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nf-osi / nfportalutils

Utilities for NF Portal project and data management
https://nf-osi.github.io/nfportalutils/
MIT License
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Refactor synapse-adjacent functions to use new reticulate-based synapser #94

Open allaway opened 1 year ago

allaway commented 1 year ago

We should drop the custom import of the synapse python client in lieu of the new reticulate-based synapser, which likely will have better ongoing support (at least compared to us maintaining a custom import of the client) and will make it easier for users of this package to import in additional synapser functions/R docs instead of having to use synapseclient via reticulate.

allaway commented 1 year ago

e.g. currently someone using nfportalutils has to use foo <- synapse$Synapse$tableQuery(.syn, "select * from syn12345")$asDataFrame() to query a table, instead of just foo <- synTableQuery("select * from syn12345")$asDataFrame()

allaway commented 8 months ago

Well, I think I discovered at least one reason to do this: #164

anngvu commented 6 months ago

Using this to keep track: Function list to check for needed conversion to synapser, meaning that we use synapser::synLogin() and can run that function without issues. Some functions that don't need touching, e.g. they just do things like make diagrams, can be checked off with NA.