Merge branch 'hotfix-1.29.13'

PavlidisLab · May 30, 2023 · c3ab512 · c3ab512
2 parents fa1abe4 + 43ea748
commit c3ab512
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Showing 8 changed files with 166 additions and 163 deletions.
diff --git a/gemma-cli/pom.xml b/gemma-cli/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.29.12</version>
+ <version>1.29.13</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-cli</artifactId>

diff --git a/gemma-core/pom.xml b/gemma-core/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.29.12</version>
+ <version>1.29.13</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-core</artifactId>

diff --git a/...e/src/main/java/ubic/gemma/persistence/service/expression/experiment/GeeqServiceImpl.java b/...e/src/main/java/ubic/gemma/persistence/service/expression/experiment/GeeqServiceImpl.java
@@ -649,7 +649,8 @@ private int leastReplicates( ExpressionExperiment ee ) {
  List<ExperimentalFactor> keepEfs = new ArrayList<>( GeeqServiceImpl.MAX_EFS_REPLICATE_CHECK );
 
  for ( BioAssay ba : bas ) {
- Collection<FactorValue> fvs = ba.getSampleUsed().getFactorValues();
+ // we need a copy here, otherwise the model will be mutated
+ Collection<FactorValue> fvs = new HashSet<>( ba.getSampleUsed().getFactorValues() );
 
  //only keep up to MAX_EFS_REPLICATE_CHECK categorical factors, ignoring batch factor and DE_EXCLUDE
  Collection<FactorValue> removeFvs = new LinkedList<>();

diff --git a/gemma-core/src/main/resources/ubic/gemma/core/ontology/valueStringToOntologyTermMappings.txt b/gemma-core/src/main/resources/ubic/gemma/core/ontology/valueStringToOntologyTermMappings.txt
diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml
@@ -3,7 +3,7 @@
  <parent>
  <artifactId>gemma</artifactId>
  <groupId>gemma</groupId>
- <version>1.29.12</version>
+ <version>1.29.13</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>gemma-web</artifactId>

diff --git a/gemma-web/src/main/java/ubic/gemma/web/services/rest/security/RestAuthEntryPoint.java b/gemma-web/src/main/java/ubic/gemma/web/services/rest/security/RestAuthEntryPoint.java
@@ -31,6 +31,7 @@
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 
 /**
  * Implementation of {@link AuthenticationEntryPoint} for the RESTful API to handle authentication.
@@ -61,7 +62,10 @@ public void commence( final HttpServletRequest request, final HttpServletRespons
  response.setContentType( MediaType.APPLICATION_JSON );
  // using 'xBasic' instead of 'basic' to prevent default browser login popup
  response.addHeader( "WWW-Authenticate", "xBasic realm=" + realm );
- response.sendError( HttpServletResponse.SC_UNAUTHORIZED, objectMapper.writeValueAsString( errorObject ) );
+ response.setStatus( HttpServletResponse.SC_UNAUTHORIZED );
+ response.setCharacterEncoding( StandardCharsets.UTF_8.name() );
+ objectMapper.writeValue( response.getWriter(), errorObject );
+ response.flushBuffer();
  }
 
  @Override

diff --git a/gemma-web/src/main/java/ubic/gemma/web/util/JsonUtil.java b/gemma-web/src/main/java/ubic/gemma/web/util/JsonUtil.java
@@ -7,7 +7,7 @@
 
 import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
-import java.io.Writer;
+import java.nio.charset.StandardCharsets;
 
 /**
  * Utilities for writing JSON payloads to {@link HttpServletResponse}.
@@ -18,24 +18,22 @@ public static void writeErrorToResponse( AuthenticationException e, HttpServletR
  JSONObject json = new JSONObject();
  json.put( "success", false );
  json.put( "message", ExceptionUtils.getRootCauseMessage( e ) );
- response.setContentType( MediaType.APPLICATION_JSON_VALUE );
- response.sendError( HttpServletResponse.SC_UNAUTHORIZED, json.toString() );
+ response.setStatus( HttpServletResponse.SC_UNAUTHORIZED );
+ writeToResponse( json, response );
  }
 
  public static void writeErrorToResponse( Exception e, HttpServletResponse response ) throws IOException {
  JSONObject json = new JSONObject();
  json.put( "success", false );
  json.put( "message", ExceptionUtils.getRootCauseMessage( e ) );
- response.setContentType( MediaType.APPLICATION_JSON_VALUE );
- response.sendError( HttpServletResponse.SC_INTERNAL_SERVER_ERROR, json.toString() );
+ response.setStatus( HttpServletResponse.SC_INTERNAL_SERVER_ERROR );
+ writeToResponse( json, response );
  }
 
  public static void writeToResponse( JSONObject json, HttpServletResponse response ) throws IOException {
- String jsonText = json.toString();
  response.setContentType( MediaType.APPLICATION_JSON_VALUE );
- response.setContentLength( jsonText.length() );
- try ( Writer out = response.getWriter() ) {
- out.write( jsonText );
- }
+ response.setCharacterEncoding( StandardCharsets.UTF_8.name() );
+ json.write( response.getWriter() );
+ response.flushBuffer();
  }
 }
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
  <name>Gemma</name>
  <groupId>gemma</groupId>
  <artifactId>gemma</artifactId>
- <version>1.29.12</version>
+ <version>1.29.13</version>
  <inceptionYear>2005</inceptionYear>
  <description>The Gemma Project for meta-analysis of genomics data</description>
  <url>https://gemma.msl.ubc.ca</url>