Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-27T05:46:16ZEcoinformatics Redmine
Redmine Bug #4904 (Resolved): NCEAS Projects list is missing from registry form dropdownhttps://projects.ecoinformatics.org/ecoinfo/issues/49042010-03-27T05:46:16ZJim Regetzregetz@nceas.ucsb.edu
<p>On the NCEAS data registry form, the dropdown menu for "NCEAS Project(s)" only has a small number of what appear to be placeholder entries, rather than the complete set of NCEAS projects.</p>
<p><a class="external" href="http://knb.ecoinformatics.org/knb/cgi-bin/register-dataset.cgi?cfg=nceas">http://knb.ecoinformatics.org/knb/cgi-bin/register-dataset.cgi?cfg=nceas</a></p>
<p>I have a vague memory (which could be wrong) of this happening after a previous Metacat upgrade.</p> Bug #4900 (Resolved): LDAP referral connection timeouthttps://projects.ecoinformatics.org/ecoinfo/issues/49002010-03-23T18:09:49Zben leinfelderleinfelder@nceas.ucsb.edu
<p>When trying to authenticate with a SANParks username from Metacat hosts that point to ldap.ecoinformatics.org, the authentication fails (localhost, saeonocean, knb, dev). When authenticating through the sanparks.org ldap with a SANParks username, the authentication is successful.<br />This points to an issue in the referral handling.</p>
<p>Upon further investigation, it appears that the AMNH referral (ldap.biodiversityinformatics.amnh.org:636) is causing the problem:<br />-------------<br />knb 20100323-11:01:11: [WARN]: AuthLdap.ldapAuthenticate - Trying to authenticate: uid=test,o=SANParks,dc=ecoinformatics,dc=org Using server: ldap://ldap.ecoinformatics.org:389/ [edu.ucsb.nceas.metacat.AuthLdap]<br />knb 20100323-11:01:11: [WARN]: Authentication exception: [LDAP: error code 49 - Invalid Credentials] [edu.ucsb.nceas.metacat.AuthLdap]<br />knb 20100323-11:01:11: [WARN]: AuthLdap.getIdentifyingName - Searching for DNs with following filter: (&(uid=test)(o=SANParks)) [edu.ucsb.nceas.metacat.AuthLdap]<br />knb 20100323-11:02:26: [ERROR]: AuthLdap.getIdentifyingName - Naming exception while getting dn: javax.naming.CommunicationException: ldap.biodiversityinformatics.amnh.org:636 [Root exception is java.net.ConnectException: Operation timed out] [edu.ucsb.nceas.metacat.AuthLdap]<br />knb 20100323-11:02:26: [ERROR]: AuthLdap.authenticate - Naming exception while authenticating in AuthLdap.authenticate: javax.naming.NamingException: Naming exception in AuthLdap.getIdentifyingName: javax.naming.CommunicationException: ldap.biodiversityinformatics.amnh.org:636 [Root exception is java.net.ConnectException: Operation timed out] [edu.ucsb.nceas.metacat.AuthLdap]<br />javax.naming.NamingException: Naming exception in AuthLdap.getIdentifyingName: javax.naming.CommunicationException: ldap.biodiversityinformatics.amnh.org:636 [Root exception is java.net.ConnectException: Operation timed out]<br /> at edu.ucsb.nceas.metacat.AuthLdap.getIdentifyingName(AuthLdap.java:411)<br /> at edu.ucsb.nceas.metacat.AuthLdap.authenticate(AuthLdap.java:158)<br /> at edu.ucsb.nceas.metacat.AuthSession.authenticate(AuthSession.java:84)<br /> at edu.ucsb.nceas.metacat.MetacatHandler.handleLoginAction(MetacatHandler.java:345)<br /> at edu.ucsb.nceas.metacat.MetaCatServlet.handleGetOrPost(MetaCatServlet.java:776)<br /> at edu.ucsb.nceas.metacat.MetaCatServlet.doPost(MetaCatServlet.java:489)<br /> at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)<br />......................</p> Bug #4871 (Resolved): Need a new tag for utilities module on Metacat 1.9.2 releasehttps://projects.ecoinformatics.org/ecoinfo/issues/48712010-03-05T01:02:05ZJing Taotao@nceas.ucsb.edu
<p>I just fixed bug 4866. <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4866">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4866</a></p>
<p>This fix involves the change on DateUtil class of utilities module. Currently the fix is the trunk. So we should create a new tag on utitlities and use this tag on our metacat build process.</p> Bug #4866 (Resolved): The date displaying on Workflow Run Schedule is incorrecthttps://projects.ecoinformatics.org/ecoinfo/issues/48662010-03-03T23:33:51ZJing Taotao@nceas.ucsb.edu
<p>I tried to schedule a workflow run on the scheduler interface. The start time is 03/03/2010 15:30:00 and end time is 03/03/2010 17:00:00. After clicking Schedule button, the result shows:</p>
<p>Start Time End Time<br />30/03/10 15:30:00 PST 00/03/10 17:00:00 PST</p>
<p>So the date displaying is incorrect. However, on 03/03/2010 15:30:00 the workflow did a run. So it is just displaying problem.</p> Bug #4850 (Resolved): Get the new TPC scheduler working with the new changes in Kepler from the K...https://projects.ecoinformatics.org/ecoinfo/issues/48502010-02-26T18:36:31ZJing Taotao@nceas.ucsb.edu
<p>On kepler side, the metadata format to describe the workflow kar file and workflow run files was changed. So TPC scheduler should be changed accordingly.</p> Bug #4841 (Resolved): Review page for new data registration omits spatial/temporal infohttps://projects.ecoinformatics.org/ecoinfo/issues/48412010-02-24T23:57:55ZJim Regetzregetz@nceas.ucsb.edu
<p>Both for the ESA and NCEAS data registries, information entered in the temporal coverage and spatial coverage sections does <strong>not</strong> appear on the review page that appears after submitting the initial registration form. This seems like an oversight, as all other fields on the form are presented for review.</p> Bug #4839 (Resolved): Fix URL in "revision notification" email sent to ESA moderatorshttps://projects.ecoinformatics.org/ecoinfo/issues/48392010-02-24T22:33:40ZJim Regetzregetz@nceas.ucsb.edu
<p>The "revise document" notification that gets sent to ESA moderators after requesting a revision contains a URL like this:</p>
<p><a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65">http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65</a></p>
<p>It probably shouldn't specify stage=modify, because the moderator is unlikely to want to modify the document at this point. A simple view action for the document would be more appropriate.</p>
<p>Alternatively, it would probably be sufficient to omit the URL altogether, and instead just indicate the docid and include a link to the ESA registry home page as a convenience.</p> Bug #4838 (Resolved): Permissions error for link contained in Data Set Citation sectionhttps://projects.ecoinformatics.org/ecoinfo/issues/48382010-02-24T22:24:33ZJim Regetzregetz@nceas.ucsb.edu
<p>It's easiest to describe this by documenting the steps to reproduce. This involves ESA, but I haven't checked whether it happens with non-public documents viewed using other registries.</p>
<p>After logging into ESA, click My Submissions (or View Submissions if logged in as a moderator), then click to view any one of the listed documents. Note that these are all documents that are <strong>not</strong> publicly readable, but should be readable by the logged-in user. The Data Set Citation section near the top of the document contains a link that refers to the document itself, e.g.: <a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/metacat/esa.65.3/esa">http://esa-dev.nceas.ucsb.edu/esa/metacat/esa.65.3/esa</a></p>
<p>Clicking on the link produces an error:</p>
<p>--------------------------------<br />This XML file does not appear to have any style information associated with it. The document tree is shown below.</p>
<p><error><br />User public does not have permission to read the document with the docid esa.65.3<br /></error><br />--------------------------------</p>
<p>The underlying URL for the example above is:<br /><a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/metacat?action=read&qformat=esa&sessionid=&docid=esa.65.3">http://esa-dev.nceas.ucsb.edu/esa/metacat?action=read&qformat=esa&sessionid=&docid=esa.65.3</a></p>
<p>Perhaps the issue is the missing session variable?</p> Bug #4837 (Resolved): Permission error when ESA moderator attempts to modify a documenthttps://projects.ecoinformatics.org/ecoinfo/issues/48372010-02-24T22:11:12ZJim Regetzregetz@nceas.ucsb.edu
<p>The "Revise document" notification emailed to moderators currently contains a URL that looks something like this:</p>
<p><a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65">http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65</a></p>
<p>If already logged in as a moderator (and not the owner of this document), clicking this link produces the following:</p>
<p>---------------------------<br />Failure<br />An error occurred. Please check the list of errors below:</p>
<ul>
<li>You don't have permission to edit this document, which is owned by uid=test,o=NCEAS,dc=ecoinformatics,dc=org. (Access Error <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">#3</a>)<br />---------------------------</li>
</ul>
<p>ESA moderators, i.e. members of cn=esa-moderators,dc=ecoinformatics,dc=org, should have ALL permissions by default, so presumably they should be able to modify this document (and there may be times when they need to be able to do so).</p> Bug #4835 (Resolved): ESA review comments don't appear to users when viewing their documentshttps://projects.ecoinformatics.org/ecoinfo/issues/48352010-02-24T21:48:54ZJim Regetzregetz@nceas.ucsb.edu
<p>After the moderator enters review comments and sends a document back for revision, those comments are visible to the moderator in the left panel when viewing the document. However, when the original document submitter logs in and views that same document, the panel on the left reports "No reviews found".</p>
<p>I would imagine the submitter <strong>should</strong> be able to see the reviews, but in any case it certainly shouldn't say "No reviews found".</p> Bug #4834 (Resolved): Request to modify document redirects to registry home after loginhttps://projects.ecoinformatics.org/ecoinfo/issues/48342010-02-24T21:39:24ZJim Regetzregetz@nceas.ucsb.edu
<p>The "Revise document" notification emailed to document submitters currently contains a URL that looks something like this:</p>
<p><a class="external" href="http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65">http://esa-dev.nceas.ucsb.edu/esa/cgi-bin/register-dataset.cgi?stage=modify&cfg=esa&docid=esa.65</a></p>
<p>This redirects to the login page if the user is not already logged in, which makes sense. However, after logging in, the user gets dumped back at the home page rather being presented with the requested page.</p>
<p>Not sure if this issue is specific to ESA.</p> Bug #4818 (Resolved): ESA does not send an email to moderators when new document is added via reg...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> Bug #4691 (Resolved): Registry mixes up users when savinghttps://projects.ecoinformatics.org/ecoinfo/issues/46912010-01-21T22:25:12ZShaun Walbridgewalbridge@nceas.ucsb.edu
<p>If different users are added for the data set owner and contact, the registry messes up the serialization and takes data from the contact form and saves it into the data set owner fields. Verified on dev.</p> Bug #4130 (Resolved): data tables in KNB display dataTable->physical->objectNamehttps://projects.ecoinformatics.org/ecoinfo/issues/41302009-06-08T18:56:18ZOliver Soongsoong@nceas.ucsb.edu
<p>KNB names data tables according to the objectName element within the physical element. By contrast, Kepler's EML 2 Dataset actor displays the entityName. This is mostly confusing for a few dataTables for which the entityName is not the same as the objectName. For example look at judithk.609.27, entityName=Dailyrainl2005.txt and objectName=rainfall2005.txt. I'm not sure which what the best way to handle this is, but it seems more intuitive to refer to the dataTable by the entityName rather than the objectName of the physical container.</p> Bug #3922 (Resolved): Registry inserts "Select state or territory here." as default valuehttps://projects.ecoinformatics.org/ecoinfo/issues/39222009-03-31T20:03:57ZJim Regetzregetz@nceas.ucsb.edu
<p>On the data registry form for new data submissions, the "U.S. State or Territory" drop down menu has a default value of "Select state or territory here." If the user does not select another value, it appears that this text string is inserted verbatim into the EML document. Presumably this field should left be blank instead.</p>
<p>This seems to be the case at least for the NCEAS and ESA registries. I haven't checked anywhere else.</p>