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draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
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COBRAparser and JSONparser failing on current bigg_models #27

Closed mephenor closed 2 years ago

mephenor commented 6 years ago
draeger commented 6 years ago

@zakandrewking Could you please check this chemical formula in model iJB785?

zakandrewking commented 6 years ago

which metabolite is that in?

mephenor commented 6 years ago

{ "id":"bm_pro_c", "name":"Protein component of biomass", "compartment":"c", "charge":0, "formula":"H70.5616C44.9625O13.1713S0.2669N12.1054R-1.0" },

zakandrewking commented 6 years ago

there's no formula for it here:

http://bigg.ucsd.edu/models/iJB785/metabolites/bm_pro_c

zakandrewking commented 6 years ago

I think we removed those decimal formulae

mephenor commented 6 years ago

The formula is still present in https://github.com/SBRG/bigg_models_data/blob/master/models/iJB785.json .

The other issue seems to be related to the Java 9 module system. With Java 8 COBRAparser works normally

matthiaskoenig commented 5 years ago

Json parser is still failing on models. See for instance also example:

java -jar ./target/ModelPolisher-noDB-1.7.jar --input="./examples/bigg/e_coli_core.json" --output="./examples/bigg/e_coli_core_json_polished.xml" --annotate-with-bigg=true --host=0.0.0.0 --port=1310 --user=postgres --passwd=postgres --dbname=bigg
mephenor commented 5 years ago

I will have a look at that

mephenor commented 4 years ago

Both parsers are now fixed in the refactoring branch, with the JSONParser now using the schema from cobrapy to create the respective objects using Jackson. Formulae are parsed using FBC and those containing non integers are currently not supported and thus dropped. Should they be added to notes instead?

draeger commented 4 years ago

As long as we are still waiting for the next FBC specification to be finalized, we should indeed keep such information (that could become valuable later on) - for now let's put it to the notes.

mephenor commented 4 years ago

Unparseable formulae in JSONParser are now added to the species notes.

Schmoho commented 2 years ago

just added a test to confirm iJB785 is parsed without error and the formula mentioned above is retained

closing and moving to tested