Cargo.lock

@@ -637,7 +637,6 @@ version = "0.1.0"
 dependencies = [
  "csv",
  "getrandom",
- "lazy_static",
  "log",
  "rand",
  "regex",

README.md

@@ -78,6 +78,13 @@ To add a new plate, click the "New Plate" button:
  Keep in mind that this will overwrite any work you currently have open,
  so you may wish to export first (see above).
 
+ #### Import Transfer from CSV (Using a picklist as a transfer)
+ If you have a CSV generated by another tool (or plate-tool),
+ you can import it as a single transfer.
+ To do so, mouse over the "File" tab, then "Import", and finally "Import Transfer from CSV".
+ When creating transfers via this method, the transfer cannot be edited.
+ This is useful if you have a pre-existing picklist that you would like to visualize in plate-tool.
+ 
  _Note 1_: JSON files are plaintext!
  By default there is little whitespace (this makes comprehending them a challenge)
  but if we pass it through a "JSON Beautifier" (enter this into your search engine of choice)
@@ -92,18 +99,6 @@ To add a new plate, click the "New Plate" button:
  that this application does not "phone home".
  Your data is stored locally (unless you choose to export it and distribute it yourself).
 
- #### Import Transfer from CSV (Using a picklist as a transfer)
- If you have a CSV generated by another tool (or plate-tool),
- you can import it as a single transfer.
- To do so, mouse over the "File" tab, then "Import", and finally "Import Transfer from CSV".
- When creating transfers via this method, the transfer cannot be edited.
- This is useful if you have a pre-existing picklist that you would like to visualize in plate-tool.
- 
- _Note_: If you try to use this feature and no plates are available to select,
- there was likely an issue parsing your picklist.
- Your browser's console may have guidance as to why parsing failed;
- plate-tool was probably expecting a different name for a column than was in your file.
-
 ### Other Neat Features
 
  #### Taking Pictures of Plates
@@ -135,7 +130,7 @@ To add a new plate, click the "New Plate" button:
 Plate tool is hosted [here](https://ilia.moe/cool-stuff/plate-tool/) for your convenience.
 However, you're absolutely welcome to host your own instance (even locally).
 Here's how:
-(_Note:_ ~~If you run Windows you're probably best off doing the following in WSL2~~ You're absolutely fine to install rustup in Powershell, and the subsequent steps should be very similar but likely with different filepaths.)
+(_Note:_ If you run Windows you're probably best off doing the following in WSL2)
 
 1. Make sure you have a working Rust toolchain
     1. Installing `rustup` is the easiest way to do this. See [their website](https://rustup.rs/),
@@ -145,7 +140,7 @@ Here's how:
 2. Install [trunk](https://trunkrs.dev/)
     - Run `cargo install --locked trunk`
 3. Clone this repository using git
-4. Enter the plate-tool-web directory and run `trunk serve`
+4. Enter the project directory and run `trunk serve`
      - You may need to check where `cargo` is installing binaries by default. For me, they're at `~/.cargo/bin`.
        If trunk is not automatically placed in your path, you would then run `/your/path/to/.cargo/bin/trunk serve`.
      - You can instead run `trunk build --release` for a more performant binary.

plate-tool-lib/Cargo.toml

@@ -14,4 +14,3 @@ serde_json = "1.0"
 csv = "1.2"
 getrandom = { version = "0.2", features = ["js"] }
 rand = { version = "0.8", features = ["small_rng"] }
-lazy_static = "1.4"

plate-tool-lib/src/csv.rs

@@ -1,12 +1,38 @@
 use crate::transfer::Transfer;
 use crate::util::*;
 
-use super::TransferRecord;
-use lazy_static::lazy_static;
-use regex::Regex;
 use serde::{Deserialize, Serialize};
 use std::error::Error;
 
+#[derive(Serialize, Deserialize, Debug)]
+pub struct TransferRecord {
+    #[serde(rename = "Source Plate", alias = "source plate", alias = "src plate")]
+    pub source_plate: String,
+    #[serde(rename = "Source Well", alias = "source well", alias = "src well")]
+    pub source_well: String,
+    #[serde(
+        rename = "Dest Plate",
+        alias = "dest plate",
+        alias = "destination plate"
+    )]
+    pub destination_plate: String,
+    #[serde(
+        rename = "Destination Well",
+        alias = "destination well",
+        alias = "dest well"
+    )]
+    pub destination_well: String,
+    #[serde(rename = "Transfer Volume", alias = "transfer volume")]
+    #[serde(default = "volume_default")]
+    pub volume: f32,
+    #[serde(rename = "Concentration", alias = "concentration")]
+    pub concentration: Option<f32>,
+}
+
+pub fn volume_default() -> f32 {
+    Transfer::default().volume
+}
+
 pub fn transfer_to_records(
     tr: &Transfer,
     src_barcode: &str,
@@ -44,21 +70,6 @@ pub fn records_to_csv(trs: Vec<TransferRecord>) -> Result<String, Box<dyn Error>
     Ok(data)
 }
 
-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();
-    }
-    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))
-        } else {
-            None
-        }
-    } else {
-        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;

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

@@ -1,173 +0,0 @@
-use super::{string_well_to_pt, TransferRecord, read_csv};
-use crate::plate::{PlateFormat, PlateType};
-use crate::plate_instances::PlateInstance;
-use crate::transfer::Transfer;
-use crate::transfer_region::{CustomRegion, Region, TransferRegion};
-
-use std::collections::HashSet;
-
-pub struct AutoOutput {
-    pub sources: Vec<PlateInstance>,
-    pub destinations: Vec<PlateInstance>,
-    pub transfers: Vec<Transfer>,
-}
-
-struct UniquePlates {
-    sources: Vec<PlateInstance>,
-    destinations: Vec<PlateInstance>,
-}
-
-const W96_COL_MAX: u8 = 12;
-const W96_ROW_MAX: u8 = 8;
-const W384_COL_MAX: u8 = 24;
-const W384_ROW_MAX: u8 = 16;
-const W1536_COL_MAX: u8 = 48;
-const W1536_ROW_MAX: u8 = 32;
-
-pub fn auto(records: &[TransferRecord]) -> AutoOutput {
-    let unique_plates = find_unique_plates(records);
-    let transfers = get_transfer_for_all_pairs(records, &unique_plates);
-
-    AutoOutput { sources: unique_plates.sources, destinations: unique_plates.destinations, transfers }
-}
-
-pub fn read_csv_auto(data: &str) -> AutoOutput {
-    let transfer_records = read_csv(data);
-    auto(&transfer_records)
-}
-
-fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
-    let mut source_names: HashSet<&str> = HashSet::new();
-    let mut destination_names: HashSet<&str> = HashSet::new();
-
-    for record in records {
-        source_names.insert(&record.source_plate);
-        destination_names.insert(&record.destination_plate);
-    }
-
-    let mut sources: Vec<PlateInstance> = Vec::with_capacity(source_names.len());
-    for source_name in source_names {
-        let filtered_records: Vec<&TransferRecord> = records
-            .iter()
-            .filter(|x| x.source_plate == source_name)
-            .collect();
-        let format_guess = guess_plate_size(&filtered_records, PlateType::Source);
-        sources.push(PlateInstance::new(
-            PlateType::Source,
-            format_guess,
-            source_name.to_string(),
-        ))
-    }
-
-    let mut destinations: Vec<PlateInstance> = Vec::with_capacity(destination_names.len());
-    for destination_name in destination_names {
-        let filtered_records: Vec<&TransferRecord> = records
-            .iter()
-            .filter(|x| x.destination_plate == destination_name)
-            .collect();
-        let format_guess = guess_plate_size(&filtered_records, PlateType::Destination);
-        destinations.push(PlateInstance::new(
-            PlateType::Destination,
-            format_guess,
-            destination_name.to_string(),
-        ))
-    }
-
-    UniquePlates {
-        sources,
-        destinations,
-    }
-}
-
-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 {
-        if let Some((row, col)) = string_well_to_pt(match which {
-            PlateType::Source => &record.source_well,
-            PlateType::Destination => &record.destination_well,
-        }) {
-            if row > W1536_ROW_MAX || col > W1536_COL_MAX {
-                return PlateFormat::W3456;
-            } else if row > W384_ROW_MAX || col > W384_COL_MAX {
-                guess = PlateFormat::W1536;
-            } else if row > W96_ROW_MAX || col > W96_COL_MAX {
-                guess = PlateFormat::W384;
-            }
-        }
-    }
-    guess
-}
-
-fn get_transfer_for_all_pairs(
-    records: &[TransferRecord],
-    unique_plates: &UniquePlates,
-) -> Vec<Transfer> {
-    let mut transfers: Vec<Transfer> = Vec::new();
-    for source_instance in &unique_plates.sources {
-        for destination_instance in &unique_plates.destinations {
-            if let Some(transfer) =
-                get_transfer_for_pair(records, source_instance, destination_instance)
-            {
-                transfers.push(transfer);
-            }
-        }
-    }
-
-    transfers
-}
-
-fn get_transfer_for_pair(
-    records: &[TransferRecord],
-    source: &PlateInstance,
-    destination: &PlateInstance,
-) -> Option<Transfer> {
-    let source_name: &str = &source.name;
-    let destination_name: &str = &destination.name;
-
-    let mut filtered_records = records
-        .iter()
-        .filter(|x| x.source_plate == source_name && x.destination_plate == destination_name)
-        .peekable();
-
-    if filtered_records.peek().is_none() {
-        return None;
-    }
-
-    let mut source_wells: HashSet<(u8, u8)> = HashSet::new();
-    let mut destination_wells: HashSet<(u8, u8)> = HashSet::new();
-    for record in filtered_records {
-        let source_point_opt = string_well_to_pt(&record.source_well);
-        let destination_point_opt = string_well_to_pt(&record.destination_well);
-
-        if source_point_opt.and(destination_point_opt).is_some() {
-            let source_point = source_point_opt.unwrap();
-            let destination_point = destination_point_opt.unwrap();
-
-            source_wells.insert(source_point);
-            destination_wells.insert(destination_point);
-        }
-    }
-    let source_wells_vec: Vec<(u8, u8)> = source_wells.into_iter().collect();
-    let destination_wells_vec: Vec<(u8, u8)> = destination_wells.into_iter().collect();
-
-    let custom_region: Region =
-        Region::Custom(CustomRegion::new(source_wells_vec, destination_wells_vec));
-
-    let transfer_region = TransferRegion {
-        source_plate: source.plate,
-        dest_plate: destination.plate,
-        interleave_source: (1, 1),
-        interleave_dest: (1, 1),
-        source_region: custom_region.clone(),
-        dest_region: custom_region,
-    };
-
-    let transfer_name = format!("{} to {}", source.name, destination.name);
-
-    Some(Transfer::new(
-        source.clone(),
-        destination.clone(),
-        transfer_region,
-        transfer_name,
-    ))
-}

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

@@ -1,9 +0,0 @@
-mod transfer_record;
-mod conversion;
-mod auto;
-
-pub use transfer_record::volume_default;
-pub use transfer_record::TransferRecord;
-pub use conversion::*;
-
-pub use auto::{auto, read_csv_auto};

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

@@ -1,33 +0,0 @@
-use serde::{Deserialize, Serialize};
-
-use crate::transfer::Transfer;
-
-#[derive(Serialize, Deserialize, Debug, Clone)]
-pub struct TransferRecord {
-    #[serde(rename = "Source Plate", alias = "source plate", alias = "src plate")]
-    pub source_plate: String,
-    #[serde(rename = "Source Well", alias = "source well", alias = "src well")]
-    pub source_well: String,
-    #[serde(
-        rename = "Dest Plate",
-        alias = "dest plate",
-        alias = "destination plate"
-    )]
-    pub destination_plate: String,
-    #[serde(
-        rename = "Destination Well",
-        alias = "destination well",
-        alias = "dest well"
-    )]
-    pub destination_well: String,
-    #[serde(rename = "Transfer Volume", alias = "transfer volume")]
-    #[serde(default = "volume_default")]
-    pub volume: f32,
-    #[serde(rename = "Concentration", alias = "concentration")]
-    pub concentration: Option<f32>,
-}
-
-pub fn volume_default() -> f32 {
-    Transfer::default().volume
-}
-

plate-tool-lib/src/plate_instances.rs

@@ -2,7 +2,7 @@ use super::plate::*;
 use serde::{Deserialize, Serialize};
 use uuid::Uuid;
 
-#[derive(PartialEq, Clone, Serialize, Deserialize, Debug)]
+#[derive(PartialEq, Clone, Serialize, Deserialize)]
 pub struct PlateInstance {
     pub plate: Plate,
     #[serde(rename = "id_v7")]

plate-tool-lib/src/transfer_region.rs

@@ -8,12 +8,6 @@ pub struct CustomRegion {
     dest: Vec<(u8, u8)>,
 }
 
-impl CustomRegion {
-    pub fn new(src: Vec<(u8, u8)>, dest: Vec<(u8, u8)>) -> Self {
-        CustomRegion { src, dest }
-    }
-}
-
 #[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
 pub enum Region {
     Rect((u8, u8), (u8, u8)),

plate-tool-lib/src/util.rs

@@ -33,7 +33,7 @@ pub fn num_to_letters(num: u8) -> Option<String> {
 
 #[cfg(test)]
 mod tests {
-    use super::{letters_to_num, num_to_letters};
+    use super::{letters_to_num, num_to_letters, RegionDisplay};
 
     #[test]
     fn test_letters_to_num() {

plate-tool-web/src/components/callbacks/import_csv_callbacks.rs

@@ -1,19 +1,22 @@
 use std::collections::HashSet;
 
+use lazy_static::lazy_static;
+use regex::Regex;
 use wasm_bindgen::{prelude::*, JsCast};
 use web_sys::{
-    FileReader, HtmlButtonElement, HtmlDialogElement, HtmlElement, HtmlFormElement,
+    FileReader, HtmlButtonElement, HtmlDialogElement, HtmlFormElement, HtmlInputElement,
-    HtmlInputElement, HtmlOptionElement, HtmlSelectElement,
+    HtmlOptionElement, HtmlSelectElement,
 };
 use yew::prelude::*;
 use yewdux::prelude::*;
 
 use crate::components::states::MainState;
+use plate_tool_lib::util::letters_to_num;
 
 use plate_tool_lib::transfer::Transfer;
 use plate_tool_lib::transfer_region::{Region, TransferRegion};
 
-use plate_tool_lib::csv::{auto, string_well_to_pt, TransferRecord};
+use plate_tool_lib::csv::TransferRecord;
 
 use super::main_window_callbacks::create_close_button;
 
@@ -112,17 +115,6 @@ pub fn import_transfer_csv_onload_callback(
 
             let window = web_sys::window().unwrap();
             let document = window.document().unwrap();
-
-            let auto_button = document
-                .create_element("button")
-                .unwrap()
-                .dyn_into::<HtmlElement>()
-                .unwrap();
-            auto_button.set_inner_text("Auto");
-            let auto_button_callback = auto_callback(main_dispatch.clone(), &records);
-            auto_button.set_onclick(Some(auto_button_callback.as_ref().unchecked_ref()));
-            auto_button_callback.forget();
-
             let form = document
                 .create_element("form")
                 .unwrap()
@@ -219,7 +211,6 @@ pub fn import_transfer_csv_onload_callback(
             form.append_child(&to_dest).unwrap();
             modal.append_child(&submit).unwrap();
             modal.append_child(&form).unwrap();
-            modal.append_child(&auto_button).unwrap();
         }
     })
 }
@@ -238,14 +229,28 @@ pub fn import_transfer_csv_submit_callback(
         let from_dest = from_dest.value();
         let to_dest = to_dest.value();
 
+        lazy_static! {
+            static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap();
+        }
         let records: Vec<((u8, u8), (u8, u8))> = records
             .iter()
             .filter(|record| record.source_plate == from_source)
             .filter(|record| record.destination_plate == from_dest)
             .map(|record| {
+                let c1 = REGEX.captures(&record.source_well).unwrap();
+                let c2 = REGEX.captures(&record.destination_well).unwrap();
+                log::debug!("{} {}", &record.source_well, &record.destination_well);
+                log::debug!("{},{}  {},{}", &c1[1], &c1[2], &c2[1], &c2[2]);
+
                 (
-                    string_well_to_pt(&record.source_well).unwrap(),
+                    (
-                    string_well_to_pt(&record.destination_well).unwrap(),
+                        letters_to_num(&c1[1]).unwrap(),
+                        c1[2].parse::<u8>().unwrap(),
+                    ),
+                    (
+                        letters_to_num(&c2[1]).unwrap(),
+                        c2[2].parse::<u8>().unwrap(),
+                    ),
                 )
             })
             .collect();
@@ -286,20 +291,3 @@ pub fn import_transfer_csv_submit_callback(
         });
     })
 }
-
-fn auto_callback(
-    main_dispatch: Dispatch<MainState>,
-    records: &[TransferRecord],
-) -> Closure<dyn FnMut(Event)> {
-    let records = Vec::from(records);
-    Closure::<dyn FnMut(_)>::new(move |_| {
-        let res = auto(&records);
-        main_dispatch.reduce_mut(|state| {
-            state.source_plates.extend(res.sources.into_iter());
-            state
-                .destination_plates
-                .extend(res.destinations.into_iter());
-            state.transfers.extend(res.transfers.into_iter());
-        });
-    })
-}