Week 12
Greetings!
After completing the code for the production of the glossary file, my next task for this project was to give the user an option to produce the output in form of a Combine Archive which contains the polished model and the glossary file.
This feature may look redundant now, but it is very helpful to keep biological models in differents formats in one Combine Archive which also contains a single glossary file which has all the annotations from the polished model.
So, for this task, I first added an option `--output-combine` for users in which they can provide a boolean to produce output as a single Combine Archive. After addition of this option, if the user provides value `true` for this option, I use binfalse/CombineArchive repository to put in the output polished model and the glossary file in a Combine Archive zip. Note that, in this case, any annotated model or glossary rdf file will not be produced.
There were multiple issues during the implementation of this feature which was solved with the help of my mentors. One of the major issues was that the URI for rdf files under combine.specifications was http://identifiers.org/combine.specifications/omex-metadata which marked it as meta-data but this was not preferred. This issue was resolved by using the URI produced by CombineFormatizer.
Further, I implemented a test: CombineArchiveTest, for testing if the archives are successfully produced and they contain the required files. Here, for the first time, I received knowledge for writing test files using JUnit.
I also updated the README, and now the README is completely updated and shall not have any major changes in the future. The major thing I added was a list of command-line options for using ModelPolisher.
In this last week I need to do the following tasks:
- Release ModelPolisher 2.0
- Write final report
- Code Formatting
- Minor changes in README
- Submit Final Evaluation
Thank You!
After completing the code for the production of the glossary file, my next task for this project was to give the user an option to produce the output in form of a Combine Archive which contains the polished model and the glossary file.
This feature may look redundant now, but it is very helpful to keep biological models in differents formats in one Combine Archive which also contains a single glossary file which has all the annotations from the polished model.
So, for this task, I first added an option `--output-combine` for users in which they can provide a boolean to produce output as a single Combine Archive. After addition of this option, if the user provides value `true` for this option, I use binfalse/CombineArchive repository to put in the output polished model and the glossary file in a Combine Archive zip. Note that, in this case, any annotated model or glossary rdf file will not be produced.
There were multiple issues during the implementation of this feature which was solved with the help of my mentors. One of the major issues was that the URI for rdf files under combine.specifications was http://identifiers.org/combine.specifications/omex-metadata which marked it as meta-data but this was not preferred. This issue was resolved by using the URI produced by CombineFormatizer.
Further, I implemented a test: CombineArchiveTest, for testing if the archives are successfully produced and they contain the required files. Here, for the first time, I received knowledge for writing test files using JUnit.
I also updated the README, and now the README is completely updated and shall not have any major changes in the future. The major thing I added was a list of command-line options for using ModelPolisher.
In this last week I need to do the following tasks:
- Release ModelPolisher 2.0
- Write final report
- Code Formatting
- Minor changes in README
- Submit Final Evaluation
Thank You!
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