Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-10-22T20:07:51ZEcoinformatics Redmine
Redmine Bug #3552 (In Progress): Annotation elements in trace file do not appear in details pane of prove...https://projects.ecoinformatics.org/ecoinfo/issues/35522008-10-22T20:07:51ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>The provenance browser shows the details for the selected data or collection element of a trace in the lower left-hand panel. When the element selected has been annotated with one or more Metadata elements, these appear as name-value pairs under the heading "Annotations" in that panel. However, if an <strong>Annotation</strong> element has been applied to the selected element, it is not displayed.</p>
<p>Annotation and Metadata elements should both appear in the details panel, probably under two distinct headings, 'Metadata' and 'Annotations'.</p>
<p>(Note that the distinction between metadata and annotations in COMAD is that the former are reserved for things that have always been true about the item it is associated with, while the former can be used for any purpose. Consequently, Metadata elements cannot be deleted or replaced during a COMAD workflow run, while Annotation elements can be.)</p> Bug #2362 (In Progress): DataSourceIcon: use new SVG Icons dynamically, instead of drawing iconhttps://projects.ecoinformatics.org/ecoinfo/issues/23622006-02-21T00:55:39ZMatthew Brookebrooke@nceas.ucsb.edu
<p>org.ecoinformatics.seek.datasource.DataSourceIcon (used by the EML200DataSource<br />actor, among others) draws its own icon dynamically - changing to show error,<br />loading and ready conditions.</p>
<p>Instead, (or in addition, depending on config), it should use the SVG icons like<br />the other actors do - changing them out dynamically to reflect the same states</p>
<p>This is not critical for 1.0, since the code has already been changed to draw<br />the icon to match the new icon-set design; however, it will become an issue<br />if/when the icon designs change.</p> Bug #2359 (In Progress): enable/disable menu items and toolbar items as appropriatehttps://projects.ecoinformatics.org/ecoinfo/issues/23592006-02-16T19:07:56ZLaura Downeyldowney@lternet.edu
<p>It is standard design practice to enable/disable menu and toolbar items as <br />appropriate. Matthew mentioned this in bug 2246. I haven't suggested this as <br />of yet because often it involves quite a bit of additional logic to the code. <br />But Matthew's mention reminded me of it and it does deserve its own bug. <br />Enabling/disabling menu/toolbar items is very useful to users in helping them <br />understand what they can do in certain contexts and with certain objects, and <br />it also helps decrease menu/toolbar complexity.</p> Bug #2342 (In Progress): MENUS: Top-Level Menu - some toolbar buttons showing texthttps://projects.ecoinformatics.org/ecoinfo/issues/23422006-01-19T22:57:36ZMatthew Brookebrooke@nceas.ucsb.edu
<p>This issue is related to the top-level menu items - when kepler menus are<br />enabled, the last 7 toolbar buttons (port/relation buttons) display text in<br />addition to their icons, and thus become much too large. The remaining buttons<br />don't do this, and it only happens when kepler menus are enabled. Something to<br />do with setting or not setting the Action.NAME property, or the LARGE_ICON prop,<br />or something similar?</p>
<p>NOTE that these 7 all have Actions in ptii, and all appear on menus in ptii. <br />The zoom toolbar buttons also have Actions and also appear on menus in ptii, but<br />do not suffer from this same text problem. Maybe compare the 2 types and see<br />what is different...</p> Bug #2271 (In Progress): Changing the Color Schemehttps://projects.ecoinformatics.org/ecoinfo/issues/22712005-11-11T22:28:36ZMatthew Brookebrooke@nceas.ucsb.edu
<p>TRANSFERRED FROM Bug <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: Investigate UI Changes (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1882">#1882</a></p>
<p>------- Additional Comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: attribute editing for EMPTY elements doesn't work (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2">#2</a> From Matthew Brooke 2005-11-08 15:56 -------</p>
<p>re: Changing the color scheme:</p>
<p>Do we really want to override the default system look & feel for background<br />colors? It would look especially odd on Mac, which uses a "pinstripe" BG under<br />Java 1.4. Would it not make more sense to let the system manage background<br />colors for these particular components, thus giving them the default platform<br />look & feel?</p>
<p>------- Additional Comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: some required elements should be optional (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/3">#3</a> From Laura Downey 2005-11-09 08:26 -------</p>
<p>There is no proposal to change the "feel" of any system components of various <br />operating systems. The proposal is to control the color scheme only so that <br />all visual elements coordiate appropriately with the proposed color palette. <br />I would assume the "striped" effect on the Mac would remain, but the shades of <br />various gray and blue gray would be the ones we specify.</p>
<p>------- Additional Comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: save as doesn't prompt before overwriting (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/4">#4</a> From Matthew Brooke 2005-11-09 09:00 -------</p>
<p>Unfortunately, that is not how it would work. The panels and window backgrounds<br />in the UI either get the native OS look, or they adopt the solid background<br />colors we specify. For example, setting the background color of a panel to gray<br />on the mac would make it solid gray, not a pinstriped version of our gray coloring.</p>
<p>------- Additional Comment <a class="issue tracker-1 status-5 priority-5 priority-highest closed" title="Bug: mde won't load because of hardcoded image paths (Closed)" href="https://projects.ecoinformatics.org/ecoinfo/issues/5">#5</a> From Laura Downey 2005-11-09 09:54 -------</p>
<p>Well then my take is this. Having one application on a Mac desktop that <br />doesn't have the striped look is not going to make the application unusable. <br />I've worked on cross platform designs in the past and they were always a pain <br />because it is often difficult to address every issue in every OS. The Mac is <br />the least prevalent OS out there so from a practical perspective, I'm not sure <br />we should spend lots of effort making sure everything looks perfect on a Mac.</p>
<p>We did have numerous discussions about controlling the colors when I first <br />started working on the visual design. I asked if we had total control and was <br />told yes since it was a java app. So as designer, of course I was going to <br />control the color palette so that everything coordinated appropriately.</p>
<p>------- Additional Comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: MCAT won't build under IRIX with Oracle 8.0.5 (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/6">#6</a> From Matthew Brooke 2005-11-09 10:52 -------</p>
<p>My rationale for making this suggestion is as follows:</p>
<p>1) It would actually involve be <strong>less</strong> effort to make this work cross-platform;<br />more effort is needed to add the background colors (see the reasons and time<br />estimates at <a class="external" href="http://kepler-project.org/Wiki.jsp?page=UIImplementation">http://kepler-project.org/Wiki.jsp?page=UIImplementation</a>).</p>
<p>2) the most-widely-used commercial Windows applications keep the system<br />look/coloring for toolbars and panels, thus providing an integrated user<br />experience - see for example all Microsoft Office & internet applications, Adobe<br />products et al. (The notable exception being Apple's iTunes, of course, whose<br />purpose is to convince windows users to switch to mac... :-)</p>
<p>Not a big deal to me either way; just wanted to point out that using system<br />colors would save time/effort <strong>and</strong> make the app "fit in" better on all<br />platforms - a win-win. Color coordination with actor icons etc. would still<br />work, since all 3 OS's have neutral (med-high value, low saturation) native app<br />BG colors.</p>
<p>------- Additional Comment <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: MCAT doesn't pass tests when built under Oracle 7.3.2 (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/7">#7</a> From Laura Downey 2005-11-09 12:58 -------</p>
<p>Applications can indeed have a different color set and still look okay on a <br />desktop -- it just needs to be done right -- with coordinated colors and <br />professionally designed graphics -- both of which we have. The current <br />proposed color set is still in the neutral gray family.</p>
<p>Also, the proposed color set will pretty much work on the silver, tan or light <br />blue windows color schemes but will of course look the best on the background <br />colors they were designed to match.</p> Bug #2270 (In Progress): TRACKING: Localization and Improvement of User-Visible Messaging Stringshttps://projects.ecoinformatics.org/ecoinfo/issues/22702005-11-11T22:21:24ZMatthew Brookebrooke@nceas.ucsb.edu
<p>There are several bugs that pertain to changing the various messaging strings<br />that the user sees (general UI text, labels etc) or may potentially see (error<br />messages etc). Relevant bugs have been marked as dependencies of this bug, for<br />tracking purposes</p>
<p>As an approach to this tasks, I suggest looking at using Java's inbuilt<br />localization functionality, which offers the following benefits:</p>
<p>1) standard and well-tested framework already in place as part of the JDK - no<br />need to create our own solution</p>
<p>2) Gathers all these strings in one place, so text changes can be addressed<br />easily now and in future</p>
<p>3) Gives us the benefit of being able to internationalize the app easily at a<br />later date, when demand escalates in non-English-speaking countries...</p> Bug #2264 (In Progress): DIALOGS: Implement New "Semantic Annotation" Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22642005-11-10T22:41:58ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New "Semantic Annotation" Dialog:</p>
<p><a class="external" href="http://kepler-project.org/Wiki.jsp?page=SemanticAnnotationDialogs">http://kepler-project.org/Wiki.jsp?page=SemanticAnnotationDialogs</a></p> Bug #2263 (In Progress): DIALOGS: Implement New "Search Ecogrid for Data Sources" Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22632005-11-10T22:39:11ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New "Search Ecogrid for Data Sources" Dialog:</p>
<p><a class="external" href="http://kepler-project.org/Wiki.jsp?page=SearchDialogs">http://kepler-project.org/Wiki.jsp?page=SearchDialogs</a></p> Bug #2262 (In Progress): DIALOGS: Implement New "Search Ecogrid for Component Sources" Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22622005-11-10T22:38:08ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New "Search Ecogrid for Component Sources" Dialog:</p>
<p>(can't find this dialog on wiki. Can see only the "Search Ecogrid for Data<br />Sources" one)</p> Bug #2260 (In Progress): DIALOGS: Implement New "Advanced Search for Components" Dialoghttps://projects.ecoinformatics.org/ecoinfo/issues/22602005-11-10T22:32:49ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Implement New "Advanced Search for Components" Dialog. See:<br /><a class="external" href="http://kepler-project.org/Wiki.jsp?page=SearchDialogs">http://kepler-project.org/Wiki.jsp?page=SearchDialogs</a></p> Bug #2251 (In Progress): Need to document how to use Kepler for phylogeneticshttps://projects.ecoinformatics.org/ecoinfo/issues/22512005-11-07T02:23:51ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>We need to write documentation for users of the phylogenetics actors in Kepler.<br /> This documentation should include:</p>
<p>1. Instructions for installing programs wrapped by phylogenetics actors and<br />configuring Kepler to use these programs.</p>
<p>2. Sample workflows and data sets demonstrating the capabilities of the<br />phylogenetics actors.</p>
<p>3. Tutorials using the sample workflows as examples.</p> Bug #2250 (In Progress): Need documentation for collection-oriented workflow approachhttps://projects.ecoinformatics.org/ecoinfo/issues/22502005-11-07T02:11:42ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>We need to write documentation describing:</p>
<p>1. How the framework supporting collection-oriented workflows works.<br />2. How to compose, configure, and run collection-oriented workflows.<br />3. How to write collection-oriented actors.</p> Bug #2249 (In Progress): Need to support a useful subset of PHYLIP (PHYlogeny Inference Package)https://projects.ecoinformatics.org/ecoinfo/issues/22492005-11-07T01:59:59ZTimothy McPhillipsmcphillips@ecoinformatics.org
<p>At present, actors wrap the following PHYLIP programs (but do not yet support<br />all features of these programs):</p>
<pre><code>consense, dnaml, dnamlk, dnapars, dnapenny, <br /> drawgram, pars, penny, proml, promlk, protpars</code></pre>
<p>At the very least, the following programs need to be wrapped by new actors and<br />their basic capabilities supported:</p>
<pre><code>dnadist, protdist, seqboot, fitch, kitsch, neighbor, factor, drawtree</code></pre> Bug #2247 (In Progress): TRACKING: Popup Dialog Changeshttps://projects.ecoinformatics.org/ecoinfo/issues/22472005-11-05T07:15:31ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Collect dialogs together in tabbed versions, per laura's designs.<br />dialog(s) in Kepler source quicker/easier; dialogs in PTII source more difficult</p>
<p>checklist so far:<br />workflow<br />director<br />actor<br />data sources<br />search Ecogrid for data sources<br />advanced search (data)<br />component sources<br />search Ecogrid for component sources<br />advanced search (component)<br />Authentication<br />semantic annotation</p> Bug #2113 (In Progress): provide mechanism for saving querieshttps://projects.ecoinformatics.org/ecoinfo/issues/21132005-06-10T18:11:17ZLaura Downeyldowney@lternet.edu
<p>provide some mechanism so users can save queries to be rerun later</p>
<p>[decision from May 2005 Estes Park mtg]</p>