Merge pull request #1532 from NCEAS/develop

First merge from the develop to main branch for 2.15.1

README.md

@@ -1,6 +1,6 @@
 # Metacat: Data Preservation and Discovery System
 
-Version: 2.15.0 Release
+Version: 2.15.1 Release
 
 Send feedback and bugs to: [email protected]
                            http://github.com/NCEAS/metacat
@@ -67,6 +67,19 @@ for the next release.
 
 ## Release Notes
 
+### Release Notes for 2.15.1
+New features and bugs fixed in this release:
+* Metacat hangs with excessive thread counts
+* Support multiple DOI shoulders
+* Update EML Semantic Annotation indexing to include and expand property URIs
+* MNodeService.getPackage() takes too long for large packages
+* Geohashes, text fields not being indexed for schema.org documents
+* Expand elements covered by EML's attribute index fields beyond just dataTable
+* EML to HTML/PDF is broken in the getPackage() method
+* Have MNCore.getCapabilities() report on auth.allowSubmitters parameter setting
+* GetPackage API doesn't work from R on Windows 
+* Add new indexes for column archvied and object_format in the systemmetadata table
+
 ### Release Notes for 2.15.0
 New features and bugs fixed in this release:
 * Support non-XML metadata objects in Metacat

build.properties

@@ -2,7 +2,7 @@
 
 #Version of this build.  This needs to be a dotted numeric version.  For
 #instance 1.9.1 is okay.  1.9.1_rc1 is not.
-metacat.version=2.15.0
+metacat.version=2.15.1
 
 #This is for packaging purposes.  leave it blank for final production release.
 metacat.releaseCandidate=

build.xml

@@ -32,7 +32,7 @@
 <project name="metacat" default="jar" basedir="."
          xmlns:artifact="antlib:org.apache.maven.artifact.ant">
 
-	<property name="metacatui-tag" value="2.15.1" />
+	<property name="metacatui-tag" value="2.16.0" />
     <property name="eml2-style-tag" value="RELEASE_EML_UTILS_1_1_2" />
 
 	<property environment="env" />
@@ -254,6 +254,7 @@
 	<target name="init" depends="config, build-metacat-common" unless="init.called">
 
 	    <property name="libdir.mvn" value="lib/maven" />
+		<delete dir="${libdir.mvn}"></delete>
 		<mkdir dir="${libdir.mvn}"/>
 
 		<path id="base.classpath">

lib/metacat.properties

@@ -34,7 +34,7 @@ server.internalPort=80
 ############### Application Values ############
 
 ## one of the few places where we use ANT tokens
-application.metacatVersion=2.15.0
+application.metacatVersion=2.15.1
 application.metacatReleaseInfo=-1
 application.readOnlyMode=false
 
@@ -134,6 +134,7 @@ database.upgradeVersion.2.13.0=upgrade-db-to-2.13.0
 database.upgradeVersion.2.14.0=upgrade-db-to-2.14.0
 database.upgradeVersion.2.14.1=upgrade-db-to-2.14.1
 database.upgradeVersion.2.15.0=upgrade-db-to-2.15.0
+database.upgradeVersion.2.15.1=upgrade-db-to-2.15.1
 
 ## for running java-based utilities
 database.upgradeUtility.1.5.0=edu.ucsb.nceas.metacat.admin.upgrade.Upgrade1_5_0
@@ -233,6 +234,8 @@ auth.moderators=
 #auth.moderators=cn=knb-prod,o=NCEAS,dc=ecoinformatics,dc=org
 #auth.moderators=cn=knb-prod,o=NCEAS,dc=ecoinformatics,dc=org:cn=esa-moderators,dc=ecoinformatics,dc=org:cn=parc-moderators,o=PARC,dc=ecoinformatics,dc=org
 auth.defaultUserManagementPage=/style/common/default-user-management.jsp
+# the size of the cache storing group information in the AuthSession class
+auth.groupCacheSize=200
 #####File-based Authentication######
 auth.file.path=/var/metacat/users/password.xml
 auth.file.hashClassName=edu.ucsb.nceas.metacat.authentication.AuthFileBCryptHash
@@ -756,6 +759,9 @@ dataone.quotas.dailyReportingUsagesTime=11:00 PM
 # use ; to separate multiple name spaces.
 dataone.quotas.portal.namespaces=https://purl.dataone.org/portals-1.0.0;https://purl.dataone.org/portals-1.1.0
 
+# Enable Metacat to append ldap groups to a session
+dataone.session.appendLdapGroups.enabled=true
+
 ############# Global Identifiers Assignment Section ######################
 guid.assignGUIDs=false
 guid.ezid.enabled=false
@@ -766,10 +772,10 @@ guid.ezid.baseurl=https://ezid.cdlib.org/
 # optional path for target. do not include hostname here. <IDENTIFIER> is replaced with real value
 guid.ezid.uritemplate.metadata=/metacatui/view/<IDENTIFIER>
 #guid.ezid.uritemplate.data=
+#The first shoulder is the primary one. It is used for minting (generating) and creating (registering) DOIs.
 guid.ezid.doishoulder.1=doi:10.5072/FK2
-#guid.ezid.doishoulder.1=doi:10.5072/FK2/KNB/
-#guid.ezid.doishoulder.3=doi:10.5072/FK2/PISCO/
-#guid.ezid.doishoulder.6=doi:10.5072/FK2/LTER/
+#The second and beyond shoulders are only for creating (registering) DOIs. You need to generate a unique DOI by yourself.
+guid.ezid.doishoulder.2=
 #The factory classes can generate the datacite document. It should be sperator by ';' if it has multiple values.
 guid.ezid.datacite.factories=edu.ucsb.nceas.metacat.doi.datacite.EML2DataCiteFactory
 

lib/style/skins/default/default.xml

@@ -31,6 +31,11 @@
   	<target publicid="-//W3C//HTML//EN">/style/skins/default/default.xsl</target>
   </doctype>
 
+<!-- eml-2.2.0 module -->
+  <doctype publicid="https://eml.ecoinformatics.org/eml-2.2.0">
+    <target publicid="-//W3C//HTML//EN">/style/skins/default/default.xsl</target>
+  </doctype>
+
 <!-- eml-2.1.1 module -->
   <doctype publicid="eml://ecoinformatics.org/eml-2.1.1">
     <target publicid="-//W3C//HTML//EN">/style/skins/default/default.xsl</target>

lib/style/skins/metacatui/eml-2/eml-semantics.xsl

@@ -39,8 +39,9 @@
 
     <xsl:template name="annotation">
         <xsl:param name="context" />
-
         <xsl:element name="div">
+            <!-- The attributes on this element are redundant with the attributes on the direct children but were kept
+            for backwards compatibility with older versions of MetacatUI. -->
             <xsl:attribute name="class">annotation</xsl:attribute>
             <xsl:attribute name="data-html">true</xsl:attribute>
             <xsl:attribute name="title"><xsl:value-of select="normalize-space(./valueURI/@label)" /></xsl:attribute>
@@ -51,15 +52,26 @@
             <xsl:attribute name="data-property-uri"><xsl:value-of select="normalize-space(./propertyURI/text())" /></xsl:attribute>
             <xsl:attribute name="data-value-label"><xsl:value-of select="normalize-space(./valueURI/@label)" /></xsl:attribute>
             <xsl:attribute name="data-value-uri"><xsl:value-of select="normalize-space(./valueURI/text())" /></xsl:attribute>
-            <div class="annotation-property"><xsl:value-of select="normalize-space(./propertyURI/@label)" /></div>
-            <div class="annotation-value"><xsl:value-of select="normalize-space(./valueURI/@label)" /></div>
-            <xsl:element name="div">
-                    <xsl:attribute name="class">annotation-findmore tooltip-this</xsl:attribute>
-                    <xsl:attribute name="data-toggle">tooltip</xsl:attribute>
-                    <xsl:attribute name="data-placement">bottom</xsl:attribute>
-                    <xsl:attribute name="title"><xsl:value-of select="concat('Click to find more datasets with measurements of ', normalize-space(./valueURI/@label), '.')" /></xsl:attribute>
-                    <div><i class="icon-long-arrow-up"></i></div>
-                </xsl:element>
+            <div class="annotation-property">
+                <xsl:attribute name="title"><xsl:value-of select="normalize-space(./propertyURI/@label)" /></xsl:attribute>
+                <xsl:attribute name="data-label"><xsl:value-of select="normalize-space(./propertyURI/@label)" /></xsl:attribute>
+                <xsl:attribute name="data-uri"><xsl:value-of select="normalize-space(./propertyURI/text())" /></xsl:attribute>
+                <xsl:attribute name="data-placement">bottom</xsl:attribute>
+                <xsl:attribute name="data-html">true</xsl:attribute>
+                <xsl:attribute name="data-content"><xsl:value-of select="concat(normalize-space(./propertyURI/@label), ' ', normalize-space(./valueURI/@label)) " /></xsl:attribute>
+                <xsl:value-of select="normalize-space(./propertyURI/@label)" />
+            </div>
+            <div class="annotation-value">
+                <xsl:attribute name="title"><xsl:value-of select="normalize-space(./valueURI/@label)" /></xsl:attribute>
+                <xsl:attribute name="data-label"><xsl:value-of select="normalize-space(./valueURI/@label)" /></xsl:attribute>
+                <xsl:attribute name="data-uri"><xsl:value-of select="normalize-space(./valueURI/text())" /></xsl:attribute>
+                <xsl:attribute name="data-placement">bottom</xsl:attribute>
+                <xsl:attribute name="data-html">true</xsl:attribute>
+                <xsl:attribute name="data-content"><xsl:value-of select="concat(normalize-space(./propertyURI/@label), ' ', normalize-space(./valueURI/@label)) " /></xsl:attribute>
+                <div class="annotation-value-text">
+                    <xsl:value-of select="normalize-space(./valueURI/@label)" />
+                </div>
+            </div>
         </xsl:element>
     </xsl:template>
 

metacat-common/pom.xml

@@ -4,7 +4,7 @@
 	<groupId>edu.ucsb.nceas.metacat.common</groupId>
 	<artifactId>metacat-common</artifactId>
 	<packaging>jar</packaging>
-	<version>2.15.0</version>
+	<version>2.15.1</version>
 	<name>metacat-common</name>
 	<url>http://maven.apache.org</url>
 	<properties>

metacat-index/pom.xml

@@ -4,13 +4,13 @@
 	<groupId>edu.ucsb.nceas.metacat.index</groupId>
 	<artifactId>metacat-index</artifactId>
 	<packaging>war</packaging>
-	<version>2.15.0</version>
+	<version>2.15.1</version>
 	<name>metacat-index</name>
 	<url>http://maven.apache.org</url>
 
 	<properties>
-        <d1_cn_index_processor_version>2.3.13</d1_cn_index_processor_version>
-        <metacat_common_version>2.15.0</metacat_common_version>
+        <d1_cn_index_processor_version>2.3.14</d1_cn_index_processor_version>
+        <metacat_common_version>2.15.1</metacat_common_version>
     </properties>
 
 	<repositories>

metacat-index/src/main/resources/application-context-eml-annotation.xml

@@ -17,7 +17,7 @@
 			<list>
 				<bean class="org.dataone.cn.indexer.parser.SolrField">
 					<constructor-arg name="name" value="sem_annotation" />
-					<constructor-arg name="xpath" value="//annotation/valueURI/text()" />
+					<constructor-arg name="xpath" value="//annotation/propertyURI/text() | //annotation/valueURI/text()" />
 					<constructor-arg name="multivalue" value="true" />
 				</bean>
 			</list>

metacat-index/src/main/resources/application-context-eml-base.xml

@@ -424,31 +424,31 @@
 	<bean id="eml.attributeName" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeName" />
 		<constructor-arg name="xpath"
-			value='//dataTable/attributeList/attribute/attributeName/text()' />
+			value='//attributeList/attribute/attributeName/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="false" />
 	</bean>
 
 	<bean id="eml.attributeLabel" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeLabel" />
 		<constructor-arg name="xpath"
-			value='//dataTable/attributeList/attribute/attributeLabel/text()' />
+			value='//attributeList/attribute/attributeLabel/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="false" />
 	</bean>
 
 	<bean id="eml.attributeDescription" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeDescription" />
 		<constructor-arg name="xpath"
-			value='//dataTable/attributeList/attribute/attributeDefinition/text()' />
+			value='//attributeList/attribute/attributeDefinition/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="false" />
 	</bean>
 
 	<bean id="eml.attributeUnit" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeUnit" />
 		<constructor-arg name="xpath"
-			value='//dataTable//standardUnit/text() | //dataTable//customUnit/text()' />
+			value='//attributeList/attribute//standardUnit/text() | //attributeList/attribute//customUnit/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="false" />
 	</bean>
@@ -461,7 +461,7 @@
 
 	<bean id="eml.attributeTextRoot" class="org.dataone.cn.indexer.parser.utility.RootElement"
 		p:name="attribute"
-		p:xPath='//dataTable/attributeList/attribute'
+		p:xPath='//attributeList/attribute'
 		p:template="[attributeName] [attributeLabel] [attributeDescription] [attributeUnit]">
 		<property name="leafs">
 			<list>
@@ -492,31 +492,31 @@
 	<bean id="eml.attributeName.noDupe" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeName_noDupe" />
 		<constructor-arg name="xpath"
-			value='//dataTable/attributeList/attribute/attributeName/text()' />
+			value='//attributeList/attribute/attributeName/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="true" />
 	</bean>
 
 	<bean id="eml.attributeLabel.noDupe" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeLabel_noDupe" />
 		<constructor-arg name="xpath"
-			value='//dataTable/attributeList/attribute/attributeLabel/text()' />
+			value='//attributeList/attribute/attributeLabel/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="true" />
 	</bean>
 
 	<bean id="eml.attributeDescription.noDupe" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeDescription_noDupe" />
 		<constructor-arg name="xpath"
-			value='//dataTable/attributeList/attribute/attributeDefinition/text()' />
+			value='//attributeList/attribute/attributeDefinition/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="true" />
 	</bean>
 
 	<bean id="eml.attributeUnit.noDupe" class="org.dataone.cn.indexer.parser.SolrField">
 		<constructor-arg name="name" value="attributeUnit_noDupe" />
 		<constructor-arg name="xpath"
-			value='//dataTable//standardUnit/text() | //dataTable//customUnit/text()' />
+			value='//attributeList/attribute//standardUnit/text() | //attributeList/attribute//customUnit/text()' />
 		<property name="multivalue" value="true" />
 		<property name="dedupe" value="true" />
 	</bean>

metacat-index/src/main/resources/application-context-json-ld.xml

@@ -28,6 +28,15 @@
 				<ref bean="schema_org_geoShape_box_west" />
 				<ref bean="schema_org_geoShape_box_north" />
 				<ref bean="schema_org_geoShape_box_east" />
+				<ref bean="schema_org_geohash_1" />
+				<ref bean="schema_org_geohash_2" />
+				<ref bean="schema_org_geohash_3" />
+				<ref bean="schema_org_geohash_4" />
+				<ref bean="schema_org_geohash_5" />
+				<ref bean="schema_org_geohash_6" />
+				<ref bean="schema_org_geohash_7" />
+				<ref bean="schema_org_geohash_8" />
+				<ref bean="schema_org_geohash_9" />
 				<ref bean="schema_org_creator_last_name" />
 				<ref bean="schema_org_prov_hadDerivation" />
 				<ref bean="schema_org_prov_instanceOfClass" />
@@ -42,6 +51,7 @@
 				<ref bean="schema_org_variableMeasured" />
 				<ref bean="schema_org_version" />
 				<ref bean="schema_org_url" />
+				<ref bean="schema_org_fullText" />
 			</list>
 		</property>
 	</bean>