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EMSL-Computing / CoreMS

CoreMS is a comprehensive mass spectrometry software framework
BSD 2-Clause "Simplified" License
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SQLite unable to open database file #6

Closed Kzra closed 3 years ago

Kzra commented 3 years ago

Running this code in corems 1.18: from corems.transient.input.brukerSolarix import ReadBrukerSolarix from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas file_path= 'Ezra MS 060532_000005.d srfa iii/' bruker_reader = ReadBrukerSolarix(file_path) bruker_transient_obj = bruker_reader.get_transient() mass_spectrum_obj = bruker_transient_obj.get_mass_spectrum(plot_result=False, auto_process=True) SearchMolecularFormulas(mass_spectrum_obj, first_hit=True).run_worker_mass_spectrum()

Gives the following error: image

I checked the url for the SQL database using from corems.encapsulation.factory.parameters import MSParameters MSParameters.molecular_search.url_database

the database is given as

'sqlite:///db/molformula.db'

this looks like a relative path to the db folder of CoreMS. However when I checked the path there is no molformula.db present. Is this a mistake or am I missing a step?

corilo commented 3 years ago

If a path is specified it will try to open an existing db file

add this line after the imports

MSParameters.molecular_search.url_database = None

This will start a new db under ./db/molformula.db (it is a relative path, so this will be created related from where you are executing your script). The software automatically generates the molecular formula db based on your parameters.

Please make sure to check your other parameters under MSParameters class

You can see more examples here:

https://github.com/EMSL-Computing/CoreMS/tree/master/examples/scripts

Kzra commented 3 years ago

Thank you, that makes sense. I added the line and the code now runs fine.