…del id is in BiGG.

Parameter access now uniformly through getters/setters.

…command to run with validation, without adb and combine archive. Hopefully secret for Slack integration is correct now

…eplaced String.format with MessageFormat.format

… error with regard to includeAnyURI. Added some form of documentation to BiGGAnnotation to give a better overview, what is done by each method.

…of String.format with MessageFormat.format

…tions and gene products out of BiGGAnnotation in to their own respective *Anntotation classes

…ady shared much of their code and moved it into CVTermAnnotation, which is now an abstract class from which both Annotation Classes and GeneProductAnnotation inherit.

…e code into own class

… is done now. Still needs a pass to implement alternative paths for code dealing with models. Removed unused/unnecessary code from SBMLPolisher class that can be directly accessed by the Parameters singleton

… as both are required and missing out on either would throw a NullPointer

…action compartment codes. These are only set, if all instances, i.e. reaction, reactants and products agree on the compartment. Polishing of Species and Reactions should now be possible without a model present

…ch components are required and should thus throw an Exception, if they are missing. Moving parsers classes into subpackages somehow broke JSONParser, which needs fixing now

…ld work again, issue was a malformed formatting placeholder in a string. German translation needs to be done for the new messages and log levels still need to be adjusted

…ng them into the resource bundle. Copied missing entries into german resource bundle, untranslated for now

…g over to call sites.

Reordered parameters in ModelPolisherOptions and Parameters to be sorted alphabetically.
Enchanced documentation in ModelPolisher class.
Fixed small issue in JSONParser - forgot to wrap notes in XML namespace in one place, leading to unknown "p" elements.
Some smaller refactoring.

…M entries cause error

Defined ModelPolisher as entrypoint, allowing to pass arguments directly to the container without need to explicitly pass java -jar ModelPolisher-?.jar, i.e. docker-compose run polisher java -jar ModelPolisher-?.jar [options] is now docker-compose run polisher [options].
Need to update README.
Next up: Dealing with MIRIAM.

… class. Correct handling of non identifiers URLs should now be possible, but integration still needs to be finished -> non identifiers.org URLs are currently not correctly handled for implemented workarounds for BiGG data

…s might exist, as testing still needs to be implemented for new code

…d namespaces leads to SBMLReader crashing on the respective inner elemnt without namespace tag

…' plugin (https://github.com/jk1/Gradle-License-Report) to get dependency licenses and removed (outdated) THIRD-PARTY.txt and licenses folder. Added instruction file (dependency-licenses.txt) on how to create the license report. Updated year in ModelPolisher license which still was 2015 (!). Further removed BuildSBMLFix, as this was outdated and not used anymore and contributor notes, as these were still based on a pre-2.0 version.

…eneReactionRules do not work currently. Notes are currently dumped as XMLString, which needs to be changed. getJSON{Gene,Metabolite,Reaction} methods need further testing

…tion to write output model as JSON

…maller tests remain