Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362007-02-09T04:27:21ZEcoinformatics Redmine
Redmine Bug #2764 (Resolved): LDAP client should handle referral failure correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/27642007-02-09T04:27:21ZJing Taotao@nceas.ucsb.edu
<p>Today, a knb website user reported that she could not register an ldap account through the knb web site. The result turned out is that a new referral, which is not up, was added to the ldap server. The failure of referral cause ldapweb.cgi failed. It seems that Morpho couldn't get ldap tree correctly either.</p>
<p>The reason of the failure is the ldap client couldn't handle the situation that referral ldap is down.</p> Bug #2748 (Resolved): MetaCatServlet.handleUploadAction() can cause data file deletion in the dat...https://projects.ecoinformatics.org/ecoinfo/issues/27482007-01-25T19:42:43ZChris Jonescjones@nceas.ucsb.edu
<p>During the upload of data documents to Metacat 1.6.x, data documents that have been previously uploaded can be deleted from Metacat's file storage area when the same file is uploaded on a second attempt. In MetaCatServlet.handleUploadAction(), DocumentImpl.registerDocument() is called after the data file has been created in the filesystem. If for some reason registerDocument() throws an exception (for instance if the docid and revision is already taken), then the data file is deleted, regardless of whether or not it happened in a previous transaction.</p>
<p>This can be critical since an entire Metcat data store could be deleted by calling action=upload on the existing data docids residing in the catalog. The existence of the data files remains registered in the catalog tables, but the file will be physically gone from the data store.</p> Bug #2747 (Resolved): AuthLdap.getGroups() doesn't follow referrals correctly when building group...https://projects.ecoinformatics.org/ecoinfo/issues/27472007-01-25T19:09:46ZChris Jonescjones@nceas.ucsb.edu
<p>EML allows for both user and group-based access control, but as of Metacat 1.6.x, access control for groups is only partially functional. The problem arises in searching for groups that are defined in LDAP databases that are referrals in the main ecoinformatics LDAP tree.</p>
<p>Given the following two EML access directives:</p>
<p><access order="allowFirst" scope="document" <br /> authSystem="ldap://ldap.ecoinformatics.org:389/dc=ecoinformatics,dc=org"><br /> <allow><br /> <principal><br /> cn=marine,dc=ecoinformatics,dc=org<br /> </principal><br /> <permission>read</permission><br /> </allow><br /></access></p>
<p>and</p>
<p><access order="allowFirst" scope="document" <br /> authSystem="ldap://ldap.ecoinformatics.org:389/dc=ecoinformatics,dc=org"><br /> <allow><br /> <principal><br /> cn=data-managers,o=PISCOGROUPS,dc=ecoinformatics,dc=org<br /> </principal><br /> <permission>read</permission><br /> </allow><br /></access></p>
<p>a search for groups will succeed for the group cn=marine, but will fail for the cn=data-managers group, and all other subsequent groups. This occurs after a NamingException is thrown when searching for group names in LDAP databases that are part of the ecoinformatics ldap tree as referrals.</p> Bug #2738 (Resolved): Announcement for when server will be unavialblehttps://projects.ecoinformatics.org/ecoinfo/issues/27382007-01-19T22:28:50ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>I think we need some kind of policy regarding what do to do when the KNB server needs is going to go offline to fix something. Maybe at least a 10-minute warning would be good. This way people can save where they are at or finish what they are doing. Currently we have a problem with the KNB Data Catalog Map is only fixed by restarting Apache. We need some kind of announcement system when the server is not going to be available.</p>
<p>Yesterday I saw a government site have at the top of the database page, in red, an announcement that their server was going to be down for repairs during a certain period. That is good for letting people know ahead of time. What can we do for when people who currently are online using the server? Is it possible to announce to those people too? A pop up box might be blocked or unavailable.</p> Bug #2716 (Resolved): KNB Data Catalog Map does not display pointshttps://projects.ecoinformatics.org/ecoinfo/issues/27162007-01-08T19:35:34ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>Metacat data bounds is not working working for the KNB Data Catalog Map. <a class="external" href="http://knb.ecoinformatics.org/index_map.jsp">http://knb.ecoinformatics.org/index_map.jsp</a> displays the map with no points representing the datasets. The option box Dataset Bounds text is crossed out.</p>
<p>Here is the errors in the server log that jing saw:<br />org.vfny.geoserver.wms.WmsException: java.util.NoSuchElementException: Could not locate FeatureTypeConfig 'metacat:data_bounds'<br />at org.vfny.geoserver.wms.requests.GetMapKvpReader.findLayer(GetMapKvpReader.java:1215)<br />at org.vfny.geoserver.wms.requests.GetMapKvpReader.parseLayersParam(GetMapKvpReader.java:1190)<br />at org.vfny.geoserver.wms.requests.GetMapKvpReader.parseLayersAndStyles(GetMapKvpReader.java:688)<br />at org.vfny.geoserver.wms.requests.GetMapKvpReader.parseMandatoryParameters(GetMapKvpReader.java:389)<br />at org.vfny.geoserver.wms.requests.GetMapKvpReader.getRequest(GetMapKvpReader.java:226)<br />at org.vfny.geoserver.servlets.AbstractService.doGet(AbstractService.java:318)</p>
<p>jing and some error about the file couldn't find:<br />/var/www/org.ecoinformatics.knb1/knb/data/metacat_shps/data_points.shp</p> Bug #2675 (Resolved): column "infinity" does not existhttps://projects.ecoinformatics.org/ecoinfo/issues/26752006-11-22T17:29:45ZChad Berkleyberkley@nceas.ucsb.edu
<p>When uploading certain xml files to metacat via the ecogrid, I get a message that says:<br /><error><br />ERROR: column "infinity" does not exist<br /></error></p>
<p>I'm not sure why it's looking for this column. You can reproduce it from kepler by trying to upload the Current Time actor to the library. Here is a full error from kepler:</p>
<p>Here's the full error:</p>
<p>[java] got lsid client<br /> [java] checking if lsid urn:lsid:kepler-project.org:actor:2:1 is already registered<br /> [java] EcogridUtils: The time to create instance is =========== 0<br /> [java] is registered? false<br /> [java] Creating transport KAR file at /Users/berkley/.kepler/cache/tmp/tmp.kar<br /> [java] done writing KAR file to /Users/berkley/.kepler/cache/tmp/tmp.kar<br /> [java] uploading kar file with id urn:lsid:kepler-project.org:kar:7:1<br /> [java] session id: 4EB5CA645287A4E729BCD30072EBCABA<br /> [java] EcogridUtils: The time to create instance is =========== 0<br /> [java] uploaded kar file with id urn:lsid:kepler-project.org:kar:7:1<br /> [java] uploading actor metadata with id urn:lsid:kepler-project.org:actor:2:1<br /> [java] session id: 4EB5CA645287A4E729BCD30072EBCABA<br /> [java] EcogridUtils: The time to create instance is =========== 0<br /> [java] repository: name=keplerRepository, repository=localhost:8080, username=uid=kepler,o=unaffiliated,dc=ecoinformatics,dc=org<br /> [java] org.kepler.objectmanager.repository.RepositoryException: java.rmi.RemoteException: <?xml version="1.0"?><br /> [java] <error><br /> [java] ERROR: column "infinity" does not exist<br /> [java] </error></p>
<pre><code>[java] at org.kepler.objectmanager.repository.EcogridRepository.put(EcogridRepository.java:176)<br /> [java] at org.kepler.gui.UploadToRepository.upload(UploadToRepository.java:273)<br /> [java] at org.kepler.gui.UploadToRepository.access$000(UploadToRepository.java:75)<br /> [java] at org.kepler.gui.UploadToRepository$UploadSwingWorker.construct(UploadToRepository.java:449)<br /> [java] at util.SwingWorker$2.run(SwingWorker.java:122)<br /> [java] at java.lang.Thread.run(Thread.java:613)</code></pre> Bug #2670 (Resolved): Test Metacat version with updates does not link to the "create a new accoun...https://projects.ecoinformatics.org/ecoinfo/issues/26702006-11-14T21:48:26ZCallie Bowdishbowdish@nceas.ucsb.edu
<p>This is not a bug for the production version of Metacat(1.6.0). The "Head" version of Metacat does not links to the form page where a user can create a new account. The productions server goes to this location:</p>
<p><a class="external" href="http://knb.ecoinformatics.org/cgi-bin/ldapweb.cgi?cfg=knb">http://knb.ecoinformatics.org/cgi-bin/ldapweb.cgi?cfg=knb</a></p>
<p>The test server does not link to the form. I only get the top of the page without the form. It has the "Register for the Knowledge Network for Biocomplexity (KNB)!" title and informaion but no form.</p>
<p>On the test Metacat server the link from the KNB homepage that says create a new account goes to <a class="external" href="http://ldap.ecoinformatics.org/cgi-bin/ldapweb.cgi">http://ldap.ecoinformatics.org/cgi-bin/ldapweb.cgi</a>. This does not work.</p>
<p>On the production server the link goes to: <a class="external" href="http://knb.ecoinformatics.org/cgi-bin/ldapweb.cgi?cfg=knb">http://knb.ecoinformatics.org/cgi-bin/ldapweb.cgi?cfg=knb</a> . This works.</p> Bug #2648 (Resolved): Update broken LTER link in web templateshttps://projects.ecoinformatics.org/ecoinfo/issues/26482006-11-07T23:17:29ZDuane Costadcosta@lternet.edu
<p>All instances of the following LTER link in metacat's web templates:</p>
<pre><code><a class="external" href="http://sql.lternet.edu/scripts/intranet/sendmemypassword.pl">http://sql.lternet.edu/scripts/intranet/sendmemypassword.pl</a></code></pre>
<p>should be replaced by the following link:</p>
<pre><code><a class="external" href="http://savanna.lternet.edu/sendpassword.php">http://savanna.lternet.edu/sendpassword.php</a></code></pre> Bug #2550 (Resolved): Dateline and polar handling for pointshttps://projects.ecoinformatics.org/ecoinfo/issues/25502006-09-11T22:08:15ZMatthew Perryperry@nceas.ucsb.edu
<p>Unfortunately for cartographers the world is not flat. When a feature crosses the dateline or the polar regions, the cartesian coordinate system and all the assumptions that go with it are invalid. For instance the west bounding coordinate would be greater than the east bounding coordinate for a bounding box that crossed the international date line.</p>
<p>This is taken care of in the polygon code by splitting such polygons into multi-polygons.</p>
<p>We need to update the point centroid generation code to reflect this reality as well.</p> Bug #2549 (Resolved): Limit spatial cache to public documentshttps://projects.ecoinformatics.org/ecoinfo/issues/25492006-09-11T22:02:20ZMatthew Perryperry@nceas.ucsb.edu
<p>Until we implement a feasible wms feature filter ( bug 2548 ) we must only put publically readable documents in the spatial cache.</p> Bug #2469 (Resolved): DocumentImpl.buildIndex() does not index XPaths with attributes correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/24692006-06-22T22:15:32ZChris Jonescjones@nceas.ucsb.edu
<p>A 1.6.x metacat installation that indexes paths from the xml_nodes table into the xml_path_index table sets the xml_path_index.path column correctly, but sets the xml_path_index.nodedata incorrectly for ATTRIBUTE nodes. This results in searches that return an incorrect subset of documents because the xml_path_index table doesn't reflect the true values in xml_nodes.</p>
<p>For example, an EML 2.0.1 document with a packageId attribute:</p>
<p><eml:eml xmlns:eml="eml://ecoinformatics.org/eml-2.0.1" <br /> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" <br /> packageId="ALEXXX_015MTBD003R00_19990906.50.1" <br /> scope="system" system="knb" <br /> xsi:schemaLocation="eml://ecoinformatics.org/eml-2.0.1 eml.xsd"><br /> <dataset scope="document"><br /> <shortName>PISCO moored temperature, ALE</shortName></p>
<pre><code>... etc ...<br /> &lt;/dataset&gt;<br />&lt;/eml:eml&gt;</code></pre>
<p>will contain an indexed record in xml_path_index with the following columns:</p>
<p>docid: ALEXXX_015MTBD003R00_19990906.50 <br />path: /eml/@packageId <br />nodedata: PISCO moored temperature, ALE</p>
<p>rather than:</p>
<p>docid: ALEXXX_015MTBD003R00_19990906.50 <br />path: /eml/@packageId <br />nodedata: ALEXXX_015MTBD003R00_19990906.50.1</p>
<p>It seems that the nodedata for the attribute is set to the node value of the next leaf node, in this case the /eml:eml/dataset/shortName field.</p>
<p>This also occurs for other attributes that are indexed in the document, such as /eml:eml/dataset/coverage/geographicCoverage/@id (which has a value of 'ALE')</p>
<p>The above @id will have an indexed value set to the geographicDescription value found in /eml:eml/dataset/coverage/geographicCoverage/geographicDescription (not 'ALE' as above)</p> Bug #2437 (Resolved): Cleaner install for spatial componentshttps://projects.ecoinformatics.org/ecoinfo/issues/24372006-05-16T16:46:47ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Make geoserver install possible from metacat build file and easier integration into the skins.</p> Bug #2186 (Resolved): Customizable web map clienthttps://projects.ecoinformatics.org/ecoinfo/issues/21862005-09-06T17:05:38ZJohn Harrisharris@nceas.ucsb.edu
<p>Currently, the spatial elements displayed within the Metacat spatial viewer are<br />lacking the standard information needed for geographic presentations. The<br />information below should be available for display within the Metacat spatial viewer:</p>
<p>Title<br />Legend<br />Scale<br />Contour Intervals<br />Source</p>
<p>... and there are probably others.</p> Bug #2178 (Resolved): Evaluate java-based web mapping applinactionshttps://projects.ecoinformatics.org/ecoinfo/issues/21782005-09-06T15:55:15ZJohn Harrisharris@nceas.ucsb.edu
<p>Currently, Metacat works with MapServer <a class="external" href="http://mapserver.gis.umn.edu/">http://mapserver.gis.umn.edu/</a>, an<br />application that is used to display spatial elements stored in Metacat. To ease<br />the incorporation of a map server into Metacat, we should evaluate the map<br />servers that are implemented as java servlets. Requirements for these<br />mapservers are that they can read/write ESRI shapefiles and read raster data.</p> Bug #1819 (Resolved): Access control - deny public/allow user read: user couldn't readhttps://projects.ecoinformatics.org/ecoinfo/issues/18192004-12-08T20:01:44ZVeronique Connollyconnolly@nceas.ucsb.edu
<p>I created three DPs for which I had set the Access Permissions so the public<br />would be denied access and I (uid=connolly,o=NCEAS,dc=ecoinformatics,dc=org)<br />would be allowed to read. When I tried accessing the data from the KNB web site<br />(after I logged in as uid=connolly,o=NCEAS,dc=ecoinformatics,dc=org), I got a<br />message saying "User public does not have permission to read the document".</p>