Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-22T17:50:42ZEcoinformatics Redmine
Redmine Metacat - Bug #4818 (Resolved): ESA does not send an email to moderators when new document is add...https://projects.ecoinformatics.org/ecoinfo/issues/48182010-02-22T17:50:42ZMichael Daigledaigle@nceas.ucsb.edu
<p>The register-dataset.cgi does not send an email when a new document is created via the ESA skin. It used to, and still should.</p> Metacat - Bug #4716 (Resolved): Metacat should run against Tomcat 6https://projects.ecoinformatics.org/ecoinfo/issues/47162010-02-01T17:46:49ZMichael Daigledaigle@nceas.ucsb.edu
<p>Matt sent:</p>
<p>Here are the two main issues I encountered in getting Metacat to run under tomcat6.</p>
<p>1) servlet-api.jar moved locations, so I needed to change build.xml. It would have been better to change it so that it could find the file in either the tomcat5 location or the tomcat6 location, but I just changed the path in place to allow compilation to continue.</p>
<p>hail:~/development/metacat jones$ svn diff build.xml <br />Index: build.xml
===================================================================<br />--- build.xml (revision 5204)<br />+++ build.xml (working copy)<br /><code>@ -48,7 +48,7 </code>@</p>
<pre><code>&lt;target name="config"&gt;<br /> &lt;property name="jsdk" <br />- value="${build.tomcat.dir}/common/lib/servlet-api.jar" /><br />+ value="${build.tomcat.dir}/lib/servlet-api.jar" /><br /> &lt;!-- usr for client testing, generally you don't need change--&gt;<br /> &lt;property name="mcuser" <br /> value="uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org" /></code></pre>
<p>2) Metacat was not allowed permission to log under tomcat6, so I had to add a new policy file to enable it:</p>
<p>grant codeBase "file:${catalina.base}/webapps/knb/-" {<br /> permission java.security.AllPermission;<br />};</p>
<p>I added that as a file (/etc/tomcat6/policy.d/51metacat.policy) where tomcat would load it. I probably should have granted a more limited set of permissions, but there were a bunch of errors related to logging so I decided to just open up the metacat code.</p>
<p>Other than that things seemed to work. I haven't run the unit tests on it in this configuration.</p> Metacat - Bug #4708 (Resolved): Handle writing a text node > 4000 characters to the db.https://projects.ecoinformatics.org/ecoinfo/issues/47082010-01-29T00:58:25ZMichael Daigledaigle@nceas.ucsb.edu
<p>Right now, the postgres db can only handle a text node of 4000 characters. Currently we break calls to DBSAXNode.writeChildNodeToDB into 4000 char data chunks in several places in the code. However, there are some places where the data is not checked or chunked.</p>
<p>We need to move the chunking into the writeChildNodeToDB method, so it is taken care of centrally.</p> Metacat - Bug #4707 (Resolved): Update release 1.9.2 release noteshttps://projects.ecoinformatics.org/ecoinfo/issues/47072010-01-28T21:48:18ZMichael Daigledaigle@nceas.ucsb.edu
<p>The final change to Metacat prior to the last release candidate should be to update the release notes.</p> Metacat - Bug #4698 (Resolved): ESA skin links are hard coded to data.esa.orghttps://projects.ecoinformatics.org/ecoinfo/issues/46982010-01-27T17:45:56ZMichael Daigledaigle@nceas.ucsb.edu
<p>The "ESA Registry" and "Search for Data" links in the ESA header are hard coded to go to data.esa.org. This causes issues on non-production systems when testing because you can inadvertently wind up on production.</p>
<p>The skin property values should be used for the home url.</p> Metacat - Bug #4680 (Resolved): Geoserver StringIndexOutOfBoundsExceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/46802010-01-20T18:46:35ZMichael Daigledaigle@nceas.ucsb.edu
<p>Geoserver is throwing many StringIndexOutOfBoundsExceptions. There is a geoserver bug listed against version 2.4.4 that seems to address this. Note that we are running version 1.4.0. We should probably update geoserver.</p>
<p>The bug info that I found is:</p>
<p>International strings in DbfFileWriter cause StringIndexOutOfBoundsException<br />----------------------------------------------------------------------------</p>
<pre><code>Key: GEOT-1926<br /> URL: <a class="external" href="http://jira.codehaus.org/browse/GEOT-1926">http://jira.codehaus.org/browse/GEOT-1926</a><br /> Project: GeoTools<br /> Issue Type: Bug<br /> Components: data shapefile<br /> Affects Versions: 2.4.4<br /> Reporter: Alexey Noskov<br /> Assignee: Jesse Eichar<br /> Attachments: DbaseInternationalTest.java</code></pre>
<p>When storing some international string using DbfFileWriter, exception <br />StringIndexOutOfBoundsException may occur if two conditions are met:<br />1) String's length less then field size<br />2) String's size in bytes more, then field size</p>
<p>Problem in DbaseFileWriter, method getFieldString(int size, String s)</p>
<p>Loop <br />for( int index=size-1; currentBytes>size; index--)<br />need change to<br />for( int index=buffer.length()-1; currentBytes>size; index--)</p>
<p>Because, when storing string in buffer through buffer.replace( 0, size, s ), <br />it's size are truncated to length of s, and there are possible no symbol at <br />index size-1</p> Metacat - Bug #4644 (Resolved): Convert build to pull eml from svn instead of cvshttps://projects.ecoinformatics.org/ecoinfo/issues/46442010-01-04T18:11:06ZMichael Daigledaigle@nceas.ucsb.edu
<p>updated build.xml to get eml from svn</p> Metacat - Bug #4616 (Resolved): Timed Replication takes many hours and drives the load up on KNBhttps://projects.ecoinformatics.org/ecoinfo/issues/46162009-12-09T16:46:08ZMichael Daigledaigle@nceas.ucsb.edu
<p>Timed replication can more than 12 hours lter and almost that long for PISCO.</p>
<p>During that time, the load on the machine can surpass 10 and java can use over 200% cpu.</p>
<p>lter has over 80K records and pisco over 60K. Only a handful of those actually need to be replicated. We need to see why it's taking so long and using so many resources.</p> Metacat - Bug #4602 (New): Enable TLS for all LDAP functionshttps://projects.ecoinformatics.org/ecoinfo/issues/46022009-12-04T16:12:25ZMichael Daigledaigle@nceas.ucsb.edu
<p>Currently TLS is only enabled for authentication in LDAP. Secure systems like the PARC LDAP need TLS for all appropriate functions.</p> Metacat - Bug #4594 (Resolved): Cannot insert replication server via guihttps://projects.ecoinformatics.org/ecoinfo/issues/45942009-12-02T22:27:45ZMichael Daigledaigle@nceas.ucsb.edu
<p>When attempting to add a replication record via the gui at</p>
<pre><code>&lt;metacat_context_url&gt;/style/skins/dev/replControl.html</code></pre>
<p>metacat throws an error:</p>
<pre><code>duplicate key value violates unique constraint "xml_replication_pk"</code></pre> Metacat - Bug #4588 (Resolved): Install parc metacathttps://projects.ecoinformatics.org/ecoinfo/issues/45882009-12-01T00:23:08ZMichael Daigledaigle@nceas.ucsb.edu
<p>installed PARC metacat on data.palmyraresearch.org. Here are the steps I took:</p>
<p>mkdir /var/parc<br /> chown webuser:webuser /var/parc<br />sudo su - postgres<br />createdb parc<br />psql parc<br />CREATE USER parc WITH UNENCRYPTED PASSWORD '<password>';<br /> (note <password> is same as esa)</p>
<p>cp /etc/http/conf/http.conf to http.conf.20091130<br />vi /etc/http/conf/http.conf and added following section (note different IP than esa):<br /> <VirtualHost 128.111.242.17:80><br /> DocumentRoot /var/www/org.palmyraresearch.data/catalog/style/skins/parc<br /> ServerName data.palmyraresearch.org<br /> ErrorLog /var/log/httpd/error_log<br /> CustomLog /var/log/httpd/access_log common</p>
<pre><code>ScriptAlias /catalog<br />/cgi-bin/ "/var/www/org.palmyraresearch.data/catalog/cgi-bin/" <br /> &lt;Directory "/var/www/org.palmyraresearch.data/catalog/cgi-bin/"&gt;<br /> AllowOverride None<br /> Options ExecCGI<br /> Order allow,deny<br /> Allow from all<br /> &lt;/Directory&gt;</code></pre>
<pre><code>&lt;Directory "/var/www/org.palmyraresearch.data/catalog/style/skins/parc"&gt;<br /> AllowOverride none<br /> Options Indexes FollowSymLinks<br /> IndexOptions FancyIndexing<br /> &lt;/Directory&gt;</code></pre>
<pre><code>&lt;Location "/var/www/org.palmyraresearch.data/catalog/style/skins/parc/parc.cfg"&gt;<br /> AllowOverride None<br /> Order allow,deny<br /> Deny from all<br /> &lt;/Location&gt;</code></pre>
<pre><code>JkMount /catalog ajp13<br /> JkMount /catalog/* ajp13<br /> JkMount /catalog/metacat ajp13<br /> JkUnMount /catalog/cgi-bin/* ajp13<br /> JkMount /*.jsp ajp13<br /> JkMount /authority ajp13<br /> JkMount /authority/* ajp13<br /> &lt;/VirtualHost&gt;</code></pre>
<p>mkdir /var/www/org.palmyraresearch.data<br /> chown webuser:webuser /var/www/org.palmyraresearch.data</p>
<p>scp knb.war from build machine to data.palmyraresearch.org:/tmp<br /> mv /tmp/knb.war /var/www/org.palmyraresearch.org/catalog.war<br /> chown webuser:webuser /var/www/org.palmyraresearch.data/catalog.war</p>
<p>Edit /usr/local/devtools/jakarta-tomcat/conf/server.conf and added following lines:<br /> <Host name="data.palmyraresearch.org" debug="0" appBase="/var/www/org.palmyraresearch.data" <br /> unpackWARs="true" autoDeploy="true" <br /> xmlValidation="false" xmlNamespaceAware="false"><br /> <Logger className="org.apache.catalina.logger.FileLogger" <br /> directory="/var/log/tomcat" prefix="data_parc_log." suffix=".log" <br /> timestamp="true"/><br /> </Host></p>
<p>/etc/init.d/http stop<br />/etc/init.d/tomcat stop<br />/etc/init.d/tomcat start<br />/etc/init.d/http start</p>
<p>chmod +x /var/www/org.palmyraresearch.data/catalog/cgi-bin/*</p>
<p>go to data.palmayraresearch.org/catalog and step through config utility<br /> -- added appropriate administrators<br /> -- set /var/parc as the root dir for all data, temp etc directories<br /> -- configured db credentials<br /> -- made parc skin default.</p> Metacat - Bug #4558 (Resolved): Create validate and isAuthorized unit testshttps://projects.ecoinformatics.org/ecoinfo/issues/45582009-11-18T21:17:54ZMichael Daigledaigle@nceas.ucsb.edu
<p>A new isValid method was created on the metacat authentication service to make validate that a session is active. A new authority service was created to make sure the user for a session has permission on a resource. Unit tests need to be created for these.</p> Metacat - Bug #4557 (Resolved): TPC Sanparks page content lenth issuehttps://projects.ecoinformatics.org/ecoinfo/issues/45572009-11-18T20:38:19ZMichael Daigledaigle@nceas.ucsb.edu
<p>If the content of a tpc list page gets to long, it breaks the page. Need to adjust the page length based on the list length.</p> Metacat - Bug #4556 (Resolved): Fix cross platform TPC GUI issueshttps://projects.ecoinformatics.org/ecoinfo/issues/45562009-11-18T20:25:07ZMichael Daigledaigle@nceas.ucsb.edu
<p>The new TPC Sanparks skins break on different OSs. Specifically, they don't work well on Windows in IE.</p> Metacat - Bug #4442 (New): Spatial indexing should not run and block metacathttps://projects.ecoinformatics.org/ecoinfo/issues/44422009-10-07T17:35:46ZMichael Daigledaigle@nceas.ucsb.edu
<p>spatial indexing runs after a fresh install the first time someone accesses metacat servlet. It blocks any calls until it is done. This can take over thirty minutes in production knb.</p>
<p>It should run it the background, and possibly be kicked off by a scheduler.</p>