libsbgn

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Improve Usability with SBML models

4

Dear SBGN team, i wanted to use SBGN for the first time and tried to convert my SBML model. However, I encountered several pitfalls that made it impossible for me:...

shoepfl

in SBGN PD the 'source and sink' element was renamed to 'emptyset'. This change is not propagated to SBGNML and libSBGN. Instead the existing 'source and sink' needs to be...

fbergmann

I found a conflicting library versions in the milestone3.2 jar provided by maven. The problem is that there is a dependency to version `1.4.01` of `xml-apis` library. However another dependency...

piotr-gawron

At some point it might be good to switch to the GitHub package repository for distribution; it is currently in beta so may not at this exact moment. * https://github.com/features/package-registry...

cannin

Incorrect SBGN file format following writing the render information

5

Hello, I am not sure whether this is related to issue #51, but I get an "invalid file format" after writing the render information. The error refers to Please see...

ibalaur

Problems writing render extension, set DocumentBuilderFactory in SbgnUtil.addAnnotation namespace aware?

2

I have some problems writing the render extension using milestone 3. I had already a brief discussion with Frank but there was not really a solution. I think I have...

tczauderna

SbgnUtil.readFrom(InputStream is) fails when conversion from Milestone 1 or 2 necessary

2

`SbgnUtil.readFrom(InputStream is)` fails when a conversion is necessary (from Milestone 1 or 2). The problem is that the input stream can only be used once. This happens here `Sbgn result...

tczauderna

Question on high level validation, ruleId=pd10112: if there are compartments defined, top-level glyphs must have a compartmentRef.

2

The high level validation (using libSBGN 3.0) failed due to not having all top-level glyphs referring to a compartment. Please see the attached files: input SBGN-ML and output validation message....

ibalaur

Given that SbgnUtil.readFromFile can read from both 2.0 and 3.0, but SbgnUtil.writeToFile exports to 3.0 only, I think it would be helpful that libSBGN provides conversion to 2.0 as well...

ibalaur

maven build not working on some systems

1

Irina was noting that the maven build on her machine failed with: ``` vn install [INFO] Scanning for projects... [INFO] [INFO] ---------------------< com.github.libsbgn:libsbgn >--------------------- [INFO] Building libSBGN 0.3-SNAPSHOT [INFO] --------------------------------[...

fbergmann