Unverified Commit cca93e17 authored by M. Haseeb's avatar M. Haseeb Committed by GitHub
Browse files

Merge pull request #32 from enasequence/ENA-3950

ENA-3950
parents d7a9644f 55bdf9cf
...@@ -11,7 +11,7 @@ plugins { ...@@ -11,7 +11,7 @@ plugins {
apply plugin: 'io.spring.dependency-management' apply plugin: 'io.spring.dependency-management'
group = 'uk.ac.ebi.ena.webin-cli' group = 'uk.ac.ebi.ena.webin-cli'
version = '3.1.0' version = '3.2.0'
sourceCompatibility = '1.8' sourceCompatibility = '1.8'
targetCompatibility = '1.8' targetCompatibility = '1.8'
...@@ -75,10 +75,10 @@ task printWebinTestCredentials { ...@@ -75,10 +75,10 @@ task printWebinTestCredentials {
} }
dependencies { dependencies {
implementation( 'uk.ac.ebi.ena.webin-cli:webin-cli-validator:1.0.9' ) implementation( 'uk.ac.ebi.ena.webin-cli:webin-cli-validator:1.0.9.1' )
implementation( 'uk.ac.ebi.ena.sequence:sequencetools:2.0.86' ) implementation( 'uk.ac.ebi.ena.sequence:sequencetools:2.0.86' )
implementation( 'uk.ac.ebi.ena.txmbtools:txmbtools:1.0.3' ) implementation( 'uk.ac.ebi.ena.txmbtools:txmbtools:1.0.3' )
implementation( 'uk.ac.ebi.ena:readtools:1.4.0' ) implementation( 'uk.ac.ebi.ena:readtools:1.6.0' )
implementation( 'org.springframework.boot:spring-boot-starter' ) implementation( 'org.springframework.boot:spring-boot-starter' )
implementation( 'org.springframework.boot:spring-boot-starter-web' ) { implementation( 'org.springframework.boot:spring-boot-starter-web' ) {
exclude group: 'org.springframework.boot', module: 'spring-boot-starter-tomcat' exclude group: 'org.springframework.boot', module: 'spring-boot-starter-tomcat'
......
...@@ -102,7 +102,7 @@ public class ReadsValidationTest { ...@@ -102,7 +102,7 @@ public class ReadsValidationTest {
.isInstanceOf(WebinCliException.class) .isInstanceOf(WebinCliException.class)
.hasMessage(""); .hasMessage("");
new ReportTester(executor).textInFileReport("invalid.fastq.gz", "does not match FASTQ regexp"); new ReportTester(executor).textInFileReport("invalid.fastq.gz", "Sequence header must start with @");
} }
@Test @Test
...@@ -202,6 +202,23 @@ public class ReadsValidationTest { ...@@ -202,6 +202,23 @@ public class ReadsValidationTest {
new ReportTester(executor).textInSubmissionReport("Multiple (1) occurrences of read name"); new ReportTester(executor).textInSubmissionReport("Multiple (1) occurrences of read name");
} }
@Test
public void uracilFastq() {
File manifestFile =
manifestBuilder()
.file(FileType.FASTQ, "uracil-bases.fastq.gz")
.build();
WebinCliExecutor<ReadsManifest, ReadsValidationResponse> executor =
executorBuilder.build(manifestFile, RESOURCE_DIR);
executor.readManifest();
SubmissionFiles submissionFiles = executor.getManifestReader().getManifest().files();
assertThat(submissionFiles.get().size()).isEqualTo(1);
assertThat(submissionFiles.get(FileType.FASTQ).size()).isOne();
executor.validateSubmission();
}
@Test @Test
public void public void
invalidCram() { invalidCram() {
......
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