- changed status to resolved
Create sample submission functionality
Rudy's notes:
input: comments.csv, controls.csv, samples.csv, slides.csv
output: excel-file; name: date_StudyId_RunName_SIS
sample import sheet (SIS):
SlideId: from slides.csv
PercentDilution: always 40
Barcode: from controls.csv; if Barcode available columns I to R should be empty
also needs verification that barcodes overlap with NO READ entries in samples.csv
SampleNotes: from comments.csv (column B); can be empty
AssayNotes: from comments.csv (column C); can be empty
SampleId: from samples.csv (column C)
SampleMatrix: should ask if (a) EDTA-Plasma, (b) Sodium Citrate Plasma or (c) Serum
SiteId: WCQ
StudyName: should ask for input
StudyId: should ask for input; format always WCQ-xx-xxx (WCQ-year-number)
RunName: should ask for input; format "Set X" (X=capital letter) can be empty
controls.csv
, samples.csv
, and slides.csv
are autogenerated by the instrument.
comments.csv
is manually created.
Need read_controls
, read_samples
, etc. fns that wrap fread
and performs checks. Probably best to make these functions chatty so the user sees what has been imported.
Then have a write_sample_submission_form
that merges the four datasets, performs more checks and writes to XLSX.
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