Misc clean up

LICENSE.md

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2014-2020 Roderick Bovee, 2020- Google
+Copyright (c) 2014- Roderick Bovee
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -16,13 +16,17 @@ Entab supports reading a variety of bioinformatics, chemoinformatics, and
 other formats.
 
  - Agilent Chemstation CH, FID, MS, MWD, and UV formats
+ - Agilent Masshunter DAD format[^1]
  - FASTA and FASTQ sequence formats
  - FCS flow cytometry format
  - Inficon Hapsite mass specotrometry format
  - PNG image format
  - SAM and BAM alignment formats
  - Thermo continuous flow isotope mass spectrometry formats
- - TSV
+ - Thermo RAW files
+ - CSV & TSV files
+
+[^1]: This format uses multiple files so it's not supported in streaming mode or in e.g. the JS bindings.
 
 ## CLI
 

entab-cli/src/lib.rs

@@ -17,6 +17,10 @@ use entab::EtError;
 
 use crate::tsv_params::TsvParams;
 
+/// Parse the provided `stdin` using `args` and write results to `stdout`.
+///
+/// # Errors
+/// If there are any issues, an `EtError` will be returned.
 pub fn run<I, T, R, W>(args: I, stdin: R, stdout: W) -> Result<(), EtError>
 where
     I: IntoIterator<Item = T>,
@@ -60,9 +64,8 @@ where
             if e.kind() == ErrorKind::DisplayHelp || e.kind() == ErrorKind::DisplayVersion {
                 e.print()?;
                 return Ok(());
-            } else {
-                return Err(e.to_string().into());
             }
+            return Err(e.to_string().into());
         }
     };
 

entab-js/LICENSE.md

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2014-2020 Roderick Bovee, 2020- Google
+Copyright (c) 2014- Roderick Bovee
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

entab-js/README.md

@@ -16,6 +16,9 @@ for (const record of reader) {
 }
 ```
 
+Note that this will require paging the entire file into memory so files that
+take >10 Mb may be slow and files >100 Mb may not work at all.
+
 ## Development
 
 Build with `wasm-pack build`.

entab-js/example/app.js

@@ -34,6 +34,7 @@ function translate(text, key = "") {
       "Pick a file": "Escoge un archivo",
       "See a sample file": "Ver un archivo de ejemplo",
       "Close file": "Cerrar el archivo",
+      "Close error": "Cerrar diálogo de error",
       "Open settings panel": "Abra el panel de configuración",
       "Close settings panel": "Cerrar el panel de configuración",
       "error-msg": "Hubo un problema al analizar el archivo.",
@@ -55,6 +56,7 @@ function translate(text, key = "") {
       "Pick a file": "Choisir un fichier",
       "See a sample file": "Voir un exemple de fichier",
       "Close file": "Fermez le fichier",
+      "Close error": "Fermer l'erreur",
       "Open settings panel": "Ouvrir le panneau paramètres",
       "Close settings panel": "Fermer le panneau paramètres",
       "error-msg": "Un problème est survenu lors de l'analyse du fichier.",
@@ -76,6 +78,7 @@ function translate(text, key = "") {
       "Pick a file": "选择文件",
       "See a sample file": "看例子",
       "Close file": "关文件",
+      "Close error": "关错误框",
       "Open settings panel": "开设置面板",
       "Close settings panel": "关设置面板",
       "error-msg": "解析文件出现问题。",
@@ -97,6 +100,7 @@ function translate(text, key = "") {
       "Pick a file": "選擇文件",
       "See a sample file": "看例子",
       "Close file": "關文件",
+      "Close error": "關錯誤框",
       "Open settings panel": "開設置面板",
       "Close settings panel": "關設置面板",
       "error-msg": "解析文件出現問題。",
@@ -122,11 +126,11 @@ const app = PetiteVue.createApp({
       const url = new URL(window.location);
       url.search = "";
       url.searchParams.set("u", this.url);
-      url.searchParams.set("p", this.graph.parser);
-      url.searchParams.set("x", this.graph.xaxis);
+      if (this.graph.parser) url.searchParams.set("p", this.graph.parser);
+      if (this.graph.xaxis) url.searchParams.set("x", this.graph.xaxis);
       if (this.graph.yaxis) url.searchParams.set("y", this.graph.yaxis);
       if (this.graph.caxis) url.searchParams.set("c", this.graph.caxis);
-      url.searchParams.set("m", this.graph.cmap);
+      if (this.graph.cmap) url.searchParams.set("m", this.graph.cmap);
       window.history.replaceState(null, "entab: plot scientific data", url);
     }
   },
@@ -171,13 +175,26 @@ const app = PetiteVue.createApp({
     this.statusType = "";
     this.statusMessage = translate("Loading file…");
     return fetch(url).then(response => {
+      if (!response.ok) {
+        throw { statusCode: response.status, statusText: response.statusText, };
+      }
       response.name = url.split("/").slice(-1)[0];
       return this.processFile(response);
     }).catch(e => {
       console.error(e);
-      this.statusType = "error";
+      this.statusType = "network-error";
       // TODO: translate
-      this.statusMessage = "A network error occured.";
+      if (!e.statusCode) {
+        this.statusMessage = "A network error occured. That server probably blocks remote requests.";
+      } else if (e.statusCode === 404) {
+        this.statusMessage = "No file exists at that URL.";
+      } else if (e.statusCode === 401 || e.statusCode === 403) {
+        this.statusMessage = "Permissions are required to access that URL.";
+      } else if (e.statusCode >= 500 && e.statusCode < 600) {
+        this.statusMessage = "A server error occured.";
+      } else {
+        this.statusMessage = "A network error occured.";
+      }
     });
   },
   closeFile() {
@@ -530,6 +547,10 @@ const FUNCTIONS = {
 
 async function calculateBounds(reader) {
   const datum = reader.next().value;
+  if (!datum) {
+    // TODO: translate
+    return new Promise((resolve, reject) => { reject("File had no records") });
+  }
   const bounds = {};
   const columns = [];
   let nPoints = 0;

entab-js/example/index.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!--
   [WIP]
-  Build the JS assets with `wasm-pack build --target web --out-dir examples/pkg`, move them into
+  Build the JS assets with `wasm-pack build --target web --out-dir example/pkg`, move them into
   this folder and serve with e.g. `python3 -m http.server 8000`.
 -->
 <html lang="en-us">
@@ -38,13 +38,19 @@
       #overlay { height: 98%; left: 0px; top: 0px; position: absolute; padding: 5px; display: flex; flex-direction: column; align-items: flex-start; justify-content: space-between; }
       .overlayButton { position: absolute; left: 0px; top: 0px; padding: 15px; font-size: 18pt; line-height: 24pt; }
       #overlay .overlayButton { font-size: 30pt; }
-      /* .closeFileButton { position: absolute; right: 0px; top: 0px; padding: 15px; font-size: 30pt; line-height: 24pt; } */
       .progress { position: absolute; right: 0px; top: 0px; padding: 15px; line-height: 24pt; display: flex; align-items: center; }
       .closeFileButton { padding-left: 20px; font-size: 30pt; }
+      .closeErrorButton { position: absolute; right: 0px; top: 0px; padding: 10px; font-size: 30pt; line-height: 24pt; } */
       .row { display: flex; align-items: center; }
       .row label, .row .label-spacer { display: inline-block; width: 80px; text-align: right; }
       #chart { height: 95%; width: 95%; top: 2.5%; left: 2.5%; position: absolute; }
-      .status, noscript { position: absolute; width: 20%; left: 30%; top: 10%; padding: 2em; text-align: center; }
+      .status, noscript { position: absolute; width: 35%; left: 25%; top: 10%; padding: 2em; text-align: center; }
+      @media only screen and (min-width: 768px) {
+        .status, noscript { width: 28%; left: 28%; }
+      }
+      @media only screen and (min-width: 992px) {
+        .status, noscript { width: 20%; left: 30%; }
+      }
       .button { margin: 0.2em; padding: 0.5em; border-radius: 5px; };
       .button:active {
         box-shadow: 0 0 0 5px rgba(0,0,0,0.2) inset; border-color: black;
@@ -93,9 +99,9 @@
       ></svg>
       <div class="buttonBar">
         <a class="overlayButton"
-           role="button" 
+           role="button"
            :aria-label="translate('Open settings panel')" 
-           tabindex="0" 
+           tabindex="0"
            @keydown.enter="toggleOverlay(true)"
            @click="toggleOverlay(true)"
         >
@@ -106,9 +112,9 @@
             {{ statusMessage }}
           </span>
           <a class="closeFileButton"
-             role="button" 
+             role="button"
              :aria-label="translate('Close file')"
-             tabindex="0" 
+             tabindex="0"
              v-if="graph.buffer || filename"
              @keydown.enter="closeFile"
              @click="closeFile"
@@ -150,16 +156,43 @@
         v-if="statusType === 'error'"
         style="background-color: #F09090"
       >
-        &#9888; {{ translate("There was a problem parsing the file.", "error-msg") }} &#9888;
+        <a class="closeErrorButton"
+           role="button"
+           :aria-label="translate('Close error')"
+           tabindex="0"
+           @keydown.enter="closeFile"
+           @click="closeFile"
+        >
+          &#xd7;
+        </a>
+        &#9888; {{ translate("There was a problem parsing the file.", "error-msg") }}
         <div style="text-align: left; font-family: monospace; font-size: 1em; white-space: pre;">
           {{ statusMessage }}
         </div>
       </div>
+      <div class="status"
+        @drop.prevent="fileDropped"
+        @dragover.prevent
+        v-if="statusType === 'network-error'"
+        style="background-color: #F09090"
+      >
+        <a class="closeErrorButton"
+           role="button"
+           :aria-label="translate('Close error')"
+           tabindex="0"
+           @keydown.enter="closeFile"
+           @click="closeFile"
+        >
+          &#xd7;
+        </a>
+        <br />
+        &#9888; {{ statusMessage }}
+      </div>
       <div id="overlay" v-if="showOverlay">
         <a class="overlayButton"
-           role="button" 
+           role="button"
            :aria-label="translate('Close settings panel')" 
-           tabindex="0" 
+           tabindex="0"
            @keydown.enter="toggleOverlay(false)"
            @click="toggleOverlay(false)"
         >

entab-js/src/lib.rs

@@ -30,7 +30,11 @@ pub struct Reader {
 }
 
 fn to_js(err: EtError) -> JsValue {
-    err.to_string().into()
+    let res = err.to_string().into();
+    // technically we could just take a &EtError, but to have a nice function signature we consume
+    // the err so we should also drop it in here to make clippy happy
+    drop(err);
+    res
 }
 
 #[wasm_bindgen]

entab-py/src/lib.rs

@@ -1,4 +1,4 @@
-#![allow(clippy::needless_option_as_deref)]
+#![allow(clippy::needless_option_as_deref, clippy::used_underscore_binding)]
 mod raw_io_wrapper;
 
 use std::collections::BTreeMap;
@@ -18,8 +18,12 @@ use crate::raw_io_wrapper::RawIoWrapper;
 create_exception!(entab, EntabError, exceptions::PyException);
 
 fn to_py(err: EtError) -> PyErr {
-    EntabError::new_err(err.to_string())
     // TODO: somehow bind err.byte and err.record in here too?
+    let res = EntabError::new_err(err.to_string());
+    // we could technically just take an `&EtError` here, but the function signature is nicer with
+    // a `EtError` so we have to drop it here to make clippy happy
+    drop(err);
+    res
 }
 
 /// Map a Value into a `PyObject`

entab-r/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2014-2020 Roderick Bovee, 2020- Google
+Copyright (c) 2014- Roderick Bovee
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

entab/Cargo.toml

@@ -11,6 +11,7 @@ categories = ["parsing", "science"]
 
 [dependencies]
 # parsing
+bytecount = "0.6.2"
 chrono = { version = "0.4", default-features=false, features = ["alloc", "serde"] }
 encoding = "0.2.33"
 memchr = "2.3"
@@ -28,7 +29,7 @@ rayon = "1.5.1"
 [features]
 default = ["compression", "std"]
 compression = ["bzip2", "xz2", "zstd"]
-std = ["chrono/std", "serde/std"]
+std = ["bytecount/runtime-dispatch-simd", "chrono/std", "serde/std"]
 
 [[bench]]
 name = "benchmarks"

entab/README.md

@@ -10,7 +10,7 @@ To parse the IDs out of a FASTA file:
 //! use entab::readers::fasta::{FastaReader, FastaRecord};
 //!
 //! let file = File::open("./tests/data/sequence.fasta")?;
-//! let mut reader = FastaReader::new(file, ())?;
+//! let mut reader = FastaReader::new(file, None)?;
 //! while let Some(FastaRecord { id, .. }) = reader.next()? {
 //!     println!("{}", id);
 //! }
@@ -21,5 +21,6 @@ To parse the IDs out of a FASTA file:
 [Chromatography Toolbox](https://github.com/chemplexity/chromatography) - Matlab - Agilent/Thermo/NetCDF/mzXML
 [Isoreader](https://github.com/isoverse/isoreader) - R - Isodat
 [Unfinnigan](https://github.com/prvst/unfinnigan) - Perl/Python - Thermo RAW
+[seqio](https://github.com/markschl/seq_io) - Rust - FASTX
 
 _Please let me know if there are others that you find useful that should be added to this list._

entab/src/filetype.rs

@@ -174,6 +174,9 @@ impl FileType {
     }
 
     /// Returns the "parser name" associated with this file type
+    ///
+    /// # Errors
+    /// If a file is unsupported, an error will be returned.
     pub fn to_parser_name<'a>(&self, hint: Option<&'a str>) -> Result<&'a str, EtError> {
         Ok(match (self, hint) {
             (FileType::AgilentChemstationFid, None) => "chemstation_fid",

entab/src/lib.rs

@@ -37,8 +37,9 @@
 //! Alternatively, you may not know the type of file when writing your code so
 //! you may want to abstract over as many types as possible. This is where the
 //! slower, generic parser framework is used (for example, in the bindings
-//! libraries also). This framework can optionally take a `parser_name` to force
-//! it to use that specific parser and optional params to control parser options.
+//! for different languages). This framework can optionally take a `parser_name`
+//! to force it to use that specific parser and optional params to control
+//! parser options.
 //! ```
 //! # #[cfg(feature = "std")] {
 //! use std::fs::File;