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implement local db / metfrag as conditional #5
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For that you need a local db running. We should have a Dockerfile floating around somewhere here https://github.com/ipb-halle/MetFragRelaunched/tree/containerize I think we should implement this in the rewrite of the tool |
The Dockerfile and instructions to build the local pubchem mirror database can be found here: https://github.com/c-ruttkies/container-metchemdata @sneumann also has recent kubernetes deployment yamls. |
@RJMW we can set this local database system up on one of the Birmingham virtual machines |
Currently in the tool the "local data base" is just a csv file. Most frequently the Galaxy tool-data loc files specify files, but its definitely possible to specify a connection string. For my curiosity: the DB you are referring to is some SQL DB? In the docker it seems to be postgres in the backend, but could be any DB (sqlite)? |
hi @bernt-matthias, We should still keep the option to have a "local database" that is just a csv file, and it should be realised as a conditional - like you mentioned in the original issue message. The database @korseby is referring to is a local PubChem database (With a few modifications - called MetChem) and can be used in replace of doing the API calls to the public PubChem instance. See xml and script. So, I will update Galaxy tool and script here for the following database options:
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I agree @Tomnl. Examples for "LocalCSV" are available from here: @korseby are there any more up-to-date csv files available? |
This is now implemented following #8 |
Since either a local db or a metfrag db has to be chosen this shoud be realised with a conditional.
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