Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-05-06T01:32:07ZEcoinformatics Redmine
Redmine 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 #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 #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> Bug #5520 (Resolved): Create replication integration test suitehttps://projects.ecoinformatics.org/ecoinfo/issues/55202011-10-27T01:59:15Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Replication integration tests should include:<br /><del>force replication between two servers -</del> A, B (write, update, delete)<br /><del>timed replication between two servers -</del> A, B<br /><del>hub/non-hub replication -</del> A, B, C (three servers)<br /><del>invalid documents (not sure how they would get in the Metacat system to begin with) -</del> A, B<br /><del>access control transferred from source to target during initial replication -</del> A, B<br /><del>access control updates propagated from source to target -</del> A, B<br /><del>replication failure for insecure target -</del> A, D (fourth server that does not have certificate?)<br />-all of the above for both data and metadata</p>
<p>Additional test ideas are welcome.</p> Bug #5515 (Resolved): change version to 2.0.0 in prep for releasehttps://projects.ecoinformatics.org/ecoinfo/issues/55152011-10-26T20:15:20ZMatt Jonesjones@nceas.ucsb.edu
<p>To prepare for the release, change te version number to 2.0.0 for all documentation, including README, Sphinx docs, etc.</p> Bug #5499 (Resolved): citation format odd for metacat data setshttps://projects.ecoinformatics.org/ecoinfo/issues/54992011-09-28T04:24:00ZMatt Jonesjones@nceas.ucsb.edu
<p>Submitting on behalf of Gail... I agree with her assesment -- what are we rendering citations this way. Somehow this escaped my attention before.</p>
<p>From Gail:</p>
<p>We are wondering why the recommended citation includes the owner’s institution - see for example <a class="external" href="http://knb.ecoinformatics.org/knb/metacat/datastar.11.13/knb">http://knb.ecoinformatics.org/knb/metacat/datastar.11.13/knb</a>, with a recommended data set citation at the top of the metadata that shows as follows:</p>
<p>Rudstam L of Cornell Biological Field Station and Jackson J of Cornell Biological Field Station.Ice Cover data for Oneida and Cazenovia Lakes, New York, 1826-2011. datastar.11.13 (<a class="external" href="http://knb.ecoinformatics.org/knb/metacat/datastar.11.13/knb">http://knb.ecoinformatics.org/knb/metacat/datastar.11.13/knb</a>).</p>
<p>Why not just:<br />Rudstam L and Jackson J. Ice Cover data for Oneida and Cazenovia Lakes, New York, 1826-2011. datastar.11.13 (<a class="external" href="http://knb.ecoinformatics.org/knb/metacat/datastar.11.13/knb">http://knb.ecoinformatics.org/knb/metacat/datastar.11.13/knb</a>).</p>
<p>Thanks for any insight or fixes,<br />Gail</p>
<p>Gail Steinhart<br />Research Data & Environmental Sciences Librarian<br />Albert R. Mann Library<br />Cornell University<br />Ithaca, NY 14853</p> Bug #5353 (Resolved): EcogridWriter doesn't work with the metacat built from trunk.https://projects.ecoinformatics.org/ecoinfo/issues/53532011-03-21T22:20:16ZJing Taotao@nceas.ucsb.edu
<p>When I used EcogridWriter to write metadata and data into dev.nceas' metadata, it worked file. I believe the version of the metadata is 1.9.3</p>
<p>I built my local metacat by revision 6013 from the svn trunk.<br />But when i used EcogridWriter to write metadata and data file into it, it gave me the following error:</p>
<p>EML document type: eml://ecoinformatics.org/eml-2.0.0<br />edu.ucsb.nceas.metacat.McdbDocNotFoundException: 2Could not find document doc.130074542695043<br /> at edu.ucsb.nceas.metacat.IdentifierManager.getDocumentInfo(IdentifierManager.java:246)<br /> at edu.ucsb.nceas.metacat.MetacatHandler.createSystemMetadata(MetacatHandler.java:3477)<br /> at edu.ucsb.nceas.metacat.MetacatHandler.createSystemMetadata(MetacatHandler.java:3618)<br /> at edu.ucsb.nceas.metacat.MetacatHandler.handleInsertOrUpdateAction(MetacatHandler.java:1862)<br /> at edu.ucsb.nceas.metacat.MetaCatServlet.handleGetOrPost(MetaCatServlet.java:885)<br /> at edu.ucsb.nceas.metacat.MetaCatServlet.doPost(MetaCatServlet.java:493)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:637)<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 #5273 (Resolved): docs with inline-data allow invalid xml into metacathttps://projects.ecoinformatics.org/ecoinfo/issues/52732011-01-13T17:37:32ZChad Berkleyberkley@nceas.ucsb.edu
<p>If you insert a document with inline-data, the data is stripped out of the document before it is validated. However, when you do a GET on the document, it is read off of the disk. So if you insert a doc with inline-data that has invalid characters in it (like unescaped ampersands), metacat will not recognize that it is invalid, but when you try to get the document, you will get a parser error if you try to parse it.</p>
<p>We should be validating the document first before stripping inline-data out of it.</p> Bug #5114 (Resolved): ESA registry: Bad link in 'register dataset' instructionshttps://projects.ecoinformatics.org/ecoinfo/issues/51142010-07-29T18:23:31ZJim Regetzregetz@nceas.ucsb.edu
<p>If you click the Register Data menu link without being logged in, it returns a page of registration instructions. Under Step 4 is a hyperlink to "ESA Data Registry Form". Clicking it produces a blank page, I imagine because the application context 'esa' is missing from the URL:<br /><a class="external" href="http://data.esa.org/cgi-bin/register-dataset.cgi?cfg=esa">http://data.esa.org/cgi-bin/register-dataset.cgi?cfg=esa</a></p>
<p>It's not a particularly useful or important link in any case (just returning the same page), but it at least shouldn't return a blank page.</p> Bug #5011 (Resolved): Add support for DataONE service APIhttps://projects.ecoinformatics.org/ecoinfo/issues/50112010-05-14T17:25:51ZMatt Jonesjones@nceas.ucsb.edu
<p>Metacat will be used within DataONE as both a Member Node and as a component of the Coordinating Node infrastructure. We need to add support for the proper REST APIs for DataONE, which are described here:</p>
<p><a class="external" href="http://mule1.dataone.org/ArchitectureDocs/index.html">http://mule1.dataone.org/ArchitectureDocs/index.html</a></p>
<p>Initial support should include the following methods:<br />MN.get()<br />MN.getSystemMetadata()<br />MN.listObjects()</p>
<p>CN.create()<br />CN.update()<br />CN.get()<br />CN.getSystemMetadata()<br />CN.resolve()</p>
<p>These tasks are a DataONE project, and so details are being tracked in the DataONE ticket system (<a class="external" href="http://trac.dataone.org">http://trac.dataone.org</a>). This is a tracking bug for the feature overall.</p> Bug #3815 (Resolved): Ampersand character not correctly encodedhttps://projects.ecoinformatics.org/ecoinfo/issues/38152009-02-10T01:35:18ZShaun Walbridgewalbridge@nceas.ucsb.edu
<p>Ampersands are encoded as "&" within register-dataset.cgi in normalize(), but documents uploaded have a "%26amp;" entry instead. "%26" is the urlencoded version of "&" and 0x0026 is the Unicode code-point.</p>
<p>An example document exhibiting the behavior:<br /><a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=nceas&docid=nceas.912.8">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=nceas&docid=nceas.912.8</a></p>
<p>The organization is set to "U.S. Fish %26amp; Wildlife Service".</p> Bug #2495 (Resolved): Charset bug: Internationalizationhttps://projects.ecoinformatics.org/ecoinfo/issues/24952006-07-19T22:31:05ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Metacat should be modified in such a way that it can handle characters from other languages also.</p>
<p>Mr. Chau Chin Lin from Taiwan has reported that they have made the following set of changes in Metacat. This enables Metacat to work with 6 languages. The changes are as following:</p>
<p>1.MetacatServlet.java (metacat-src-1.4.0\metacat-1.4.0\src\edu\<br />ucsb\nceas\metacat\ MetacatServlet.java)</p>
<p>HandleGetOrPost()<br />if (action.equals("query")) {<br />/*line:421*/ /*add this line*/response.setContentType("text/xml;<br />charset=UTF-8");<br />PrintWriter out = response.getWriter();<br />handleQuery(out, params, response, username, groupnames,<br />sess_id);<br />out.close();</p>
<p>handleReadAction(){<br />/*line:1030*/ /*add this line*/response.setContentType("text/xml;<br />charset=UTF-8");<br />ServletOutputStream out = null;<br />ZipOutputStream zout = null;<br />PrintWriter pw = null;<br />boolean zip = false;</p>
<p>2.build.properties<br />line 27:jdbc-connect=jdbc:postgresql://localhost/metacat?charSet=UTF-8</p>
<p>3.jsp files(metacat-src-1.4.0\metacat-1.4.0\lib\style\skins\default)<br /><%@ page contentType="text/html; charset=UTF-8" %></p>
<p>UTF-8 is enforced as the character encoding for all types of communication.</p>
<p>Also worth noting is the way geoserver does things. It has an entry in web.xml which specifies a filter to encoding conversion</p>
<p><filter><br /> <filter-name>Set Character Encoding</filter-name><br /><filter-class>org.vfny.geoserver.filters.SetCharacterEncodingFilter</filter-class><br /> <init-param><br /> <param-name>encoding</param-name><br /> <param-value>UTF-8</param-value><br /> </init-param><br /> </filter></p>
<p>A test document with chinese characters can be found here: <a class="external" href="http://bugs.tfri.gov.tw/tfri/servlet/metacat?action=read&qformat=default&docid=test100.4.9">http://bugs.tfri.gov.tw/tfri/servlet/metacat?action=read&qformat=default&docid=test100.4.9</a></p>
<p>A chat log explaing related issues:</p>
<p>[10:05] <sid> the changes which i made for storing all the possible characters in &xxx; form in metacat will probably break things for Lin<br />[10:06] <sid> i am trying to debug it.. but we will probably need to change a bunch of code later on<br />[10:10] <matt> yep<br />[10:12] <sid> this document: <a class="external" href="http://bugs.tfri.gov.tw/tfri/servlet/metacat?action=read&qformat=xml&docid=test100.4.9">http://bugs.tfri.gov.tw/tfri/servlet/metacat?action=read&qformat=xml&docid=test100.4.9</a><br />[10:13] <sid> comes back as this document: <a class="external" href="http://indus.msi.ucsb.edu/knb/metacat?action=read&qformat=xml&docid=sgtest.100.1">http://indus.msi.ucsb.edu/knb/metacat?action=read&qformat=xml&docid=sgtest.100.1</a><br />[10:14] <matt> if you insert it in 1.6+<br />[10:14] <matt> ?<br />[10:14] <sid> yes<br />[10:14] <matt> with or without their patches?<br />[10:14] <sid> i havnt tried the patches yet<br />[10:15] <matt> i think you need them<br />[10:15] <matt> in order to store the characters in postgres as UTF-8<br />[10:16] <sid> its mainly because of this code<br />[10:16] <sid> str.append("&#");<br />[10:16] <sid> str.append(Integer.toString(ch));<br />[10:16] <sid> str.append(';');<br />[10:16] <sid> so any character that we are not familiar with is converted to &#xxx; format<br />[10:17] <sid> the characters that we are familiar with are the characters in the range of 31 and 128 when converted to int.. newline, carriage return, tab, &, <, ><br />[10:18] <sid> so that is good enough for most of the documents<br />[10:19] <sid> but it screws up when we have a character which is not between integer values 0 and 255 <br />[10:19] <sid> which is the case for all other languages<br />[10:19] <sid> so i can try taking out this code and try setting the encoding to UTF-8 for postgres<br />[10:21] <sid> so any character that we are not familiar with, we try to store it as it is in metacat<br />[10:21] <sid> actually in that case i think we can just take away the normalize function<br />[10:22] <sid> as in maybe we wont need any normalization<br />[10:23] <sid> but this will probably screw up if the document being inserted has an encoding other than UTF-8<br />[10:24] <sid> so we will have to enforce that encoding or maybe have an encoding convertor filter</p>