EML: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-07-03T18:11:39ZEcoinformatics Redmine
Redmine 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> 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> Feature #6079 (New): Support JSON or XML output from emlparserhttps://projects.ecoinformatics.org/ecoinfo/issues/60792013-09-06T18:12:45Zben leinfelderleinfelder@nceas.ucsb.edu
<p>The online parser servlet returns HTML, but there has been a request to support alternate output formats for programatic interactions.</p>
<p>Matt's proposed schema<br /><pre>
<!ELEMENT response (validation+)>
<!ELEMENT validation (message*)>
<!ATTLIST validation type (#PCDATA) #REQUIRED>
<!ATTLIST validation status (passed | failed) #REQUIRED>
<!ELEMENT message (#PCDATA)>
</pre></p>
<p>and example:</p>
<pre>
<response>
<validation type="emlparse" status="failed">
<message>Missing key for reference to node "154A12"</message>
<message>Missing key for reference to node "26A467"</message>
</validation>
<validation type="saxparse" status="passed" />
</response>
</pre> 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> Bug #4939 (New): buildDocBook.xsl missing from release distributionhttps://projects.ecoinformatics.org/ecoinfo/issues/49392010-04-15T22:41:40ZMatt Jonesjones@nceas.ucsb.edu
<p>Gallagher reports:</p>
<p>Anyway, the file buildDocBook.xsl is missing from the tar.gz dist of eml<br />2.1.0. This shows when the clean target is run because that target<br />erases the docs. The docs target requires the xsl...</p> Bug #4393 (New): Use datamanager for EML QA/QChttps://projects.ecoinformatics.org/ecoinfo/issues/43932009-09-17T20:24:06Zben leinfelderleinfelder@nceas.ucsb.edu
<p>As discussed at the LTER meeting this year:<br />------------<br />Work Group: Metrics and reports for EML data package quality<br />The EML data manager library (contributors: Costa, Tao, Leinfelder, Servilla) was created to parse EML metadata documents and insert the described data entity into a relational database. Our experience using the library with data packages contributed to the LTER NIS indicates that a large fraction do not have metadata of sufficient quality for the data to be used in this way. The primary contribution from LTER sites to the NIS is data sets, which are intended to be used in cross-site synthesis projects. Clearly, for cross-site synthesis to make use of the NIS a certain minimum level of metadata and data quality is required.<br />The goals for this group:<br />1. establish a set of metrics for LTER EML data package quality,<br />2. recommend content for a report to be produced by the EML data manager library, and<br />3. consider implementation strategies, e.g. should the report be another choice on the EML parser page? a shell script similar to that included with the EML parser?</p>
<p>The quality reports can be used to<br />1. inform the dataset contributor about the content of the data package, and indicate whether data are of sufficient quality to be machine-readable. Our data catalog (metacat) has no quality standards beyond basic XML and EML compliance, so a data package that fails these quality metrics can still be uploaded or harvested, although its usefulness is limited.<br />2. in the LTER context, reports can produce a list of failure modes for LTER metadata and data entities. Such a list could provide input for the design of specific tools for data providers, or help identify gaps in a site's IM system. A site requesting supplemental funding for its IMS could use the reports as part of the proposal justification.</p>
<p>As a starting point for our discussion, I have started a flowchart based on my own experience with the data manager library and SBC's EML data packages.</p>
<p>Here is the current membership (on this cc list, and present in Estes Park):<br />Margaret O'Brien, SBC<br />Emery Boose, HFR<br />Dan Bahauddin, CDR<br />James Brunt, LNO<br />Mark Servilla, LNO<br />Duane Costa, LNO<br />Mark Shildhauer, NCEAS<br />Ben Leinfelder, NCEAS</p> Bug #3499 (New): attribute BoundsGroup may be retyped in a future schema-1.1https://projects.ecoinformatics.org/ecoinfo/issues/34992008-09-30T21:33:50ZMargaret O'Brienmob@msi.ucsb.edu
<p>Resolution of bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: Base datatypes in eml-attribute BoundsGroup preclude scientific notation (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2272">#2272</a> will be to retype boundsGroup's limits to xs:float. <br />However, schema-1.1 may include a new data type which will have features of both float and decimal, called xs:precisionDecimal. see bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: Base datatypes in eml-attribute BoundsGroup preclude scientific notation (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2272">#2272</a> or links below:</p>
<p><a class="external" href="http://www.w3.org/TR/xmlschema11-2/#precisionDecimal">http://www.w3.org/TR/xmlschema11-2/#precisionDecimal</a><br /><a class="external" href="http://www.w3.org/XML/2007/dc.pd.html">http://www.w3.org/XML/2007/dc.pd.html</a> (and its references)<br /><a class="external" href="http://754r.ucbtest.org/">http://754r.ucbtest.org/</a></p> Bug #3181 (New): xs:string to ComplexType TextType, minOccurs=0, judiciously appliedhttps://projects.ecoinformatics.org/ecoinfo/issues/31812008-03-21T23:13:51ZMargaret O'Brienmob@msi.ucsb.edu
<p>This is a summary of a recent discussion on eml-dev which does not appear to have been entered in bugzilla.<br />Several people have expressed a need for additional structure in leaf nodes that are currently designated xs:string, generally to accommodate formatting for species binomials, chemical notation and lists. Examples include <title>, <method>, and <protocol>.</p>
<p>One solution is to change these from xs:string to txt:TextType. Since TextType is mixed content, it will not affect existing documents containing strings. The nodes to apply this change should be agreed on by this group, and this is not meant to be a work-around for eml which needs enhancement. Database implementations will need to correctly interpret the data typing when searching these elements. For more info on TextType, see bug 2703, and the docbook schema (<a class="external" href="http://www.docbook.org/specs/">http://www.docbook.org/specs/</a>).</p>
<p>EML 2.0.1 title element:<br /><xs:element name="title" type="xs:string" maxOccurs="unbounded"></p>
<p>EML 2.0.2 proposed title element:<br /><xs:element name="title" type="txt:TextType" maxOccurs="unbounded"></p>
<p>Either of these is valid:<br /><eml><br /> <dataset><br /> <title>Uptake of nitrogen by Alnus tenuifolia and Alnus crispa in six different successional habitats</title><br /> ...<br /> </dataset><br /></eml></p>
<p><eml><br /> <dataset><br /> <title>Uptake of nitrogen by<br /> <emphasis>Alnus tenuifolia</emphasis> and<br /> <emphasis>Alnus crispa</emphasis><br /> in six different successional habitats</title><br /> ...<br /> </dataset><br /></eml></p> Bug #2702 (New): Data Manager Library: Support for online URL referenceshttps://projects.ecoinformatics.org/ecoinfo/issues/27022006-12-15T16:44:49ZDuane Costadcosta@lternet.edu
<p>Next release. Again, this will be rare. Not much to be gained from a URL reference.</p>
<p>Matt</p>
<p>Duane Costa wrote:</p>
<blockquote>
<p>Matt, Mark:</p>
<p>Do you think that handling references to online URLs should be a <br />requirement for the first release of the Data Manager Library (1.0.0), or recorded as an enhancement for the next release (1.1.0)?</p>
<p>Thanks,<br />Duane</p>
<blockquote>
<p>-----Original Message-----<br />From: Jing Tao [mailto:<a class="email" href="mailto:tao@nceas.ucsb.edu">tao@nceas.ucsb.edu</a>]<br />Sent: Wednesday, December 13, 2006 9:06 PM<br />To: Duane Costa<br />Cc: 'inigo san gil'; 'Mark Servilla'<br />Subject: RE: In-line data</p>
<p>Hi, Duane:</p>
<p>Yeah, current eml parser coudn't handle the reference for online url. <br />It can handle reference for attributeList and attribute. We can add <br />supporting online url reference as new feature into our data manager <br />library.</p>
<p>Thanks,</p>
<p>Jing</p>
<p>Jing Tao<br />National Center for Ecological<br />Analysis and Synthesis (NCEAS)<br />735 State St. Suite 204<br />Santa Barbara, CA 93101</p>
<p>On Wed, 13 Dec 2006, Duane Costa wrote:</p>
<blockquote>
<p>Date: Wed, 13 Dec 2006 15:37:27 -0700<br />From: Duane Costa <<a class="email" href="mailto:dcosta@lternet.edu">dcosta@lternet.edu</a>><br />To: 'Jing Tao' <<a class="email" href="mailto:tao@nceas.ucsb.edu">tao@nceas.ucsb.edu</a>><br />Cc: 'inigo san gil' <<a class="email" href="mailto:isangil@lternet.edu">isangil@lternet.edu</a>>,<br />'Mark Servilla' <<a class="email" href="mailto:servilla@lternet.edu">servilla@lternet.edu</a>><br />Subject: RE: In-line data</p>
<p>Hi Jing,</p>
<p>Inigo and I have looked into the second issue below a</p>
</blockquote>
<p>little more (the</p>
<blockquote>
<p>question about FTP protocol). The problem was not the FTP</p>
</blockquote>
<p>protocol --</p>
<blockquote>
<p>we changed to HTTP and the Data Manager library had the</p>
</blockquote>
<p>same problem downloading the data. The problem is that the metadata <br />is using a reference to the URL to the data like this:</p>
<blockquote>
<p><dataTable><br />.<br />.<br />.<br /><distribution><br /><references>distributionReference</references><br /></distribution></p>
<p>In another part of the EML, we have:</p>
<p><distribution id="distributionReference"> <online><br /><url><br /><a class="external" href="http://lternet.lternet.edu/~isangil/NIN/nin_met_1982.txt">http://lternet.lternet.edu/~isangil/NIN/nin_met_1982.txt</a><br /></url><br /></online><br /></distribution></p>
<p>Because of the reference, Data Manager has no value for the</p>
</blockquote>
<p>entity identifier, and the download handler is not able to download <br />the</p>
<blockquote>
<p>data. So it seems that this is a legal EML document but the</p>
</blockquote>
<p>EML parser is not able to follow the reference to the URL for the <br />data.</p>
<blockquote>
<p>Here is a link to the document that is having the problem:</p>
<p><a class="external" href="http://lternet.lternet.edu/~isangil/NIN/nin_lter_met_1982.xml">http://lternet.lternet.edu/~isangil/NIN/nin_lter_met_1982.xml</a></p>
<p>Could you take a look?</p>
<p>Thanks,<br />Duane</p>
</blockquote></blockquote></blockquote> Bug #2701 (New): Data Manager Library: Support for inline datahttps://projects.ecoinformatics.org/ecoinfo/issues/27012006-12-15T16:42:45ZDuane Costadcosta@lternet.edu
<p>Wait for the next release -- as far as I know there is very little or no inline data out there in the KNB collection.</p>
<p>Matt</p>
<p>Duane Costa wrote:</p>
<blockquote>
<p>Matt, Mark:</p>
<p>Do you think that handling inline data should be a priority for <br />release 1.0.0 of the Data Manager Library, or something that should be recorded in Bugzilla as an enhancement for the next release, 1.1.0?</p>
<p>Thanks,<br />Duane</p>
<blockquote>
<p>-----Original Message-----<br />From: Jing Tao [mailto:<a class="email" href="mailto:tao@nceas.ucsb.edu">tao@nceas.ucsb.edu</a>]<br />Sent: Wednesday, December 13, 2006 8:59 PM<br />To: Duane Costa<br />Subject: Re: In-line data</p>
<p>Hi, Duane:</p>
<p>Our datamanager couldn't handle inline data so far. Do you think this <br />feature has very high priority?</p>
</blockquote>
<p>.<br />.<br />.</p>
<blockquote>
<p>Jing</p>
<p>Jing Tao<br />National Center for Ecological<br />Analysis and Synthesis (NCEAS)<br />735 State St. Suite 204<br />Santa Barbara, CA 93101</p>
<p>On Wed, 13 Dec 2006, Duane Costa wrote:</p>
<blockquote>
<p>Date: Wed, 13 Dec 2006 12:20:05 -0700<br />From: Duane Costa <<a class="email" href="mailto:dcosta@lternet.edu">dcosta@lternet.edu</a>><br />To: 'Jing Tao' <<a class="email" href="mailto:tao@nceas.ucsb.edu">tao@nceas.ucsb.edu</a>><br />Subject: In-line data</p>
<p>Hi Jing,</p>
<p>We have some metadata that contains <inline> tags to the</p>
</blockquote>
<p>data. Is the</p>
<blockquote>
<p>Data Manager download handler able to use this to download the data?</p>
</blockquote></blockquote>
<p>.<br />.<br />.</p>
<blockquote><blockquote>
<p>Thanks,<br />Duane</p>
</blockquote></blockquote></blockquote> Bug #2688 (New): embedded text format ignored by Metacathttps://projects.ecoinformatics.org/ecoinfo/issues/26882006-12-06T21:58:17ZInigo Gilisangil@lternet.edu
<p>When metacat displays metadata documents, the original format is often lost. Newlines, new paragraphs, bullets and the like are largely ignored by the metacat stylesheets, and all spaced is lumped together, creating undesired results.</p>
<p>A number of solutions are being considered and some are deployed in the development metacat at the LTER network office.</p>
<p>A broad approach would be to prepend an html <pre> tag wherever the user has specified within EML that the content should be treated as <literalLayout>.
Another broad approach is to plant <pre> tags in critical sections such as methodology descriptions (I.e: eml/dataset/methods/description/) or in inline data.
Other workarounds are to explore trimming white space in targeted locations (at beginning and end, not everywhere). There are a handful of different XSL treatments of whitespace, carriage returns, line feeds and new line characters discussed at http://www.dpawson.co.uk/xsl/sect2/N8321.html</p></pre> Bug #1634 (New): units not in eml-unitDictionaryhttps://projects.ecoinformatics.org/ecoinfo/issues/16342004-07-10T00:44:32ZMargaret O'Brienmob@msi.ucsb.edu
<p>As requested, here is the list of customUnits used by sbclter (to date). The<br />current version of this list can be found at the url above. Several of these<br />units need addional attributes or definition. These are commonly-used units in <br />oceanography and limnology.</p>
<p><unit id="reciprocalMeter" name="reciprocalMeter" unitType="lengthReciprocal" <br />abbreviation="m-1" parentSI="meter" multiplerToSI="1"><br /><description>per meter, describes optical properties</description><br /></unit><br /><del><br /><unit id="reciprocalMetersPerSteradian" name="reciprocalMetersPerSteradian" <br />unitType="lengthReciprocal" abbreviation="m-1*sr-1" parentSI="meter" <br />multiplerToSI=""><br /><description>describes directional optical measurements</description><br /></unit><br /></del><br /><unit id="microwattsPerSquareCentimeterPerNanometer" <br />name="microwattsPerSquareCentimeterPerNanometer" unitType="power" parentSI="joule"><br /><description>irradance unit</description><br /></unit><br /><del><br /><unit id="microwattsPerSquareCentimeterPerNanometerPerSteradian" <br />name="microwattsPerSquareCentimeterPerNanometerPerSteradian" unitType="power" <br />parentSI="joule"><br /><description>directional irradiance unit</description><br /></unit><br /></del><br /><unit id="microeinsteinsPerSquareMeterPerSecond" <br />name="microeinsteinsPerSquareMeterPerSecond" unitType="energy" parentSI="joule"><br /><description><br />PAR irradiance unit, Seabird 911. 1Ein = energy of 1 mole photons<br /></description><br /></unit><br /><del><br /><unit id="microeinsteinsPerSquareCentimeterPerSecond" <br />name="microeinsteinsPerSquareCentimeterPerSecond" unitType="energy" <br />parentSI="joule"><br /></del><br /><description><br />PAR Scalar irradiance unit. 1Ein = energy of 1 mole photons<br /></description><br /></unit><br /><del><br /><unit id="decibar" name="decibar" unitType="pressure" abbreviation="dbar" <br />parentSI="pascal" multiplerToSI="10,000"><br /><description>pressure, oceanography</description><br /></unit><br /></del><br /><unit id="hectoPascal" name="hectoPascal" unitType="pressure" abbreviation="hPa" <br />parentSI="pascal" multiplerToSI="100"><br /><description><br />SI unit for atmospheric pressure, equivalent in magnitude to millibar<br /></description><br /></unit><br />-<br /><unit id="percent" name="percent" unitType="massPerMass" abbreviation="o/o" <br />parentSI="gramsPerGram" multiplerToSI=".01"><br /><description>parts per hundred</description><br /></unit></p>
<p><unit id="permil" name="permil" unitType="massPerMass" abbreviation="o/oo" <br />parentSI="gramsPerGram"><br /><description><br />parts per thousand relative to a std composition. UC-delta used for isotope<br />enrichment = (Rx / Rs - 1) ·1000. o/oo used for salinity<br /></description><br /></unit><br /><del><br /><unit id="sigma_unit" name="sigma_unit" unitType="massDensity" <br />parentSI="killogramsPerCubicMeter" constantToSI="-1000" multiplerToSI="1"><br /><description>seawater density = kg/m3 -1000</description><br /></unit><br /></del><br /><unit id="millimolesPerCubicMeter" name="millimolesPerCubicMeter" <br />unitType="amountOfSubstanceConcentration" abbreviation="mmol*m-3" <br />parentSI="molesPerCubicMeter" multiplerToSI=".001"><br /><description>concentration unit</description><br /></unit><br /><del><br /><unit id="micromolesPerLiter" name="micromolesPerLiter" <br />unitType="amountOfSubstanceConcentration" parentSI="molesPerCubicMeter" <br />multiplerToSI=".001"><br /><description><br />concentration, same magnitude as micromolar (for a dissolved constituent)<br /></description><br /></unit><br /></del><br /><unit id="microequivalentsPerLiter" name="microequivalentsPerLiter" <br />unitType="amountOfSubstanceConcentration" parentSI="molesPerCubicMeter" <br />multiplerToSI=""><br /><description><br />concentration of charge (on dissolved ions). A single multiplier to SI is not<br />possible, since conversion includes valence of ion.<br /></description><br /></unit><br /><del><br /><unit id="siemensPerMeter" name="siemensPerMeter" unitType="conductance" <br />abbreviation="S*m-1" parentSI="siemen" multiplerToSI="1"><br /><description>conductivity unit, seawater</description><br /></unit><br /></del><br /><unit id="microsiemensPerCentimeter" name="microsiemensPerCentimeter" <br />unitType="conductance" parentSI="siemen" multiplerToSI=".0001"><br /><description>conductivity unit, freshwater</description><br /></unit><br /><del><br /><unit id="milligramsPerSquareMeterPerDay" name="milligramsPerSquareMeterPerDay" <br />unitType="areaMassDensityRate" abbreviation="mg*m-2*d-1" <br />parentSI="kilogramsPerSquareMeterPerSecond" multiplerToSI="8.64E10"><br /><description><br />areal primary production rate, often in mg-Carbon for an integrated water column<br /></description><br /></unit><br /></del><br /><unit id="kilogramsPerSquareMeterPerDay" name="kilogramsPerSquareMeterPerDay" <br />unitType="areaMassDensityRate" abbreviation="kg*m-2*d-1" <br />parentSI="kilogramsPerSquareMeterPerSecond" multiplerToSI="86400"><br /><description><br />areal primary production rate, may be kg-DW, <del>Carbon or -nitrogen for kelp<br /></description><br /></unit><br /></del><br /><unit id="milligramsPerCubicMeterPerDay" name="milligramsPerCubicMeterPerDay" <br />unitType="volumetricMassDensityRate" abbreviation="mg*m-3*d-1" parentSI="" <br />multiplerToSI=""><br /><description><br />volumetric primary production rate, in a parcel of water<br /></description><br /></unit></p> Bug #1197 (New): dictionary needed for externallyDefinedFormathttps://projects.ecoinformatics.org/ecoinfo/issues/11972003-10-31T17:17:21ZPeter McCartneypeter.mccartney@asu.edu
<p>Externally defined format is useless for automatic processing unless you have<br />some idea what to look for. This is a step backwards from FGDC which at least<br />provided enumerations for the common file formats at the time.</p> Bug #1193 (New): Temporal Description Missing?https://projects.ecoinformatics.org/ecoinfo/issues/11932003-10-27T18:21:58ZChristy Bowlesbowles@nceas.ucsb.edu
<p>A temporal description field is not currently available. Should a temporal <br />description field (paragraph format) be available in EML 2?</p> Bug #501 (New): change in documentation structurehttps://projects.ecoinformatics.org/ecoinfo/issues/5012002-05-09T16:11:17ZChad Berkleyberkley@nceas.ucsb.edu
<p>We should change the structure of the documentation xsd so that each of the<br />documentation tags (summary, tooltip and description) are inlined into one bit<br />of text instead of sibling elements. The new documentation should look<br />something like</p>
<p><description><summary>The <tooltip>title field</tooltip> is used to generally<br />describe the resource.</summary> It is typically 15 to 20 words long, and<br />provides a concise yet thorough descrition of the resource.</documentation></p>