Activity for jlibsedml
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Chris Myers committed [r453]
Removed unused import
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Here is the function modified with your changes; public static String getSEDBaseAnnotation(SEDBase...
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Here is the getSEDBaseAnnotation method I wrote. public static String getSEDBaseAnnotation(SEDBase...
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Richard Adams modified ticket #26
Improve Annotation handling
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I've committed in some improved methods to set Annotation, to add top-level elements...
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annotation helper
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Nevermind. Found the problem. āsā is not a full path. It is only the filename. When...
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I just tried again with these two print statements included: for (String s : new...
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Hi Chris I put your code into a unit test 'testExportBugReport' in Libsedml test...
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This sounds fine. I did not realize libkisao was not maintained. Probably best to...
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Below is the code. When I unzip the SED-ML archive, it only has the SED-ML file and...
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There is a class called SBMLSupport: file:///Users/myers/Downloads/jlibsedml-2.2.3/javadoc/index.html...
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general formatting and minor bug fixes
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Are you talking about LocalParameters in SBML? In which case, I don't think that...
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Online Validator: claims that a plot2d output as invali
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Online Validator: claims that a plot2d output as invali
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The online validator no longer exists, it is now at tools.jlibsedml.org, and this...
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Problem with Mathml
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This again seems fixed, e.g. in a DataGenerator <math:math xmlns:math="http://www.w3.org/1998/Math/MathML">...
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This again seems fixed, e.g. <math:math xmlns:math="http://www.w3.org/1998/Math/MathML">...
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This again seems fixed, e.g. `<math:math xmlns:math="http://www.w3.org/1998/Math/MathML">...
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This again seems fixed, e.g. <math:math xmlns:math="http://www.w3.org/1998/Math/MathML">...
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Problem with Mathml
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jlibsedml writes out incorrect language!
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This is already fixed.... at some point over the last 5 years ....
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SEDML archive not include model files
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There is a unit test public void testCreateWriteReadRoundTrip() throws Exception...
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SEDML archive not include model files
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Missing Kisao terms
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updated kisao to latest version
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I had a look at this - yes, the .obo file was very out of date! .obo no longer seems...
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I had a look at this - yes, the .obo file was very out of date! .obo no longer seems...
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Missing Kisao terms
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Yes, that should work. On Jul 24, 2016, at 4:18 PM, Richard Adams otter606@users.sf.net...
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I've committed in a test 'testExtensionSymbolMean()' in org.jlibsedml.mathsymbols.SymbolTests...
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example code for 'mean' function
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I agree it is invalid, but I think I also tried other functions and all functions...
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Function name in data generator not preserved
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Hi Chris, 'mean' isn't a supported MathML function in SED-ML level 1 - the only vector...
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Problems retrieving model from URI resource
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Don't know - the URL is different from that resolved from the URN - which is http://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000012...
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This now works, but wonder why there were characters that could not be parsed. Were...
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OK, I could reproduce the error in the sense that XML couldn't be parsed. . Looks...
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Problems retrieving model from URI resource
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bugs 9 - filter out invalid XML characters
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Add Gradle build support + remove hardcoded paths from build.
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Add Gradle build support + remove hardcoded paths from build.
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Gradle wrapper added and removed requirement for fop installation for document g...
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Add Gradle build support + remove hardcoded paths from build.
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updated developer notes
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I think I did something like this: Libsedml.parseFormulaString(mean(X)); And I think...
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Here are some more details about this one (see below). I get the document as a String,...
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ensure gradle compile&test runs if fop document...
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add gradle wrapper
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Add clearXXX methods to remove all items from a list
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added clearXXX methods to Model and top-level SEDML class
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removed failing test
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added clearXXX methods to SEDML class
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fixed and unit test added
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Removing a change did not work!
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Removing a change did not work!
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fix bug#11 and add clearChanges() method
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Removing a change did not work!
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Add clearXXX methods to remove all items from a list
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Can you send some code you've tried, or an example of the MathML you'd expect, just...
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Function name in data generator not preserved
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Problems retrieving model from URI resource
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So not fixing as I think this is a usage issue, not an actual bug
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So,there are various implementations of IModelResolver that can load models from...
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updated build notes
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Problems retrieving model from URI resource
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Implement copy constructors
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Function name in data generator not preserved
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10 issues reported by Chris Meyrs
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Problems retrieving model from URI resource
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10 issues reported by Chris Meyrs
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Add clearXXX methods to remove all items from a list
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10 issues reported by Chris Meyrs
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Yes, the Kisao terms are hardcoded as a resource file and are probably out of da...
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Missing Kisao terms
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Missing Kisao terms
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I've got a project on Github https://github.com/otter606/sedml-validator/tree/master/Omex...
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SEDML archive not include model files
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Implement function getReactionIdFromXPathIdentifier
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Validate against l1 v2 documents
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validation against l1v2 schema implemented
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Ticket moved from /p/jlibsedml/bugs/6/
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Improve Annotation handling
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update version
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update version
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Frank Bergmann created ticket #5
10 issues reported by Chris Meyrs
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- commit patch from Martin Scharm that fixes a ...
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jlibsedml released /jlibsedml-2.2.3.zip
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tag of 2.2.3 release
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updated pom.xml dependencies for Maven release ...
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2.2.3
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formatting
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check level and version in constructors
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update for l1v2
