Recent changes to bugshttps://sourceforge.net/p/jsbml/bugs/2017-03-09T16:02:53.108000ZRecent changes to bugs#87 Encoding error in org.sbml.jsbml.xml.stax.SBMLWriter2017-03-09T16:02:53.108000Z2017-03-09T16:02:53.108000ZNicolas Rodriguezhttps://sourceforge.net/u/niko-rodrigue/https://sourceforge.net7283f3794e7e14bd1b43e15f98f58b7f5ec37816<div class="markdown_content"><ul>
<li><strong>status</strong>: open-accepted --> closed-fixed</li>
</ul></div>#90 update SBO term PHYSICAL_STIMULATION2017-03-09T15:57:51.656000Z2017-03-09T15:57:51.656000ZNicolas Rodriguezhttps://sourceforge.net/u/niko-rodrigue/https://sourceforge.net5a33721f495e6b67a2fe5b2dac2704ca12ff662c<div class="markdown_content"><ul>
<li><strong>status</strong>: pending --> closed-wont-fix</li>
<li><strong>assigned_to</strong>: Andreas Dräger</li>
</ul></div>#91 Incorrect date in output SBML2017-03-09T15:53:37.912000Z2017-03-09T15:53:37.912000ZNicolas Rodriguezhttps://sourceforge.net/u/niko-rodrigue/https://sourceforge.net37fb19012f2e10979856dd3898cc4191ddae7ea9<div class="markdown_content"><ul>
<li><strong>status</strong>: unread --> closed-fixed</li>
<li><strong>assigned_to</strong>: Nicolas Rodriguez</li>
</ul></div>Incorrect date in output SBML2016-02-18T23:20:41.919000Z2016-02-18T23:20:41.919000ZAnonymoushttps://sourceforge.net/u/userid-None/https://sourceforge.netdc644a276cff51f16726f58ecf4a800cea6d5ed0<div class="markdown_content"><p>I exported SBML using new SBMLWriter("MyApp","1.0") ...</p>
<p>The output has the wrong month in the second line:</p>
<p>I'm sure this is a simple fix where the format specifier for the minute was used where the month was supposed to go; notice the month and the minute are the same... this is always true in all the SBML files I've generated.</p></div>Incorrect date in output SBML2016-02-18T23:20:41.919000Z2016-02-18T23:20:41.919000ZAnonymoushttps://sourceforge.net/u/userid-None/https://sourceforge.netcacb5b2ce9bc9473f6586d89ad945321bf3f43c8<div class="markdown_content"><p>Ticket 91 has been modified: Incorrect date in output SBML<br/>
Edited By: Nicolas Rodriguez (niko-rodrigue)<br/>
Status updated: u'unread' => u'closed-fixed'<br/>
Owner updated: None => u'niko-rodrigue'</p></div>#90 update SBO term PHYSICAL_STIMULATION2015-11-10T08:29:56.052000Z2015-11-10T08:29:56.052000ZAndreas Drägerhttps://sourceforge.net/u/andreas-draeger/https://sourceforge.net60e738a48d2875e1c33b32e344043aac7a6ba46b<div class="markdown_content"><ul>
<li><strong>labels</strong>: --> annotation</li>
<li>Description has changed:</li>
</ul>
<p>Diff:</p>
<div class="codehilite"><pre><span class="gd">--- old</span>
<span class="gi">+++ new</span>
<span class="gu">@@ -1,2 +1 @@</span>
<span class="gd">-</span>
In Alias2SBO.cfg, the term PHYSICAL_STIMULATION is 21, but it should possibly be replaced with the number 459 (see http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460).
</pre></div>
<ul>
<li><strong>status</strong>: unread --> pending</li>
</ul></div>#90 update SBO term PHYSICAL_STIMULATION2015-11-10T08:29:19.301000Z2015-11-10T08:29:19.301000ZAndreas Drägerhttps://sourceforge.net/u/andreas-draeger/https://sourceforge.netfb38c9d5221850dc7d292bd2dcf25abe0d6aac49<div class="markdown_content"><p>Thanks for reporting this issue. Could you please tell a bit more how you run into this problem? Originally, the file Alias2SBO.cfg was used as a mapping between CellDesigner's graphical display and SBO terms. Some of CellDesigner's shapes etc. have no direct correspondence in the SBO. This is also reflected by the comments in the file Alias2SBO.cfg.</p>
<p>Now, if we change PHYSICAL_STIMULATION from SBO term 21 to 459, there would be a clash with TRANSLATIONAL_ACTIVATION. What we could do is, swap the SBO terms of both that are both not directly reflected in the SBO. However, tools that already rely on this scheme might experience different behavior.</p>
<p>Would this solve the problem or cause more problems?</p></div>update SBO term PHYSICAL_STIMULATION2015-10-23T10:20:51.936000Z2015-10-23T10:20:51.936000ZPiero Dalle Pezzehttps://sourceforge.net/u/pdp10/https://sourceforge.netb00751e3694a0c43103227429ee318d1e3a21b05<div class="markdown_content"><p>In Alias2SBO.cfg, the term PHYSICAL_STIMULATION is 21, but it should possibly be replaced with the number 459 (see <a href="http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460" rel="nofollow">http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460</a>). </p></div>update SBO term PHYSICAL_STIMULATION2015-10-23T10:20:51.936000Z2015-10-23T10:20:51.936000ZPiero Dalle Pezzehttps://sourceforge.net/u/pdp10/https://sourceforge.net712ee022c917b91f17ffb80043728695ff050670<div class="markdown_content"><p>Ticket 90 has been modified: update SBO term PHYSICAL_STIMULATION<br/>
Edited By: Andreas Dräger (andreas-draeger)<br/>
Status updated: u'unread' => u'pending'<br/>
Description updated:<br/>
--- description-old</p>
<p>+++ description-new</p>
<p>@@ -1,3 +1,2 @@</p>
<p>-<br/>
In Alias2SBO.cfg, the term PHYSICAL_STIMULATION is 21, but it should possibly be replaced with the number 459 (see <a href="http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460" rel="nofollow">http://www.ebi.ac.uk/sbo/main/display?open=-460&nodeId=460</a>). </p></div>update SBO term PHYSICAL_STIMULATION2015-10-23T10:20:51.936000Z2015-10-23T10:20:51.936000ZPiero Dalle Pezzehttps://sourceforge.net/u/pdp10/https://sourceforge.netf936956a760748b38bff511c686be7ae8052c5c8<div class="markdown_content"><p>Ticket 90 has been modified: update SBO term PHYSICAL_STIMULATION<br/>
Edited By: Nicolas Rodriguez (niko-rodrigue)<br/>
Status updated: u'pending' => u'closed-wont-fix'<br/>
Owner updated: None => u'andreas-draeger'</p></div>