Merge branch 'master' of https://github.com/genepi/imputationserver i…

…nto release
statgen · Sep 12, 2023 · bf8ec3c · bf8ec3c
2 parents 5bb17b6 + 3769d4c
commit bf8ec3c
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diff --git 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 <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-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
@@ -1,7 +1,7 @@
 id: imputationserver-hla
 name: Genotype Imputation HLA (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-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
@@ -1,7 +1,7 @@
 id: imputationserver-pgs
 name: Genotype Imputation (PGS Calc Integration)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.3
+version: 1.7.4
 website: https://imputationserver.readthedocs.io
 category:
 

diff --git 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 <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.3
+version: 1.7.4
 website: https://imputationserver.readthedocs.io
 category:
 

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 	<groupId>genepi</groupId>
 	<artifactId>imputationserver</artifactId>
 
-	<version>1.7.3</version>
+	<version>1.7.4</version>
 
 	<packaging>jar</packaging>
 
@@ -19,11 +19,11 @@
 
 	<repositories>
 		<repository>
-			<id>jfrog-genepi-maven</id>
-			<name>jfrog-genepi-maven</name>
-			<url>https://genepi.jfrog.io/artifactory/maven/</url>
+			<id>imed-genepi-maven</id>
+			<name>imed-genepi-maven</name>
+			<url>https://genepi.i-med.ac.at/maven</url>
 		</repository>
-
+		
 		<repository>
 			<id>cloudera</id>
 			<url>https://repository.cloudera.com/artifactory/cloudera-repos/</url>

diff --git a/src/main/java/genepi/imputationserver/steps/InputValidation.java b/src/main/java/genepi/imputationserver/steps/InputValidation.java
@@ -4,6 +4,8 @@
 import java.io.IOException;
 import java.util.*;
 
+import org.apache.commons.lang.StringEscapeUtils;
+
 import cloudgene.sdk.internal.WorkflowContext;
 import cloudgene.sdk.internal.WorkflowStep;
 import genepi.hadoop.importer.ImporterFactory;
@@ -122,7 +124,7 @@ 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;
 		}
 
@@ -248,7 +250,7 @@ private boolean checkVcfFiles(WorkflowContext context) {
 
 			} catch (IOException e) {
 
-				context.endTask(e.getMessage() + " (see <a href=\"/start.html#!pages/help\">Help</a>).",
+				context.endTask(StringEscapeUtils.escapeHtml(e.getMessage()) + " (see <a href=\"/start.html#!pages/help\">Help</a>).",
 						WorkflowContext.ERROR);
 				return false;
 

diff --git 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";