Recent changes to bugs

#87 Encoding error in org.sbml.jsbml.xml.stax.SBMLWriter

Nicolas Rodriguez — Thu, 09 Mar 2017 16:02:53 -0000

status: open-accepted --> closed-fixed

#90 update SBO term PHYSICAL_STIMULATION

Nicolas Rodriguez — Thu, 09 Mar 2017 15:57:51 -0000

status: pending --> closed-wont-fix
assigned_to: Andreas Dräger

#91 Incorrect date in output SBML

Nicolas Rodriguez — Thu, 09 Mar 2017 15:53:37 -0000

status: unread --> closed-fixed
assigned_to: Nicolas Rodriguez

Incorrect date in output SBML

Anonymous — Thu, 18 Feb 2016 23:20:41 -0000

I exported SBML using new SBMLWriter("MyApp","1.0") ...

The output has the wrong month in the second line:

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.

Incorrect date in output SBML

Anonymous — Thu, 18 Feb 2016 23:20:41 -0000

Ticket 91 has been modified: Incorrect date in output SBML
Edited By: Nicolas Rodriguez (niko-rodrigue)
Status updated: u'unread' => u'closed-fixed'
Owner updated: None => u'niko-rodrigue'

#90 update SBO term PHYSICAL_STIMULATION

Andreas Dräger — Tue, 10 Nov 2015 08:29:56 -0000

labels: --> annotation
Description has changed:

Diff:

--- old
+++ new
@@ -1,2 +1 @@
-
 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).

status: unread --> pending

#90 update SBO term PHYSICAL_STIMULATION

Andreas Dräger — Tue, 10 Nov 2015 08:29:19 -0000

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.

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.

Would this solve the problem or cause more problems?

update SBO term PHYSICAL_STIMULATION

Piero Dalle Pezze — Fri, 23 Oct 2015 10:20:51 -0000

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).

update SBO term PHYSICAL_STIMULATION

Piero Dalle Pezze — Fri, 23 Oct 2015 10:20:51 -0000

Ticket 90 has been modified: update SBO term PHYSICAL_STIMULATION
Edited By: Andreas Dräger (andreas-draeger)
Status updated: u'unread' => u'pending'
Description updated:
--- description-old

+++ description-new

@@ -1,3 +1,2 @@

-
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).

update SBO term PHYSICAL_STIMULATION

Piero Dalle Pezze — Fri, 23 Oct 2015 10:20:51 -0000

Ticket 90 has been modified: update SBO term PHYSICAL_STIMULATION
Edited By: Nicolas Rodriguez (niko-rodrigue)
Status updated: u'pending' => u'closed-wont-fix'
Owner updated: None => u'andreas-draeger'