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> Support #6838 (In Progress): LTER user can't log inhttps://projects.ecoinformatics.org/ecoinfo/issues/68382015-08-28T23:41:47ZJing Taotao@nceas.ucsb.edu
<p>marco: ldap.lternet.edu should still work<br />[4:32pm] Jing: but why the search doesn’t work?<br />[4:32pm] Jing: and i can’t log in it from knb web page.<br />[4:34pm] marco: my guess is that the connection is trying to connect to 389, which IIRC is where startTLS initiates<br />[4:34pm] marco: port 389 is now blocked - not my decision<br />[4:34pm] Jing: aha.<br />[4:35pm] Jing: thanks, marco<br />[4:35pm] marco: if necessary, 389 can be opened for a specific IP or range<br />[4:35pm] marco: and startTLS enabled<br />[4:37pm] marco: we'll work with mark schildhauer next week to figure out the disposition of LDAP</p> Support #6793 (In Progress): Update DOIs from KNB to redirect to view servicehttps://projects.ecoinformatics.org/ecoinfo/issues/67932015-07-02T19:00:00ZMatt Jonesjones@nceas.ucsb.edu
<p>In <a class="issue tracker-2 status-3 priority-2 priority-default closed" title="Feature: Create a new service to update DOI pointers (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/6530">#6530</a> and <a class="issue tracker-5 status-5 priority-2 priority-default closed" title="Story: Keep DOI registrations current and resolvable (Closed)" href="https://projects.ecoinformatics.org/ecoinfo/issues/6440">#6440</a>, we added features to update DOI registrations, but we still have many originally assigned DOIs that redirect to the raw EML document rather than our landing page for a data set. We need to fix all of the /AA/ DOI registrations in the KNB and ensure they point to the right View service page. For DOIs for metadata, that would be the associated /view url for that DOI. For data files and resource maps, its to the view for the associated metadata. E.g.,</p>
<ul>
<li>Metadata doi:10.5063/AA/nceas.227.15 should redirect to <a class="external" href="https://knb.ecoinformatics.org/#view/doi:10.5063/AA/nceas.227.15">https://knb.ecoinformatics.org/#view/doi:10.5063/AA/nceas.227.15</a></li>
<li>Data doi:10.5063/AA/wtyburczy.30.1 should redirect to the same metadata file <a class="external" href="https://knb.ecoinformatics.org/#view/doi:10.5063/AA/nceas.227.15">https://knb.ecoinformatics.org/#view/doi:10.5063/AA/nceas.227.15</a></li>
</ul>
<p>Also, when a user updates metadata for a package (but doesn't change the data), the DOI redirect for the data will need to be updated to point to the new metadata. Let's verify that this is happening automatically in Metacat.</p> Feature #6416 (In Progress): Do not allow restrictive access control change to content with a DOIhttps://projects.ecoinformatics.org/ecoinfo/issues/64162014-02-11T18:34:16Zben leinfelderleinfelder@nceas.ucsb.eduFeature #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 #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 #5518 (In Progress): Track down the performance issue of metacat query.https://projects.ecoinformatics.org/ecoinfo/issues/55182011-10-26T22:47:27ZJing Taotao@nceas.ucsb.edu
<p>Matt queried knb with the word "water". It took one minute and half. We need to figured out why it so slow.</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 #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 #3402 (In Progress): internal dtds are not handledhttps://projects.ecoinformatics.org/ecoinfo/issues/34022008-06-19T18:52:33ZChad Berkleyberkley@nceas.ucsb.edu
<p>XML documents with internal DTDs are not handled by metacat. The internal dtd entity callback in the sax parser is blank and doesn't do anything when presented with an internal dtd.</p>