DataONE Tasks: Issueshttps://redmine.dataone.org/https://redmine.dataone.org/favicon.ico2019-03-12T16:54:08ZDataONE Tasks
Redmine CN REST - Task #8778 (New): Ensure SystemMetadata replica auditing updates are saved and broadcasthttps://redmine.dataone.org/issues/87782019-03-12T16:54:08ZChris Jonescjones@nceas.ucsb.edu
<p>In <code>MNAuditTask.call()</code>, we process a batch of pids in need of auditing per Member Node. For each <code>pid</code> in the <code>auditPIDs</code> list, we call <code>MN.getChecksum()</code>. Regardless of success or failure, we set the <code>Replica.replicaVerified</code> date in the <code>SystemMetadata</code>. However, the task has a copy of the system metadata from <code>hzSystemMetadata.get()</code>, and the task doesn't subsequently call <code>hzSystemMetadata.put(pid, sysmeta)</code>. This means that while we are auditing content, we may just not be recording the results! I need to look at the code more to see if we make an API call to <code>CN.updateSystemMetadata()</code> elsewhere, but I would expect the<code>MNAuditTask</code> to do this. Also, if this happens in the task, we also need to broadcast the system metadata change to the authoritative MN and all replica MNS. Lastly, we need to update the <code>serialVersion</code> field to show the other CNs what the most recent replica list is.</p>
CN REST - Task #8777 (New): Configure CN to audit objects greater than 1GBhttps://redmine.dataone.org/issues/87772019-03-12T16:47:42ZChris Jonescjones@nceas.ucsb.edu
<p>The replication auditor currently limits auditing of objects at 1GB. There are currently 4 objects greater than 1TB in size, and 3,588 objects greater than 1GB in size, both being very small counts compared to the 2,769,111 objects less than 1GB in size in the network. Nonetheless, they should still be audited if feasible. The limiting factor is likely HTTP timeout limits during the call to <code>MN.getChecksum()</code>. For reference, I'm seeing the following general times for calculating MD5 and SHA-1 checksums:</p>
<pre>Size MD5 SHA-1
---- ------- -------
1GB 00m02.5s 00m02.6s
10GB 00m25.9s 00m30.0s
100GB 03m28.0s 04m01.8s
1TB 50m14.2s 67m38.6s
</pre>
<p>10GB and 100GB objects seem pretty feasible if we set the HTTP client timeout to > 5 minutes, whereas the few > 1TB files may be challenging just due to the timeouts. The other factor is that the <code>AbstractReplicationAuditor</code> sets a default timeout to 60 seconds, and if the task future doesn't return in that time frame, the future gets cancelled. So the HTTP timeout and this timeout need to be increased and coordinated in order to handle larger object auditing.</p>
CN REST - Task #8776 (New): Set valid replica status to completedhttps://redmine.dataone.org/issues/87762019-03-12T15:57:36ZChris Jonescjones@nceas.ucsb.edu
<p>In <code>MNAuditTask.call()</code> we audit replica checksums, but on success, we only set the <code>Replica.replicaVerified</code> field to the current date. We don't set the <code>Replica.replicationStatus</code> field to <code>COMPLETED</code>. This is an issue because the <code>Replica</code> entry in the <code>SystemMetadata</code> may have been set to <code>FAILED</code> or <code>INVALIDATED</code>, but may now be valid, and so would need to be updated.</p>
CN REST - Story #8757 (New): Fix getChecksum() in MNAuditTask to use dynamic checksum algorithmshttps://redmine.dataone.org/issues/87572019-01-14T16:46:33ZChris Jonescjones@nceas.ucsb.edu
<p>The <code>MNAuditTask.call()</code> method is hardcoded to use <code>MD5</code> checksums on line 277. It requests the Member Node to generate an <code>MD5</code> checksum, and then compares that checksum to the checksum stated in the Coordinating Node<code>s cached</code>SystemMetadata.checksum<code>field for the object. This obviously will fail for objects that submitted objects using</code>SHA-1` or other algorithms.</p>
CN REST - Story #8756 (New): Ensure replica auditor is effectivehttps://redmine.dataone.org/issues/87562019-01-12T20:25:18ZChris Jonescjones@nceas.ucsb.edu
<p>The replication auditor service is currently configured to audit all objects every 90 days. As documented in <a class="issue tracker-4 status-1 priority-4 priority-default child" title="Story: Replica Auditing service is throwing errors (New)" href="https://redmine.dataone.org/issues/8582">#8582</a>, the auditor is not working correctly. While the errors being thrown that are described in that ticket seem to be limited to <code>pid</code>s with certain characters in them, I think the whole auditor process is not keeping up with our content.</p>
<p>Looking at the number of objects on each member node that haven't been audited in the last 90 days, auditing is well behind (if we consider it working at all):</p>
<pre>SELECT sm.authoritive_member_node, count(smr.guid) AS count
FROM systemmetadata sm INNER JOIN smreplicationstatus smr
ON sm.guid = smr.guid
WHERE
smr.member_node != 'urn:node:CN' AND
sm.date_uploaded < (SELECT CURRENT_DATE - interval '90 days') AND
smr.date_verified < (SELECT CURRENT_DATE - interval '90 days')
GROUP BY sm.authoritive_member_node
ORDER BY count DESC;
authoritive_member_node | count
-------------------------+--------
urn:node:ARCTIC | 771872
urn:node:PANGAEA | 507456
urn:node:LTER | 416339
urn:node:DRYAD | 374439
urn:node:CDL | 242115
urn:node:PISCO | 235791
urn:node:KNB | 86075
urn:node:TDAR | 75639
urn:node:NCEI | 50974
urn:node:USGS_SDC | 40290
urn:node:TERN | 31671
urn:node:ESS_DIVE | 28830
urn:node:NMEPSCOR | 16042
urn:node:GOA | 9266
urn:node:IARC | 7677
urn:node:NRDC | 6673
urn:node:TFRI | 6478
urn:node:PPBIO | 3464
urn:node:ORNLDAAC | 3328
urn:node:FEMC | 2430
urn:node:EDI | 2098
urn:node:GRIIDC | 2065
urn:node:mnTestKNB | 2010
urn:node:SANPARKS | 2008
urn:node:ONEShare | 1874
urn:node:R2R | 1787
urn:node:USGSCSAS | 1151
urn:node:EDACGSTORE | 1075
urn:node:US_MPC | 1032
urn:node:RW | 970
urn:node:KUBI | 516
urn:node:NEON | 487
urn:node:LTER_EUROPE | 343
urn:node:IOE | 279
urn:node:RGD | 273
urn:node:ESA | 272
urn:node:NKN | 218
urn:node:OTS_NDC | 126
urn:node:BCODMO | 115
urn:node:SEAD | 90
urn:node:mnTestNKN | 50
urn:node:EDORA | 28
urn:node:ONEShare.pem | 22
urn:node:CLOEBIRD | 17
urn:node:mnTestBCODMO | 11
urn:node:USANPN | 10
urn:node:mnTestTDAR | 10
urn:node:MyMemberNode | 1
</pre>
<p>The table above represents the number of un-audited objects (in the last 90 days), but I get the feeling that the auditor isn't able to audit any of the content it is charged to audit given 1) the frequency, 2) the number of threads allotted, and 3) the configured batch count (seems way too low). <del>Note that this query excludes replicated content - this is just the original objects</del> (After looking at my query again, I think the join is including all replicas - the total is 2,935,787, which is greater than the total objects in the system (2,751,136), so this query needs to be refined).</p>
<p>We need to evaluate the true effectiveness of the auditor. Some strategies may include: 1) looking to see if we may be in an infinite loop on processing a few <code>pid</code>s due to the issues in <a class="issue tracker-4 status-1 priority-4 priority-default child" title="Story: Replica Auditing service is throwing errors (New)" href="https://redmine.dataone.org/issues/8582">#8582</a>, 2) seeing if we can increase the batch size by increasing the total threads allocated in the executor, and 3) decide if we need to offload the process from the CNs and distribute the workload across a cluster of workers that can do the auditing faster. Needs some thought and discussion.</p>
Member Nodes - Task #8697 (New): ESSDIVE: anonymous download issuehttps://redmine.dataone.org/issues/86972018-09-13T19:40:48ZAmy Forresteraforres4@utk.edu
<p>We do have one small issue that we will want to discuss with you and that will be figuring out if we can deal with anonymous download of our data. We had promised our users that they would be notified about downloads and who downloaded. We had not thought about that replication into DataONE of the data itself would violate that promise. I don't think it changes our join schedule and enthusiasm for joining, it just means we have an issue to work out soon.</p>
Infrastructure - Story #8639 (New): Replication performance is too slow to service demandhttps://redmine.dataone.org/issues/86392018-07-04T11:17:55ZDave Vieglaisdave.vieglais@gmail.com
<p>The replication process is operating too slowly to service demand resulting in lengthy delays to completion of replication tasks for new and changed content.</p>
<p>This is particularly apparent in the stage environment where perhaps the number of orphaned objects and deprecated / defunct nodes is interfering with expected behaviors.</p>
<p>Goal of this story is to identify and address the immediate issues. Any significant refactoring of the replication process should be captured under another story / epic.</p>
Search UI - Task #7498 (In Progress): Search UI deployments need to be automatedhttps://redmine.dataone.org/issues/74982015-11-20T23:19:19ZChris Jonescjones@nceas.ucsb.edu
<p>We need to be able to install the Search UI code with minimal to no manual intervention. Create a debian package for the Search UI based on the cn-buildout project. Integrate this into the Jenkins build system so the debian package can be installed from the unstable, beta, and stable channels.</p>
Infrastructure - Task #7466 (In Progress): Some objects not accessible on the CN via REST APIhttps://redmine.dataone.org/issues/74662015-11-04T18:41:38ZBryce Mecummecum@nceas.ucsb.edu
<p>While doing other work, I noticed that a good number (not sure how many) of objects listed on the CN's Solr index are not accessible via the REST API get() and resolve() methods. Instead of returning the object, they return a NotFound error. </p>
<p>To reproduce,</p>
<ol>
<li>Visit <a href="https://cn.dataone.org/cn/v1/query/solr/?fl=identifier,title,authoritativeMN,datasource&q=formatType:METADATA+AND+-obsoletedBy:*&rows=100&start=0">https://cn.dataone.org/cn/v1/query/solr/?fl=identifier,title,authoritativeMN,datasource&q=formatType:METADATA+AND+-obsoletedBy:*&rows=100&start=0</a></li>
<li>Pick a PID from the query result, e.g.</li>
</ol>
<ul>
<li>knb-lter-cap.148.9</li>
<li>CLOEBDMETADATA.10242013.1</li>
</ul>
<ol>
<li>Attempt to resolve() or get() the object via the REST API like: <a href="https://cn.dataone.org/cn/v1/object/CLOEBDMETADATA.10242013.1">https://cn.dataone.org/cn/v1/object/CLOEBDMETADATA.10242013.1</a></li>
<li>Receive a NotFound error instead of the object.</li>
</ol>
<p>Notes:</p>
<p>In IRC, Skye noticed that the objects can be retrieved via their respective MN so it appears this issue may be a Metacat replication issue.</p>
Java Client - Task #7389 (Testing): V2 D1Object fails to download V1 contenthttps://redmine.dataone.org/issues/73892015-09-28T17:34:30ZChris Jonescjones@nceas.ucsb.edu
<p>During testing of services in the mixed V1/V2 DEV2 environment, D1Object fails to download content listed in the ObjectLocationList from a V1-only Member Node. The symptom is a null pointer exception when trying to close a non-existent temporary file where the bytes of the object should have been located. Fix download() to call V1 endpoints on V1-only MNs.</p>
Java Client - Task #7120 (Testing): Fix DataPackage.insertRelationship() to handle any URI for ex...https://redmine.dataone.org/issues/71202015-05-21T16:49:34ZChris Jonescjones@nceas.ucsb.edu
<p>DataPackage currently provides two insertRelationship() methods - one to add ORE relationships between metadata and data members of the aggregation, and a second to provide any relationship using predicates from other namespaces (such as PROV). The latter method assumes that all identifiers should be treated as objects using the CN Base URL when constructing the subject and object URIs. This isn't always the case. Change or override the method to accept any URI as subject and object components of the triple, and fix any tests that use this method.</p>
Infrastructure - Task #6843 (In Progress): Update the prov instance of the RdfXmlSubprocessor to ...https://redmine.dataone.org/issues/68432015-02-06T23:18:48ZChris Jonescjones@nceas.ucsb.edu
<p>In the "sem-prov-design issue 66":<a href="https://github.com/DataONEorg/sem-prov-design/issues/66">https://github.com/DataONEorg/sem-prov-design/issues/66</a> we have renamed the provenance-based Solr fields to include 'prov_' as a prefix, and have added new fields. See also "issue 99":<a href="https://github.com/DataONEorg/sem-prov-design/issues/99">https://github.com/DataONEorg/sem-prov-design/issues/99</a> and "issue 100":<a href="https://github.com/DataONEorg/sem-prov-design/issues/100">https://github.com/DataONEorg/sem-prov-design/issues/100</a>.<br>
Modify the provRdfXmlSubprocessor bean to handle the renaming scheme, the new fields, and the inverse fields determined to be useful. Also, add these fields as static Solr fields so we can remove the '_sm' suffixes from the names.</p>
Infrastructure - Task #6394 (New): Resolve SSL certificate connection errors for UNM Epscor Tier ...https://redmine.dataone.org/issues/63942014-09-18T18:36:20ZBruce Wilsonbwilso27@utk.edu
<p>Per discussion 2014-09-18 in MN Forum, Hayes is having problems getting SSL connections to work. One question is what certificate store is being used. They use InCommon Certificates.</p>
Infrastructure - Task #6250 (New): CN methods return 500 ServiceFailure when called with bogus te...https://redmine.dataone.org/issues/62502014-08-29T16:58:54ZRoger Dahldahl@unm.edu
<p>A number of the test for the Python CN Client currently fail due to 500 ServiceFailure responses from the server. The CN calls are not meant to complete successfully because they're performed with random values and without certificates, but the tests expect specific exceptions, such as 401 NotAuthorized when calling an API without a certificate.</p>
<p>While 500 ServiceFailure is not exactly a bug, it would be great to get an exception that relates to the actual issue with the request.</p>
<p>For instance, a call to CNIdentity.registerAccount() gives:</p>
<p><?xml version="1.0" encoding="UTF-8"?><br>
<br>
Could not counstruct partial tree: Invalid name: Sidalcea</p>
<p>I'm not sure how many of APIs this applies to, but it's at least several of these:</p>
<p>CNCore.setObsoletedBy()</p>
<p>CNAuthorization.setRightsHolder()<br>
CNAuthorization.isAuthorized()</p>
<p>CNIdentity.registerAccount()<br>
CNIdentity.updateAccount()<br>
CNIdentity.verifyAccount()<br>
CNIdentity.getSubjectInfo()<br>
CNIdentity.listSubjects()<br>
CNIdentity.mapIdentity()<br>
CNIdentity.removeMapIdentity()<br>
CNIdentity.requestMapIdentity()<br>
CNIdentity.confirmMapIdentity()<br>
CNIdentity.denyMapIdentity()<br>
CNIdentity.createGroup()<br>
CNIdentity.addGroupMembers()<br>
CNIdentity.removeGroupMembers()</p>
<p>CNReplication.setReplicationStatus()<br>
CNReplication.updateReplicationMetadata()<br>
CNReplication.setReplicationPolicy()<br>
CNReplication.isNodeAuthorized()</p>
<p>CNRegister.updateNodeCapabilities()<br>
CNRegister.register()</p>
Infrastructure - Task #6168 (New): CNAuthorization.setRightsHolder() returns 500 ServiceFailurehttps://redmine.dataone.org/issues/61682014-08-29T16:01:00ZRoger Dahldahl@unm.edu
<p>CNAuthorization.setRightsHolder() returns 500 ServiceFailure when called with invalid pid.</p>