feature: Improved CSV Parsing

1. Superior field detection: short of having actual typos, most ways to
   express a field should now be properly registered. Further, it will
   be considerably easier to add new variants.
2. Numeric well parsing: some systems do not use alphanumeric wells like
   H12 or E7. Purely numeric wells will now be supported but only if the
   plate format is manually specified; this feels like a good tradeoff
   since a failed detection would yield very odd behaviour to a user.

plate-tool-lib/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "plate-tool-lib"
-version = "0.3.0"
+version = "0.3.1"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

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

@@ -1,7 +1,7 @@
 use crate::transfer::Transfer;
 use crate::util::*;
 
-use super::TransferRecord;
+use super::{TransferRecord, transfer_record::TransferRecordDeserializeIntermediate, mangle_headers::mangle_headers};
 use lazy_static::lazy_static;
 use regex::Regex;
 use serde::{Deserialize, Serialize};
@@ -47,29 +47,28 @@ pub fn records_to_csv(trs: Vec<TransferRecord>) -> Result<String, Box<dyn Error>
 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();
+        static ref REGEX_ALT: Regex = Regex::new(r"(\d+)").unwrap();
     }
     if let Some(c1) = REGEX.captures(input) {
         if let (Some(row), Some(col)) = (letters_to_num(&c1[1]), c1[2].parse::<u8>().ok()) {
-            Some((row, col))
+            return Some((row, col))
         } else {
-            None
+            return None
         }
-    } else {
-        None
     }
+    None
 }
 
 pub fn read_csv(data: &str) -> Vec<TransferRecord> {
-    let (header, data) = data.split_at(data.find('\n').unwrap());
-    let modified: String = header.to_lowercase() + data;
-
+    let modified = mangle_headers(data);
     let mut rdr = csv::Reader::from_reader(modified.as_bytes());
     let mut records: Vec<TransferRecord> = Vec::new();
-    for record in rdr.deserialize::<TransferRecord>() {
+    for record in rdr.deserialize::<TransferRecordDeserializeIntermediate>() {
         match record {
             Ok(r) => {
-                //log::debug!("{:?}", r);
-                records.push(r);
+                if !r.is_empty() {
+                    records.push(r.into());
+                }
             }
             Err(e) => {
                 log::debug!("{:?}", e);

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

@@ -0,0 +1,58 @@
+pub fn mangle_headers(data: &str) -> String {
+    let (header, rows) = data.split_at(data.find('\n').unwrap());
+    let fields = header.trim().split(",");
+    let mut modified_headers: Vec<String> = Vec::new();
+    for field in fields {
+        if let Some(f) = detect_field(field) {
+            modified_headers.push(f.to_string());
+        }
+    }
+
+    modified_headers.join(",") + "\n" + rows
+}
+
+fn detect_field(field: &str) -> Option<Field> {
+    match field.trim().to_lowercase() {
+        x if x.contains("source") || x.contains("src") => match x {
+            _ if x.contains("plate") => Some(Field::SourcePlate),
+            _ if x.contains("well") => Some(Field::SourceWell),
+            _ if x.contains("format") || x.contains("fmt") => Some(Field::SourceFormat),
+            _ => None,
+        },
+        x if x.contains("destination") || x.contains("dest") => match x {
+            _ if x.contains("plate") => Some(Field::DestinationPlate),
+            _ if x.contains("well") => Some(Field::DestinationWell),
+            _ if x.contains("format") || x.contains("fmt") => Some(Field::DestinationFormat),
+            _ => None,
+        },
+        x if x.contains("volume") => Some(Field::Volume),
+        x if x.contains("concentration") => Some(Field::Concentration),
+        _ => None,
+    }
+}
+
+enum Field {
+    SourcePlate,
+    DestinationPlate,
+    SourceWell,
+    DestinationWell,
+    SourceFormat,
+    DestinationFormat,
+    Volume,
+    Concentration,
+}
+
+impl ToString for Field {
+    fn to_string(&self) -> String {
+        match self {
+            Field::SourcePlate => "sourceplate".to_string(),
+            Field::DestinationPlate => "destinationplate".to_string(),
+            Field::SourceWell => "sourcewell".to_string(),
+            Field::DestinationWell => "destinationwell".to_string(),
+            Field::SourceFormat => "sourceformat".to_string(),
+            Field::DestinationFormat => "destinationformat".to_string(),
+            Field::Volume => "volume".to_string(),
+            Field::Concentration => "concentration".to_string(),
+        }
+    }
+}

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

@@ -1,6 +1,7 @@
 mod transfer_record;
 mod conversion;
 mod auto;
+mod mangle_headers;
 
 pub use transfer_record::volume_default;
 pub use transfer_record::TransferRecord;

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

@@ -1,33 +1,100 @@
 use serde::{Deserialize, Serialize};
 
-use crate::transfer::Transfer;
+use crate::{plate::PlateFormat, transfer::Transfer, util::num_to_letters};
 
-#[derive(Serialize, Deserialize, Debug, Clone)]
+#[derive(Serialize, Debug, Clone)]
 pub struct TransferRecord {
-    #[serde(rename = "Source Plate", alias = "source plate", alias = "src plate")]
+    #[serde(rename = "Source Plate")]
     pub source_plate: String,
-    #[serde(rename = "Source Well", alias = "source well", alias = "src well")]
+    #[serde(rename = "Source Well")]
     pub source_well: String,
-    #[serde(
-        rename = "Dest Plate",
-        alias = "dest plate",
-        alias = "destination plate"
-    )]
+    #[serde(rename = "Dest Plate")]
     pub destination_plate: String,
-    #[serde(
-        rename = "Destination Well",
-        alias = "destination well",
-        alias = "dest well"
-    )]
+    #[serde(rename = "Destination Well")]
     pub destination_well: String,
-    #[serde(rename = "Transfer Volume", alias = "transfer volume")]
-    #[serde(default = "volume_default")]
+    #[serde(rename = "Transfer Volume")]
     pub volume: f32,
-    #[serde(rename = "Concentration", alias = "concentration")]
+    #[serde(rename = "Concentration")]
     pub concentration: Option<f32>,
 }
 
+#[derive(Deserialize, Debug, Clone)]
+pub struct TransferRecordDeserializeIntermediate {
+    #[serde(rename = "sourceplate")]
+    source_plate: String,
+    #[serde(rename = "destinationplate")]
+    destination_plate: String,
+    #[serde(rename = "sourcewell")]
+    source_well: String,
+    #[serde(rename = "sourceformat")]
+    source_format: Option<String>,
+    #[serde(rename = "destinationwell")]
+    destination_well: String,
+    #[serde(rename = "destinationformat")]
+    destination_format: Option<String>,
+    #[serde(rename = "volume")]
+    volume: Option<f32>,
+    #[serde(rename = "concentration")]
+    concentration: Option<f32>,
+}
+
+impl From<TransferRecordDeserializeIntermediate> for TransferRecord {
+    fn from(value: TransferRecordDeserializeIntermediate) -> Self {
+        let mut source_well: String = value.source_well;
+        if let Some(pformat) = value
+            .source_format
+            .and_then(|x| PlateFormat::try_from(x.as_str()).ok())
+        {
+            if let Ok(well_number) = source_well.parse::<u16>() {
+                if let Some(alphanumeric) = numeric_well_to_alphanumeric(well_number, pformat) {
+                    source_well = alphanumeric;
+                }
+            }
+        }
+
+        let mut destination_well: String = value.destination_well;
+        if let Some(pformat) = value
+            .destination_format
+            .and_then(|x| PlateFormat::try_from(x.as_str()).ok())
+        {
+            if let Ok(well_number) = destination_well.parse::<u16>() {
+                if let Some(alphanumeric) = numeric_well_to_alphanumeric(well_number, pformat) {
+                    destination_well = alphanumeric;
+                }
+            }
+        }
+
+        let volume = value.volume.unwrap_or(volume_default());
+
+        TransferRecord {
+            source_plate: value.source_plate,
+            destination_plate: value.destination_plate,
+            source_well,
+            destination_well,
+            volume,
+            concentration: value.concentration,
+        }
+    }
+}
+
+impl TransferRecordDeserializeIntermediate {
+    pub fn is_empty(&self) -> bool {
+        self.source_plate.is_empty()
+            || self.destination_plate.is_empty()
+            || self.source_well.is_empty()
+            || self.destination_well.is_empty()
+    }
+}
+
+fn numeric_well_to_alphanumeric(input: u16, pformat: PlateFormat) -> Option<String> {
+    let column_height: u16 = pformat.size().0 as u16;
+    let column = input.div_ceil(column_height);
+    let row = input % column_height;
+    let row_str = num_to_letters(row as u8)?;
+
+    Some(format!("{}{}", row_str, column))
+}
+
 pub fn volume_default() -> f32 {
     Transfer::default().volume
 }
-

plate-tool-lib/src/plate.rs

@@ -77,6 +77,20 @@ impl TryFrom<&str> for PlateFormat {
         }
     }
 }
+impl From<&PlateFormat> for u16 {
+    fn from(value: &PlateFormat) -> Self {
+        match value {
+            PlateFormat::W6 => 6,
+            PlateFormat::W12 => 12,
+            PlateFormat::W24 => 24,
+            PlateFormat::W48 => 48,
+            PlateFormat::W96 => 96,
+            PlateFormat::W384 => 384,
+            PlateFormat::W1536 => 1536,
+            PlateFormat::W3456 => 3456,
+        }
+    }
+}
 
 impl PlateFormat {
     pub fn size(&self) -> (u8, u8) {