Add some doc comments to lib

plate-tool-lib/src/csv/alternative_formats.rs

@@ -2,9 +2,10 @@ use serde::Serialize;
 
 use super::TransferRecord;
 
-// Format preferred by the Echo Client when using the Pick-List function.
-// Note that this does not export plate info!
-// Exports of this type should combine all transfers between the two actively selected plates.
+/// Format preferred by the Echo Client when using the Pick-List function.
+///
+/// Note that this does not export plate info!
+/// Exports of this type should combine all transfers between the two actively selected plates.
 #[derive(Serialize, Debug)]
 pub struct EchoClientTransferRecord {
     #[serde(rename = "SrcWell")]

plate-tool-lib/src/csv/auto.rs

@@ -1,3 +1,8 @@
+//! Auto module for importing picklists without creating plates first
+//!
+//! Before the auto module, it was necessary for a user to create the plates
+//! used in an imported transfer before import.
+
 use super::{string_well_to_pt, TransferRecord, read_csv};
 use crate::plate::{PlateFormat, PlateType};
 use crate::plate_instances::PlateInstance;
@@ -12,6 +17,7 @@ pub struct AutoOutput {
     pub transfers: Vec<Transfer>,
 }
 
+/// Two lists of plates that are guaranteed to be unique (no duplicate plates)
 struct UniquePlates {
     sources: Vec<PlateInstance>,
     destinations: Vec<PlateInstance>,
@@ -24,6 +30,12 @@ const W384_ROW_MAX: u8 = 16;
 const W1536_COL_MAX: u8 = 48;
 const W1536_ROW_MAX: u8 = 32;
 
+/// Main function for the auto module
+/// Takes a list of pre-deserialized transfer records and generates output
+/// This output is 3 lists of:
+/// 1. The source plates used in the picklist
+/// 2. The destination plates used in the picklist
+/// 3. All of the transfers between those plates
 pub fn auto(records: &[TransferRecord]) -> AutoOutput {
     let unique_plates = find_unique_plates(records);
     let transfers = get_transfer_for_all_pairs(records, &unique_plates);
@@ -31,11 +43,18 @@ pub fn auto(records: &[TransferRecord]) -> AutoOutput {
     AutoOutput { sources: unique_plates.sources, destinations: unique_plates.destinations, transfers }
 }
 
+/// Helper function that reads a CSV and immediately dumps the resulting transfer records
+/// into the auto function defined in this module.
 pub fn read_csv_auto(data: &str) -> AutoOutput {
     let transfer_records = read_csv(data);
     auto(&transfer_records)
 }
 
+/// Looks through a list of transfer records and generates two lists
+/// of all of the unique plates found in those transfers.
+/// Worth noting that the Transfer struct requires two associated PlateInstances;
+/// these PlateInstance structs are generated here---they are not present in a TransferRecord.
+/// See notes on the UniquePlates struct
 fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
     let mut source_names: HashSet<&str> = HashSet::new();
     let mut destination_names: HashSet<&str> = HashSet::new();
@@ -79,6 +98,12 @@ fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
     }
 }
 
+/// Tries to guess the format of a plate given the southeastern-est well used.
+/// A picklist does not necessarily contain plate format info; this method guesses
+/// based on the well furthest from A1 that exists in a transfer.
+/// It's possible for a 1536 well plate to be seen as a 384 well if all of the wells
+/// used could have fit in the top-left quadrant of a 384 well plate
+/// (i.e. all lower than P24 in this case)
 fn guess_plate_size(plate_filtered_records: &[&TransferRecord], which: PlateType) -> PlateFormat {
     let mut guess = PlateFormat::W96; // Never guess smaller than 96
     for record in plate_filtered_records {
@@ -116,6 +141,17 @@ fn get_transfer_for_all_pairs(
     transfers
 }
 
+/// Given a source and destination plate, get all of the wells transferred
+/// from source to destination and turn this into a Transfer.
+/// 
+/// Note that even if you have what looks like two separate transfers,
+/// this will join all transfers for a given source-dest pair.
+/// For example:
+/// Consider expanding all of src:A1 to the column dst:A 
+/// and src:B1 -> row dst:1
+/// If you were making this transfer in plate tool, it would be easiest
+/// to do this as two separate transfers.
+/// On import, this would be seen as one transfer.
 fn get_transfer_for_pair(
     records: &[TransferRecord],
     source: &PlateInstance,

plate-tool-lib/src/csv/conversion.rs

@@ -52,9 +52,12 @@ pub fn records_to_echo_client_csv(trs: Vec<TransferRecord>) -> Result<String, Bo
     Ok(data)
 }
 
+/// Converts "spreadsheet format" well identification to coordinates
 pub fn string_well_to_pt(input: &str) -> Option<(u8, u8)> {
     lazy_static! {
         static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap();
+
+        // Can this be removed?
         static ref REGEX_ALT: Regex = Regex::new(r"(\d+)").unwrap();
     }
     if let Some(c1) = REGEX.captures(input) {

plate-tool-lib/src/csv/mangle_headers.rs

@@ -1,3 +1,12 @@
+//! This contains the `mangle_headers` function and its helpers
+//!
+//! Mangling headers is necessary to normalize CSV column names before
+//! deserialization can be done by Serde.
+//! Field detection occurs in `detect_field`.
+//!
+//! As of lib 0.4.0, unrecognized headers are ignored and left untouched by mangling.
+//! However, they are not passed through to any subsequent exports from plate-tool.
+
 pub fn mangle_headers(data: &str) -> String {
     let (header, rows) = data.split_at(data.find('\n').unwrap());
     let fields = header.trim().split(",");

plate-tool-lib/src/csv/transfer_record.rs

@@ -2,6 +2,10 @@ use serde::{Deserialize, Serialize};
 
 use crate::{plate::PlateFormat, transfer::Transfer, util::num_to_letters};
 
+/// Represents a single line of a CSV picklist.
+/// In practice, this is generated from the deserialize intermediate.
+/// A list of `TransferRecord`s can be used to create a `transfer::Transfer` struct;
+/// see the `auto` module for this.
 #[derive(Serialize, Debug, Clone)]
 pub struct TransferRecord {
     #[serde(rename = "Source Barcode")]
@@ -18,6 +22,12 @@ pub struct TransferRecord {
     pub concentration: Option<f32>,
 }
 
+/// The deserialization intermediate is generated from a mangled CSV s.t.
+/// the column headers are standardized to those given to the derive macro.
+///
+/// `TransferRecord` can *always* be generated from the intermediate.
+/// Currently there's no reason why the inverse couldn't be true,
+/// but there's no reason to convert back into the deserialize-only intermediate.
 #[derive(Deserialize, Debug, Clone)]
 pub struct TransferRecordDeserializeIntermediate {
     #[serde(rename = "sourceplate")]
@@ -78,6 +88,7 @@ impl From<TransferRecordDeserializeIntermediate> for TransferRecord {
 }
 
 impl TransferRecordDeserializeIntermediate {
+    /// Used to cull malformed picklist entries that lack required information
     pub fn is_empty(&self) -> bool {
         self.source_plate.is_empty()
             || self.destination_plate.is_empty()
@@ -95,6 +106,7 @@ fn numeric_well_to_alphanumeric(input: u16, pformat: PlateFormat) -> Option<Stri
     Some(format!("{}{}", row_str, column))
 }
 
+// Why is this here?
 pub fn volume_default() -> f32 {
     Transfer::default().volume
 }