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 #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 #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 #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>
Requirements - Requirement #768 (New): (Requirement) Need default authz policies that resolve pro...https://redmine.dataone.org/issues/7682010-08-11T00:33:39ZMatthew Jonesjones@nceas.ucsb.edu
<p>When principals die, retire, change careers, or lose interest in a research area, they may leave in the system data objects that would be otherwise useful to science but are restricted access. The authorization system should have carefully crafted default policies that encourage the public release and sharing of data, the expiration of embargo periods, and the movement of data into the public domain when it is legal and ethical to do so. Principals should be able to override these defaults to create more restrictive policies (e.g., for human subjects data) that will be respected indefinitely, but the defaults should encourage openness and sharing.</p>
<p>Fit Criteria</p>
<ul>
<li>Defaults encourage openness and sharing, without alienating principals through unexpected release of their data, etc.</li>
</ul>
Requirements - Requirement #767 (New): (Requirement) Users need to be able to express embargo rul...https://redmine.dataone.org/issues/7672010-08-11T00:14:36ZMatthew Jonesjones@nceas.ucsb.edu
<p>These embargo rules allow data to be published in the system, but not released until a particular date. By operating this way, users can use the system in their daily management of their data without worry of losing track of publication of the data at a later date. It encourages people to start using the system even long before they want to publicly release the data.</p>
<p>Fit Criteria</p>
<p>*<br>
*<br>
*</p>
Requirements - Requirement #766 (New): (Requirement) Users should be able to easily assign proxy ...https://redmine.dataone.org/issues/7662010-08-11T00:11:26ZMatthew Jonesjones@nceas.ucsb.edu
<p>When users need to execute processes asynchronously, they need to be able to grant proxy privileges (e.g., to a workflow or grid system) to operate on their behalf in particular contexts. In addition, at times some users want others to be able to run and access data and operate on behalf of another, such as in a faculty student situation where the student acts as a proxy for the faculty member.</p>
<p>Fit Criteria</p>
<p>*<br>
*<br>
*</p>
Requirements - Requirement #762 (New): (Requirement) User identities can be derived from existing...https://redmine.dataone.org/issues/7622010-08-10T22:55:56ZMatthew Jonesjones@nceas.ucsb.edu
<p>Many existing directory services are in use in the environmental sciences, and participating member nodes should be able to expose their directories through a standardized mechanism to allow users to make use of existing identities. For example, the KNB LDAP server is a federation of multiple LDAP systems from around the world, and these identities have been used in access rules for many existing objects.Rationale: Re-use of existing infrastructure reduces cost of participation and minimizes confusion over which accounts to use and which rules are associated with what account. </p>
<p>Fit Criteria</p>
<ul>
<li>The system provides a mechanism for exsiting directory services to join * The system provides a namespacing mechanism to differentiate users with the same id in different original directories (e.g., mjones@LTER, mjones@UCNRS)</li>
<li>The same email address can be associated with multiple identities</li>
<li>The same person or system can possess multiple identities </li>
<li>If a user has multiple identities, the user can express equivalence rules that indicate that they are linked, equivalent identities for the purposes of authentication and authorization</li>
</ul>
Requirements - Requirement #592 (New): DataONE needs to synchronize metadata between MNs and CNshttps://redmine.dataone.org/issues/5922010-04-23T00:53:56ZMatthew Jonesjones@nceas.ucsb.edu
<p><a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> functions by having CNs that provide a central index of all metadata in the system. This allows for rapid search of the whole network while maintaining autonomy of MNs.</p>