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CBIIT / R-cometsAnalytics

R package development for COMETS Analytics
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COMETS 1.5 Rapid UID upload #43

Closed nateappel closed 1 year ago

nateappel commented 6 years ago

After harmonization of study data, in our updated process, we will need to update COMETS with a new UID file to account for new metabolites added. Is there a way to automate this where when the files has changes, we can upload it to a specific spot and is used by COMETS without any input processing?

Does the file we send need to be modified to make something like this work.

ellatemprosa commented 6 years ago

@nateappel there is a processing routine that we run to compile the uid file, there is also a convention that you should add to your uid file to put the date as the worksheet name so we can keep track of the version. do you want to take care of doing the processing and plop in the needed rds and uid file? the functions for processing is called processuid.R

nateappel commented 6 years ago

@ellatemprosa , that sounds great. We will start dating the UID worksheet. I will also take the processuid function and try to generate the desired output. We can test the from there.

nateappel commented 6 years ago

Ella, Does the processuid function run everytime an analysis is done, or just when a new COMETS file is delivered? Thanks, Nathan

ellatemprosa commented 6 years ago

only when there is an update to the uid file. it processes the file to make the look up faster when cohorts do their harmonization

steven-moore commented 6 years ago

We are currently in discussions about revising the UID file to make it a relational database. We should discuss whether this in 1.4 or 1.5 functionality.

steven-moore commented 6 years ago

Also, I am tagging issue #30 as it raised similar concerns. That issue is now closed because it is redundant with this one, but I wanted to make sure it's documentation was available here.

steven-moore commented 6 years ago

Switched to COMETS 1.5, as this is intertwined with our update to a relational DB format for this file