DataONE Tasks: Issueshttps://redmine.dataone.org/https://redmine.dataone.org/favicon.ico2019-06-19T01:44:19ZDataONE Tasks
Redmine Infrastructure - Bug #8822 (New): Account queries in STAGE-2 failing from web browserhttps://redmine.dataone.org/issues/88222019-06-19T01:44:19ZBryce Mecummecum@nceas.ucsb.edu
<p>Steps to reproduce:</p>
<ol>
<li>Visit <a href="https://search-stage-2.test.dataone.org/">https://search-stage-2.test.dataone.org/</a></li>
<li>Log in</li>
<li>Navigate to <a href="https://search-stage-2.test.dataone.org/data">https://search-stage-2.test.dataone.org/data</a></li>
<li>Observe an HTTP 500 in the Network pane of whichever browser you're using to <a href="https://search-stage-2.test.dataone.org/cn/v2/accounts/?query=%7BYOUR_DN%7D">https://search-stage-2.test.dataone.org/cn/v2/accounts/?query={YOUR_DN}</a></li>
</ol>
<p>Response body:</p>
<pre><?xml version="1.0" encoding="UTF-8"?>
<error detailCode="500" errorCode="500" name="ServiceFailure">
<description>Internal Server Error: The server encountered an unexpected condition which prevented it from fulfilling the request.</description>
</error>
</pre>
<p>Some notes:</p>
<ul>
<li>I notice this in multiple browsers</li>
<li>I notice this only when the request is issued from MetacatUI, not when I visit the URL in my browser or hit it with curl</li>
<li>I don't notice this error on search.dataone.org</li>
<li>MetacatUI on search.dataone.org doesn't even issue this request</li>
<li>MetacatUI on stage-2 is at v2.4.2 and on search is at 2.6.1</li>
</ul>
<p>It seems like a bug to me that we see a service failure but I'm not sure if this is a MetacatUI bug or an issue in the CN stack (i.e., Apache config or something) but I wanted to file it for someone to take a look.</p>
Infrastructure - Story #7807 (New): cn.synchronize should support synchronization failure correct...https://redmine.dataone.org/issues/78072016-05-13T16:56:25ZRob Nahfrnahf@epscor.unm.edu
<p>cn.synchronize(session, identifier) works well for its original purpose (supporting MN-driven system metadata updates, and MN-driven push synchronization), but doesn't seem to work for manual synchronization failure workflows. The main problem is that the request can only be made by the MN itself (using the MN client certificate). </p>
<p>As we envision a centralized dashboard for monitoring failed synchronization items, how do we address this situation? </p>
<p>The synchronization processing queue needs both the pid and a nodeId from where to retrieve the object. the NodeId is not specified directly in the method call, but gleaned from the session by a reverse lookup from the certificate. (It uses the first node found in the NodeList where the Node.subject field matches the certificate subject).</p>
<p>Should we allow node.contactSubjects into the algorithm?<br>
Should we add nodeId as a parameter?</p>
Member Nodes - MNDeployment #7758 (New): Polar Rock Repository (PRR) at Ohio Statehttps://redmine.dataone.org/issues/77582016-05-02T23:50:40ZLaura Moyerslmoyers1@utk.edu
<p>The Polar Rock Repository (PRR) at the Ohio State University holds over 40,000 physical specimens which are available to be "checked out" by users. Laura/Mark met with Anne Grunow and Wes Haines 4/28/16 to discuss DataONE, the PRR, and how we might work together. See <a href="https://epad.dataone.org/pad/p/PRR_and_DataONE">https://epad.dataone.org/pad/p/PRR_and_DataONE</a></p>
Infrastructure - Bug #7698 (New): Exclude SLF4J jars in d1_solr_extensions.jarhttps://redmine.dataone.org/issues/76982016-03-28T16:22:54ZRobert Waltz
<p>Dave reported:<br>
when running “service solr status” on a CN, I see a complaint about multiple SLF4J bindings:<br>
(12:05:53 PM) vieglais: SLF4J: Class path contains multiple SLF4J bindings.<br>
(12:05:53 PM) vieglais: SLF4J: Found binding in <a href="12:05:55 PM" class="external">jar:file:/var/solr/server/solr-webapp/webapp/WEB-INF/lib/d1_solr_extensions.jar!/org/slf4j/impl/StaticLoggerBinder.class</a> vieglais: SLF4J: Found binding in <a href="12:05:56 PM" class="external">jar:file:/var/solr/server/lib/ext/slf4j-log4j12-1.7.7.jar!/org/slf4j/impl/StaticLoggerBinder.class</a> vieglais: SLF4J: See <a href="http://www.slf4j.org/codes.html#multiple_bindings">http://www.slf4j.org/codes.html#multiple_bindings</a> for an explanation.<br>
(12:05:56 PM) vieglais: SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]</p>
<p>looks like a class conflict due to the shaded d1_solr_extensions.jar that includes SLF4J and solr jetty that also includes SLF4J.</p>
<p>try excluding SLF4J jars in d1_solr_extensions.jar.</p>
DataONE API - Bug #7684 (New): Call to MNStorage.update() via REST API returns java.lang.StackOve...https://redmine.dataone.org/issues/76842016-03-21T23:07:39ZBryce Mecummecum@nceas.ucsb.edu
<p>I was trying to update an object via the REST API via cURL and forgot to enter the correct URL. The cURL command I used and response is:</p>
<p>$ curl -X PUT -H "Authorization: Bearer $TOKEN" -F "pid=resourceMap_doi:10.5065/D6G44NFV" -F "object=@object.xml" -F "sysmeta=@sysmeta.xml" -F "newPid=resourceMap_doi:10.5065/D6G44NFV_v3" $URL<br>
<?xml version="1.0" encoding="UTF-8"?><br>
java.lang.StackOverflowError<br>
</p>
<p>Where $URL was '<a href="https://arcticdata.io/metacat/d1/mn/v2/object">https://arcticdata.io/metacat/d1/mn/v2/object</a>' instead of '<a href="https://arcticdata.io/metacat/d1/mn/v2/object/resourceMap_doi:10.5065/D6G44NFV">https://arcticdata.io/metacat/d1/mn/v2/object/resourceMap_doi:10.5065/D6G44NFV</a>'</p>
<p>I expected to receive some sort of warning/error that I had forgotten to specify the URL properly for this call but instead saw a StackOverflowError.</p>
Python GMN - Task #7162 (New): Member node does not check with coordinating node before replicatinghttps://redmine.dataone.org/issues/71622015-06-05T23:49:44ZMark Flynnflynnm@dataone.unm.edu
<p>Replication is supposed to follow a sequence:<br>
CN — MN.replicate( ) —> newReplicaMN<br>
newReplicatMN —- MN.getReplica( ) —> sourceMN<br>
sourceMN — CN.isNodeAuthorized() —> CN<br>
newReplicaMN — CN.setReplicationStatus( ) —> CN</p>
<p>However, CN.isNodeAuthorized is not called before sourceMN replicates to newReplicaMN</p>
Member Nodes - MNDeployment #7145 (New): PlutoFhttps://redmine.dataone.org/issues/71452015-06-03T12:52:55ZLaura Moyerslmoyers1@utk.edu
<p>PlutoF is hosted at the University of Tartu in Estonia and "provides cloud database and computing services for the taxonomical, ecological, phylogenetical, etc. research. The purpose of the platform is to provide synergy through common modules for the classifications, taxon names, analytical tools, etc. It allows to address integrated questions in ecology and coevolution of taxa. Different types of the species occurrences, viz. preserved specimens, DNA sequences, human observations, references can be stored in PlutoF as well. PlutoF has no restrictions on taxon and geographic coverage and therefore can be used for the databasing interacting taxa. It includes also collection management module. Few examples of the public web outputs from PlutoF are Estonian eBiodiversity (<a href="http://elurikkus.ut.ee">http://elurikkus.ut.ee</a>), and molecular key for fungi (<a href="https://unite.ut.ee)">https://unite.ut.ee)</a>."</p>
<p>Anticipate GMN for this implementation. They currently hold ~500,000 biodiversity records.</p>
<p>For more information about PlutoF, see references in these articles: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023303/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023303/</a>, </p>
<p><a href="http://www.la-press.com/plutofa-web-based-workbench-for-ecological-and-taxonomic-research-with-article-a2406">http://www.la-press.com/plutofa-web-based-workbench-for-ecological-and-taxonomic-research-with-article-a2406</a></p>
Member Nodes - MNDeployment #3691 (New): National Institute for Amazon Researchhttps://redmine.dataone.org/issues/36912013-03-22T17:04:37ZLaura Moyerslmoyers1@utk.edu
<p>From DataONE website "contact us" – How to contribute, I have something to offer</p>
<p>Website: <a href="http://www.inpa.gov.br/">http://www.inpa.gov.br/</a> (in Portuguese)<br>
Entity: National Institute for Amazon Research<br>
POC: <a href="mailto:lcampos@inpa.gov.br">lcampos@inpa.gov.br</a><br>
Date of inquiry: 6/26/12<br>
Responder: Matt Jones<br>
Date of response: 7/19/12<br>
Response: Let's meet and discuss</p>
Member Nodes - MNDeployment #3683 (New): Purdue University Librarieshttps://redmine.dataone.org/issues/36832013-03-22T16:56:43ZLaura Moyerslmoyers1@utk.edu
<p>From DataONE website "contact us" – Want to be DUG member 2nd request</p>
<p>Website: <a href="http://www.lib.purdue.edu/">http://www.lib.purdue.edu/</a><br>
Entity: Purdue University Libraries<br>
POC: <a href="mailto:jcarlso9@gmail.com">jcarlso9@gmail.com</a><br>
Date of inquiry: 12/19/12<br>
Responder: Amber Budden<br>
Date of response: 1/2/13<br>
Response: Added to list. Please send welcome letter.</p>
Member Nodes - MNDeployment #3241 (New): ALA - Atlas of Living Australia member nodehttps://redmine.dataone.org/issues/32412012-09-07T01:46:59ZDave Vieglaisdave.vieglais@gmail.com
<p>The Atlas of Living Australia has been identified as a potential member node. This issue track progress towards that goal.</p>
<p>ALA - <a href="http://www.ala.org.au/">http://www.ala.org.au/</a></p>
Member Nodes - MNDeployment #3240 (New): AZGS - Arizona Geological Survey member nodehttps://redmine.dataone.org/issues/32402012-09-07T01:45:24ZDave Vieglaisdave.vieglais@gmail.com
<p>The Arizona Geological Survey (AZGS) has been identified as a potential member node. This issue track progress towards that goal.</p>
<p>Lee Allison has been identified as an initial contact.</p>
<p><a href="http://www.azgs.az.gov/">http://www.azgs.az.gov/</a></p>
Member Nodes - MNDeployment #3235 (New): LITS - Long-Term Individual base Time Series project me...https://redmine.dataone.org/issues/32352012-09-07T01:19:49ZDave Vieglaisdave.vieglais@gmail.com
<p>LITS - the UK Long-term Individual based Time Series project has been identified as a potential member node. This issue track progress towards that goal.</p>
<p><a href="http://lits.bio.ic.ac.uk:8080/litsproject/">http://lits.bio.ic.ac.uk:8080/litsproject/</a></p>
Infrastructure - Task #991 (New): implement HEAD /resolve/<guid>https://redmine.dataone.org/issues/9912010-10-11T17:41:17ZRob Nahfrnahf@epscor.unm.edu
<p>The resolution service supports the HEAD method:<br>
HEAD Returns basic information resolve response document<br>
Last-Modified: Date the resolve information was last updated for that identifier. This is helpful to clients that may cache resolve responses.</p>
Requirements - Requirement #433 (New): (Requirement) Data and metadata is replicated to at least ...https://redmine.dataone.org/issues/4332010-03-25T03:01:56ZDave Vieglaisdave.vieglais@gmail.com
<p>Data is copied verbatim to at least one other node.</p>
<p>Rationale<br>
Replicating information helps to ensure availability after (random or intentional) node inaccessibility. Choices for multiple data retrieval locations improves access efficiency and scalability.</p>
<p>Fit Criteria</p>
<ul>
<li>Copies of data and metadata are available from more than a single node</li>
<li>Node failure does not prevent data availability</li>
<li>Data and metadata are replicated to at least one other node within XXX minutes of appearing on a Member Node</li>
</ul>
Requirements - Requirement #386 (New): (Requirement) Deploy at least three Member Nodeshttps://redmine.dataone.org/issues/3862010-03-17T13:39:36ZDave Vieglaisdave.vieglais@gmail.com
<p>As part of the cooperative agreement, it is necessary for <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> to stand up three Member Nodes by the end of the first year.</p>
<p>Rationale</p>
<p>This is a requirement of the CA. The intent is perhaps to demonstrate significant progress on the implementation of the proposed infrastructure.</p>
<p>Fit Criteria</p>
<ul>
<li>Prototype member node functionality is designed</li>
<li>Targets for the prototype member nodes have been identified</li>
<li>Software implementations for the target member nodes are available</li>
<li>Deployed member nodes effectively participate in the <a class="wiki-page new" href="https://redmine.dataone.org/projects/d1req/wiki/DataONE">DataONE</a> cyberinfrastructure</li>
</ul>