feat: extensively provide associated external identifiers for rxns and mets

[haowang-bioinfo]

Main improvements in this PR:

• This PR is to address feat: provide the stoichiometric matrix with comprehensive external association and annotation #107.
• Scripts getHuman1RxnAssoc and getHuman1MetAssoc are made for refining/retrieving previously prepared association/annotation to reactions and metabolites, respectively.
• 6 identifiers from different databases or human GEMs were assigned to reactions, and 10 identifiers for metabolites.
• The sorted external identifiers are saved to HumanGEMRxnAssoc and HumanGEMMetAssoc, both are organized in JSON format, as discussed in Apply JSON files for storing curation/annotation information #75.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected devel as a target branch

[JonathanRob]

Ok, it will be very nice to have all the external ID information organized as you have done here. I have only two small comments:

1. I'm not sure if you're planning to merge the already generated JSON files directly, or regenerate the JSON files after merging. If you are going to merge them directly, just make sure that they're updated. The reason I'm saying this is because the current humanGemRxnAssoc.JSON file does not appear to be updated with your latest Recon3D ID additions.

2. How about humanGEMRxnAssoc.JSON instead of humanGemRxnAssoc.JSON (and same with the metabolite file)? Since GEM is the normal usage of the term, I would recommend using it that way.

[haowang-bioinfo]

@JonathanRob can you specify any "latest Recon3D ID additions" so that they can be retrieved if missing.

[JonathanRob]

@Hao-Chalmers What I meant was that when I ran the getHuman1RxnAssoc script, the new humanGemRxnAssoc.JSON file that it generated did not match the existing humanGemRxnAssoc.JSON file. It seemed that this was because the existing JSON file was an older version that you had generated before commit 7a40123. However, it looks like I ran it right before you updated the file in your next commit, so the issue has been solved.