Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-11-17T21:19:00ZEcoinformatics Redmine
Redmine Bug #7229 (New): Mis-Formatting of Data Package Contentshttps://projects.ecoinformatics.org/ecoinfo/issues/72292017-11-17T21:19:00ZThomas Thelen
<p>In MetacatUI we're getting a slight mis-formatting when displaying data package contents. This can be seen in the attached images. The issue was initially reported in MetacatUI as issue 379.</p>
<p><a class="external" href="https://github.com/NCEAS/metacatui/issues/379">https://github.com/NCEAS/metacatui/issues/379</a></p>
<p>From Bryce,</p>
<p>"The HTML in question is actually produced by Metacat and MetcatUI is just rendering it without modification from Metacat's View Service. ... The fix would involve changing the underlying eml-2 XSLT."</p> Bug #7182 (New): Allow partial package downloads when some of the objects are private https://projects.ecoinformatics.org/ecoinfo/issues/71822017-04-13T15:10:57ZLauren Walkerwalker@nceas.ucsb.edu
<p>When you try to download a package that has at least one private object, you get a 401 - Unauthorized response. When I am authorized to read at least one object in a package, I would expect to still be able to download the .zip package with those objects.</p>
<p>It's difficult for MetacatUI to tell when the "Download All" will fail, since it would need to check the /isAuthorized/{pid}?action=read result for every single object in the package, which can sometimes be >100. So right now we have an issue where users are getting a failed package download.</p> Bug #6959 (New): http response charset not includedhttps://projects.ecoinformatics.org/ecoinfo/issues/69592016-02-11T00:29:11ZPeter Slaughterslaughter@nceas.ucsb.edu
<p>Metacat doesn't include the content type charset in the http response headers:</p>
<p>curl -o test.dat -v "https://knb.ecoinformatics.org/knb/d1/mn/v2/object/solson.25.5" returns</p>
<p>Content-Type: text/csv</p>
<p>but should be something like:</p>
<p>Content-Type: text/xml;charset=UTF-8</p>
<p>so that the client doesn't have to assume the charset</p> Feature #6848 (New): Add link to send another verification emailhttps://projects.ecoinformatics.org/ecoinfo/issues/68482015-09-30T16:29:26ZLauren Walkerwalker@nceas.ucsb.edu
<p>This has been something suggested by a few users when they don't get their original verification email</p> Feature #6034 (New): Simplify configuration for certificate delegationhttps://projects.ecoinformatics.org/ecoinfo/issues/60342013-07-09T21:32:35Zben leinfelderleinfelder@nceas.ucsb.edu
<p>So we don't loose this in the shuffle - we could probably fill out some of the MyProxy configuration values based on Metacat properties. But I don't think we can really generate provate keys and register nodes with CILogon...</p> Bug #5836 (New): Logshttps://projects.ecoinformatics.org/ecoinfo/issues/58362013-01-30T18:16:16ZBrendan Hahnhahn@nceas.ucsb.edu
<p>Logs are kind of a mess, mixing multiple logging object types along with System.* output. Metacat has its own log directory, but only replication events are recorded there. Default build/distribution has uneven log levels set.</p> Bug #5835 (New): Leakshttps://projects.ecoinformatics.org/ecoinfo/issues/58352013-01-30T17:44:53ZBrendan Hahnhahn@nceas.ucsb.edu
<p>There are significant memory leaks that will eventually hang or kill the application server if metacat is restarted without terminating the entire server process. E.g. use of log4j dynamic configuration leaves orphan threads about (not really metacat's fault -- I'm amazed this is <strong>still</strong> a problem). Other threads, classloaders, etc along with the associated resources get left behind as well.</p>
<p>In short: should clean up better.</p> Bug #5821 (New): Allow certificate-based Metacat administrationhttps://projects.ecoinformatics.org/ecoinfo/issues/58212013-01-24T22:12:04Zben leinfelderleinfelder@nceas.ucsb.edu
<p>As we move toward the DataONE API where the MN does not provide identity and authorization services, perhaps the Metacat administrative functions should also follow suit. This would be a pretty large change for our users, but ultimately will simplify things so that we are not using two different identity/auth schemes to manage a single server.</p>
<p>In cases where the Metacat administrator did not have a useable (CILogon) identity we cold provide a utility to generate a client certificate for administrative use (or something akin to this). Ultimately this would need to be available in a browser UI where the bulk of our admin/config is performed.</p> Bug #5522 (New): download linked KNB data and convert links in EML to ORE packageshttps://projects.ecoinformatics.org/ecoinfo/issues/55222011-10-28T21:06:37ZMatt Jonesjones@nceas.ucsb.edu
<p>The KNB data sets, and EML data in general, represent linkages to data as online/url linkages in EML documents. When we convert to the KNB to a DataONE Member Node, we need a mechanism to convert these EML packages to create DataONE ORE-base data packages. Depending on the specific situation, different steps will need to be taken:</p>
<p>1) For packages that arrive via the DataONE services, do nothing<br />2) For packages that arrive via the Metacat and EcoGrid services, check all online/url links:<br /> a) if it is an ecogrid:// link, then create the corresponding link in an ore document<br /> b) if it is a URL marked as "information" in EML, ignore it<br /> c) if it is a URL marked as "download" in EML, then:<br /> i) attempt to download the data, and if successful<br /> -- check if it is real data (hard to do, but filtering out obvious HTML errors, login pages, HTML pages, etc would be tractable)<br /> -- insert it into the MN using the permissions and policies specified in the EML document (need to determine what the ID would be for this object -- maybe the original URL, but need to ensure uniqueness and < 800 chars, etc)<br /> -- add a link to the ORE document for this dataset<br /> d) insert the final ORE document that's been assembled (need to determine the identifier to use)</p>
<p>This utility method should be callable in two ways:<br />1) For an existing EML document already in metacat, likely to be run on initial conversion and periodically to be sure all proper data packages are created<br /> -- need to be sure that this doesn't create duplicate packages<br />2) On any INSERT or UPDATE calls<br /> -- when EML is updated, need to rebuild the package<br /> -- when data objects are updated, need to rebuild the package<br /> -- but need to watch out for sequential ops not interfering (e.g., when Morpho updates a data file, then updates a EML file to point at the new data file in a second step, we should only create one new ORE package version)<br /> -- on update calls, be sure to set appropriate obseletes/obsoletedBy properties on the ORE package (the update() calls themselves should handle these properties for the sysmeta for EML and data objects already)</p> Bug #4886 (New): "DatabaseService is already registered" error after configuring Metacathttps://projects.ecoinformatics.org/ecoinfo/issues/48862010-03-17T20:33:20ZJing Taotao@nceas.ucsb.edu
<p>I installed Metacat from 1.9.2 branch and configured it successfully. Then I typed<br />the url on the browser:<br /><a class="external" href="http://chico1.dyndns.org/knb/metacat?action=read&qformat=knb&docid=tao.14547">http://chico1.dyndns.org/knb/metacat?action=read&qformat=knb&docid=tao.14547</a></p>
<p>I got the error:<br />javax.servlet.ServletException: Service problem while intializing MetaCat Servlet: ServiceService.registerService - Service: DatabaseService is already registered. Use ServiceService.reregister() to replace the service.<br /> edu.ucsb.nceas.metacat.MetaCatServlet.initSecondHalf(MetaCatServlet.java:490)<br /> edu.ucsb.nceas.metacat.MetaCatServlet.handleGetOrPost(MetaCatServlet.java:696)<br /> edu.ucsb.nceas.metacat.MetaCatServlet.doGet(MetaCatServlet.java:519)<br /> javax.servlet.http.HttpServlet.service(HttpServlet.java:690)<br /> javax.servlet.http.HttpServlet.service(HttpServlet.java:803)<br /> org.vfny.geoserver.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:122)</p>
<p>I had to restart tomcat and error was gone.</p>
<p>Paul Were sent an email to metacat-dev describing that he got the same error:</p>
<p>I installed metacat 192RC4 and configured it ok.</p>
<p>I am now attempting run the registry.</p>
<p>I get the Registry login page but whenever I try to log in it fails. I get the following error.</p>
<p>knb 20100316-11:49:55: [ERROR]: MetaCatServlet.initSecondHalf - Service problem while initializing MetaCat Servlet: ServiceService.registerService - Service:<br />DatabaseService is already registered. Use ServiceService.reregister() to replace the service. [edu.ucsb.nceas.metacat.MetaCatServlet]</p>
<p>I am able to login into the admin page with no error as</p>
<p>uid=pwere,o=unaffiliated,dc=ecoinformatics,dc=org</p>
<p>and that is the same login I am using for the registry.</p>
<p>Jing's comment: i guess the "registry" in Paul's email means metacat.</p> 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> 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> Bug #4437 (New): allow-public-read rule is not being honoredhttps://projects.ecoinformatics.org/ecoinfo/issues/44372009-10-06T21:00:39ZMargaret O'Brienmob@msi.ucsb.edu
<p>This EML201 doc: knb-lter-sbc.3.7 contains 4 datatables. It has a dataset level access tree which includes an allow-public-read statment. Each data table also has additionalMetadata tree referencing it, also with allow-public-read statements. But one of the tables returns this message:</p>
<p>User public does not have permission to read the document with the docid sbclter.728.1</p>
<p>When you look at the doc, be sure to include the revision number. the most recent revision will have all those additionalMetadata trees removed.</p> Bug #3509 (New): Fix XML Schema filesystem namespace conflicts and backupshttps://projects.ecoinformatics.org/ecoinfo/issues/35092008-10-08T15:45:26ZMichael Daigledaigle@nceas.ucsb.edu
<p>Currently, two schema files with the same name but different namespaces will try to get written to the /schema directory. This will cause conflicts. The file should be written to /schema/<namespace> directory.</p>
<p>Also, schema files should be backed up to an external directory from the application. In this way, custom schemas will not get lost when metacat is upgraded.</p> Bug #2130 (New): Not able to delete DPs from KNBhttps://projects.ecoinformatics.org/ecoinfo/issues/21302005-06-17T17:57:04ZSaurabh Gargsgarg@nceas.ucsb.edu
<p>Not able to delete rwilliams.4.1 and rwilliams.10.1 from KNB. The message sent <br />back by Metacat is <br />Docid rwillliams.4.1 does not exsist. Please check that you have specified the <br />revision number of the document also</p>
<p>This error is generated in DocumentImpl after running followign query:<br />"SELECT * FROM xml_documents WHERE docid = ?" (The logs indicate that ? was <br />replaced by rwilliams.4)</p>
<p>If no record is found, then the above error is generated. Otherwise the <br />document is deleted. Hence it means no document was found.</p>
<p>However, running the same query via sqlplus returns one record. Weird.</p>