Week 8

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Greetings!

As mentioned in the previous blog my targets for this week included:
  • Test containerization completely.
  • Add updates to README about containerization.
  • Solve the issue of restructuring ModelPolisher.
  • Open PR for the above tasks.
  • Figure out and test queries for getting annotations from ADB.
  • Complete integration of AnnotateDB.
I was able to complete most of these tasks, here are the details:
  • CONTAINERISATION: The ModelPolisher is successfully containerized, and is available here currently. ModelPolisher has been divided into three containers/services, namely - BiGGDB, ADB, Java. The first two services host the respective databases with Postgres as base images, the third service with OpenJDK-11 as the base, is used to run ModelPolisher jar in a container. The containerization of ModelPolisher has been successfully tested by me. The ModelPolisher can now be run simply in two steps:
    • Run `docker-compose up`
    • Polish models using `docker-compose run` command. More details available in README.
  • RESTRUCTURING ModelPolisher: ModelPolisher has been successfully restructured as required by the issue and also the required changes have been made in the build procedure. So, now one can successfully build the restructured ModelPolisher and it is running successfully.
  • Integration of ANNOTATEDB: I have integrated AnnotateDB in ModelPolisher which should the feature of adding annotations in ModelPolisher from ADB also (and still have annotations from BiGGDB). The following major steps were there in this integration:
    • Adding/Changing parameters to add the option to annotate models with ADB and pass the host, port and other info of AnnotateDB. I have assumed that we will provide support for AnnotateDB available from Postgres server.
    • Formulating the queries to get annotations from ADB.
      ExampleQuery: `SELECT m.target_term, ac.urlpattern FROM mapping_view m, adb_collection ac WHERE  m.source_namespace = 'bigg.metabolite' AND m.source_term = '10fthf' AND ac.namespace = m.target_namespace`
    • Creating classes and support similar to what is available in ModelPolisher for BiGGDB.
    • Using `ResultSet` to get annotations from ADB.
    • Add annotations as CV terms to elements (species and reactions)
I still need to completely test this integration and confirm what are the test cases to be added.
Major points to discuss in today's meeting:
  • Confirm if any changes required in the functionality of ModelPolisher after integration.
  • Discuss issues with PR's of solved issues, especially restructuring of ModelPolisher.
  • Currently, the files required while building images for docker are stored in my personal AWS s3 server. Discuss where to host them.
  • Discuss tasks for next weeks, especially tasks related to third evaluation.
  • Confirm any further tasks for this evaluation.
Thank You!

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