Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-07-03T18:11:39ZEcoinformatics Redmine
Redmine EML - Bug #6574 (New): document use of ORCID ids in userId fieldhttps://projects.ecoinformatics.org/ecoinfo/issues/65742014-07-03T18:11:39ZMatt Jonesjones@nceas.ucsb.edu
<p>Kyle Braak [GBIF] has requested that we document how to use ORCID ids in EML documentation. He writes:</p>
<blockquote>
<p>Just a thought, but to promote ORCIDs a bit, how about adding <a class="external" href="http://orcid.org/">http://orcid.org/</a> to the list of examples in the "directory" documentation: <a class="external" href="https://knb.ecoinformatics.org/#external//emlparser/docs/eml-2.1.1/./eml-party.html#directory">https://knb.ecoinformatics.org/#external//emlparser/docs/eml-2.1.1/./eml-party.html#directory</a>? Another candidate could be Researcher IDs (e.g. <a class="external" href="http://www.researcherid.com/rid/C-4862-2011">http://www.researcherid.com/rid/C-4862-2011</a>).</p>
</blockquote>
<p>This includes describing the use of the <a class="external" href="http://orcid.org">http://orcid.org</a> site as the directory, and showing an example of an ORCID in the text. We should also mak eit clear that a userId from a public source like ORCID is much more useful than a local userid from a site-specific system.</p> Community Dynamics Toolbox - Task #6392 (New): Create workflow encapsulating Sid's analysishttps://projects.ecoinformatics.org/ecoinfo/issues/63922014-01-16T21:56:40ZMatt Jonesjones@nceas.ucsb.edu
<p>Wrap R code in Kepler, and prepare demo.</p> EML - Feature #6283 (New): add field to reference data usage citationshttps://projects.ecoinformatics.org/ecoinfo/issues/62832013-12-06T15:51:34ZMatt Jonesjones@nceas.ucsb.edu
<p>Consider adding an optional top level field to eml-dataset to provide this, possibly something like:</p>
<p><code>/eml/dataset/dataUsageCitation which would be of type CitationType<br /></code></p>
<p>See discussion on eml-dev regarding this issue:<br /> <a class="external" href="http://lists.nceas.ucsb.edu/ecoinformatics/pipermail/eml-dev/2013-December/002004.html">http://lists.nceas.ucsb.edu/ecoinformatics/pipermail/eml-dev/2013-December/002004.html</a></p> MetacatUI - Feature #6032 (In Progress): Add schema.org dataset annotations to dataset viewshttps://projects.ecoinformatics.org/ecoinfo/issues/60322013-07-09T20:10:20ZMatt Jonesjones@nceas.ucsb.edu
<p>The current view page is envisioned as an HTML representation of a data set. Adding in RDFa tags using the schema.org datasets extension will allow machine parsers to trace their way back to the machine-readable versions of the datasets, including the direct download links. Will need to resolve the difference between a dcat:Dataset and an OAI-ORE ResourceMap-based package as we've defined in DataONE.</p>
<p>See <a class="external" href="http://www.w3.org/TR/vocab-dcat/">http://www.w3.org/TR/vocab-dcat/</a></p>
<p>See <a class="external" href="http://www.w3.org/wiki/WebSchemas/Datasets">http://www.w3.org/wiki/WebSchemas/Datasets</a><br /><a class="external" href="http://www.w3.org/wiki/WebSchemas/SchemaDotOrgProposals">http://www.w3.org/wiki/WebSchemas/SchemaDotOrgProposals</a></p>
<p>Good introduction (longer/ with more context):<br /><a class="external" href="http://www.slideshare.net/joshsh/semantic-markup-using-schemaorg">http://www.slideshare.net/joshsh/semantic-markup-using-schemaorg</a></p> EML - Feature #5998 (New): Add publication date property to keywordSethttps://projects.ecoinformatics.org/ecoinfo/issues/59982013-06-06T17:53:02Zben leinfelderleinfelder@nceas.ucsb.edu
<p>From Éamonn Ó Tuama [GBIF] <<a class="email" href="mailto:eotuama@gbif.org">eotuama@gbif.org</a>>:<br />---------<br />Both EML and ISO19115 provide fields for keywords and the name/title of associated thesaurus. However, if the thesaurus name is provided, in the case, of ISO19115, a publication date must also be included. In order to ensure maximum information transfer in cross walks from EML to the new North American Profile of ISO19115 [1], consider adding a conditional date (and date type) property to the EML keywordSet. See example in [2].</p>
<p>[1] <a class="external" href="http://nap.geogratis.gc.ca/metadata/napMetadata-eng.html">http://nap.geogratis.gc.ca/metadata/napMetadata-eng.html</a><br />[2] <a class="external" href="http://nap.geogratis.gc.ca/metadata/examples/napEx1.xml">http://nap.geogratis.gc.ca/metadata/examples/napEx1.xml</a></p> MetacatUI - Feature #5982 (New): Plans pagehttps://projects.ecoinformatics.org/ecoinfo/issues/59822013-05-25T01:10:02ZMatt Jonesjones@nceas.ucsb.eduMetacatUI - Task #5979 (In Progress): Choose new site namehttps://projects.ecoinformatics.org/ecoinfo/issues/59792013-05-25T01:07:21ZMatt Jonesjones@nceas.ucsb.edu
<p>The possibilities are endless....</p> MetacatUI - Feature #5972 (New): Implement pre-caching of one or more prior and next result pages...https://projects.ecoinformatics.org/ecoinfo/issues/59722013-05-25T00:55:10ZMatt Jonesjones@nceas.ucsb.eduEML - Bug #5731 (New): parser does not recognize attribute/@id in additionalMetadata/describeshttps://projects.ecoinformatics.org/ecoinfo/issues/57312012-11-08T21:03:03ZMargaret O'Brienmob@msi.ucsb.edu
<p>A document has an additionalMetadata section which describes a dataTable attribute. But the parser rejects it saying the referenced id does not exist in the given keys.</p>
<p>I think this is because "//attribute" was left off the list of elements in the <key name="identifierKey"> that the parser checks. I am assuming this was not deliberate.</p>
<p>example config file with <key name="identifierKey">:<br /><a class="external" href="http://svn.lternet.edu/websvn/filedetails.php?repname=EML&path=%2Ftrunk%2Feml-2.1.0%2Flib%2Fconfig.xml">http://svn.lternet.edu/websvn/filedetails.php?repname=EML&path=%2Ftrunk%2Feml-2.1.0%2Flib%2Fconfig.xml</a></p>
<p>Although the parser I used was <a class="external" href="http://knb.ecoinformatics.org/emlparser/index.html">http://knb.ecoinformatics.org/emlparser/index.html</a></p>
<p>Below is some skeleton EML. Obviously, the doc is not in Metacat because it is invalid.</p>
<p><dataset><br />...<br /> <attribute id="entity_1.NH4_uM" system="sbclter" scope="system"><br /> <attributeName>NH4_uM</attributeName><br />...<br /> </attribute><br />...<br /></dataset><br /><additionalMetadata><br /> <describes>entity_1.NH4_uM</describes><br /> <metadata><br /> <annotation> ... </annotation><br /> </metadata><br /></additionalMetadata></p> EML - Bug #5728 (New): I18N is incomplete in EML 2.1.1https://projects.ecoinformatics.org/ecoinfo/issues/57282012-11-05T07:29:39ZMAITA Eiichimaita.eiichi@nies.go.jp
<p>Multi-language extention of EML 2.1.1 is a good news<br />for Japan LTER Network because we intend to share<br />our data both nationally and internationally.<br />But I18N is incomplete in EML 2.1.1 for us,<br />so we hope that more textual elements are modified to<br />the i18n elements, especially the following elements;</p>
<p>project/title <br /> eml-project.xsd: 102</p>
<p>method/instrumentation<br /> eml-methods.xsd: 391</p>
<p>geographicCoverage/geographicDescription<br /> eml-coverage.xsd: 487<br />taxonCoverage/commonName<br /> eml-coverage.xsd: 1283</p>
<p>citation/article/journal<br /> eml-literature.xsd: 294<br />citation/article/volume<br /> eml-literature.xsd: 308<br />citation/article/issue<br /> eml-literature.xsd: 320<br />citation/book/edition<br /> eml-literature.xsd: 424<br />citation/book/volume<br /> eml-literature.xsd: 435<br />citation/report/reportNumber<br /> eml-literature.xsd: 603</p> EML - Bug #5704 (New): update documentation for species binomialshttps://projects.ecoinformatics.org/ecoinfo/issues/57042012-09-04T16:06:32ZMargaret O'Brienmob@msi.ucsb.edu
<p>The EML documentation needs an update to reflect correct practice when including a taxonomic species name. Taxonomically speaking, the 'species name' is a genus and the specific epithet. But looking at it from a strictly hierarchical node structure the specific epithet looks and acts like the other nodes. However a node 'alterniflora' has no taxon rank by itself.</p>
<p>LTER already reccommends this construction in its Best Practices, but actual implementations are inconsistent, perhaps because of the normative documentation.</p>
<p>Another note: The normative docs also seem to refer to "Acer rubrum" as the 'common name' of Red Maple, which is incorrect..</p>
<p>Here is an example of 2 implementations sent to eml-dev (from Wade Sheldon):</p>
<p>with binomial:</p>
<p><taxonomicClassification><br /> <taxonRankName>Genus</taxonRankName><br /> <taxonRankValue>Spartina</taxonRankValue><br /> <taxonomicClassification><br /> <taxonRankName>Species</taxonRankName><br /> <taxonRankValue>Spartina alterniflora</taxonRankValue><br /> </taxonomicClassification><br /></taxonomicClassification></p>
<p>without binomial:</p>
<p><taxonomicClassification><br /> <taxonRankName>Genus</taxonRankName><br /> <taxonRankValue>Spartina</taxonRankValue><br /> <taxonomicClassification><br /> <taxonRankName>Species</taxonRankName><br /> <taxonRankValue>alterniflora</taxonRankValue><br /> </taxonomicClassification><br /></taxonomicClassification></p>
<p>Here is the text from the EML 2.1.1 normative docs:<br />(<a class="external" href="http://knb.ecoinformatics.org/software/eml/eml-2.1.1/eml-coverage.html">http://knb.ecoinformatics.org/software/eml/eml-2.1.1/eml-coverage.html</a>)<br />seem to suggest the opposite approach:</p>
<p>"The name representing the taxonomic rank of the taxon being described.<br />The values included may be referenced from an authoritative source such<br />as the Integrated Taxonomic Information System (ITIS)in the U.S.<br />(<a class="external" href="http://www/itis.usda.gov">http://www/itis.usda.gov</a>) and in Canada<br />(<a class="external" href="http://sis.agr.gc.ca/pls/itisca/taxaget">http://sis.agr.gc.ca/pls/itisca/taxaget</a>). Also, Species2000 is another<br />source of taxonomic information, found at (<a class="external" href="http://www.sp2000.org">http://www.sp2000.org</a>)<br />Example(s):<br />Acer would be an example of a genus rank value, and rubrum would be an<br />example of a species rank value, together indicating the common name of<br />red maple. It is recommended to start with Kingdom and include ranks<br />down to the most detailed level possible."</p> EML - Bug #5617 (New): date time format strings need a systemhttps://projects.ecoinformatics.org/ecoinfo/issues/56172012-06-05T20:45:23ZMargaret O'Brienmob@msi.ucsb.edu
<p>EML has a formatString element that takes text strings, and the spec give several examples. Translating dates would be much easier if the system which specified the format was included.</p>
<p>This data: 01May2007</p>
<p>The spec example suggests DDWWWYYYY<br />which is specified by the system [unknown]</p>
<p>Another representation of this date is</p>
<p><formatString>DDMonYYYY</formatString></p>
<p>which can be read directly by postgresql. So using something like this:<br /><formatString system="sql">DDMonYYYY</formatString></p>
<p>would be more informative and make interpretation easier for code like the DML.</p>
<p>example doc using this date format: knb-lter-sbc.61.1</p> SEEK - Bug #2422 (New): Changing Logging Options Prevent Metadata Downloadshttps://projects.ecoinformatics.org/ecoinfo/issues/24222006-04-20T18:37:01ZDavid Sledgedsledge@lternet.edu
<p>In the file log4j.properties in kepler's base directory, changing the line that reads:</p>
<pre><code>log4j.rootLogger=WARN, CONSOLE, R</code></pre>
<p>to:</p>
<pre><code>log4j.rootLogger=DEBUG, CONSOLE, R</code></pre>
<p>prevents Metadata from being downloaded from Metacat. With the ecogrid webapp--which uses the same API that kepler uses to access data on the ecogrid--the lack of a log4j.properties file prevented the metadata from being downloaded.</p>
<p>In both cases, org.ecoinformatics.ecogrid.queryservice.stub.EcoGridQueryLevelOneServiceStub.get() threw a ClassCastException.</p>
<p>Kepler:</p>
<p>java.lang.ClassCastException: java.lang.String<br /> at <br />org.ecoinformatics.ecogrid.queryservice.stub.EcoGridQueryLevelOneServiceStub.get(EcoGridQueryLevelOneServiceStub.java:310)<br /> at <br />org.ecoinformatics.ecogrid.queryservice.EcogridGetToStreamClient.get(EcogridGetToStreamClient.java:81)<br /> ...</p>
<p>Webapp:</p>
<p>java.lang.ClassCastException: java.lang.String<br /> at org.ecoinformatics.ecogrid.queryservice.stub.EcoGridQueryLevelOneServiceStub.get(Unknown Source)<br /> at org.ecoinformatics.ecogrid.queryservice.EcogridGetToStreamClient.get(Unknown Source)<br /> ...</p> EML - Bug #1605 (In Progress): missing or erroneous SI units in unitDictionaryhttps://projects.ecoinformatics.org/ecoinfo/issues/16052004-06-16T16:36:53ZMargaret O'Brienmob@msi.ucsb.edu
<p>1. The SI-derived unit "steradian" (sr) appears to be missing. it describes a<br />solid angle, and is the 3-dimensional equivalent of "radian". I dont believe it<br />can be described in terms of any other unit.</p>
<p>2. the "waveNumber" unit is more correctly called reciprocalMeter (m-1), and<br />waveNumber is one of the measurements expressed by this unit (ie, waveNumber=the<br />number of wave cycles in 1 meter). Other measurements which are expressed in m-1<br />include absorbance, scattering and transmittance.</p>
<p>3. the unit "kilogramPerCubicMeter" is named inconsistently. It seems that it<br />should be plural, ie kilogramsPerCubicMeter. This is consistent with other unit<br />names (milligramsPerCubicMeter) and also how it is referenced as a ParentSI<br />attribute.</p> Morpho - Bug #570 (In Progress): convert editor/DocFrame to use MorphoFramehttps://projects.ecoinformatics.org/ecoinfo/issues/5702002-08-22T18:27:48ZMatt Jonesjones@nceas.ucsb.edu
<p>The current editor package has a class DocFrame that extends JFrame. It needs<br />to be changed so that all editor windows are instances of MorphoFrame so that<br />they get all of the menus and toolbars. DocFrame is complex, so this might take<br />some redesign.</p>