Semtools: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-05-12T17:44:52ZEcoinformatics Redmine
Redmine Bug #5004 (New): oboe: create an oboe-examples ontology for documenting "best practices"https://projects.ecoinformatics.org/ecoinfo/issues/50042010-05-12T17:44:52ZShawn Bowersbowers@gonzaga.edu
<p>Should be comprised of a set of examples from the oboe "getting started" guide. These examples should also encode "best practices" with respect to using oboe.</p> Bug #5003 (New): oboe: develop a high-level "getting started" guide / documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/50032010-05-12T17:41:51ZShawn Bowersbowers@gonzaga.edu
<p>This should also include a set of simple examples and a corresponding ontology oboe-examples simply for the sake of the guide.</p> Bug #5002 (New): oboe-unit: create new oboe-unit for oboe-corehttps://projects.ecoinformatics.org/ecoinfo/issues/50022010-05-12T17:38:51ZShawn Bowersbowers@gonzaga.edu
<p>Modify the current oboe-unit to conform to the new oboe-core structure. Primarily requires modifying the characteristic hierarchy (simplify).</p> Bug #5001 (New): oboe-core: ensure new characteristic structure still supports unit conversionhttps://projects.ecoinformatics.org/ecoinfo/issues/50012010-05-12T16:12:58ZShawn Bowersbowers@gonzaga.edu
<p>This needs to be done using some examples ... maybe a "unit-test" ontology (not sure what this would be)?</p> Bug #4946 (New): Look-ahead search freezeshttps://projects.ecoinformatics.org/ecoinfo/issues/49462010-04-19T20:18:43Zben leinfelderleinfelder@nceas.ucsb.edu
<p>In the ontology browser, quick typing will render the popup useless.<br />My hunch is that it will go away when we stop searching the class descriptions.</p> Bug #4935 (New): Lazily load semtools pluginhttps://projects.ecoinformatics.org/ecoinfo/issues/49352010-04-07T21:06:51Zben leinfelderleinfelder@nceas.ucsb.edu
<p>While Morpho has a good framework for developing and loading plugins for the application, it does not have a way to enable/disable plugins that are installed. Nor does it have a mechanism for installing or upgrading plugins on an existing installation.<br />I think it's unlikely that we'll get to the install/upgrade phase, but I think it would be nice (as does MOB) to have the choice of enabling the annotation menus and tables so that it's not always in your face.</p>
<p>I suppose this would be controlled in something like a File->Manage Plugins... action. <br />Ideally you would not have to restart Morpho after changing the plugins that are enabled, but I think it could get ugly if not (menu bars, for instance).</p> 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> 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> 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> 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> 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> 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> 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> 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> Bug #4675 (New): EML:DataTable:Annotation cardinalityhttps://projects.ecoinformatics.org/ecoinfo/issues/46752010-01-15T17:58:22Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Currently we have the following relationships:<br />(1) EML Datapackage<br />(1...n) DataTables in the Datapackage<br />(1) Annotation per DataTable</p>
<p>Option A (as is):<br />It is possible to have multiple Annotations per DataTable (an additional file for each annotation-datatable pair) but this is not yet implemented in the Morpho plugin.</p>
<p>Option B (enhancement):<br />Alternatively, we might want to have a single Annotation annotate multiple dataTables (one file for multiple datatable annotations). This is not yet implemented/supported in the Annotation Schema.</p>