Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362009-03-20T22:46:58ZEcoinformatics Redmine
Redmine Bug #3913 (Resolved): "forget password page" (ldap) on dev doesn't work for nceas organizationhttps://projects.ecoinformatics.org/ecoinfo/issues/39132009-03-20T22:46:58ZJing Taotao@nceas.ucsb.edu
<p>I was trying to figure out the issue that "forget password page" doesn't work for UCNRS. After changing the username/password for UCNRS in ldapweb.cfg file, it still doesn't work -giving an error "User not found in database. Please try again"</p>
<p>So I decided to try a nceas account, the page still doesn't work, gave the same error as the the UCNRS account.</p>
<p>I also monitor the error log of apache, both nceas and UCNRS accounts showed the same error message:<br /> [Fri Mar 20 16:42:29 2009] [error] [client 98.208.91.162] LDAPweb: started with stage resetpass, cfg knb, referer: <a class="external" href="http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb">http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb</a><br />[Fri Mar 20 16:42:29 2009] [error] [client 98.208.91.162] Use of uninitialized value in concatenation (.) or string at /var/www/edu.ucsb.nceas.dev/knb/cgi-bin/ldapweb.cgi line 422., referer: <a class="external" href="http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb">http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb</a><br />[Fri Mar 20 16:42:29 2009] [error] [client 98.208.91.162] Use of uninitialized value in concatenation (.) or string at /var/www/edu.ucsb.nceas.dev/knb/cgi-bin/ldapweb.cgi line 422., referer: <a class="external" href="http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb">http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb</a><br />[Fri Mar 20 16:42:29 2009] [error] [client 98.208.91.162] Use of uninitialized value in concatenation (.) or string at /var/www/edu.ucsb.nceas.dev/knb/cgi-bin/ldapweb.cgi line 439., referer: <a class="external" href="http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb">http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb</a><br />[Fri Mar 20 16:42:29 2009] [error] [client 98.208.91.162] LDAPweb: ldap server: ldap://ldap.ecoinformatics.org:389/, referer: <a class="external" href="http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb">http://dev.nceas.ucsb.edu/knb/cgi-bin/ldapweb.cgi?stage=resetpass&cfg=knb</a></p>
<p>We tested unaffiliated accounts and they worked.</p>
<p>I guess "change password page" will have some problem.</p>
<p>Mike, when you work on this bug, don't user UCNRS account. This account may have more issues.</p> Bug #3908 (Resolved): replication data user permission errorhttps://projects.ecoinformatics.org/ecoinfo/issues/39082009-03-19T16:57:38ZMichael Daigledaigle@nceas.ucsb.edu
<p>From Jing</p>
<p>I observed some error message during the replication from LTER to KNB:<br /> Failed to write doc pisco_recruitment.314.1 into db because User does not have<br />permission to update of access rules for data file pisco_recruitment.120<br />[edu.ucsb.nceas.metacat.ReplicationHandler]<br />Metacat: [ERROR]: error to handle update doc in xml_documents in time<br />replicationUser does not have permission to update of access rules for data<br />file pisco_recruitment.120 [edu.ucsb.nceas.metacat.ReplicationHandler]<br />Metacat: [ERROR]: Error in Eml200SAXHanlder.handleOnlineUrlDataFile is User<br />does not have permission to update of access rules for data file<br />pisco_recruitment.120 [edu.ucsb.nceas.metacat.Eml200SAXHandler]</p>
<p>I think this is an issue ( which may NOT relative to Margaret's one). During<br />the replication, there no user login, so the user is null and it should have<br />all permission to write documents into the db. Obviously, this access control<br />rule was modified.</p> Bug #3907 (Resolved): Zero length documents are getting written to diskhttps://projects.ecoinformatics.org/ecoinfo/issues/39072009-03-19T15:44:34ZMichael Daigledaigle@nceas.ucsb.edu
<p>From jim r:</p>
<p>As promised, below are some DPs that return a blank page when I attempt to view them on the web. Note that in both cases I know there were issues with imported data tables (in Morpho) that failed to save to the network. I have no idea whether this commonality has anything to do with the fact that both sets of DPs now return blank pages.</p>
Case 1:
<ul>
<li>Go to <a class="external" href="http://knb.ecoinformatics.org">http://knb.ecoinformatics.org</a></li>
<li>Search for "budden" </li>
<li>Returns one DP: xhan.4.5</li>
<li>Clicking the link to open it returns a blank page</li>
</ul>
Case 2:
<ul>
<li>Go to <a class="external" href="http://data.nceas.ucsb.edu">http://data.nceas.ucsb.edu</a></li>
<li>Search for "tatoosh intertidal" </li>
<li>Returns three DPs: nceas.953, reeves.56, reeves.54</li>
<li>Clicking to view any of these returns a blank page</li>
</ul>
<p>(Note that there is clearly a separate issue here insofar as we have 3 separate DPs for what I assume is the same data product, but I'll check with Rick about that when he gets back from his trip. I suspect it had to do with him repeatedly trying to import and save a table.)</p>
<p>I'm afraid I haven't tested to see what happens if I try to access these DPs in Morpho, and I don't have Morpho here (on my home machine). But I am certain xhan.4 was opening fine both in Morpho and on the web a couple of weeks ago (though with an invalid reference to the imported table that evidently failed to save).</p>
<p>I'd be happy to help troubleshoot this more in the AM, over IRC.</p> Bug #3906 (Resolved): Can't read files whose names are a pathhttps://projects.ecoinformatics.org/ecoinfo/issues/39062009-03-19T15:41:57ZMichael Daigledaigle@nceas.ucsb.edu
<p>During replication, Metacat is getting a lot of errors that look like:</p>
<p>knb 06:35:44,975: [ERROR]: error to handle update doc in xml_revisions in time replication<error>Error reading document /export/home/tcat/prd/metacat_data/metacat/documents/knb-lter-hfr.120.3 from disk: null</error></p> Bug #3889 (Resolved): KNB and LTER metacats not replicating some 210 test docshttps://projects.ecoinformatics.org/ecoinfo/issues/38892009-03-16T20:38:03ZMargaret O'Brienmob@msi.ucsb.edu
<p>Mike asked me to put this info into a bug.</p>
<p>sbc_eml210_test.6.2 (<a class="external" href="http://knb.ecoinformatics.org/knb/metacat/sbc_eml210_test.6.2/default">http://knb.ecoinformatics.org/knb/metacat/sbc_eml210_test.6.2/default</a><br />This doc was inserted directly to knb with the form at dev/style/skins/loadxml.html It does not appear at LTER.</p>
<p>5 other docs were inserted at LTER via dev/style/skins/loadxml.html but are not present at KNB<br />sbc_eml210_test.1.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.1.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.1.1/lter</a><br />sbc_eml210_test.2.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.2.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.2.1/lter</a><br />sbc_eml210_test.3.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.3.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.3.1/lter</a><br />sbc_eml210_test.4.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.4.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.4.1/lter</a><br />sbc_eml210_test.5.2 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.5.2/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.5.2/lter</a></p>
<p>. <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need more extensive element documentation (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1">#1</a> and <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: attribute editing for EMPTY elements doesn't work (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2">#2</a> are citations, <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: some required elements should be optional (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/3#note-5">#3-5</a> are datasets. sbc_eml210_test.6.2 (at KNB) is identical to sbc_eml210_test.5.2 (at LNO), except for the docid, so there should be 6 documents total in both metacats.</p> Bug #3884 (Resolved): Perl modules missing from 1.9.0 installhttps://projects.ecoinformatics.org/ecoinfo/issues/38842009-03-11T20:21:52ZMichael Daigledaigle@nceas.ucsb.edu
<p>Per Matt</p>
<p>Go to NCEAS skin (<a class="external" href="http://knb.ecoinformatics.org/knb/style/skins/nceas/">http://knb.ecoinformatics.org/knb/style/skins/nceas/</a>)<br /> then search for 'soil' which will list bowdish.251.9 as one result<br /> then click on 'Edit' button, which generates an error from<br />register-dataset.cgi:<br /> (The server encountered an internal error or misconfiguration and<br />was unable to complete your request.) The error_log says:<br /> [Wed Mar 11 00:24:18 2009] [error] [client 206.174.86.39] Premature<br />end of script headers: register-dataset.cgi, referer:<br /><a class="external" href="http://knb.ecoinformatics.org/knb/metacat">http://knb.ecoinformatics.org/knb/metacat</a><br />[Wed Mar 11 00:26:20 2009] [error] [client 206.174.86.39] Can't locate<br />Config/Properties.pm in @INC<br /> which I interpret to mean that register-dataset.cgi is missing at<br />least Config::Properties</p> Bug #3883 (Resolved): OBFS skins still using ant tokenshttps://projects.ecoinformatics.org/ecoinfo/issues/38832009-03-11T20:19:31ZMichael Daigledaigle@nceas.ucsb.edu
<p>After the 1.9.0 Metacat release, Matt wrote:</p>
<p>Go to <a class="external" href="http://knb.ecoinformatics.org/knb/style/skins/obfs/">http://knb.ecoinformatics.org/knb/style/skins/obfs/</a><br /> Search for 'soil', results include obfs.46.4 (first record)<br /> Click on record to display eml, but no styles display<br /> Looks like there's some errant ant tokens in the CSS and JS paths<br />for the OBFS skin:<br /> "<code>style-skins-path</code>/obfs/obfs.css" <br /> "<code>style-skins-path</code>/obfs/obfs.js" <br /> "<code>style-common-path</code>/branding.js" <br /> This problem does not occur for the knb, nceas, sanparks, esa, and nrs skins</p> Bug #3882 (Resolved): KNB Web links don't work correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/38822009-03-11T20:17:49ZMichael Daigledaigle@nceas.ucsb.edu
<p>There are several issues with links and hardcoded paths in knbweb. These have been reproduced in a dev environment.</p>
<p>Per Matt:</p>
<p>4) Go to main KNB site (<a class="external" href="http://knb.ecoinformatics.org">http://knb.ecoinformatics.org</a>), click on<br />register online link<br /> 4a) Login form shows up but is missing styles (looks like same css<br />problem as (1) above)<br /> 4b) Filling in my username and password results in a 404 error:<br /> "The requested URL /register-dataset.cgi was not found on this server." <br /> This is a bit confusing as it should get the same error as the<br />NCEAS skin in (2) above, so is it a different install of<br />register-dataset.cgi? Or is this a misconfigured login form that's<br />pointing to a non-existent script location? Probably the latter.</p> Bug #3881 (Resolved): Replication not working between KNB and LTER metacatshttps://projects.ecoinformatics.org/ecoinfo/issues/38812009-03-11T20:13:43ZMichael Daigledaigle@nceas.ucsb.edu
<p>After the 1.9.0 upgrade on knb and lter, docs are not replicating from knb to lter. Jing is working with Duane C to resolve this issue.</p> Bug #3853 (Resolved): Make sure the sbclter and pisco skins work with token replacementhttps://projects.ecoinformatics.org/ecoinfo/issues/38532009-03-02T17:51:03ZMichael Daigledaigle@nceas.ucsb.edu
<p>Work with Margaret to knock out the remaining display issues on the sbclter skin.</p> Bug #3849 (Resolved): Some perl make files are not included in metacat war installhttps://projects.ecoinformatics.org/ecoinfo/issues/38492009-02-26T23:15:20ZMichael Daigledaigle@nceas.ucsb.edu
<p>The old perl "make install" would create a file named /usr/local/share/perl/5.8.8/auto/Metacat/autosplit.ix ...</p>
<p>This file is not included in the packaged version of metacat. There may be others. Not having autosplit.ix keeps register-dataset.cgi from running.</p> Bug #3848 (Resolved): Update metacat to use new EML tagshttps://projects.ecoinformatics.org/ecoinfo/issues/38482009-02-26T22:53:12ZMichael Daigledaigle@nceas.ucsb.edu
<p>The separate tags for EML schema and styles work a little differently than before. Only the affected directories are being tagged whereas before, the entire repository was tagged with each tag.</p>
<p>We need to change the tags in build.xml and make sure they work.</p> Bug #3826 (Resolved): Remove jdbc properties from build.properties if not neededhttps://projects.ecoinformatics.org/ecoinfo/issues/38262009-02-18T00:32:25ZMichael Daigledaigle@nceas.ucsb.edu
<p>Per Duane Costa:</p>
<p>In build.properties:</p>
<p>The 'database' property and all the 'jdbc' properties<br /> are still in the build.properties file but they are all<br /> commented-out. Is there a reason they still need to be<br /> present in the build.properties file? It might be less<br /> confusing to Metacat administrators if these properties<br /> could be removed from the file prior to releasing the<br /> distribution.</p> Bug #3825 (Resolved): indexPaths should be more readable in build.propertieshttps://projects.ecoinformatics.org/ecoinfo/issues/38252009-02-18T00:29:57ZMichael Daigledaigle@nceas.ucsb.edu
<p>Per Duane Costa:</p>
<p>In build.properties:</p>
<p>'indexPaths' is an important property, but its value is<br /> very difficult to read and edit.</p>
<pre><code>(i) It would be helpful if the 'indexPaths' entries were alphabetized so<br /> that some kind of ordering is imposed. Right now it is<br /> a huge unordered list, so hunting down individual entries<br /> is like finding a needle in the haystack.</code></pre>
<pre><code>(ii) Is there some way to break up a property value over<br /> several lines? If so, it would be good to list the<br /> 'indexPaths' entries one per line, instead of all<br /> on a single line several hundred characters long.<br /> This would make it easy to 'diff' a modified 'indexPaths'<br /> value with its original value.</code></pre> Bug #3824 (Resolved): Normalize the app deploy dir in build.propertieshttps://projects.ecoinformatics.org/ecoinfo/issues/38242009-02-18T00:27:53ZMichael Daigledaigle@nceas.ucsb.edu
<p>Per Duane Costa:</p>
<p>in build.properties file:</p>
<p>app.deploy.dir=/usr/local/devtools/jakarta-tomcat/webapps</p>
<pre><code>It would be nice if this could be changed to:</code></pre>
<pre><code>app.deploy.dir=${build.tomcat.dir}/webapps</code></pre>
<pre><code>This would mean that many installations would be able to use<br /> the default value, hence, one less property that needs to be edited<br /> for many Metacat administrators.</code></pre>