Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362013-09-06T18:12:45ZEcoinformatics Redmine
Redmine EML - 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> Metacat - Task #6040 (New): Metacat-index does not handle <references>https://projects.ecoinformatics.org/ecoinfo/issues/60402013-07-26T00:01:50Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I indexed a document from EVOS that uses a reference for a creator rather than the details of the person:<br /><pre>
<creator><references>1359152217358</references></creator>
</pre><br />But in the index it shows up as "||" instead of following the reference back the the id where it was declared:<br /><pre>
<associatedParty id="1359152217358">...
</pre></p>
<p><a class="external" href="http://evos.nceas.ucsb.edu/evos/metacat/df35c.9.14/default">http://evos.nceas.ucsb.edu/evos/metacat/df35c.9.14/default</a></p> Semtools - Bug #5371 (New): AnnotationManager: query performancehttps://projects.ecoinformatics.org/ecoinfo/issues/53712011-04-04T21:30:41Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Identify long-running aspects of semquery. First glance indicates that returning the metadata/annotation content to be displayed in Metacat is the biggest bottleneck. This is good and bad. It means using the DB for managing annotations is pretty efficient, but it also means that returning large results sets will not be so efficient.<br />Probable solution: include only a subset of annotation information in the resultset rather than the entire annotation xml content.</p> Semtools - Bug #5368 (New): Compound query conditionshttps://projects.ecoinformatics.org/ecoinfo/issues/53682011-04-04T21:05:18Zben leinfelderleinfelder@nceas.ucsb.edu
<p>We allow grouping of semantic query conditions, but not in the web UI. Adding grouping makes the UI much more complicated, but allows exact query authoring. We've taken a simpler approach that is largely based on browsing and drilling down iteratively after applying a set of conditions (thereby making an implicit intersection of the criteria and their results).<br />This is a place-holder bug to track whether we need to support super-expressive compound grouping.</p> Semtools - Bug #5367 (New): Verify "same observation as" query criteriahttps://projects.ecoinformatics.org/ecoinfo/issues/53672011-04-04T21:02:40Zben leinfelderleinfelder@nceas.ucsb.edu
<p>The "strict=true" query condition mode indicates that the criteria in that group must come from the same observation in order to be considered true. During testing, we should make sure that the query results reflect the desired distinction is being made.</p> Semtools - Bug #5366 (New): Integrate semantic query with keyword and spatial queryhttps://projects.ecoinformatics.org/ecoinfo/issues/53662011-04-04T20:53:23Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Combining semantic, keyword and spatial criteria will allow a smoother transition from non-semantic metadata to semantically annotated data. It will also allow us to refine query results further by limiting to specific organizations, locations, people, etc.</p>
<p>Metacat should support combining "squery", "semquery" and "spatialquery" actions in an extensible way that lets future query mechanisms contribute conditions to the query so that additional (or fewer) matches are returned.</p>
<p>This may require additional or wrapper syntax for specifying a compound, multi-faceted query.</p> Semtools - Bug #5365 (New): Context-based semantic queryhttps://projects.ecoinformatics.org/ecoinfo/issues/53652011-04-04T20:48:07Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Include interace for expressing context criteria for a semantic query. The query syntax allows context criteria, but there is no GUI for it. The criteria assume a basic context template rather than any specific entity (because of the general nature of the query there is not a concrete observation before submitting the query). Context is defined as <Entity> <Relationship> <Entity> and can be combined to further expand/refine context conditions. The classes are expanded using the ontology as you would expect.</p> Semtools - Bug #4856 (New): Ontology Browser as a non-modal palettehttps://projects.ecoinformatics.org/ecoinfo/issues/48562010-03-01T17:42:42Zben leinfelderleinfelder@nceas.ucsb.edu
<p>From Shawn:<br />---<br />5. I still think we should display the current drop-down term<br />selection as a panel in the right-hand side portion of the editor<br />(where the plain old metadata is viewed now). There are multiple<br />reasons for this: (a) currently when it is viewed as a drop down it<br />hides the table (i.e., what we are trying to annotate); (b) it<br />prohibits any kind of static interaction with the component, e.g., i<br />can't search it or look through it without performing an annotation;<br />and (c) I think we could add more features to the panel to make it<br />easier to search and see search results if it were a static widget on<br />the canvas, as opposed to a drop down. I think we could make this<br />context sensitive, but not "focus stealing". So, e.g., if I were to<br />click on the <characteristic> in the madlib, i'd only see active in<br />the "ontology palette" the characteristic portion.</p> Semtools - Bug #4855 (New): Reorder the Full Annotation rows to match madlib orderhttps://projects.ecoinformatics.org/ecoinfo/issues/48552010-03-01T17:39:36Zben leinfelderleinfelder@nceas.ucsb.edu
<p>From Shawn:<br />---<br />2. The full annotation should be more closely aligned to the terms<br />used in the madlib. So, e.g., It should go in this order:</p>
<pre><code>Characteristic<br /> Entity<br /> Standard<br /> Protocol<br /> Context</code></pre>
<p>3. This would mean we use a different identifier than ox -- maybe just<br />a number (and drop the o part, or Entity1, Entity2, etc.)</p> Semtools - Bug #4854 (New): Integrate Context Annotation tab with Column Annotation tabhttps://projects.ecoinformatics.org/ecoinfo/issues/48542010-03-01T17:37:57Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Make one compete madlib for the column annotation.<br />---<br />1. I'd like to see the context annotation tab be folded into the<br />column annotation tab. Specifically, I think the column annotation<br />should contain two madlib sentences:</p>
<pre><code>The &lt;characteristic&gt; of the &lt;entity&gt; was recorded using the<br />&lt;standard&gt; standard and the &lt;protocol&gt; protocol.</code></pre>
<pre><code>The &lt;entity&gt; was observed &lt;relationship&gt; the &lt;existing-entity&gt; [Add...]</code></pre>
<p>Where [Add...] is a button that adds another context sentence that can<br />be filled in.</p> Semtools - Bug #4772 (New): Annotation cell selection also selects data table cellhttps://projects.ecoinformatics.org/ecoinfo/issues/47722010-02-08T18:15:47Zben leinfelderleinfelder@nceas.ucsb.edu
<p>It seems that part of column model sharing between the annotation table and the data table results in the cell selection also being shared. It's not a huge deal, but it does make the data table get marked as "dirty" and then you're prompted to save the changes even if you haven't made any changes.</p>
<p>I want the columns to continue to be aligned, but I want different cell selection models. Oh, and I also want the column selection models to be shared. Hmm...</p> Semtools - Bug #4771 (New): Decide permission policy for Annotations and Ontologies in Metacathttps://projects.ecoinformatics.org/ecoinfo/issues/47712010-02-07T06:55:35Zben leinfelderleinfelder@nceas.ucsb.edu
<p>My proposal:<br />-public read on all Ontologies<br />-same permissions as EML for Annotations that annotate that EML</p>
<p>This will be set via the recently-new setAccess API in Metacat.</p> Semtools - Bug #4770 (New): Load Annotations from Metacat in Annotation pluginhttps://projects.ecoinformatics.org/ecoinfo/issues/47702010-02-07T06:48:30Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Currently only locally stored annotations are loaded (at startup when the Annotation Plugin is initialized).<br />For a large local corpus of EML data packages that all have annotations, this could get costly. Moreover, loading <em>all</em> remote annotations would be a nightmare if we did it at start up (worst case scenario).<br />I think the best approach for remote files will be to search for and load their annotations when they themselves are opened.<br />We want to continue to load local annotations (until we run into a memory limit and have to solve that problem) so that we can continue to support the current annotation-based searching.</p>
<p>So back to the topic of this bug:<br /><del>when a DP is opened from the remote repository, the associated annotation[s] should be downloaded and loaded into the SMS manager. This will allow us to continue annotating the DP as though it were local. (Perhaps we should force a network</del>>local synchronization before annotation begins? TBD)</p> Semtools - Bug #4769 (New): Save annotations to networkhttps://projects.ecoinformatics.org/ecoinfo/issues/47692010-02-07T06:41:44Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Currently only supporting saving Annotations to local store<br />This has implications for loading Annotations as well since that currently happens when the Annotation Plugin loads at start up.</p> Semtools - Bug #4724 (New): Mark data package as changed when Annotation is editedhttps://projects.ecoinformatics.org/ecoinfo/issues/47242010-02-02T21:32:27Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Currently you can make as many changes as you want to an Annotation without ever changing the EML data package that it is referring to. This means:<br /><del>you can close the data package without being prompted to save the annotation<br />-if you use the File</del>>Save... menu you will not be able to save the the location you are currently working from ("local" will be greyed out in the most typical case).</p>
<p>If we mark the EML package as dirty, then we will always save both EML and Annotations when the save is invoked.<br />Unfortunately this will inflate the EML revision number and also makes it look like Annotating is an act of "editing" the EML.</p>
<p>At this point there is a separate "Save Annotations" option in the Annotation menu bar but it has rightly been deemed confusing.</p>