DataONE Tasks: Issueshttps://redmine.dataone.org/https://redmine.dataone.org/favicon.ico2018-09-12T00:18:51ZDataONE Tasks
Redmine Infrastructure - Bug #8696 (New): double indexing of a resource map and another not processed bec...https://redmine.dataone.org/issues/86962018-09-12T00:18:51ZRob Nahfrnahf@epscor.unm.edu
<p>In production, the ORE 'a1a0e96a-3cde-4f3c-829c-29650b09f22b' was not processed because a member was also referenced by the ORE it obsoleted, 'dc39515e-440b-4673-9f63-962c7374bf48'. The task failed without being requeued. Below is the log output.</p>
<pre>rnahf@cn-orc-1:/var/log/dataone/index$ grep a1a0e96a-3cde-4f3c-829c-29650b09f22b cn-index-processor-daemon.log.*
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:27,384 (IndexTaskProcessor:saveTask:865) IndexTaskProcess.saveTask save the index task a1a0e96a-3cde-4f3c-829c-29650b09f22b
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:27,384 (IndexTaskProcessor:getNextIndexTask:610) Start of indexing pid: a1a0e96a-3cde-4f3c-829c-29650b09f22b
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:34,832 (IndexTaskProcessor:getNextIndexTask:664) the original index task - IndexTask [id=18085996, pid=a1a0e96a-3cde-4f3c-829c-29650b09f22b, formatid=http://www.openarchives.org/ore/terms, objectPath=/var/metacat/data/autogen.2018091015425874434.1, dateSysMetaModified=1536087134490, deleted=false, taskModifiedDate=1536619467383, priority=3, status=IN PROCESS]
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:34,832 (IndexTaskProcessor:getNextIndexTask:671) the new index task - IndexTask [id=18085996, pid=a1a0e96a-3cde-4f3c-829c-29650b09f22b, formatid=http://www.openarchives.org/ore/terms, objectPath=/var/metacat/data/autogen.2018091015425874434.1, dateSysMetaModified=1536087134490, deleted=false, taskModifiedDate=1536619467383, priority=3, status=IN PROCESS]
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:34,901 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:35,402 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:35,902 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:36,402 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:36,903 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:37,403 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:37,903 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:38,403 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:38,904 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:39,404 (IndexTaskProcessor:checkReadinessProcessResourceMap:369) ###################Another resource map is process the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 as well. So the thread to process id a1a0e96a-3cde-4f3c-829c-29650b09f22b has to wait 0.5 seconds.
cn-index-processor-daemon.log.6:[ERROR] 2018-09-10 22:44:39,904 (IndexTaskProcessor:checkReadinessProcessResourceMap:384) We waited for another thread to finish indexing a resource map which has the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 for a while. Now we quited and can't index id a1a0e96a-3cde-4f3c-829c-29650b09f22b
cn-index-processor-daemon.log.6:[ERROR] 2018-09-10 22:44:39,904 (IndexTaskProcessor:processTask:297) Unable to process task for pid: a1a0e96a-3cde-4f3c-829c-29650b09f22b
cn-index-processor-daemon.log.6:java.lang.Exception: We waited for another thread to finish indexing a resource map which has the referenced id ee73cf7f-1005-4b89-bab9-3a7fa01d27c6 for a while. Now we quited and can't index id a1a0e96a-3cde-4f3c-829c-29650b09f22b
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:39,906 (IndexTaskProcessor:newOrFailedIndexTaskExists:890) IndexTaskProcess.newOrFailedIndexTaskExists for id a1a0e96a-3cde-4f3c-829c-29650b09f22b
rnahf@cn-orc-1:/var/log/dataone/index$ date
Tue Sep 11 23:46:56 UTC 2018
rnahf@cn-orc-1:/var/log/dataone/index$ grep dc39515e-440b-4673-9f63-962c7374bf48 cn-index-processor-daemon.log.*
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:12,133 (HZEventFilter:filter:127) HZEventFilter.filter - the system metadata for the index event shows shows dc39515e-440b-4673-9f63-962c7374bf48 having a newer version than the SOLR server. So this event should be granted for indexing.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:13,347 (HZEventFilter:filter:127) HZEventFilter.filter - the system metadata for the index event shows shows dc39515e-440b-4673-9f63-962c7374bf48 having a newer version than the SOLR server. So this event should be granted for indexing.
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:18,677 (IndexTaskProcessor:saveTask:865) IndexTaskProcess.saveTask save the index task dc39515e-440b-4673-9f63-962c7374bf48
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:18,677 (IndexTaskProcessor:getNextIndexTask:610) Start of indexing pid: dc39515e-440b-4673-9f63-962c7374bf48
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:25,783 (IndexTaskProcessor:getNextIndexTask:664) the original index task - IndexTask [id=18086020, pid=dc39515e-440b-4673-9f63-962c7374bf48, formatid=http://www.openarchives.org/ore/terms, objectPath=/var/metacat/data/autogen.2017072514144216470.1, dateSysMetaModified=1536087137440, deleted=false, taskModifiedDate=1536619458675, priority=3, status=IN PROCESS]
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:25,783 (IndexTaskProcessor:getNextIndexTask:671) the new index task - IndexTask [id=18086020, pid=dc39515e-440b-4673-9f63-962c7374bf48, formatid=http://www.openarchives.org/ore/terms, objectPath=/var/metacat/data/autogen.2017072514144216470.1, dateSysMetaModified=1536087137440, deleted=false, taskModifiedDate=1536619458675, priority=3, status=IN PROCESS]
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:27,221 (IndexTaskProcessor:processTask:284) *********************start to process update index task for dc39515e-440b-4673-9f63-962c7374bf48 in thread 20
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:43,513 (IndexTaskProcessor:processTask:288) *********************end to process update index task for dc39515e-440b-4673-9f63-962c7374bf48 in thread 20
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:44:43,519 (IndexTaskProcessor:processTask:315) Indexing complete for pid: dc39515e-440b-4673-9f63-962c7374bf48
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:11,604 (IndexTaskProcessor:saveTask:865) IndexTaskProcess.saveTask save the index task dc39515e-440b-4673-9f63-962c7374bf48
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:11,604 (IndexTaskProcessor:getNextIndexTask:610) Start of indexing pid: dc39515e-440b-4673-9f63-962c7374bf48
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:18,731 (IndexTaskProcessor:getNextIndexTask:664) the original index task - IndexTask [id=18086015, pid=dc39515e-440b-4673-9f63-962c7374bf48, formatid=http://www.openarchives.org/ore/terms, objectPath=/var/metacat/data/autogen.2017072514144216470.1, dateSysMetaModified=1536087137440, deleted=false, taskModifiedDate=1536619571603, priority=3, status=IN PROCESS]
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:18,732 (IndexTaskProcessor:getNextIndexTask:671) the new index task - IndexTask [id=18086015, pid=dc39515e-440b-4673-9f63-962c7374bf48, formatid=http://www.openarchives.org/ore/terms, objectPath=/var/metacat/data/autogen.2017072514144216470.1, dateSysMetaModified=1536087137440, deleted=false, taskModifiedDate=1536619571603, priority=3, status=IN PROCESS]
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:20,164 (IndexTaskProcessor:processTask:284) *********************start to process update index task for dc39515e-440b-4673-9f63-962c7374bf48 in thread 20
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:36,252 (IndexTaskProcessor:processTask:288) *********************end to process update index task for dc39515e-440b-4673-9f63-962c7374bf48 in thread 20
cn-index-processor-daemon.log.6:[ INFO] 2018-09-10 22:46:36,255 (IndexTaskProcessor:processTask:315) Indexing complete for pid: dc39515e-440b-4673-9f63-962c7374bf48
cn-index-processor-daemon.log.7:[ INFO] 2018-09-10 21:44:09,798 (HZEventFilter:compareRaplicaList:256) HZEventFilter.compareReplicaList - the system metadata for the index event shows dc39515e-440b-4673-9f63-962c7374bf48 having the same replica list as the solr doc.
cn-index-processor-daemon.log.7:[ INFO] 2018-09-10 21:44:09,798 (HZEventFilter:filter:164) HZEventFilter.filter - the system metadata for the index event shows dc39515e-440b-4673-9f63-962c7374bf48 having the same modification date as the SOLR server. Also both have the same replica list. So this event has been filtered out for indexing (no indexing).
rnahf@cn-orc-1:/var/log/dataone/index$
</pre> Infrastructure - Bug #4674 (New): Ask Judith, Mike and Virgina Perez.2.1 to obsolete those pids w...https://redmine.dataone.org/issues/46742014-03-31T18:02:41ZJing Taotao@nceas.ucsb.edu
<p>doi:10.5063/AA/Virginia Perez.2.1<br>
judith botha.1.1<br>
judith botha.2.1<br>
judith kruger.1.1<br>
judith kruger.2.1<br>
judith kruger.3.1<br>
judith kruger.4.1<br>
judith kruger.5.1<br>
doi:10.6085/AA/ SHLX00_XXXITV2XLSR03_20111128.40.1 (PISCO)</p>
Infrastructure - Task #4210 (Testing): Metacat does not set serialVersion correctly in CNodeServi...https://redmine.dataone.org/issues/42102013-12-20T15:22:50ZChris Jonescjones@nceas.ucsb.edu
<p>For DATA and METADATA, CNodeService.archive() and D1NodeService.archive(), respectively, don't increment the serialVersion field. Check this for delete() as well. D1NodeService delegates to DocumentImpl to call the HZ put() method, so the fix needs to be there, and in CNodeService.</p>
Member Nodes - MNDeployment #3521 (Operational): SEAD Member Nodehttps://redmine.dataone.org/issues/35212013-01-25T21:19:12ZRebecca Koskelarkoskela@unm.edu
<p>SEAD (Sustainable Environment - Actionable Data), another DataNet, would like to become a DataONE Member Node<br>
(<a href="http://sead-data.net/">http://sead-data.net/</a>)</p>
Infrastructure - Bug #3492 (In Progress): Invalid PIDs in production (whitespace)https://redmine.dataone.org/issues/34922013-01-17T15:13:44ZDave Vieglaisdave.vieglais@gmail.com
<p>Recording this for future reference. </p>
<p>There are nine PIDs in the production environment that contain whitespace. This appears to have no functional effect - sysmeta and objects can be retrieved so no action is required other than to ensure no more sneak in.</p>
<p>The PIDs in question are:</p>
<a name="guid"></a>
<h2 > guid <a href="#guid" class="wiki-anchor">¶</a></h2>
<p>doi:10.5063/AA/Virginia Perez.2.1<br>
judith kruger.3.1<br>
judith kruger.4.1<br>
judith botha.1.1<br>
judith kruger.1.1<br>
judith kruger.2.1<br>
judith kruger.5.1<br>
judith botha.2.1<br>
resourceMap_Lin Cheng-Jung.1.1<br>
resourceMap_Lin Cheng-Jung.1.2<br>
resourceMap_Lin Cheng-Jung.1.3<br>
Lin Cheng-Jung.1.1<br>
Lin Cheng-Jung.1.2<br>
Lin Cheng-Jung.1.3<br>
doi:10.6085/AA/ SHLX00_XXXITV2XLSR03_20111128.40.1</p>
Member Nodes - MNDeployment #3118 (Operational): Dryad Member Nodehttps://redmine.dataone.org/issues/31182012-08-05T17:05:51ZDave Vieglaisdave.vieglais@gmail.com
<p>The Dryad MN will operate as a tier 1 member node.</p>
<p>Base_URL: <a href="https://datadryad.org/mn">https://datadryad.org/mn</a><br>
Node_ID: urn:node:DRYAD<br>
Deployment_Contact: Ryan Scherle<br>
Software: Custom on modified DSpace (Dryad)<br>
Target_Tier: 1<br>
Content_Volume_GB: 20</p>
Requirements - Requirement #822 (New): (Requirement) Object access and manipulation should be res...https://redmine.dataone.org/issues/8222010-09-06T03:32:31ZDave Vieglaisdave.vieglais@gmail.com
<p>The system should respond within a reasonable time when a user requests content or changes are made to content.</p>
<p>Rationale</p>
<p>An unresponsive system will be an impediment to adoption.</p>
<p>Fit Criteria</p>
<ul>
<li><p>Object lists always respond within XX seconds</p></li>
<li><p>Get object always returns within XX seconds</p></li>
<li><p>resolve object always responds within XX seconds</p></li>
<li><p>create and update operations always respond within XX seconds</p></li>
</ul>
Requirements - Requirement #821 (New): (Requirement) Sponsor required functionalityhttps://redmine.dataone.org/issues/8212010-09-06T03:23:56ZDave Vieglaisdave.vieglais@gmail.com
<p>(Requirement) Sponsor required functionality</p>
Requirements - Requirement #820 (New): (Requirement) Common API for authentication and authorizat...https://redmine.dataone.org/issues/8202010-09-06T02:37:34ZDave Vieglaisdave.vieglais@gmail.com
<p>There should be a common API utilized by the major software components of the infrastructure for <a href="for all <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataNet">DataNet</a>?" class="external">[DataONE]</a> for authentication and authorization operations.</p>
<p>Rationale</p>
<p>A common API will help minimize inconsistencies that arise from functional and semantic mis-match when interacting across multiple systems.</p>
<p>Fit Criteria</p>
<ul>
<li>CN, MN, and ITK libraries share a common API for authn and authz</li>
<li>Differing component implementations pass integration testing</li>
</ul>
Requirements - Requirement #795 (New): (Requirement) System must support revocation of user permi...https://redmine.dataone.org/issues/7952010-08-27T14:51:51ZMark Servillamark.servilla@gmail.com
<p>The system should be able to revoke any user's permissions and, ultimately, their direct access to the system, if the user is misbehaving within the system.</p>
<p>Although it is unclear as to who assigns permissions, I believe that the final responsibility and authority for access control is the <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> administrator. As such, permissions and simple access to any part of the <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> infrastructure, and perhaps member node infrastructure that is accessed through <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a>, should be revokable.</p>
<p>Fit Criteria</p>
<ul>
<li>Administrator can change permissions for a user for any object</li>
<li>Permission changes are propagated through the system within XXX seconds</li>
<li>Read, write access rules can be altered for a user for all content in the system</li>
</ul>
Requirements - Requirement #777 (New): (Requirement) Authorization rules should support common pe...https://redmine.dataone.org/issues/7772010-08-11T07:53:45ZMatthew Jonesjones@nceas.ucsb.edu
<p>Several types of access directives are in common use in data packages in the environmental sciences, and the authorization system should support these. The most common authorization levels would include:</p>
<p>** read: the ability to display or download an object</p>
<p>** write: the ability to change the content of an object through an update operation (which does not mean it actually changes the object -- it may just create a new version that obsoletes the old)</p>
<p>** changePermission: the ability to change access control rules on the object</p>
<p>Often, the permission levels are nested, in that higher privilege levels encompass the lower levels as well (e.g., write access to an object implies read access).</p>
<p>See the EML access control module for a detailed explanation of these levels (eml-access module).</p>
<p>In addition to specifying levels of permissions on the individual data objects, the authorization system should allow node administrators to specify what services principals can utilize on their nodes, and any resource constraints that may apply. For example, a Member Node operator may want to specify for their node several rules, such as:</p>
<p>** user joe can insert or update objects on node 32</p>
<p>** user jack can not update objects on node 21</p>
<p>** user joe has an aggregate storage limit of 1TB (may want to consider soft and hard resource limits)</p>
<p>** user joe has a network bandwidth transfer limit of 10mb/s</p>
<p>Note that these types of node-level resource limitations may not be implemented currently on most member nodes, but the authorization system should be expressive enough to allow node operators to build in these restrictions.</p>
Requirements - Requirement #772 (New): (Requirement) Authentication services should be compatible...https://redmine.dataone.org/issues/7722010-08-11T03:04:41ZMatthew Jonesjones@nceas.ucsb.edu
<p>Many applications will need to be adapted to work with the authentication and authorization services provided. Ideally, the services chosen will be compatible with existing systems and support those systems through standard protocols. Applications will need to commonly connect to, for example, web applications using HTTP Basic Authentication for Apache and JAAS for servlets like Tomcat. In addition, some applications may want to connect via PAM and similar security mechanisms. Some identity services, such as LDAP, are commonly supported in these scenarios.</p>
<p>Fit Criteria<br>
** Software in common use at Member Nodes and as clients should be able to easily utilize the authentication and authorization services with minimal configuration</p>
Requirements - Requirement #771 (New): (Requirement) User identities should have simple string se...https://redmine.dataone.org/issues/7712010-08-11T00:46:18ZMatthew Jonesjones@nceas.ucsb.edu
<p>When user identities can be drawn from multiple providers, we need to be able to serialize both the id and the provider namespace, for example by encapsulating both in a single distinguished name (DN). Ideally this serialization would be relatively short, persistent, and human understandable, and ideally it should not contain spaces or other characters that make it difficult to utilize in a variety of contexts (such as command line applications).</p>
<p>An example DN that has worked for the KNB network is:</p>
<p>uid=jones,o=NCEAS,dc=ecoinformatics,dc=org</p>
<p>Fit Criteria</p>
<p>*<br>
*<br>
*</p>
Requirements - Requirement #770 (New): (Requirement) Authorization system should be able to expre...https://redmine.dataone.org/issues/7702010-08-11T00:41:53ZMatthew Jonesjones@nceas.ucsb.edu
<p>There should be well-known mechanisms in the authorization system to allow access rules that explicitly grant access to pseudo-principals, including:</p>
<ul>
<li>public: anonymous, non-authenticated users</li>
<li>valid-user: authenticated user</li>
<li>registered-user: authenticated user with explicit minimal contact information</li>
<li>verified-user: authenticated user with explicit minimal contact information that has been verified as belonging to a real account holder</li>
</ul>
<p>Fit Criteria</p>
<p>*</p>
Requirements - Requirement #769 (New): (Requirement) Authorization should support critical roles,...https://redmine.dataone.org/issues/7692010-08-11T00:36:00ZMatthew Jonesjones@nceas.ucsb.edu
<p>While the principals contributing data should be able to specify access, they frequently struggle with the software systems intended to do so, and at times make mistakes. The system should support certain roles with elevated privielges for groups of objects to allow, e.g, a system administrator or data curator to change objects for which they are not otherwise granted access. For example, all objects that are associated with a particular field station might be managed by the information manager at that field station, and the person filling that role through time might change. Individual principals should be able to determine who has access to objects, both through explicit grants of access and through indirect roles that may be only implicitly defined.</p>
<p>Fit Criteria</p>
<ul>
<li>Its possible for access by some roles to be assigned implicitly through certain membership criteria (e.g., a data object is part of an LTER site)</li>
</ul>