SEEK: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-02-11T22:05:25ZEcoinformatics Redmine
Redmine Bug #3145 (New): Fix [or remove] web interface for ecogrid queryhttps://projects.ecoinformatics.org/ecoinfo/issues/31452008-02-11T22:05:25Zben leinfelderleinfelder@nceas.ucsb.edu
<p>The Kepler user manual docs (chapter 6) have link to:<br /><a class="external" href="http://seek.ecoinformatics.org/Wiki.jsp?page=EarthGridPortal">http://seek.ecoinformatics.org/Wiki.jsp?page=EarthGridPortal</a><br />which in turn has a link to:<br /><a class="external" href="http://ecogrid.ecoinformatics.org/ecogrid/advancedQuery.jspx">http://ecogrid.ecoinformatics.org/ecogrid/advancedQuery.jspx</a></p>
<p>This search returns no data for KNB. Jing and I suspect it is due to the change in ecogrid query service names. The search should probably be updated to reflect those new endpoints. Also note that it has an option for searching GEON, too. The GEON service has not been operational for sometime, and could also be commented out, at the very least.</p> Bug #2731 (New): Make TCS document the direct data sourcehttps://projects.ecoinformatics.org/ecoinfo/issues/27312007-01-17T01:35:00Zxianhua liurobertliu325@yahoo.com
<p>Develop new functions to directly access TCS document.</p> Bug #2730 (New): Publication problemhttps://projects.ecoinformatics.org/ecoinfo/issues/27302007-01-17T01:30:39Zxianhua liurobertliu325@yahoo.com
<p>For publication let's use be use to implement both short and long full text and guid. The rest is unnecessary for now.</p> Bug #2729 (New): Support third party parent-child relationshiphttps://projects.ecoinformatics.org/ecoinfo/issues/27292007-01-17T01:28:45Zxianhua liurobertliu325@yahoo.com
<p>Third party parent-child, and should we allow parents to be specified for genus in definition.</p> Bug #2728 (New): XML Output problemhttps://projects.ecoinformatics.org/ecoinfo/issues/27282007-01-17T01:23:45Zxianhua liurobertliu325@yahoo.com
<p>Mostly validation was fine, but one minor problem was <br />identified. TaxonRankEnum X puts in string like genus, when <br />should be TaxonomicRankGenusEnum. Suggest validate with XMLSpy or <br />Oxygen</p> Bug #2727 (New): lost data during importhttps://projects.ecoinformatics.org/ecoinfo/issues/27272007-01-17T01:20:04Zxianhua liurobertliu325@yahoo.com
<p>One problem is that superfluous stuff is lost. For example:<br /><teeth>Y-5 molar pattern</teeth><br />We should capture all this in some form of buffer so it can be <br />exported. For example, all 18 relationship types shoudl come in and go out.</p> Bug #2694 (New): Change get operation in EcoGridQueryInterfaceLevelOne from soap binding to http ...https://projects.ecoinformatics.org/ecoinfo/issues/26942006-12-09T00:20:15ZJing Taotao@nceas.ucsb.edu
<p>Since ecogrid now is using pure axis web service, it is time to change get operation from soap binding to http binding. Http binding will use streaming and wouldn't use huge memory for getting big data set.</p> Bug #2693 (New): Ecogrid doesn't support relative URI in namespace element of query.xsdhttps://projects.ecoinformatics.org/ecoinfo/issues/26932006-12-09T00:13:40ZJing Taotao@nceas.ucsb.edu
<p>In query.xsd there is a elemen named namespace and its type is anyURI. In auto-generated stub, the element was assigned a java object - org.apache.axis.types.URI and used consctutor is <abbr title="String url">URI</abbr>. This consctor doesn't support relative URI.</p> Bug #2682 (New): Add start and stop dates to concepts and relationshipshttps://projects.ecoinformatics.org/ecoinfo/issues/26822006-11-27T17:10:40ZRobert Peetpeet@unc.edu
<p>We need to add start (and probably stop) dates to concepts and relationships for use with references that are continuously changing. We track Alan Weakley's concepts and relationships in conceptmapper, but Alan is continuously making changes and we need to be able to reconstruct his perspective at any given time, beause otherwise the work is not citable. The alternative solution is to have an enormous number of Weakley references, perhaps thousands in any given year. We could use just start dates and do some logical sorting to find the most recent relevant concept or relationship, but the inclusion of end dates (a minor denormalization?) would make the situation clearer and computationally more tractable. I am not at all sure how to embed start and stop dates in TCS. Perhaps we need our own upgrade to TCS. I will copy this to Jessie and Aimee to see if they have advice.</p> Bug #2650 (New): ecogrid returnfields need to support more xpathhttps://projects.ecoinformatics.org/ecoinfo/issues/26502006-11-08T18:26:25ZChad Berkleyberkley@nceas.ucsb.edu
<p>When you are dealing with documents that store a lot of information in xml attributes instead of CDATA nodes, it is imperative that xpath attribute queries work correctly. AFAICT, they don't work at all with the ecogrid returnfields. For instance, the element:</p>
<p><property name="semanticType000" class="org.kepler.sms.SemanticType" <br /> value="urn:lsid:localhost:onto:1:1#Variable"><br /></property></p>
<p>The only meaniful way to get one of the attributes values based on another is via an attribute query like:</p>
<p>//property/[@name='semanticType000']/@value</p>
<p>which should return the value attribute of any property node with a name attribute equal to 'semanticType000'.</p> Bug #2649 (New): Ecogrid returnfields don't return enough informationhttps://projects.ecoinformatics.org/ecoinfo/issues/26492006-11-08T18:21:16ZChad Berkleyberkley@nceas.ucsb.edu
<p>When using returnfields in an ecogrid query, the original xpath used in the returnfield is not returned with the results, making it very difficult to parse the results. When a query is submited, a ResultsetTypeRecordReturnfield object is returned. This object only has two useful methods: get_value() and getId(). I thought getId() would return the original xpath query used to create the returnfield, but instead it returns a cryptic identifier starting with 'f' then a number.</p>
<p>Example:<br />Given these returnfields:<br /><returnField>/entity/@name</returnField><br /><returnField>/entity/property/@name</returnField><br /><returnField>/entity/property/@value</returnField></p>
<p>And this input document:</p>
<p><entity name="Variable Setter" class="ptolemy.kernel.ComponentEntity"><br /> <property name="entityId" value="urn:lsid:kepler-project.org:actor:10:2" <br /> class="org.kepler.moml.NamedObjId"/><br /> <property name="documentation" class="org.kepler.moml.DocumentationAttribute"><br /> null<br /> </property></p>
<pre><code>&lt;property name="class" value="ptolemy.actor.lib.SetVariable" <br /> class="ptolemy.kernel.util.StringAttribute"><br /> &lt;property name="id" value="null" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;/property&gt;</code></pre>
<pre><code>&lt;property name="kepler:input" class="org.kepler.moml.PortAttribute"&gt;<br /> &lt;property name="direction" value="input" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;property name="dataType" value="unknown" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;property name="isMultiport" value="false" <br /> class="ptolemy.kernel.util.StringAttribute"/><br /> &lt;/property&gt;</code></pre>
<pre><code>&lt;property name="variableName" class="ptolemy.kernel.util.StringAttribute" <br /> value="parameter"><br /> &lt;/property&gt;<br /> &lt;property name="delayed" class="ptolemy.data.expr.Parameter" value="true"&gt;<br /> &lt;/property&gt;<br /> &lt;property name="semanticType000" class="org.kepler.sms.SemanticType" <br /> value="urn:lsid:localhost:onto:1:1#Variable"><br /> &lt;/property&gt;<br /> &lt;property name="semanticType111" class="org.kepler.sms.SemanticType" <br /> value="urn:lsid:localhost:onto:2:1#LocalInput"><br /> &lt;/property&gt;<br /> &lt;property name="_location" class="ptolemy.kernel.util.Location" <br /> value="{250, 300}"><br /> &lt;/property&gt;<br /> &lt;property name="karId" class="ptolemy.kernel.util.StringAttribute" <br /> value="urn:lsid:kepler-project.org:kar:11:1"><br /> &lt;/property&gt;<br />&lt;/entity&gt;</code></pre>
<p>You will get returnfields (in the format getId():get_value()) like this:<br />returnfield: f0:Variable Setter<br />returnfield: f1:entityId<br />returnfield: f2:urn:lsid:kepler-project.org:actor:10:2<br />returnfield: f1:documentation<br />returnfield: f1:class<br />returnfield: f2:ptolemy.actor.lib.SetVariable<br />returnfield: f1:kepler:input<br />returnfield: f1:variableName<br />returnfield: f2:parameter<br />returnfield: f1:delayed<br />returnfield: f2:true<br />returnfield: f1:semanticType000<br />returnfield: f2:urn:lsid:localhost:onto:1:1#Variable<br />returnfield: f1:semanticType111<br />returnfield: f2:urn:lsid:localhost:onto:2:1#LocalInput<br />returnfield: f1:_location<br />returnfield: f2:{250, 300}<br />returnfield: f1:karId<br />returnfield: f2:urn:lsid:kepler-project.org:kar:11:1</p>
<p>Instead, there either needs to be a new method, getQuery(), that would return the query for each field, or the getId() should return the query or some other more meaninful identifier.</p> Bug #2491 (New): Get ecogrid endpoints from Ecogrid registryhttps://projects.ecoinformatics.org/ecoinfo/issues/24912006-07-17T18:31:06ZDavid Sledgedsledge@lternet.edu
<p>Sibling bug to bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: Get ecogrid endpoints from Ecogrid registry (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2490">#2490</a> in kepler.</p>
<p>Currently, individual endpoints for SRB, metacat, GEON, and Digir ecogrid implementations are stored in a config file for the ecogrid portal. Unfortunately, these endpoint may change. Ecogrid needs to be updated to retreive these from the Ecogrid registry (daily? hourly?) so that they can change and just send new values to the registry.</p> 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> Bug #2364 (New): Records Crossing the International Datelinehttps://projects.ecoinformatics.org/ecoinfo/issues/23642006-02-21T20:33:19ZDavid Sledgedsledge@lternet.edu
<p>Because the language used for querying ecogrid nodes can only compare fields to<br />constants:</p>
<p><condition operator="LESS THAN" concept="westBoundary">-23.0</condition></p>
<p>it's possible for records whose bounding coordinates cross the International<br />Date Line to be returned when they shouldn't be and to not return when<br />circumstances dictate that they should.</p>
<p>In order to construct a query to correctly handle such records, a means is<br />needed to compare a field to another field within a record (e.g. westBoundary ><br />eastBoundary).</p> Bug #2006 (New): workflow development for biodiversity/productivity use casehttps://projects.ecoinformatics.org/ecoinfo/issues/20062005-03-10T00:51:55ZDeana Penningtondpennington@lternet.edu
<p>Develop Kepler workflow for biodiversity/productivity use case. Involves:</p>
<p>composite workflow 1<br />a) input is multiple data sets annotated with terms from a standard ontology. <br />In this case, experimental data comparing species richness and productivity on<br />control plots and treated plots with nitrogen added, from many LTER sites (Elsa<br />Cleland will be working on these as part of her postdoc at NCEAS)<br />b) KR/SMS constructs an integrated dataset from the annotations<br />c) requires conversion of biomass and cover% values to a common measure of NPP.<br /> We have partial details on this conversion; will be specified in full at a<br />meeting in September (or earler by e-mail, if we get to this earlier)</p>
<p>composite workflow 2<br />a) Input data is output from data integration piece developed in KR/SMS in<br />composite workflow 1<br />b) Construct site by species matrix<br />c) Use bootstrapping to calculate average number of species for different areas<br />d) Output species count/area data file<br />e) Logistic regression model of data<br />f) Output graph with points and curves</p>
<p>composite workflow 3<br />compare multiple graphs. Specifications to come later</p>
<p>composite workflow 4<br />link experimental findings with broad scale study of increased nitrogen<br />deposition due to urban sprawl. Specifications to come later</p>
<p>Contacts:<br />Deana, Steve Cox (who has some of the code in R), David Chalcraft, Evan Weiher,<br />Elsa Clelans, Katie Suding</p>
<p>Will hold follow up meeting in late Sep at NCEAS to further develop workflows.</p>