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> Member Nodes - Bug #8622 (New): IOE repository is not respondinghttps://redmine.dataone.org/issues/86222018-06-18T19:04:55ZDave Vieglaisdave.vieglais@gmail.com
<p>Possibly related to <a class="issue tracker-4 status-1 priority-4 priority-default child parent" title="Story: Upgrade Member Node to current version of Metacat (IOE) (New)" href="https://redmine.dataone.org/issues/8244">#8244</a></p>
<p>The IOE repository is not responding at the expected baseURL of:</p>
<p><a href="https://data.rcg.montana.edu/catalog/d1/mn">https://data.rcg.montana.edu/catalog/d1/mn</a></p>
<p>and instead returns an error that SSL connection is not available. Attempting to use http instead of https returns a 404 error.</p>
<p>Contact the server administrator and have them check the service availability.</p>
Member Nodes - Task #7686 (Testing): tDAR - Enable URL links out to data from search results https://redmine.dataone.org/issues/76862016-03-23T16:59:05ZLaura Moyerslmoyers1@utk.edu
<p>Adam Brin would like his search results to show links out to his content from DataONE search results. We can do this with EML (see "Online Distribution Info"), so we'd need to develop a stylesheet for DCX (tDAR's metadata) such that search results display the desired link to tDAR content. See attached for a mock-up. </p>
<p>Here are some tDAR DCX identifiers:<br><br>
doi:10.6067:XCV848701_meta<br>
doi:10.6067:XCV848702_meta<br>
doi:10.6067:XCV848525_meta<br>
doi:10.6067:XCV848630_meta</p>
<p>Note they're behind a firewall. </p>
Member Nodes - MNDeployment #6544 (Operational): TERN Australia (powered by AEKOS)https://redmine.dataone.org/issues/65442014-11-03T00:35:54ZLaura Moyerslmoyers1@utk.edu
<p>AEKOS is the data repository component of TERN Eco-informatics. Their metadata standard is RIF-CS (the Australian National Data Service standard), but we intend to use EML for the DataONE MN:</p>
<p><a href="https://releases.dataone.org/online/api-documentation-v1.2.0/design/SearchMetadata_eml.html">https://releases.dataone.org/online/api-documentation-v1.2.0/design/SearchMetadata_eml.html</a></p>
<p>and use GMN as the MN stack.</p>
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 #3556 (Operational): ESA Data Registryhttps://redmine.dataone.org/issues/35562013-02-07T03:58:02ZDave Vieglaisdave.vieglais@gmail.comMember 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 #3238 (Operational): Idaho Northwest Knowledge Network member node https://redmine.dataone.org/issues/32382012-09-07T01:30:43ZDave Vieglaisdave.vieglais@gmail.com
<p>The Northwest Knowledge network (NKN) at Idaho has been identified as a potential member node, and expressed interest at the 2012 DUG.</p>
<p>Initial contact is Greg Goldberg: CI/NKN/FRAMES Program Manager University of Idaho 208-885-9756 <a href="mailto:gollberg@uidaho.edu">gollberg@uidaho.edu</a></p>
Member Nodes - MNDeployment #3221 (Operational): EDAC member node https://redmine.dataone.org/issues/32212012-09-05T03:39:05ZDave Vieglaisdave.vieglais@gmail.com
<p>This issue is to track the deployment or otherwise of the EDAC (Earth Data and Analysis Center) as a member node.</p>
<p>Base_URL: <a href="http://gstore.unm.edu/apps/dataone">http://gstore.unm.edu/apps/dataone</a><br>
Node_ID: urn:node:EDAC-GSTORE<br>
Deployment_Contact: Soren Scott<br>
Software: Custom python service layer<br>
Target_Tier: 1<br>
Content_Volume_GB: 20,000</p>
<p>Test system<br>
Base_URL: <a href="http://129.24.63.115/dataone">http://129.24.63.115/dataone</a><br>
Node_ID: urn:node:EDACGSTORE ?</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 #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 #391 (New): (Requirement) Enable different classes of users commensura...https://redmine.dataone.org/issues/3912010-03-17T16:15:31ZDave Vieglaisdave.vieglais@gmail.com
<p>There are several types of users that will be interacting with the <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> infrastructure, as such it is necessary to ensure that user roles can be supported by the identity management infrastructure. Closely related to <a href="https://trac.dataone.org/ticket/390">https://trac.dataone.org/ticket/390</a></p>
<p>Rationale: Different user classes or groups provides an effective mechanismfor indicating the types of interaction that might be supported by the system. The alternative is to specifically assign privileges for each user - an<br>
approach that is inefficient and potentially insecure as it is easy to miss an<br>
individual when setting privileges for a large number of users.</p>
<p>Fit Criteria</p>
<ul>
<li><p>A well defined set of standard groups is identified and can be easily manage (e.g. administrators, data contributors, data readers)</p></li>
<li><p>Users can be assigned to and removed from groups </p></li>
<li><p>Additional groups can be created to support group functions as necessary </p></li>
<li><p>Users can create their own groups for ad-hoc collaboration when needed and without approval of system administrators </p></li>
<li><p>Access control rules can be associated with groups and operate as expected.</p></li>
</ul>
Requirements - Requirement #390 (New): (Requirement) Consistent mechanism for identifying usershttps://redmine.dataone.org/issues/3902010-03-17T16:10:03ZDave Vieglaisdave.vieglais@gmail.com
<p>It is necessary to provide a mechanism for users to be identified in the <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> system. There are several distinct roles that need to be supported for users.Rationale: Identity of users, contributors and other participants in <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> is necessary to ensure appropriate policies for data sharing (read, write), attribution, and notification (e.g. subscription to types of data).</p>
<p>Fit Criteria</p>
<ul>
<li>Users can identify themselves in the <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> system </li>
<li>Identity is consistent across all nodes (i.e. identity associated with an object is consistent regardless of where the object is retrieved from or acted on) </li>
<li>Users can associate various accounts with a single identity</li>
<li>Identity information is sufficient to ensure appropriate attribution to content </li>
<li>Authentication and authorization mechanisms are recognized consistently by all participant nodes and services of the cicore.<br></li>
<li>Existing user directories in use in environmental science community can directly contribute identities (not "yet another" identity system)</li>
</ul>