Merge pull request #8 from gf-dcc/feat/manage-sample-ids

Add prelim script

manage-sample-ids/README.md

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+## Sample ID Management
+
+Collection of utility scripts that help with managing sample entities for the BEN Collaborative Project / Breast Atlas in Synapse. 
+There is potential functionality for extracting ids, inferring linkage of existing sample entities with data files, etc., that may be more automated eventually.

manage-sample-ids/extract.R

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+library(synapser)
+
+synapser::synLogin(authToken = Sys.getenv("SYNAPSE_AUTH_TOKEN"))
+
+# It is easiest to use a fileview to get all nested children in "Samples"
+SampleTracking <- "syn52225331"
+
+tb <- synapser::synTableQuery(glue::glue("select id from {SampleTracking}"))
+ids <- as.data.frame(tb)$id
+
+asPatientID <- function(s) regmatches(s, regexpr("[A-Z]+[0-9]?-?[0-9]+", s))
+
+errors <- c()
+
+for(i in ids) {
+
+  entity <- synapser::synGet(i, downloadFile = FALSE)
+  pID <- asPatientID(entity$properties$name)
+  entity$annotations$PatientID <- pID
+
+  # For now, let's just use the entity name as sample name
+  entity$annotations$SampleID <- entity$properties$name
+  tryCatch(synapser::synStore(entity), error = function(e) { cat("Skipped ", i, "\n"); errors <- append(errors, i) })
+}
+
+
+