DataONE Tasks: Issueshttps://redmine.dataone.org/https://redmine.dataone.org/favicon.ico2019-11-06T22:31:11ZDataONE Tasks
Redmine Infrastructure - Story #8851 (New): CN sends error doc with "pid" to v2 endpointhttps://redmine.dataone.org/issues/88512019-11-06T22:31:11ZRoger Dahldahl@unm.edu
<p>Error XML type with "pid" is correct re. 2.0 arch docs but not 2.0 schemas. Let's discuss in maint. call.</p>
<ul>
<li>2.0 arch doc says 'pid': <a href="https://releases.dataone.org/online/api-documentation-v2.0/apis/Exceptions.html#Exceptions.SynchronizationFailed">https://releases.dataone.org/online/api-documentation-v2.0/apis/Exceptions.html#Exceptions.SynchronizationFailed</a></li>
<li>1.1 schema says 'pid': <a href="https://releases.dataone.org/online/d1-schemas-1.1.1/dataoneErrors.xsd">https://releases.dataone.org/online/d1-schemas-1.1.1/dataoneErrors.xsd</a> </li>
<li>2.0 schema says 'identifier': <a href="https://releases.dataone.org/online/d1-schemas-2.0.1/dataoneErrors.xsd">https://releases.dataone.org/online/d1-schemas-2.0.1/dataoneErrors.xsd</a>
<ul>
<li>Presumably because it can be a PID or a SID</li>
</ul></li>
<li>GMN expects "pid" in /v1 and "identifier" in /v2</li>
</ul>
<p>Example error sent to GMN v2 MNRead.synchronizationFailed() by the CN:</p>
<p><?xml version="1.0" encoding="UTF-8"?><br>
<br>
Synchronization task of [PID::] <a href="https://pasta.lternet.edu/package/data/eml/edi/443/1/0271719552fcd1ce830fcb2ee8efae71">https://pasta.lternet.edu/package/data/eml/edi/443/1/0271719552fcd1ce830fcb2ee8efae71</a> [::PID] failed. Cause: InvalidSystemMetadata: The checksum for pid: <a href="https://pasta.lternet.edu/package/data/eml/edi/443/1/0271719552fcd1ce830fcb2ee8efae71">https://pasta.lternet.edu/package/data/eml/edi/443/1/0271719552fcd1ce830fcb2ee8efae71</a> does not match the actual checksum supplied by the member node: urn:node:EDI. Actual checksum: null. System metadata checksum: eaaac8b49e6e8c13d30005a69e3600e7e17c9b3a</p>
Infrastructure - Story #8848 (New): A minor difference of annotation index between CN and MNhttps://redmine.dataone.org/issues/88482019-11-01T21:37:01ZJing Taotao@nceas.ucsb.edu
<p>The solr index on CN is:</p>
<pre><arr name="sem_annotation">
<str>http://purl.dataone.org/odo/ECSO_00000512</str>
<str>
http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType
</str>
<str>http://purl.dataone.org/odo/ECSO_00001102</str>
<str>http://purl.dataone.org/odo/ECSO_00001243</str>
<str>http://purl.dataone.org/odo/ECSO_00000629</str>
<str>http://purl.dataone.org/odo/ECSO_00000518</str>
<str>http://www.w3.org/2000/01/rdf-schema#Resource</str>
<str>http://purl.dataone.org/odo/ECSO_00000516</str>
<str>http://purl.obolibrary.org/obo/UO_0000301</str>
</arr>
</pre>
<p>The mn is:</p>
<pre><arr name="sem_annotation">
<str>http://purl.dataone.org/odo/ECSO_00000512</str>
<str>
http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#MeasurementType
</str>
<str>http://purl.dataone.org/odo/ECSO_00001102</str>
<str>http://purl.dataone.org/odo/ECSO_00001243</str>
<str>http://purl.dataone.org/odo/ECSO_00000629</str>
<str>http://purl.dataone.org/odo/ECSO_00000518</str>
<str>http://purl.dataone.org/odo/ECSO_00000516</str>
<str>http://purl.obolibrary.org/obo/UO_0000301</str>
</arr>
</pre>
<p>The cn has an extra <code><str>http://www.w3.org/2000/01/rdf-schema#Resource</str></code><br>
Bryce and I discussed it and thought it wouldn't affect the feature. But we still need to figure it out.</p>
Member Nodes - Story #8835 (New): Add ability for scanner to stop after a certain number of errorshttps://redmine.dataone.org/issues/88352019-08-12T19:16:39ZJohn Evans
<p>Right now the scanner will try to go thru the entire list of sitemap documents, regardless of whether they all fail or not. We should add the ability to abort further checks if a certain error threshold is crossed.</p>
Infrastructure - Story #8806 (New): Cleanup from OS upgradeshttps://redmine.dataone.org/issues/88062019-05-21T12:45:17ZDave Vieglaisdave.vieglais@gmail.com
<p>There's a few items that need to be addressed after the OS upgrades from 14.04 to 18.04.</p>
Infrastructure - Story #8762 (New): Add new formats to CNhttps://redmine.dataone.org/issues/87622019-02-07T19:58:28ZPeter Slaughterslaughter@nceas.ucsb.edu
<p>Add a new formatId for Python notebooks: application/x-ipynb+json. This is the current popular Media Type for Python notebooks (<a href="https://jupyter.readthedocs.io/en/latest/reference/mimetype.html">https://jupyter.readthedocs.io/en/latest/reference/mimetype.html</a>), but as it has the 'x-' prefix it is 'unregistered' and<br>
not recognized by IANA (<a href="https://www.iana.org/assignments/media-types/media-types.xhtml">https://www.iana.org/assignments/media-types/media-types.xhtml</a>).</p>
<p>The new entry should be:<br>
<objectFormat><br>
<formatId>application/x-ipynb+json</formatId><br>
<formatName>Jupyter Notebook</formatName><br>
<formatType>DATA</formatType><br>
<mediaType name="application/x-ipynb+json"/><br>
<extension>ipynb</extension><br>
</objectFormat></p>
Member Nodes - Story #8589 (New): ARM: Re-Discovery & Planninghttps://redmine.dataone.org/issues/85892018-05-10T20:35:03ZAmy Forresteraforres4@utk.edu
<p><strong>5/10/2018:</strong> Meeting at ORNL - Giri Prakash expressed re-interest in becoming a MN. Following on USGS_SDC GMN implementation (~Fall 2018), Aaron Stokes can turn attention to ARM installation</p>
Member Nodes - Story #8521 (New): CAFF: Testing & Developmenthttps://redmine.dataone.org/issues/85212018-03-26T15:07:58ZAmy Forresteraforres4@utk.edu
<p>The repository and DataONE have agreed to proceed with deployment as a member node. Install or develop a functional member node to be registered to a non-production environment.</p>
Infrastructure - Story #8307 (New): Check node subject on node registration and subsequent callshttps://redmine.dataone.org/issues/83072018-02-06T20:04:39ZDave Vieglaisdave.vieglais@gmail.com
<p>The <code>/node/subject</code> entry of the node document should match the subject of the certificate used to register the node (unless the call is being made by a CN certificate).</p>
Infrastructure - Story #8204 (New): Adjust memory allocation for services running under JVM on CNshttps://redmine.dataone.org/issues/82042017-10-24T15:29:28ZDave Vieglaisdave.vieglais@gmail.com
<p>Most services on CNs run in JVM instances, each with separate restrictions on memory use.</p>
<p>Current configurations were mostly based on defaults and have not changed much despite significantly higher memory use for systems such as Solr and Hazelcast.</p>
<p>The goal of this story is to evaluate the memory configuration of each JVM instance on the CNs and tune as necessary with the primary goal of avoiding out of memory errors, secondary goal is improving performance.</p>
<p>Note that with increased heap allocation, garbage collection may become a significant bottleneck, with application freeze in the order of several minutes possible or likely with higher heap allocations (e.g. 16GB)</p>
Infrastructure - Story #8173 (New): add checks for retrograde systemMetadata changeshttps://redmine.dataone.org/issues/81732017-09-01T19:42:33ZRob Nahfrnahf@epscor.unm.edu
<p>with the ability to prioritize and the introduction of parallelized index task processing, the effective queue is not guaranteed to be time-ordered. If there are two valid system metadata changes resulting in two tasks and the second change hits the index first, the earlier task should be rejected, as its changes are out of date.</p>
Infrastructure - Story #8044 (New): certificate manager should check expiration of CAs it loads i...https://redmine.dataone.org/issues/80442017-03-14T18:28:54ZRob Nahfrnahf@epscor.unm.edu
<p>currently, libclient checks for duplicates before it adds the shipped certificates into the trustStore. It does not check for expiration date. Evaluate whether it should. (Would our shipped set be more up-to-date than the java runtime?</p>
Infrastructure - Story #7859 (New): Add formatID for the STL 3d model file formathttps://redmine.dataone.org/issues/78592016-08-04T19:02:58ZBryce Mecummecum@nceas.ucsb.edu
<p>The STL file format is a domain standard file format for storing 3d models and is the most common way I've managed 3d models used while 3d printing. Given that 3d printing is seeing increased usage in the sciences, I would say this is a good candidate for inclusion in the controlled list of format ids.</p>
<p>Type: DATA<br>
Id: STL<br>
Name: StereoLithography File Format<br>
Media type: application/sla (unofficial)<br>
Extension: .stl</p>
<p>There is an ASCII form and a Binary form of this format. They don't see to be distinguished according to any standard. What do we do in this case?</p>
<p>References: <br>
- <a href="https://en.wikipedia.org/wiki/STL_(file_format)">https://en.wikipedia.org/wiki/STL_(file_format)</a><br>
- <a href="https://reference.wolfram.com/language/ref/format/STL.html">https://reference.wolfram.com/language/ref/format/STL.html</a></p>
Java Client - Story #6850 (New): automate Java Client releases https://redmine.dataone.org/issues/68502015-02-11T20:33:42ZRob Nahfrnahf@epscor.unm.edu
<p>We would like the self-contained jars for the Java Client Libraries to be built and automatically deployed from jenkins to releases.dataone.org.</p>
Infrastructure - Story #4650 (New): Allow MN to bias resolve to the authoritative MNhttps://redmine.dataone.org/issues/46502014-03-28T18:17:40ZBruce Wilsonbwilso27@utk.edu
<p>In the MN workshop (IDCC, Feb 2014) and in a MN forum discussion, several MN's asked if the resolve could be biased so that the authoritative MN was the somehow biased, so that users would be more likely to retrieve the data from the authoritative MN. A suggestion that met with a very positive response was to ensure that CN.resolve() returns the authoritative MN as the first item in the list. My understanding is that the order in the CN.resolve() results is indeterminate. </p>
Infrastructure - Story #2488 (New): Changing the authoritativeMembernode will require all replica...https://redmine.dataone.org/issues/24882012-03-14T19:08:19ZRobert Waltz
<p>Modifying the authoritativeMembernode requires human intervention. A tool should be created to perform the modification and then call MNStorage.systemMetadataChanged() on all replicas of the object.</p>