From fd1a42c4da3fdb84bdbef58ed913537d1296bf68 Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Fri, 1 Sep 2023 10:16:27 +0200 Subject: [PATCH 1/3] Update genepi maven repository (#114) --- pom.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index f3569eb5..53419fe3 100644 --- a/pom.xml +++ b/pom.xml @@ -19,11 +19,11 @@ - jfrog-genepi-maven - jfrog-genepi-maven - https://genepi.jfrog.io/artifactory/maven/ + imed-genepi-maven + imed-genepi-maven + https://genepi.i-med.ac.at/maven - + cloudera https://repository.cloudera.com/artifactory/cloudera-repos/ From df82d7a38d0d26f51d3647e9d9697b26128c6aa2 Mon Sep 17 00:00:00 2001 From: Sebastian Schoenherr Date: Wed, 6 Sep 2023 16:01:57 +0200 Subject: [PATCH 2/3] Add escape to error messages (#117) Co-authored-by: Lukas Forer --- .../java/genepi/imputationserver/steps/InputValidation.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/main/java/genepi/imputationserver/steps/InputValidation.java b/src/main/java/genepi/imputationserver/steps/InputValidation.java index 798e13a6..4c825c9a 100644 --- a/src/main/java/genepi/imputationserver/steps/InputValidation.java +++ b/src/main/java/genepi/imputationserver/steps/InputValidation.java @@ -6,6 +6,8 @@ import java.util.List; import java.util.Vector; +import org.apache.commons.lang.StringEscapeUtils; + import cloudgene.sdk.internal.WorkflowContext; import cloudgene.sdk.internal.WorkflowStep; import genepi.hadoop.importer.ImporterFactory; @@ -118,7 +120,7 @@ private boolean checkVcfFiles(WorkflowContext context) { return false; } } catch (Exception e) { - context.error("Unable to parse reference panel '" + reference + "': " + e.getMessage()); + context.error("Unable to parse reference panel '" + reference + "': " + StringEscapeUtils.escapeHtml(e.getMessage())); return false; } @@ -244,7 +246,7 @@ private boolean checkVcfFiles(WorkflowContext context) { } catch (IOException e) { - context.endTask(e.getMessage() + " (see Help).", + context.endTask(StringEscapeUtils.escapeHtml(e.getMessage()) + " (see Help).", WorkflowContext.ERROR); return false; From 3769d4cc3dd2b309be3bac05892d4386e86442d6 Mon Sep 17 00:00:00 2001 From: seppinho Date: Wed, 6 Sep 2023 16:10:51 +0200 Subject: [PATCH 3/3] Prepare release v1.7.4 --- files/imputationserver-beagle.yaml | 2 +- files/imputationserver-hla.yaml | 2 +- files/imputationserver-pgs.yaml | 2 +- files/minimac4.yaml | 2 +- pom.xml | 2 +- .../imputationserver/steps/imputation/ImputationPipeline.java | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/files/imputationserver-beagle.yaml b/files/imputationserver-beagle.yaml index f369f9fe..fb2c263d 100644 --- a/files/imputationserver-beagle.yaml +++ b/files/imputationserver-beagle.yaml @@ -1,7 +1,7 @@ id: imputationserver-beagle name: Genotype Imputation supporting Beagle (Minimac4) description: This is the new Michigan Imputation Server Pipeline using Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.7.3 +version: 1.7.4 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-hla.yaml b/files/imputationserver-hla.yaml index 31293ed9..8fd7a0a6 100644 --- a/files/imputationserver-hla.yaml +++ b/files/imputationserver-hla.yaml @@ -1,7 +1,7 @@ id: imputationserver-hla name: Genotype Imputation HLA (Minimac4) description: This is the new Michigan Imputation Server Pipeline using Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.7.3 +version: 1.7.4 website: https://imputationserver.readthedocs.io category: diff --git a/files/imputationserver-pgs.yaml b/files/imputationserver-pgs.yaml index e7bb775c..ec8d0615 100644 --- a/files/imputationserver-pgs.yaml +++ b/files/imputationserver-pgs.yaml @@ -1,7 +1,7 @@ id: imputationserver-pgs name: Genotype Imputation (PGS Calc Integration) description: This is the new Michigan Imputation Server Pipeline using Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.7.3 +version: 1.7.4 website: https://imputationserver.readthedocs.io category: diff --git a/files/minimac4.yaml b/files/minimac4.yaml index a7812b6a..fa6d5448 100644 --- a/files/minimac4.yaml +++ b/files/minimac4.yaml @@ -1,7 +1,7 @@ id: imputationserver name: Genotype Imputation (Minimac4) description: This is the new Michigan Imputation Server Pipeline using Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.7.3 +version: 1.7.4 website: https://imputationserver.readthedocs.io category: diff --git a/pom.xml b/pom.xml index 53419fe3..fa7f0908 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ genepi imputationserver - 1.7.3 + 1.7.4 jar diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index 86d44251..428ead2f 100644 --- a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java +++ b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java @@ -24,7 +24,7 @@ public class ImputationPipeline { - public static final String PIPELINE_VERSION = "michigan-imputationserver-1.7.3"; + public static final String PIPELINE_VERSION = "michigan-imputationserver-1.7.4"; public static final String IMPUTATION_VERSION = "minimac4-1.0.2";