Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-06-14T00:37:23ZEcoinformatics Redmine
Redmine Bug #6003 (Closed): The "war" target in the metacat will build the metacat-index.war https://projects.ecoinformatics.org/ecoinfo/issues/60032013-06-14T00:37:23ZJing Taotao@nceas.ucsb.edu
<p>The "war" target in the metacat doesn't build the metacat-index.war in the dist directory. It only builds knb.war and geoserver.war.</p> Bug #5597 (Resolved): eml xsl templates incompletehttps://projects.ecoinformatics.org/ecoinfo/issues/55972012-05-06T01:32:07Zgastil gastilmarygastil@yahoo.com
<p>Some xslt templates for eml transform to html are incomplete in metacat 2.0.0 (on lava).</p>
<p>Attached are two screenshots showing how the link to a protocol document within methods disappears, as compared to Chris Jones and Margaret's stylesheets. The example docId is knb-lter-mcr.10.29</p>
<p>I looked at lava.lternet.edu so if there is a more recent version, just refer me to that and I'll re-test.</p>
<p>Also see knb-lter-mcr.5005.3 for an example where a ulink within an abstract does not transform to an a href link. Also in that example the abstract gets truncated. Also the methodStep paragraphs get truncated.</p>
<p>Also in knb-lter-mcr.5005.3 the enumerated domain display is empty. Note that both these docs look fine using the xslt at MCR, SBC, VCR or even the current LTER skin for metacat 1.9.5 at LNO. (Although that xslt does not handle the ulink.)</p> Bug #5572 (Resolved): Couldn't upload a kar file from kepler to metacathttps://projects.ecoinformatics.org/ecoinfo/issues/55722012-02-02T23:51:58ZJing Taotao@nceas.ucsb.edu
<p>I used "ant clean install" a metacat. Then I went through the web pages to configure the metacat with a fresh db.</p>
<p>When I tried upload a kar file from kepler.2.3, i got this error:<br />[ERROR]: MetacatHandler.handleUploadAction - Upload Error: Hazelcast Instance is not active! [edu.ucsb.nceas.metacat.MetacatHandler</p>
<p>Ben suggested to restart tomcat. So i restarted tomcat and uploaded another kar file. But got this error:<br />knb 20120202-15:42:37: [ERROR]: MetacatHandler.handleUploadAction - Upload Error: null [edu.ucsb.nceas.metacat.MetacatHandler]</p>
<p>Each time i chose to make the kar file public readable.</p> Bug #5569 (Resolved): The sanparks skin doesn't show welcome message when user login again (after...https://projects.ecoinformatics.org/ecoinfo/issues/55692011-12-21T21:41:01ZJing Taotao@nceas.ucsb.edu
<p>When user first time logins, the sanpark skin will show a welcome message, upload data link and search form.</p>
<p>However, if user logouts then logins again, the page only shows a search form, no welcome message and upload data link.</p> Bug #5568 (Resolved): Get an exception during startup metacathttps://projects.ecoinformatics.org/ecoinfo/issues/55682011-12-20T19:52:07ZJing Taotao@nceas.ucsb.edu
<p>I got an exception when i started metacat. However, it seems that metacat still can work.</p>
<p>SEVERE: /127.0.0.1:5701 [DataONE] null<br />java.lang.RuntimeException<br /> at edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap.load(SystemMetadataMap.java:70)<br /> at edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap.loadAll(SystemMetadataMap.java:79)<br /> at com.hazelcast.impl.concurrentmap.MapStoreWrapper.loadAll(MapStoreWrapper.java:148)<br /> at com.hazelcast.impl.FactoryImpl.loadKeys(FactoryImpl.java:586)<br /> at com.hazelcast.impl.FactoryImpl.checkInitialization(FactoryImpl.java:568)<br /> at com.hazelcast.impl.FactoryImpl.getOrCreateProxyByName(FactoryImpl.java:522)<br /> at com.hazelcast.impl.FactoryImpl.getMap(FactoryImpl.java:490)<br /> at com.hazelcast.impl.FactoryImpl$HazelcastInstanceProxy.getMap(FactoryImpl.java:224)<br /> at com.hazelcast.core.Hazelcast.getMap(Hazelcast.java:140)<br /> at edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService.init(HazelcastService.java:195)<br /> at edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService.<init>(HazelcastService.java:121)<br /> at edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService.getInstance(HazelcastService.java:141)<br /> at edu.ucsb.nceas.metacat.MetaCatServlet.initSecondHalf(MetaCatServlet.java:438)<br /> at edu.ucsb.nceas.metacat.MetaCatServlet.init(MetaCatServlet.java:310)<br /> at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173)<br /> at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)<br /> at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4387)<br /> at org.apache.catalina.core.StandardContext.start(StandardContext.java:4700)<br /> at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)<br /> at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)<br /> at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)<br /> at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:905)<br /> at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:740)<br /> at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:500)<br /> at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)<br /> at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)<br /> at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)<br /> at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1061)<br /> at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)<br /> at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)<br /> at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)<br /> at org.apache.catalina.core.StandardService.start(StandardService.java:525)<br /> at org.apache.catalina.core.StandardServer.start(StandardServer.java:701)<br /> at org.apache.catalina.startup.Catalina.start(Catalina.java:585)<br /> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br /> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br /> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br /> at java.lang.reflect.Method.invoke(Method.java:597)<br /> at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)<br /> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)<br />Caused by: java.lang.NullPointerException<br /> at java.math.BigInteger.<init>(BigInteger.java:270)<br /> at java.math.BigInteger.<init>(BigInteger.java:447)<br /> at edu.ucsb.nceas.metacat.IdentifierManager.getSystemMetadata(IdentifierManager.java:276)<br /> at edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap.load(SystemMetadataMap.java:63)<br /> ... 39 more</p> Bug #5567 (Resolved): Click the schedule button on sankparks skin got an blank pagehttps://projects.ecoinformatics.org/ecoinfo/issues/55672011-12-15T18:31:35ZJing Taotao@nceas.ucsb.edu
<p>Click TPC worklfow link on the sanparks skin, user will get a list of workflows. Every workflow has three associated actions. One of them is Schedule. But click the button, it just shows a blank page. It worked, but i don't know why it doesn't work any more.</p> Bug #5566 (Resolved): Click View Run link get 0 result if user doesn't login on the sanparks skinhttps://projects.ecoinformatics.org/ecoinfo/issues/55662011-12-07T22:42:33ZJing Taotao@nceas.ucsb.edu
<p>On the sanparks skin, if you click the TPC workflows link, you will get a list of workflows. There are three actions for each workflow - View Run, Schedule and Download.</p>
<p>When user click View Run link, it shows no run even though user can see some public readable runs.</p>
<p>If user logged in, he will see some runs when he/she clicks the View Run link.</p> Bug #5563 (Resolved): Kepler can't get search result from metacat 2.0.0https://projects.ecoinformatics.org/ecoinfo/issues/55632011-12-06T23:48:59ZJing Taotao@nceas.ucsb.edu
<p>I used kepler 2.3 to do a % query against a metacat which was built from the trunk. It didn't show any result. Actually, it should show lots of result.</p>
<p>I also used Kepler 2.3 to do a % query against the kepler library which is metacat 1.9.5. It worked.</p> Bug #5562 (Resolved): Got an NPE when upgrade db from 1.9.5 to 2.0.0https://projects.ecoinformatics.org/ecoinfo/issues/55622011-12-02T19:23:36ZJing Taotao@nceas.ucsb.edu
<p>knb 20111202-11:20:14: [ERROR]: SkinsAdmin.configureSkins - Could not find properties for skin: semtools [edu.ucsb.nceas.metacat.admin.SkinsAdmin]<br />knb 20111202-11:20:22: [ERROR]: SkinsAdmin.configureSkins - Could not find metadata for skin: semtools [edu.ucsb.nceas.metacat.admin.SkinsAdmin]<br />knb 20111202-11:20:35: [ERROR]: Error updating date time node data: null [edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime]<br />java.lang.NullPointerException<br /> at edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime.upgradeSingleTable(UpgradeNodeDataDatetime.java:129)<br /> at edu.ucsb.nceas.metacat.admin.upgrade.UpgradeNodeDataDatetime.upgrade(UpgradeNodeDataDatetime.java:61)<br /> at edu.ucsb.nceas.metacat.admin.upgrade.Upgrade2_0_0.upgrade(Upgrade2_0_0.java:40)<br /> at edu.ucsb.nceas.metacat.admin.DBAdmin.upgradeDatabase(DBAdmin.java:804)<br /> at edu.ucsb.nceas.metacat.admin.DBAdmin.configureDatabase(DBAdmin.java:208)<br /> at edu.ucsb.nceas.metacat.admin.MetacatAdminServlet.handleGetOrPost(MetacatAdminServlet.java:167)<br /> at edu.ucsb.nceas.metacat.admin.MetacatAdminServlet.doGet(MetacatAdminServlet.java:74)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)<br /> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)<br /> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)<br /> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)<br /> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)<br /> at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)<br /> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)<br /> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)<br /> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)<br /> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)<br /> at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)<br /> at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)<br /> at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:776)<br /> at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:705)<br /> at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:898)<br /> at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)<br /> at java.lang.Thread.run(Thread.java:619)</p> Bug #5561 (Resolved): Got a SQL error when click TPC workflows or TPC link on sanparks skinhttps://projects.ecoinformatics.org/ecoinfo/issues/55612011-12-02T18:31:43ZJing Taotao@nceas.ucsb.edu
<p>Clicked TPC status, I saw:</p>
<p>knb 20111202-10:30:51: [ERROR]: DBQuery.createResultDocument - SQL Error: The column index is out of range: 17, number of columns: 16. [edu.ucsb.nceas.metacat.DBQuery] on tomcat log.</p>
<p>Clicked TPC Workflows, I saw:<br />knb 20111202-10:31:36: [ERROR]: DBQuery.createResultDocument - SQL Error: The column index is out of range: 23, number of columns: 22. [edu.ucsb.nceas.metacat.DBQuery]</p> Bug #5560 (Resolved): Upgrade access control rules in Metacat DBhttps://projects.ecoinformatics.org/ecoinfo/issues/55602011-12-02T17:02:59Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Metacat handles a single access control policy for ALL revisions of an object whereas DataONE allows different access control rules for each revision (revisions are not a closely tied to one another in the DataONE model as they are in the Metacat docid.rev approach).<br />After a lengthy discussion, Matt and I decided the upgrade procedure for Metacat 1.x to 2.x should duplicate access control rules for a document into every revision so that Metacat would have distinct access control policies for every revision -- matching DataONE's model for access control.<br />This is the general upgrade approach:<br />1. create GUID mappings in the 'identifier' table for every scope.docid.rev<br />2. alter xml_access table to include the GUID column.<br />3. insert xml_access rows for each GUID in the identifier table, copying the xml_access row that exists for that docid (no revision).<br />4. clean-up xml_access by removing the rows that have no GUID value (the rows we copied from).<br />5. alter the xml_access table to remove unused columns: accessfileid, ticket and node-based columns.</p>
<p>This means that Metacat 2.0 should only insert and read xml_access records using the GUID. If we are interacting with Metacat using the legacy API, we will first need to look up the GUID from the identifier table. This will ultimately simplify the acces DAO classes.</p>
<p>One question I have is whether the Metacat API should continue to (a) function as it has been where a call to "setaccess" will update access control rules for <em>every</em> revision of a document. Another possible policy would be (b) to only update the the given revision if the revision was provided in the docid parameter. If it was simply scope.docid we could update every revision since we wouldn't know which one to specifically update. Or (c) we could update only the latest revision if no docid were provided. Option (a) would effectively look as though Metacat access control handling had not changed from v1.x to v2.x.</p> Bug #5551 (Resolved): Set public access button on the FGDC document display page doesn't work (on...https://projects.ecoinformatics.org/ecoinfo/issues/55512011-11-23T19:09:10ZJing Taotao@nceas.ucsb.edu
<p>When I tried to grant a public readable access to a nonpublic readable document, i got an error:<br /> User public does not have permission to read the document with the docid kepler_kepler.19.1</p>
<p>When i tried to revoke a public readable access from a public readable document, i got a message "null" on the top of the page.</p>
<p>Both documents still keep the original access rules after click the buttons.</p> Bug #5544 (Resolved): the footer of the output page after clicking TPC status/workflow can't be r...https://projects.ecoinformatics.org/ecoinfo/issues/55442011-11-17T22:40:51ZJing Taotao@nceas.ucsb.edu
<p>The text of the footer of the output page is black and can be read when a user click TPC workflow/status menu.</p> Bug #5543 (Resolved): Can't upload a FGDC metadata file with a data file in SANParks skinhttps://projects.ecoinformatics.org/ecoinfo/issues/55432011-11-16T22:55:18ZJing Taotao@nceas.ucsb.edu
<p>I tried to use the data package upload form to upload a FGDC file, it succeeded. However, if i uploaded a FGDC file with a data file, it failed:</p>
<p>edu.ucsb.nceas.metacat.client.MetacatException: <?xml version="1.0"?><br /><error><br />Error: problem reading multipart data: Corrupt form data: premature ending<br /></error></p>
<pre><code>at edu.ucsb.nceas.metacat.client.MetacatClient.upload(MetacatClient.java:711)<br /> at edu.ucsb.nceas.metacat.clientview.ClientViewHelper.handlePackageUpload(ClientViewHelper.java:453)<br /> at edu.ucsb.nceas.metacat.clientview.ClientViewHelper.handleClientRequest(ClientViewHelper.java:270)<br /> at edu.ucsb.nceas.metacat.clientview.ClientViewHelper.clientRequest(ClientViewHelper.java:180)<br /> at org.apache.jsp.style.skins.sanparks.SaeonUpload_jspx._jspService(SaeonUpload_jspx.java:108)<br /> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)<br /> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:386)<br /> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)<br /> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)<br /> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)<br /> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)<br /> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:646)<br /> at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:551)<br /> at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:488)<br /> at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:968)<br /> at org.apache.jsp.style.skins.sanparks.upload_jsp._jspService(upload_jsp.java:312)<br /> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)<br /> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:386)<br /> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)<br /> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)<br /> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)<br /> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)<br /> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)<br /> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)<br /> at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)<br /> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)<br /> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)<br /> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)<br /> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)<br /> at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)<br /> at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)<br /> at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:776)<br /> at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:705)<br /> at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:898)<br /> at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)<br /> at java.lang.Thread.run(Thread.java:619)</code></pre> Bug #5542 (Resolved): Data Package Upload form in SANParks skin missing the description texthttps://projects.ecoinformatics.org/ecoinfo/issues/55422011-11-16T22:45:25ZJing Taotao@nceas.ucsb.edu
<p>It misses the text like:<br />Enter the Meta Data File (<strong>.xml) <br />Enter Data File 1 (</strong>.shp)<br />Enter Data File 2 (*.dbf)<br />....</p>