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Merged
merged 1 commit into from
Apr 15, 2025
Merged

replace publish plugin in cqp-api #21

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170 changes: 4 additions & 166 deletions cqp-api/build.gradle.kts
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Original file line number Diff line number Diff line change
@@ -1,187 +1,25 @@
import java.net.HttpURLConnection
import kotlin.io.encoding.Base64
import kotlin.io.encoding.ExperimentalEncodingApi

plugins {
`java-library`
`maven-publish`
signing
id("com.diffplug.spotless") version "7.0.2"
id("com.quantori.cqp-build")
}

group = "com.quantori"
description = "Chem query platform. Compound quick search"
version = "0.0.10"
description = "Chem query platform. Storage API"
version = "0.0.11"

repositories {
mavenLocal()
mavenCentral()
}

java {
toolchain {
languageVersion = JavaLanguageVersion.of(17)
}
withSourcesJar()
withJavadocJar()
}

publishing {
publications {
create<MavenPublication>("mavenJava") {
from(components["java"])

pom {
artifactId = "cqp-api"
name = project.name
description = project.description
packaging = "jar"
url = "https://github.com/quantori/chem-query-platform"

licenses {
license {
name = "The Apache License, Version 2.0"
url = "https://www.apache.org/licenses/LICENSE-2.0.txt"
}
}

developers {
developer {
id = "artem.chukin"
name = "Artem Chukin"
email = "artem.chukin@quantori.com"
}
developer {
id = "dmitriy gusev"
name = "Dmitriy Gusev"
email = "dmitriy.gusev@quantori.com"
}

developer {
id = "valeriy burmistrov"
name = "Valeriy Burmistrov"
email = "valeriy.burmistrov@quantori.com"
}

developer {
id = "boris sukhodoev"
name = "Boris Sukhodoev"
email = "boris.sukhodoev@quantori.com"
}
}

scm {
connection = "scm:git:git://github.com/quantori/chem-query-platform.git"
developerConnection = "scm:git:ssh://github.com/quantori/chem-query-platform.git"
url = "https://github.com/quantori/chem-query-platform"
}
}
}
}
repositories {
maven {
name = "localStaging"
// change URLs to point to your repos, e.g. http://my.org/repo
val releasesRepoUrl = uri(layout.buildDirectory.dir("repos/releases"))
val snapshotsRepoUrl = uri(layout.buildDirectory.dir("repos/snapshots"))
url = if (version.toString().endsWith("SNAPSHOT")) snapshotsRepoUrl else releasesRepoUrl
}
}
}

tasks.test {
useJUnitPlatform()
testLogging {
events("passed", "skipped", "failed")
}
}

artifacts {
archives(tasks.named("javadocJar"))
archives(tasks.named("sourcesJar"))
}

signing {
setRequired {
!version.toString().endsWith("SNAPSHOT") && gradle.taskGraph.hasTask("publish")
}
val signingSecretKey = findProperty("signing.secretKey") as String? ?: System.getenv("GPG_SIGNING_SECRET_KEY")
val signingPassword = findProperty("signing.password") as String? ?: System.getenv("GPG_SIGNING_PASSWORD")

useInMemoryPgpKeys(signingSecretKey, signingPassword)
sign(publishing.publications["mavenJava"])
sign(configurations.archives.get())
}

// Fix Javadoc warnings on JDK 9+ (optional but recommended)
if (JavaVersion.current().isJava9Compatible) {
tasks.withType<Javadoc>().configureEach {
(options as StandardJavadocDocletOptions).addStringOption("Xdoclint:none", "-quiet")
(options as StandardJavadocDocletOptions).addBooleanOption("html5", true)
}
}

@OptIn(ExperimentalEncodingApi::class)
fun String.toBase64(): String {
return Base64.encode(this.toByteArray(Charsets.UTF_8))
}

val publishToLocalStaging = tasks.getByName("publishMavenJavaPublicationToLocalStagingRepository")

publishToLocalStaging.outputs.dir(layout.buildDirectory.dir("repos/releases"))

val zipBundle by tasks.registering(Zip::class) {
archiveFileName = "central-bundle.zip"
destinationDirectory = project.layout.buildDirectory.dir("distributions")
inputs.files(publishToLocalStaging.outputs.files)
from(publishToLocalStaging.outputs.files.files)
}

val uploadToMavenCentral by tasks.registering {
val url = uri("https://central.sonatype.com/api/v1/publisher/upload").toURL()
val boundary = "----WebKitFormBoundary7MA4YWxkTrZu0gW"
inputs.file(zipBundle.map { it.archiveFile }.get())
doLast {
val file = zipBundle.get().archiveFile.get().asFile
val mavenCentralUsername =
findProperty("mavenCentralUsername") as String? ?: System.getenv("MAVEN_CENTRAL_USERNAME")
val mavenCentralPassword =
findProperty("mavenCentralPassword") as String? ?: System.getenv("MAVEN_CENTRAL_PASSWORD")
val token = "$mavenCentralUsername:$mavenCentralPassword\n".toBase64()

val connection = (url.openConnection() as HttpURLConnection).apply {
requestMethod = "POST"
doOutput = true
setRequestProperty("Authorization", "Bearer $token")
setRequestProperty("Content-Type", "multipart/form-data; boundary=$boundary")
}

val outputStream = connection.outputStream
outputStream.bufferedWriter().use { writer ->
writer.append("--$boundary\r\n")
writer.append("Content-Disposition: form-data; name=\"bundle\"; filename=\"${file.name}\"\r\n")
writer.append("Content-Type: application/octet-stream\r\n\r\n")
writer.flush()

file.inputStream().use { it.copyTo(outputStream) }

writer.append("\r\n--$boundary--\r\n")
writer.flush()
}

val responseCode = connection.responseCode
println("Response Code: $responseCode")
println("Response Message: ${connection.inputStream.bufferedReader().readText()}")
}
}

dependencies {
implementation("commons-codec:commons-codec:1.15")
compileOnly(libs.jackson)

implementation(libs.javax.validation)
implementation(libs.bundles.indigo)
implementation(libs.common.text)
compileOnly(libs.jackson)

compileOnly(libs.lombok)
annotationProcessor(libs.lombok)
Expand Down
130 changes: 130 additions & 0 deletions cqp-api/src/test/java/com/quantori/cqp/api/ProcessChiralStructuresTest.java
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package com.quantori.cqp.api;

import static org.junit.Assert.assertTrue;

import com.epam.indigo.Indigo;
import com.quantori.cqp.api.indigo.IndigoMatcher;
import com.quantori.cqp.api.indigo.IndigoProvider;
import com.quantori.cqp.api.model.ExactParams;
import com.quantori.cqp.api.model.SubstructureParams;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;

class ProcessChiralStructuresTest {

private final IndigoProvider indigoProvider = new IndigoProvider(100, 5);

@ParameterizedTest
@ValueSource(strings = {
"C1C=CC=C2C=CC=CC=12",
"N1([C@@]2(SC(=N1)C(=O)C)N(N=C(c1ccc(cc1)Br)CC2)c1ccccc1)c1c(cc(cc1)Cl)Cl",
"""
X-17641
MACCS-II09195910443D 1 0.00000 0.00000 0
MOE2004 3D
38 42 0 0 0 0 999 V2000 \s
9.7920 2.1040 0.0000 C 0 0 0 0 0
4.2870 7.1000 0.0000 C 0 0 0 0 0
8.5870 7.0150 0.0000 C 0 0 0 0 0
7.3550 2.1040 0.0000 N 0 0 0 0 0
7.3550 4.9100 0.0000 C 0 0 0 0 0
8.5660 4.2090 0.0000 C 0 0 0 0 0
9.7920 6.3200 0.0000 C 0 0 0 0 0
8.5660 8.4170 0.0000 O 0 0 0 0 0
8.5660 0.0070 0.0000 N 0 0 0 0 0
8.5660 2.8130 0.0000 C 0 0 2 0 0
7.3550 9.1050 0.0000 C 0 0 0 0 0
12.2010 2.1040 0.0000 O 0 0 0 0 0
0.7160 3.5140 0.0000 C 0 0 0 0 0
6.0370 0.2620 0.0000 S 0 0 0 0 0
4.2020 4.7400 0.0000 F 0 0 0 0 0
2.7850 4.7400 0.0000 C 0 0 0 0 0
11.0040 0.0000 0.0000 C 0 0 0 0 0
11.0040 4.2090 0.0000 O 0 0 0 0 0
5.5900 3.8690 0.0000 O 0 0 0 0 0
5.0160 9.2460 0.0000 C 0 0 0 0 0
2.0830 5.9520 0.0000 C 0 0 0 0 0
5.6970 7.0850 0.0000 O 0 0 0 0 0
7.3550 6.2990 0.0000 C 0 0 0 0 0
9.7920 4.9100 0.0000 C 0 0 0 0 0
3.8690 8.4250 0.0000 C 0 0 0 0 0
0.0140 2.3030 0.0000 Cl 0 0 0 0 0
6.0370 2.5300 0.0000 C 0 0 0 0 0
3.8050 1.4030 0.0000 C 0 0 0 0 0
6.1570 8.3960 0.0000 C 0 0 0 0 0
2.0830 3.5290 0.0000 C 0 0 0 0 0
5.2010 1.4030 0.0000 C 0 0 0 0 0
9.7920 0.6870 0.0000 C 0 0 0 0 0
13.4130 2.8060 0.0000 C 0 0 0 0 0
11.0040 2.8060 0.0000 C 0 0 0 0 0
0.0000 4.7400 0.0000 C 0 0 0 0 0
7.3550 0.6870 0.0000 C 0 0 0 0 0
0.7160 5.9590 0.0000 C 0 0 0 0 0
7.3550 10.5010 0.0000 O 0 0 0 0 0
4 36 1 0 0 0
4 27 1 0 0 0
4 10 1 0 0 0
36 9 2 0 0 0
36 14 1 0 0 0
1 10 1 0 0 0
1 32 2 0 0 0
1 34 1 0 0 0
27 31 1 0 0 0
27 19 2 0 0 0
31 14 1 0 0 0
31 28 2 0 0 0
9 32 1 0 0 0
10 6 1 0 0 0
32 17 1 0 0 0
28 30 1 0 0 0
30 13 2 0 0 0
30 16 1 0 0 0
11 29 1 0 0 0
11 8 1 0 0 0
11 38 2 0 0 0
34 18 2 0 0 0
34 12 1 0 0 0
29 22 1 0 0 0
29 20 2 0 0 0
6 24 2 0 0 0
6 5 1 0 0 0
8 3 1 0 0 0
22 2 1 0 0 0
13 26 1 0 0 0
13 35 1 0 0 0
16 15 1 0 0 0
16 21 2 0 0 0
20 25 1 0 0 0
2 25 2 0 0 0
24 7 1 0 0 0
5 23 2 0 0 0
3 23 1 0 0 0
3 7 2 0 0 0
12 33 1 0 0 0
37 21 1 0 0 0
37 35 2 0 0 0
M END
"""
})
void test_exact_match(String structure) {
var indigoObject = new Indigo().loadMolecule(structure);
var exactParams = ExactParams.builder().searchQuery(structure).build();
assertTrue(new IndigoMatcher(indigoProvider).isExactMatch(indigoObject.serialize(), exactParams));
}

@ParameterizedTest
@ValueSource(strings = {
"N1([C@@](C=C(C1=O)Nc1ccc(I)cc1)(C(=O)OCC)C)c1ccc(cc1)I",
"N1([C@@]2(SC(=N1)C(=O)C)N(N=C(c1ccc(cc1)Br)CC2)c1ccccc1)c1c(cc(cc1)Cl)Cl",
"c1(c(c2c([nH]c1=O)ccc(c2)Cl)c1ccccc1)C1=NN(C(Nc2ccccc2)=S)[C@H](C1)c1ccc(cc1)OC",
"c1(c(c2c([nH]c1=O)ccc(c2)Cl)c1ccccc1)C1=NN([C@H](C1)c1cc(c(cc1)OC)OC)C(=O)CCC(=O)O",
"N1(N=C(c2c(c3c(nc2C)ccc(c3)Br)c2ccccc2)C[C@H]1c1ccc(cc1)C)C(=O)CCC(=O)O",
"c12n(c(c3c(n1c(nn2)SCC(c1ccc(cc1)Cl)=O)sc1c3CC[C@H](C1)C(C)(C)C)=O)c1c(C)cccc1",
"c12n([C@H](C(F)(F)F)C[C@H](N2)c2ccc(cc2)Br)ncc1C(Nc1cc(c(c(c1)OC)OC)OC)=O"
})
void test_sub_search(String structure) {
var indigoObject = new Indigo().loadMolecule(structure);
var substructureParams = SubstructureParams.builder().searchQuery(structure).heteroatoms(false).build();
assertTrue(new IndigoMatcher(indigoProvider).isSubstructureMatch(indigoObject.serialize(), substructureParams));
}
}
65 changes: 65 additions & 0 deletions cqp-api/src/test/java/com/quantori/cqp/api/ProcessStructureTest.java
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package com.quantori.cqp.api;

import com.quantori.cqp.api.indigo.IndigoMatcher;
import com.quantori.cqp.api.indigo.IndigoProvider;
import com.quantori.cqp.api.model.SubstructureParams;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;

import java.util.stream.Stream;

class ProcessStructureTest {

private static Stream<Arguments> molecules() {
return Stream.of(
Arguments.of("C1C=CC=C2CCC=12>>C1CCC1",
"[NH2:1][C:2]1=[CH:3][CH:4]=[C:5]([C:8]2=[CH:9][N:10]=[C:11]([C:13]3([CH2:14][CH2:15][CH2:16]3)[O:17]"
+ "[CH2:18][C:19](=[O:20])[O:21]C)[S:12]2)[CH:6]=[CH:7]1.[CH:23]1([CH2:24][C:25]2=[C:26]1[CH:27]="
+ "[CH:28][CH:29]=[CH:30]2)[C:31](=[O:32])O.CN1CCOCC1.O.ON1N=NC2=C1C=CC=C2.Cl.C(C)N=C=NCCCN(C)C>CN(C=O)"
+ "C>[C:25]12=[CH:30][CH:29]=[CH:28][CH:27]=[C:26]1[CH:23]([C:31](=[O:32])[NH:1][C:2]1=[CH:3][CH:4]"
+ "=[C:5]([C:8]3=[CH:9][N:10]=[C:11]([C:13]4([CH2:14][CH2:15][CH2:16]4)[O:17][CH2:18][C:19](=[O:20])"
+ "[OH:21])[S:12]3)[CH:6]=[CH:7]1)[CH2:24]2 |f:3.4,5.6|"),

Arguments.of("C1C=CC=C2CCC=12>>C1CCC1",
"[NH2:1][C:2]1=[CH:3][CH:4]=[C:5]([C:8]2=[CH:9][N:10]=[C:11]([C:13]3([CH2:14][CH2:15][CH2:16]3)[O:17]"
+ "[CH2:18][C:19](=[O:20])[O:21]C)[S:12]2)[CH:6]=[CH:7]1.[CH:23]1([CH2:24][C:25]2=[C:26]1[CH:27]="
+ "[CH:28][CH:29]=[CH:30]2)[C:31](=[O:32])O.CN1CCOCC1.O.ON1N=NC2=C1C=CC=C2.Cl.C(C)N=C=NCCCN(C)C>CN(C=O)"
+ "C>[C:25]12=[CH:30][CH:29]=[CH:28][CH:27]=[C:26]1[CH:23]([C:31](=[O:32])[NH:1][C:2]1=[CH:3][CH:4]="
+ "[C:5]([C:8]3=[CH:9][N:10]=[C:11]([C:13]4([CH2:14][CH2:15][CH2:16]4)[O:17][CH2:18][C:19](=[O:20])"
+ "[OH:21])[S:12]3)[CH:6]=[CH:7]1)[CH2:24]2 |f:3.4,5.6|"),

Arguments.of("C1C=CC=C2CCC=12>>C1CCC1",
"[NH2:1][C:2]1=[CH:3][CH:4]=[C:5]([C:8]2=[CH:9][N:10]=[C:11]([C:13]3([CH2:14][CH2:15][CH2:16]3)[O:17]"
+ "[CH2:18][C:19](=[O:20])[O:21]C)[S:12]2)[CH:6]=[CH:7]1.[CH:23]1([CH2:24][C:25]2=[C:26]1[CH:27]="
+ "[CH:28][CH:29]=[CH:30]2)[C:31](=[O:32])O.CN1CCOCC1.O.ON1N=NC2=C1C=CC=C2.Cl.C(C)N=C=NCCCN(C)C>CN(C=O)"
+ "C>[C:25]12=[CH:30][CH:29]=[CH:28][CH:27]=[C:26]1[CH:23]([C:31](=[O:32])[NH:1][C:2]1=[CH:3][CH:4]="
+ "[C:5]([C:8]3=[CH:9][N:10]=[C:11]([C:13]4([CH2:14][CH2:15][CH2:16]4)[O:17][CH2:18][C:19](=[O:20])"
+ "[OH:21])[S:12]3)[CH:6]=[CH:7]1)[CH2:24]2 |f:3.4,5.6|\n"),

Arguments.of("C1C=CC=[C:3]2[CH2:8][CH2:7][C:2]=12>>[CH2:2]1[CH2:7][CH2:8][CH2:3]1",
"[NH2:1][C:2]1=[CH:3][CH:4]=[C:5]([C:8]2=[CH:9][N:10]=[C:11]([C:13]3([CH2:14][CH2:15][CH2:16]3)[O:17]"
+ "[CH2:18][C:19](=[O:20])[O:21]C)[S:12]2)[CH:6]=[CH:7]1.[CH:23]1([CH2:24][C:25]2=[C:26]1[CH:27]="
+ "[CH:28][CH:29]=[CH:30]2)[C:31](=[O:32])O.CN1CCOCC1.O.ON1N=NC2=C1C=CC=C2.Cl.C(C)N=C=NCCCN(C)C>CN(C=O)"
+ "C>[C:25]12=[CH:30][CH:29]=[CH:28][CH:27]=[C:26]1[CH:23]([C:31](=[O:32])[NH:1][C:2]1=[CH:3][CH:4]="
+ "[C:5]([C:8]3=[CH:9][N:10]=[C:11]([C:13]4([CH2:14][CH2:15][CH2:16]4)[O:17][CH2:18][C:19](=[O:20])"
+ "[OH:21])[S:12]3)[CH:6]=[CH:7]1)[CH2:24]2 |f:3.4,5.6|\n"),

Arguments.of("C1C=CC=[C:3]2[CH2:8][CH2:7][C:2]=12>>[CH2:2]1[CH2:7][CH2:8][CH2:3]1",
"[NH2:1][C:2]1=[CH:3][CH:4]=[C:5]([C:8]2=[CH:9][N:10]=[C:11]([C:13]3([CH2:14][CH2:15][CH2:16]3)[O:17]"
+ "[CH2:18][C:19](=[O:20])[O:21]C)[S:12]2)[CH:6]=[CH:7]1.[CH:23]1([CH2:24][C:25]2=[C:26]1[CH:27]="
+ "[CH:28][CH:29]=[CH:30]2)[C:31](=[O:32])O.CN1CCOCC1.O.ON1N=NC2=C1C=CC=C2.Cl.C(C)N=C=NCCCN(C)C>CN(C=O)"
+ "C>[C:25]12=[CH:30][CH:29]=[CH:28][CH:27]=[C:26]1[CH:23]([C:31](=[O:32])[NH:1][C:2]1=[CH:3][CH:4]="
+ "[C:5]([C:8]3=[CH:9][N:10]=[C:11]([C:13]4([CH2:14][CH2:15][CH2:16]4)[O:17][CH2:18][C:19](=[O:20])"
+ "[OH:21])[S:12]3)[CH:6]=[CH:7]1)[CH2:24]2 |f:3.4,5.6|")
);
}

@ParameterizedTest
@MethodSource("molecules")
void test(String source, String target) {
var substructureParams = SubstructureParams.builder().searchQuery(source).heteroatoms(false).build();
Assertions.assertTrue(new IndigoMatcher(new IndigoProvider(100, 5)).isReactionSubstructureMatch(target, substructureParams));
}
}
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