Merge pull request #2439 from intermine/dev

Release 5.0.8
intermine · Jun 23, 2022 · cc5b746 · cc5b746
2 parents f6360f9 + d6ef5b5
commit cc5b746
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@ InterMine
 
 Master: [![InterMine CI](https://github.com/intermine/intermine/workflows/InterMine%20CI/badge.svg?branch=master)](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
 Dev: [![InterMine CI](https://github.com/intermine/intermine/workflows/InterMine%20CI/badge.svg?branch=dev)](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
-[![Version](http://img.shields.io/badge/version-5.0.7-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
+[![Version](http://img.shields.io/badge/version-5.0.8-blue.svg?style=flat)](https://github.com/intermine/intermine/releases)
 [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE)
 [![Research software impact](http://depsy.org/api/package/pypi/intermine/badge.svg)](http://depsy.org/package/python/intermine)
 [![Conda](https://anaconda.org/anaconda/conda-build/badges/installer/conda.svg)](https://anaconda.org/bioconda/intermine)
@@ -66,7 +66,7 @@ This product includes software developed by the
 InterMine Development Roadmap
 -----------------------------
 
-For more information about the upcoming releases, please visit the [InterMine Development Roadmap](https://intermine.readthedocs.io/en/latest/intermine/roadmap/#intermine-development-roadmap). For the roadmap, please see [here](https://github.com/intermine/intermine/projects/7).
+For more information about the upcoming releases, please visit the [InterMine Development Roadmap](http://intermine.org/im-docs/docs/intermine/roadmap/). For the roadmap, please see [here](https://github.com/intermine/intermine/projects/7).
 
 Please cite
 ------------------------

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -7,6 +7,10 @@
  * information or http://www.gnu.org/copyleft/lesser.html.
  *
  */
+InterMine 5.0.8 (June 2022)
+
+- Improved user input checks
+
 InterMine 5.0.7 (April 2022)
 
 #2419 - Updated the WS /templates to return dataTypes

diff --git a/bio/build.gradle b/bio/build.gradle
@@ -1,6 +1,6 @@
 subprojects {
     group = 'org.intermine'
-    version = '5.0.7'
+    version = '5.0.8'
 
     apply plugin: "java"
     apply plugin: "maven"

diff --git a/bio/gradle.properties b/bio/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.7
-systemProp.bioVersion=5.0.7
+systemProp.imVersion=5.0.8
+systemProp.bioVersion=5.0.8
 
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!

diff --git a/bio/postprocess-test/build.gradle b/bio/postprocess-test/build.gradle
@@ -17,7 +17,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.7'
+    version = '5.0.8'
 
     apply plugin: 'java'
     apply plugin: 'maven'

diff --git a/bio/postprocess-test/gradle.properties b/bio/postprocess-test/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.7
-systemProp.bioVersion=5.0.7
+systemProp.imVersion=5.0.8
+systemProp.bioVersion=5.0.8
 
 systemProp.flymineVersion=4.2.0
 

diff --git a/bio/postprocess/build.gradle b/bio/postprocess/build.gradle
@@ -16,7 +16,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.7'
+    version = '5.0.8'
 
     apply plugin: 'java'
     apply plugin: 'maven'

diff --git a/bio/postprocess/gradle.properties b/bio/postprocess/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.7
-systemProp.bioVersion=5.0.7
+systemProp.imVersion=5.0.8
+systemProp.bioVersion=5.0.8
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

diff --git a/bio/sources/build.gradle b/bio/sources/build.gradle
@@ -16,7 +16,7 @@ ext {
 
 subprojects {
     group = 'org.intermine'
-    version = '5.0.7'
+    version = '5.0.8'
 
     apply plugin: 'java'
     apply plugin: 'maven'

diff --git a/bio/sources/gradle.properties b/bio/sources/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.7
-systemProp.bioVersion=5.0.7
+systemProp.imVersion=5.0.8
+systemProp.bioVersion=5.0.8
 
 # some unit tests need additional classes that aren't in the core model.
 # we use flymine's model. don't touch!

diff --git a/config/run-ws-tests.sh b/config/run-ws-tests.sh
@@ -17,7 +17,8 @@ if [ "$CLIENT" = "JS" ]; then
     # The error only happens in a fresh environment without node_modules and
     # bower_components installed, so devs don't usually see the error,
     # but Travis always does.
-    npm install acorn
+    # try to no install acorn anymore
+    # npm install acorn
     npm install # installs deps
     grunt test  # runs tests
 

diff --git a/intermine/build.gradle b/intermine/build.gradle
@@ -1,6 +1,6 @@
 subprojects {
     group = 'org.intermine'
-    version '5.0.7'
+    version '5.0.8'
 
     apply plugin: "java"
     apply plugin: "maven"

diff --git a/intermine/gradle.properties b/intermine/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.7
-systemProp.bioVersion=5.0.7
+systemProp.imVersion=5.0.8
+systemProp.bioVersion=5.0.8
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

diff --git a/intermine/webapp/src/main/java/org/intermine/web/logic/Constants.java b/intermine/webapp/src/main/java/org/intermine/web/logic/Constants.java
@@ -227,7 +227,7 @@ private Constants() {
     /**
      * Current version of the InterMine code
      */
-    public static final String INTERMINE_VERSION = "5.0.7";
+    public static final String INTERMINE_VERSION = "5.0.8";
 
     /**
      * Key for a Map from class name to Boolean.TRUE for all classes in the model that do not have

diff --git a/intermine/webapp/src/main/java/org/intermine/web/struts/HtmlHeadController.java b/intermine/webapp/src/main/java/org/intermine/web/struts/HtmlHeadController.java
@@ -15,6 +15,7 @@
 import javax.servlet.http.HttpSession;
 import javax.servlet.http.Cookie;
 
+import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.apache.struts.action.ActionForm;
@@ -138,7 +139,7 @@ public ActionForward execute(ComponentContext context,
                 LOG.warn("Could not correctly set the page title for object ID - " + objectId, e);
             }
         }
-        request.setAttribute("htmlPageTitle", htmlPageTitle);
+        request.setAttribute("htmlPageTitle", StringEscapeUtils.escapeHtml(htmlPageTitle));
 
         // Can we employ user tracking?
         String userTrackingMessage = (String) SessionMethods.getWebProperties(

diff --git a/intermine/webapp/src/main/java/org/intermine/web/struts/KeywordSearchResultsController.java b/intermine/webapp/src/main/java/org/intermine/web/struts/KeywordSearchResultsController.java
@@ -23,6 +23,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.apache.struts.action.ActionForm;
@@ -144,7 +145,7 @@ public ActionForward execute(ComponentContext context,
         // there are needed in the form too so we have to use request (i think...)
         request.setAttribute("searchResults", searchResultsParsed);
         request.setAttribute("searchTerm", searchTerm);
-        request.setAttribute("searchBag", searchBag);
+        request.setAttribute("searchBag", StringEscapeUtils.escapeHtml(searchBag));
         request.setAttribute("searchFacetValues", facetValues);
 
         // used for re-running the search in case of creating a list for ALL results
@@ -230,7 +231,8 @@ private Map<String, String> getFacetValues(HttpServletRequest request,
                         }
                     }
                     if (found) {
-                        facetValues.put(facetField, requestParameter.getValue()[0]);
+                        facetValues.put(facetField,
+                            StringEscapeUtils.escapeHtml(requestParameter.getValue()[0]));
                     }
                 }
             }

diff --git a/plugin/build.gradle b/plugin/build.gradle
@@ -4,7 +4,7 @@ apply plugin: 'maven'
 apply plugin: 'signing'
 
 group 'org.intermine'
-version '5.0.7'
+version '5.0.8'
 
 sourceCompatibility = 1.8
 

diff --git a/plugin/gradle.properties b/plugin/gradle.properties
@@ -1,5 +1,5 @@
-systemProp.imVersion=5.0.7
-systemProp.bioVersion=5.0.7
+systemProp.imVersion=5.0.8
+systemProp.bioVersion=5.0.8
 
 systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
 

diff --git a/testmine/build.gradle b/testmine/build.gradle
@@ -1,5 +1,5 @@
 ext {
-    imVersion = "5.0.7"
+    imVersion = "5.0.8"
     taskGroup = "InterMine"
     minePropertyFileName = "testmodel.properties"
     minePropertyFile = "${System.env.HOME}/.intermine/$minePropertyFileName"