emilia
/
plate-tool
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Format 

(I should set up `cargo fmt` as a commit hook)
This commit is contained in:
Emilia Allison 2023-06-07 16:14:19 -04:00
parent 658ab3082a
commit 85670fe86e
Signed by: emilia
GPG Key ID: 7A3F8997BFE894E0
9 changed files with 207 additions and 112 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

107
src/components/main_window.rs
View File

@ -1,9 +1,9 @@
#![allow(non_snake_case)]
use js_sys::Array;
use wasm_bindgen::{prelude::*, JsCast, JsValue};
use web_sys::{Blob, HtmlAnchorElement, HtmlDialogElement, HtmlFormElement, HtmlInputElement, Url};
use yew::prelude::*;
use yewdux::prelude::*;
use wasm_bindgen::{JsValue, JsCast, prelude::*};
use web_sys::{Blob, Url, HtmlAnchorElement, HtmlDialogElement, HtmlInputElement, HtmlFormElement};
use js_sys::Array;
use super::new_plate_dialog::NewPlateDialog;
use super::plates::plate_container::PlateContainer;
@ -11,8 +11,8 @@ use super::states::{CurrentTransfer, MainState};
use super::transfer_menu::TransferMenu;
use super::tree::Tree;
use crate::data::plate_instances::PlateInstance;
use crate::data::csv::state_to_csv;
use crate::data::plate_instances::PlateInstance;
#[function_component]
pub fn MainWindow() -> Html {
@ -59,7 +59,8 @@ pub fn MainWindow() -> Html {
let ct_dispatch = ct_dispatch.clone();
Callback::from(move |_| {
let window = web_sys::window().unwrap();
let confirm = window.confirm_with_message("This will reset all plates and transfers. Proceed?");
let confirm =
window.confirm_with_message("This will reset all plates and transfers. Proceed?");
if let Ok(confirm) = confirm {
if confirm {
main_dispatch.set(MainState::default());
@ -73,8 +74,11 @@ pub fn MainWindow() -> Html {
let main_state = main_state.clone();
Callback::from(move |_| {
if main_state.transfers.len() == 0 {
web_sys::window().unwrap().alert_with_message("No transfers to export.").unwrap();
return ()
web_sys::window()
.unwrap()
.alert_with_message("No transfers to export.")
.unwrap();
return ();
}
web_sys::window().unwrap().alert_with_message("CSV export is currently not importable. Export as JSON if you'd like to back up your work!").unwrap();
if let Ok(csv) = state_to_csv(&main_state) {
@ -89,7 +93,10 @@ pub fn MainWindow() -> Html {
if let Ok(json) = serde_json::to_string(&main_state) {
save_str(&json, "plate-tool-state.json");
} else {
web_sys::window().unwrap().alert_with_message("Failed to export.").unwrap();
web_sys::window()
.unwrap()
.alert_with_message("Failed to export.")
.unwrap();
}
})
};
@ -100,7 +107,11 @@ pub fn MainWindow() -> Html {
let window = web_sys::window().unwrap();
let document = window.document().unwrap();
let body = document.body().unwrap();
let modal = document.create_element("dialog").unwrap().dyn_into::<HtmlDialogElement>().unwrap();
let modal = document
.create_element("dialog")
.unwrap()
.dyn_into::<HtmlDialogElement>()
.unwrap();
modal.set_text_content(Some("Import File:"));
let onclose_callback = {
let modal = modal.clone();
@ -111,8 +122,16 @@ pub fn MainWindow() -> Html {
modal.set_onclose(Some(&onclose_callback.as_ref().unchecked_ref()));
onclose_callback.forget();
let form = document.create_element("form").unwrap().dyn_into::<HtmlFormElement>().unwrap();
let input = document.create_element("input").unwrap().dyn_into::<HtmlInputElement>().unwrap();
let form = document
.create_element("form")
.unwrap()
.dyn_into::<HtmlFormElement>()
.unwrap();
let input = document
.create_element("input")
.unwrap()
.dyn_into::<HtmlInputElement>()
.unwrap();
input.set_type("file");
input.set_accept(".json");
form.append_child(&input).unwrap();
@ -121,33 +140,38 @@ pub fn MainWindow() -> Html {
let main_dispatch = main_dispatch.clone();
let modal = modal.clone();
Closure::<dyn FnMut(_)>::new(move |e: Event| {
if let Some(input) = e.current_target() {
let input = input.dyn_into::<HtmlInputElement>().expect("We know this is an input.");
if let Some(files) = input.files() {
if let Some(file) = files.get(0) {
let fr = web_sys::FileReader::new().unwrap();
fr.read_as_text(&file).unwrap();
let fr1 = fr.clone(); // Clone to avoid outliving closure
let main_dispatch = main_dispatch.clone(); // Clone to satisfy FnMut
// trait
let modal = modal.clone();
let onload = Closure::<dyn FnMut(_)>::new(move |e: Event| {
log::debug!("{:?}",&fr1.result());
if let Some(value) = &fr1.result().ok().and_then(|v| v.as_string()) {
let ms = serde_json::from_str::<MainState>(value);
match ms {
Ok(ms) => main_dispatch.set(ms),
Err(e) => log::debug!("{:?}", e),
};
modal.close();
}
});
fr.set_onload(Some(&onload.as_ref().unchecked_ref()));
onload.forget(); // Magic (don't touch)
if let Some(input) = e.current_target() {
let input = input
.dyn_into::<HtmlInputElement>()
.expect("We know this is an input.");
if let Some(files) = input.files() {
if let Some(file) = files.get(0) {
let fr = web_sys::FileReader::new().unwrap();
fr.read_as_text(&file).unwrap();
let fr1 = fr.clone(); // Clone to avoid outliving closure
let main_dispatch = main_dispatch.clone(); // Clone to satisfy FnMut
// trait
let modal = modal.clone();
let onload = Closure::<dyn FnMut(_)>::new(move |e: Event| {
log::debug!("{:?}", &fr1.result());
if let Some(value) =
&fr1.result().ok().and_then(|v| v.as_string())
{
let ms = serde_json::from_str::<MainState>(value);
match ms {
Ok(ms) => main_dispatch.set(ms),
Err(e) => log::debug!("{:?}", e),
};
modal.close();
}
});
fr.set_onload(Some(&onload.as_ref().unchecked_ref()));
onload.forget(); // Magic (don't touch)
}
}
}
}
})};
})
};
input.set_onchange(Some(&input_callback.as_ref().unchecked_ref()));
input_callback.forget(); // Magic straight from the docs, don't touch :(
@ -187,15 +211,18 @@ pub fn MainWindow() -> Html {
}
fn save_str(data: &str, name: &str) {
let blob = Blob::new_with_str_sequence(
&Array::from_iter(std::iter::once(JsValue::from_str(data))));
let blob =
Blob::new_with_str_sequence(&Array::from_iter(std::iter::once(JsValue::from_str(data))));
if let Ok(blob) = blob {
let url = Url::create_object_url_with_blob(&blob).expect("We have a blob, why not URL?");
// Beneath is the cool hack to download files
let window = web_sys::window().unwrap();
let document = window.document().unwrap();
let anchor = document.create_element("a").unwrap()
.dyn_into::<HtmlAnchorElement>().unwrap();
let anchor = document
.create_element("a")
.unwrap()
.dyn_into::<HtmlAnchorElement>()
.unwrap();
anchor.set_download(name);
anchor.set_href(&url);
anchor.click();

13
src/components/plates/destination_plate.rs
View File

@ -61,8 +61,11 @@ pub fn DestinationPlate(props: &DestinationPlateProps) -> Html {
let mut color_counter: u8 = 0;
let color_map = {
let ts = main_state.transfers.iter().filter(|t| t.dest_id == props.destination_plate.get_uuid());
let mut color_map: HashMap<(u8,u8), u8> = HashMap::new();
let ts = main_state
.transfers
.iter()
.filter(|t| t.dest_id == props.destination_plate.get_uuid());
let mut color_map: HashMap<(u8, u8), u8> = HashMap::new();
for t in ts {
color_counter += 1;
let dws = t.transfer_region.get_destination_wells();
@ -142,7 +145,7 @@ pub struct DestPlateCellProps {
pub selected: bool,
pub mouse: Callback<(u8, u8, MouseEventType)>,
pub in_transfer: Option<bool>,
color: Option<(u8,u8)>,
color: Option<(u8, u8)>,
}
#[function_component]
@ -156,8 +159,8 @@ fn DestPlateCell(props: &DestPlateCellProps) -> Html {
_ => None,
};
let color = match props.color {
Some(num) => PALETTE.get_u8(num.0,num.1),
None => [255.0,255.0,255.0]
Some(num) => PALETTE.get_u8(num.0, num.1),
None => [255.0, 255.0, 255.0],
};
let mouse = Callback::clone(&props.mouse);
let mouse2 = Callback::clone(&props.mouse);

15
src/components/plates/source_plate.rs
View File

@ -41,8 +41,11 @@ pub fn SourcePlate(props: &SourcePlateProps) -> Html {
let mut color_counter: u8 = 0;
let color_map = {
let ts = main_state.transfers.iter().filter(|t| t.source_id == props.source_plate.get_uuid());
let mut color_map: HashMap<(u8,u8), u8> = HashMap::new();
let ts = main_state
.transfers
.iter()
.filter(|t| t.source_id == props.source_plate.get_uuid());
let mut color_map: HashMap<(u8, u8), u8> = HashMap::new();
for t in ts {
color_counter += 1;
let sws = t.transfer_region.get_source_wells();
@ -139,7 +142,7 @@ pub struct SourcePlateCellProps {
selected: bool,
mouse: Callback<(u8, u8, MouseEventType)>,
in_transfer: Option<bool>,
color: Option<(u8,u8)>,
color: Option<(u8, u8)>,
}
#[derive(Debug)]
pub enum MouseEventType {
@ -158,8 +161,8 @@ fn SourcePlateCell(props: &SourcePlateCellProps) -> Html {
_ => None,
};
let color = match props.color {
Some(num) => PALETTE.get_u8(num.0,num.1),
None => [255.0,255.0,255.0]
Some(num) => PALETTE.get_u8(num.0, num.1),
None => [255.0, 255.0, 255.0],
};
let mouse = Callback::clone(&props.mouse);
let mouse2 = Callback::clone(&props.mouse);
@ -174,7 +177,7 @@ fn SourcePlateCell(props: &SourcePlateCellProps) -> Html {
onmouseenter={move |_| {
mouse2.emit((i,j, MouseEventType::MOUSEENTER))
}}>
<div class="plate_cell_inner"
<div class="plate_cell_inner"
style={format!("background: rgba({},{},{},1);", color[0], color[1], color[2])}/>
</td>
}

28
src/components/plates/util.rs
View File

@ -17,16 +17,16 @@ impl ColorPalette {
pub fn get(&self, t: f64) -> [f64; 3] {
[
(self.a[0] + self.b[0]*f64::cos(6.28318*(self.c[0]*t+self.d[0])))*255.0,
(self.a[1] + self.b[1]*f64::cos(6.28318*(self.c[1]*t+self.d[1])))*255.0,
(self.a[2] + self.b[2]*f64::cos(6.28318*(self.c[2]*t+self.d[2])))*255.0,
(self.a[0] + self.b[0] * f64::cos(6.28318 * (self.c[0] * t + self.d[0]))) * 255.0,
(self.a[1] + self.b[1] * f64::cos(6.28318 * (self.c[1] * t + self.d[1]))) * 255.0,
(self.a[2] + self.b[2] * f64::cos(6.28318 * (self.c[2] * t + self.d[2]))) * 255.0,
]
}
pub fn get_u8(&self, t: u8, n: u8) -> [f64; 3] {
assert!(t>0, "t must be greater than zero!");
assert!(n>0, "There cannot be zero points!");
self.get((t-1) as f64 / (n-1) as f64)
assert!(t > 0, "t must be greater than zero!");
assert!(n > 0, "There cannot be zero points!");
self.get((t - 1) as f64 / (n - 1) as f64)
}
}
@ -36,15 +36,15 @@ pub struct Palettes;
#[allow(dead_code)]
impl Palettes {
pub const RAINBOW: ColorPalette = ColorPalette {
a: [0.500,0.500,0.500],
b: [0.500,0.500,0.500],
c: [0.800,0.800,0.800],
d: [0.000,0.333,0.667],
a: [0.500, 0.500, 0.500],
b: [0.500, 0.500, 0.500],
c: [0.800, 0.800, 0.800],
d: [0.000, 0.333, 0.667],
};
pub const YELLOW_PINK: ColorPalette = ColorPalette {
a: [0.500,0.500,0.320],
b: [0.500,0.500,0.500],
c: [0.100,0.500,0.360],
d: [0.000,0.000,0.650],
a: [0.500, 0.500, 0.320],
b: [0.500, 0.500, 0.500],
c: [0.100, 0.500, 0.360],
d: [0.000, 0.000, 0.650],
};
}

31
src/components/transfer_menu.rs
View File

@ -3,9 +3,9 @@
use lazy_static::lazy_static;
use regex::Regex;
use serde::{Deserialize, Serialize};
use uuid::Uuid;
use wasm_bindgen::JsCast;
use web_sys::{EventTarget, HtmlInputElement};
use uuid::Uuid;
use yew::prelude::*;
use yewdux::prelude::*;
@ -28,10 +28,9 @@ pub fn TransferMenu() -> Html {
ct_dispatch.reduce_mut(|state| {
state.transfer.name = input.value().clone();
});
}
}
)};
})
};
let on_src_region_change = {
let ct_dispatch = ct_dispatch.clone();
@ -174,19 +173,24 @@ pub fn TransferMenu() -> Html {
spi.clone(),
dpi.clone(),
ct_state.transfer.transfer_region,
ct_state.transfer.name.clone()
ct_state.transfer.name.clone(),
);
main_dispatch.reduce_mut(|state| {
state.transfers.push(new_transfer);
state.selected_transfer = state.transfers.last()
.expect("An element should have just been added")
.get_uuid();
state.selected_transfer = state
.transfers
.last()
.expect("An element should have just been added")
.get_uuid();
});
}
}
} else {
if let Some(index) = main_state.transfers.iter()
.position(|t| t.get_uuid() == main_state.selected_transfer) {
if let Some(index) = main_state
.transfers
.iter()
.position(|t| t.get_uuid() == main_state.selected_transfer)
{
main_dispatch.reduce_mut(|state| {
state.transfers[index] = ct_state.transfer.clone();
});
@ -205,8 +209,11 @@ pub fn TransferMenu() -> Html {
if main_state.selected_transfer.is_nil() {
() // Maybe reset transfer?
} else {
if let Some(index) = main_state.transfers.iter()
.position(|t| t.get_uuid() == ct_state.transfer.get_uuid()) {
if let Some(index) = main_state
.transfers
.iter()
.position(|t| t.get_uuid() == ct_state.transfer.get_uuid())
{
main_dispatch.reduce_mut(|state| {
state.transfers.remove(index);
state.selected_transfer = Uuid::nil();

19
src/components/tree.rs
View File

@ -104,9 +104,11 @@ pub fn Tree(props: &TreeProps) -> Html {
if let Some(li) = li {
if let Ok(id) = u128::from_str_radix(li.id().as_str(), 10) {
let id = Uuid::from_u128(id);
if let Some(transfer) = main_state.transfers
.iter().find(|transfer| transfer.get_uuid() == id) {
if let Some(transfer) = main_state
.transfers
.iter()
.find(|transfer| transfer.get_uuid() == id)
{
main_dispatch.reduce_mut(|state| {
state.selected_source_plate = transfer.source_id;
state.selected_dest_plate = transfer.dest_id;
@ -237,11 +239,12 @@ fn PlateInfoModal(props: &PlateInfoModalProps) -> Html {
let id = props.id;
Callback::from(move |e: Event| {
log::debug!("Changed name");
let input = e.target().expect("Event must have target")
.dyn_into::<HtmlInputElement>().unwrap();
main_dispatch.reduce_mut(|state| {
state.rename_plate(id, &input.value())
})
let input = e
.target()
.expect("Event must have target")
.dyn_into::<HtmlInputElement>()
.unwrap();
main_dispatch.reduce_mut(|state| state.rename_plate(id, &input.value()))
})
};

37
src/data/csv.rs
View File

@ -1,9 +1,9 @@
use crate::data::transfer::Transfer;
use crate::components::transfer_menu::num_to_letters;
use crate::components::states::MainState;
use crate::components::transfer_menu::num_to_letters;
use crate::data::transfer::Transfer;
use std::{error::Error};
use serde::Serialize;
use std::error::Error;
#[derive(Serialize, Debug)]
struct TransferRecord {
@ -24,13 +24,23 @@ struct TransferRecord {
pub fn state_to_csv(state: &MainState) -> Result<String, Box<dyn Error>> {
let mut records: Vec<TransferRecord> = Vec::new();
for transfer in &state.transfers {
let src_barcode = state.source_plates.iter().find(|spi| spi.get_uuid() == transfer.source_id)
.ok_or("Found unpurged transfer")?;
let dest_barcode = state.destination_plates.iter().find(|dpi| dpi.get_uuid() == transfer.dest_id)
.ok_or("Found unpurged transfer")?;
records.append(&mut transfer_to_records(transfer, &src_barcode.name, &dest_barcode.name))
let src_barcode = state
.source_plates
.iter()
.find(|spi| spi.get_uuid() == transfer.source_id)
.ok_or("Found unpurged transfer")?;
let dest_barcode = state
.destination_plates
.iter()
.find(|dpi| dpi.get_uuid() == transfer.dest_id)
.ok_or("Found unpurged transfer")?;
records.append(&mut transfer_to_records(
transfer,
&src_barcode.name,
&dest_barcode.name,
))
}
return records_to_csv(records)
return records_to_csv(records);
}
fn transfer_to_records(
@ -47,17 +57,18 @@ fn transfer_to_records(
let dest_wells = map(s_well);
if let Some(dest_wells) = dest_wells {
for d_well in dest_wells {
records.push(TransferRecord {
records.push(TransferRecord {
source_plate: src_barcode.to_string(),
source_well: format!("{}{}", num_to_letters(s_well.0).unwrap(), s_well.1),
destination_plate: dest_barcode.to_string(),
destination_well: format!("{}{}", num_to_letters(d_well.0).unwrap(), d_well.1),
volume: 2.5, // Default value since not yet implemented
concentration: None })
concentration: None,
})
}
}
}
return records
return records;
}
fn records_to_csv(trs: Vec<TransferRecord>) -> Result<String, Box<dyn Error>> {
@ -66,5 +77,5 @@ fn records_to_csv(trs: Vec<TransferRecord>) -> Result<String, Box<dyn Error>> {
wtr.serialize(record)?
}
let data = String::from_utf8(wtr.into_inner()?)?;
return Ok(data)
return Ok(data);
}

2
src/data/mod.rs
View File

@ -1,5 +1,5 @@
pub mod csv;
pub mod plate;
pub mod plate_instances;
pub mod transfer;
pub mod transfer_region;
pub mod csv;

67
src/data/transfer_region.rs
View File

@ -515,19 +515,48 @@ mod tests {
let transfer2 = TransferRegion {
source_plate: Plate::new(PlateType::Source, PlateFormat::W384),
dest_plate: Plate::new(PlateType::Destination, PlateFormat::W384),
source_region: Region::Rect((1,1), (2,3)),
dest_region: Region::Rect((2,2), (11,16)),
source_region: Region::Rect((1, 1), (2, 3)),
dest_region: Region::Rect((2, 2), (11, 16)),
interleave_source: (1, 1),
interleave_dest: (2, 2),
};
let transfer2_source = transfer2.get_source_wells();
let transfer2_dest = transfer2.get_destination_wells();
assert_eq!(transfer2_source, vec![(1,1),(1,2),(1,3),(2,1),(2,2),(2,3)], "Failed type replicate 2 source");
assert_eq!(transfer2_dest,
vec![(2,2),(2,8),(6,2),(6,8),(2,4),(2,10),(6,4),(6,10),(2,6),(2,12),(6,6),(6,12),
(4,2),(4,8),(8,2),(8,8),(4,4),(4,10),(8,4),(8,10),(4,6),(4,12),(8,6),(8,12)],
"Failed type replicate 2 destination");
assert_eq!(
transfer2_source,
vec![(1, 1), (1, 2), (1, 3), (2, 1), (2, 2), (2, 3)],
"Failed type replicate 2 source"
);
assert_eq!(
transfer2_dest,
vec![
(2, 2),
(2, 8),
(6, 2),
(6, 8),
(2, 4),
(2, 10),
(6, 4),
(6, 10),
(2, 6),
(2, 12),
(6, 6),
(6, 12),
(4, 2),
(4, 8),
(8, 2),
(8, 8),
(4, 4),
(4, 10),
(8, 4),
(8, 10),
(4, 6),
(4, 12),
(8, 6),
(8, 12)
],
"Failed type replicate 2 destination"
);
}
#[test]
@ -536,8 +565,8 @@ mod tests {
let transfer1 = TransferRegion {
source_plate: Plate::new(PlateType::Source, PlateFormat::W384),
dest_plate: Plate::new(PlateType::Destination, PlateFormat::W384),
source_region: Region::Rect((1,4),(3,7)),
dest_region: Region::Point((1,9)),
source_region: Region::Rect((1, 4), (3, 7)),
dest_region: Region::Point((1, 9)),
interleave_source: (1, 1),
interleave_dest: (0, 2),
};
@ -547,8 +576,20 @@ mod tests {
transfer1_dest.dedup(); // Makes our check easier, otherwise we have repeated wells
let transfer1_map = transfer1.calculate_map();
// Skipping source check---it's just 12 wells.
assert_eq!(transfer1_dest, vec![(1,9),(1,11),(1,13),(1,15)], "Failed type pool 1 dest");
assert_eq!(transfer1_map((2,6)), Some(vec![(1,13)]), "Failed type pool 1 map 1");
assert_eq!(transfer1_map((3,7)), Some(vec![(1,15)]), "Failed type pool 1 map 2");
assert_eq!(
transfer1_dest,
vec![(1, 9), (1, 11), (1, 13), (1, 15)],
"Failed type pool 1 dest"
);
assert_eq!(
transfer1_map((2, 6)),
Some(vec![(1, 13)]),
"Failed type pool 1 map 1"
);
assert_eq!(
transfer1_map((3, 7)),
Some(vec![(1, 15)]),
"Failed type pool 1 map 2"
);
}
}