
@@ -46,14 +48,43 @@
</prerequisites>
<developers>
<developer>
- <name>John May</name>
+ <name>John Mayfield (né May)</name>
<email>https://github.com/johnmay</email>
<url>http://www.github.com/johnmay/</url>
- <organization>EMBL-EBI</organization>
- <organizationUrl>http://ebi.ac.uk</organizationUrl>
+ <organization>NextMove Software</organization>
+ <organizationUrl>https://www.nextmovesoftware.com</organizationUrl>
<timezone>GMT</timezone>
</developer>
</developers>
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.13.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.hamcrest</groupId>
+ <artifactId>hamcrest-core</artifactId>
+ <version>2.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.hamcrest</groupId>
+ <artifactId>hamcrest-all</artifactId>
+ <version>2.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.hamcrest</groupId>
+ <artifactId>hamcrest</artifactId>
+ <version>2.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-core</artifactId>
+ <version>4.11.0</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
<profiles>
<profile>
<id>ossrh</id>
@@ -63,7 +94,7 @@
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.3</version>
- <extensions>true</extensions>
+ <extensions>false</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
@@ -113,6 +144,32 @@
</plugins>
</build>
</profile>
+ <profile>
+ <id>coverage</id>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.jacoco</groupId>
+ <artifactId>jacoco-maven-plugin</artifactId>
+ <version>0.8.5</version>
+ <executions>
+ <execution>
+ <id>prepare-agent</id>
+ <goals>
+ <goal>prepare-agent</goal>
+ </goals>
+ </execution>
+ <execution>
+ <id>report</id>
+ <goals>
+ <goal>report</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
</profiles>
<build>
<plugins>
@@ -121,8 +178,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.1</version>
<configuration>
- <source>1.7</source>
- <target>1.7</target>
+ <source>1.8</source>
+ <target>1.8</target>
</configuration>
</plugin>
</plugins>
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-core/1.3.5/beam-core-1.3.5.pom -rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-exec/1.3.5/beam-exec-1.3.5.pom -rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-func/1.3.5/beam-func-1.3.5.pom -rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam/1.3.5/beam-1.3.5.pom lrwxrwxrwx root/root /usr/share/java/beam-core-1.3.5.jar -> beam-core.jar lrwxrwxrwx root/root /usr/share/java/beam-exec-1.3.5.jar -> beam-exec.jar lrwxrwxrwx root/root /usr/share/java/beam-func-1.3.5.jar -> beam-func.jar lrwxrwxrwx root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-core/1.3.5/beam-core-1.3.5.jar -> ../../../../../../../java/beam-core.jar lrwxrwxrwx root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-exec/1.3.5/beam-exec-1.3.5.jar -> ../../../../../../../java/beam-exec.jar lrwxrwxrwx root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-func/1.3.5/beam-func-1.3.5.jar -> ../../../../../../../java/beam-func.jar
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-core/1.3.3/beam-core-1.3.3.pom -rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-exec/1.3.3/beam-exec-1.3.3.pom -rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-func/1.3.3/beam-func-1.3.3.pom -rw-r--r-- root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam/1.3.3/beam-1.3.3.pom lrwxrwxrwx root/root /usr/share/java/beam-core-1.3.3.jar -> beam-core.jar lrwxrwxrwx root/root /usr/share/java/beam-exec-1.3.3.jar -> beam-exec.jar lrwxrwxrwx root/root /usr/share/java/beam-func-1.3.3.jar -> beam-func.jar lrwxrwxrwx root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-core/1.3.3/beam-core-1.3.3.jar -> ../../../../../../../java/beam-core.jar lrwxrwxrwx root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-exec/1.3.3/beam-exec-1.3.3.jar -> ../../../../../../../java/beam-exec.jar lrwxrwxrwx root/root /usr/share/maven-repo/uk/ac/ebi/beam/beam-func/1.3.3/beam-func-1.3.3.jar -> ../../../../../../../java/beam-func.jar
No differences were encountered in the control files