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Refactor synapse-adjacent functions to use new reticulate-based synapser #94

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allaway opened this issue Mar 24, 2023 · 3 comments · Fixed by #168, #170 or #171
Open

Refactor synapse-adjacent functions to use new reticulate-based synapser #94

allaway opened this issue Mar 24, 2023 · 3 comments · Fixed by #168, #170 or #171
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allaway commented Mar 24, 2023 •
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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.
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allaway commented Mar 24, 2023 •
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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()

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allaway commented Dec 20, 2023

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

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anngvu commented Feb 23, 2024 •
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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.

This was linked to pull requests Feb 23, 2024
change people functions to synapser #168
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Add synapser update ci #170
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synapser refactor phase a #171
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@anngvu anngvu mentioned this issue Feb 23, 2024
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@anngvu anngvu moved this to In Progress in NF-OSI Sprints Mar 3, 2024
This was referenced Mar 4, 2024
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@anngvu anngvu self-assigned this Mar 4, 2024
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