Menu ▾ ▴

#5 10 issues reported by Chris Meyrs

2.3
open
nobody
None
5
2016-07-13
2016-07-12
Frank Bergmann
No

1) Only Model has a copy constructor, and I’m not sure it is a deep copy. I ended up implementing my own though they are likely not complete (see attached Java file).

2) SubTask is not derived from SEDBase. Not sure if that is intended or not.

7)

9) getChangedModel fails on model3 for oscli-delete from same website.

There are probably a few more things, but I usually could find a workaround. I will log them on the tracker from now on, and can even moves these to the tracker, if you like. I’m also happy to try to fix some of them as they come up. We are developing libSBOLj to support SBOL in our group, and I’ve actually been quite involved in the coding (more fun than the things I should be doing).

Discussion

  • Richard Adams

    Richard Adams - 2016-07-13
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -1,15 +1,8 @@
-
 1) Only Model has a copy constructor, and I’m not sure it is a deep copy.  I ended up implementing my own though they are likely not complete (see attached Java file).

 2) SubTask is not derived from SEDBase.  Not sure if that is intended or not.

-3) The getAnnotation method returns a list of Annotations even though there is only one Annotation on each object.  This function is marked as deprecated, so I suspect that you know this, but I cannot find a replacement.  I assume addAnnotation should also be deprecated and setAnnotation should take a single item.  It would also be nice to have some functions to help build and parse annotations.  See getSEDBaseAnnotation in the attached as an example.

-4) You can create XPath expressions for LocalParameters, and you can get the Id from this expression.  However, there is no function to get the ReactionId from this expression.  See my attempt at one in the attached file, getReactionIdFromXPathIdentifier.
-
-5) When I write a SEDML archive, it seems to not include the body of the model files.  Granted this is low priority as I should likely move to COMBINE archive, but I thought it might be nice to use if it worked.
-
-6) The ALGORITHM_WITH_DETERMINISTIC_RULES does not seem to work.  I think your kisao version is missing a lot of terms which is likely part of the problem.  Again, likely low priority, since I should be using the Kisao library.

 7) I wanted to include functions in my math for DataGenerators, but it always turns them into “misc” and does not preserve the function name.  I was thinking to use this to indicate, for example, “mean” of a result of a repeated task.

@@ -19,6 +12,6 @@

 9) getChangedModel fails on model3 for oscli-delete from same website.

-10) It would be nice to have methods to remove all objects from a list.  For example, removing all the Changes from a Model proved to be quite tricky, since you can only get them by iterating through the list, but if you remove them while iterating, you get current modification exception.  It would be nice to have “clear” methods remove everything from the list.
+

 There are probably a few more things, but I usually could find a workaround.  I will log them on the tracker from now on, and can even moves these to the tracker, if you like.  I’m also happy to try to fix some of them as they come up.  We are developing libSBOLj to support SBOL in our group, and I’ve actually been quite involved in the coding (more fun than the things I should be doing).
     

  • Richard Adams

    Richard Adams - 2016-07-13
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -6,9 +6,7 @@

 7) I wanted to include functions in my math for DataGenerators, but it always turns them into “misc” and does not preserve the function name.  I was thinking to use this to indicate, for example, “mean” of a result of a repeated task.

-8) The method to get from a URI resource does not seem to work properly.  This fails for me for BIOMD0000000012 found here:

-http://svn.code.sf.net/p/libsedml/code/trunk/Samples/sedx-archives/

 9) getChangedModel fails on model3 for oscli-delete from same website.
    • Group: v1.0_(example) --> 2.3
     

  • Richard Adams

    Richard Adams - 2016-07-13
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -4,7 +4,7 @@



-7) I wanted to include functions in my math for DataGenerators, but it always turns them into “misc” and does not preserve the function name.  I was thinking to use this to indicate, for example, “mean” of a result of a repeated task.
+7)
     
MongoDB Logo MongoDB