Remove Global Tauri Invoke/open

observablehq.config.ts

@@ -41,17 +41,17 @@ export default {
   ],
 
   // Some additional configuration options and their defaults:
-  theme: "default", // try "light", "dark", "slate", etc.
+  // theme: "default", // try "light", "dark", "slate", etc.
   // header: "", // what to show in the header (HTML)
   // head: ({
   //   path,
   // }) => `<link rel="canonical" href="${path.replace(/\/index$/, "/")}">
   //   <link rel="apple-touch-icon" href="/logo.png">
   //   <link rel="icon" type="image/png" href="/logo.png" sizes="32x32">`,
+  head: '<link rel="icon" href="icon.png" type="image/png" sizes="32x32">',
 
   // footer: "Built with Observable.", // what to show in the footer (HTML)
   toc: true, // whether to show the table of contents
   // pager: true, // whether to show previous & next links in the footer
   // output: "dist", // path to the output root for build
-  dynamicPaths: ["./icon.png"],
 };

package.json

@@ -10,10 +10,10 @@
     "tauri": "tauri"
   },
   "dependencies": {
-    "@observablehq/framework": "latest",
+    "@observablehq/framework": "^1.12.0",
     "@tauri-apps/api": "latest",
-    "@tauri-apps/plugin-dialog": "^2.0.0",
-    "@tauri-apps/plugin-shell": "^2.0.0",
+    "@tauri-apps/plugin-dialog": "latest",
+    "@tauri-apps/plugin-shell": "latest",
     "d3-dsv": "^3.0.1",
     "d3-time-format": "^4.1.0",
     "ideogram": "^1.47",

src-tauri/tauri.conf.json

@@ -12,7 +12,7 @@
     "security": {
       "csp": null
     },
-    "withGlobalTauri": true,
+    "withGlobalTauri": false,
     "windows": [
       {
         "fullscreen": false,

src/components/fasta_processing.js

@@ -0,0 +1,39 @@
+import { open } from "@tauri-apps/plugin-dialog";
+import { invoke } from "npm:@tauri-apps/api/core";
+import { html } from "npm:htl";
+
+function choosefasta() {
+  const selected = open({
+    multiple: false,
+    filters: [
+      {
+        name: "Fasta",
+        extensions: ["fa", "fasta", "fna"],
+      },
+    ],
+  });
+  return selected;
+}
+
+function choosefastq() {
+  const selected = open({
+    multiple: false,
+    filters: [
+      {
+        name: "Fastq",
+        extensions: ["fq", "fastq"],
+      },
+    ],
+  });
+  return selected;
+}
+
+export async function getFastaStats() {
+  const fasta = await choosefasta();
+  const stats = await invoke("get_stats", { filename: fasta });
+  return html`<div>
+    <h3>Fasta Statistics</h3>
+    <p>Record Count: ${stats.recordcount}</p>
+    <p>Maximum Length: ${stats.maxlength}</p>
+  </div>`;
+}

src/dna/restriction_enzyme_analysis.md

@@ -6,7 +6,7 @@
 
 
 ```js
-let invoke = window.__TAURI__.core.invoke;
+import { invoke } from "npm:@tauri-apps/api/core";
 let text = view(Inputs.textarea({label: "DNA For Searching", placeholder: "DNA Goes here", submit: true}));
 // let re_sites =  (text == "") ? []: invoke("check_restriction_sites", {sequence: text})
 text
@@ -23,4 +23,3 @@ if (text != "") {
 // display( re_sites)
 
 ```
-

src/dna/translation.md

@@ -7,7 +7,7 @@ Simple DNA->Protiein Translation using the [protein_translate](https://docs.rs/p
 
 
 ```js
-let invoke = window.__TAURI__.core.invoke;
+import { invoke } from "npm:@tauri-apps/api/core";
 let dna_text = view(Inputs.textarea({label: "DNA For Translation", placeholder: "DNA Here", submit: true}));
 let dna_text_realized;
 
@@ -28,4 +28,4 @@ display(dna_text)
 >NC_000913.3:1728347-1728994 rnt [organism=Escherichia coli str. K-12 substr. MG1655] [GeneID=946159] [chromosome=]
 ATGTCCGATAACGCTCAACTTACCGGTCTGTGCGACCGTTTTCGTGGTTTTTATCCTGTTGTGATCGATGTTGAAACAGCCGGATTTAACGCCAAAACCGATGCGCTGCTTGAGATTGCCGCCATCACCCTGAAAATGGATGAACAAGGCTGGCTGATGCCGGACACCACATTACATTTCCACGTCGAACCATTTGTCGGCGCAAATTTGCAACCAGAAGCCCTCGCCTTCAACGGCATTGACCCGAACGATCCCGATCGCGGCGCGGTCAGCGAATACGAGGCGCTGCACGAAATTTTTAAAGTTGTACGTAAAGGTATTAAAGCGAGCGGCTGTAACCGCGCCATTATGGTGGCGCACAATGCCAATTTTGATCACAGCTTTATGATGGCCGCCGCAGAACGCGCCTCACTGAAACGTAACCCGTTCCACCCTTTCGCCACTTTTGACACTGCTGCACTGGCCGGGCTGGCACTCGGACAAACCGTATTGTCAAAGGCTTGCCAGACCGCTGGCATGGACTTCGACAGCACCCAGGCGCACTCCGCGCTGTACGACACCGAACGCACTGCTGTGCTGTTTTGTGAAATCGTCAACCGCTGGAAACGTCTGGGAGGCTGGCCGCTATCTGCCGCCGAAGAGGTGTAA
 
-```
+```

src/fastx/fasta_simple.md

@@ -4,51 +4,21 @@ title: "Simple Fasta"
 
 Simplest example. uses Noodles to loop throught a fasta file and return the record count and maximul length in the file
 
-```js
-let open = window.__TAURI__.dialog.open;
-let invoke = window.__TAURI__.core.invoke;
-
-// use the tauri open to get absolute file paths
-async function choosefasta(){
-    const selected = open({
-        multiple: false,
-        filters: [{
-            name: 'Fasta',
-            extensions: ['fa', 'fasta', 'fna']}]
-    });
-    return selected
-};
-
-async function choosefastq(){
-    const selected = open({
-        multiple: false,
-        filters: [{
-            name: 'Fastq',
-            extensions: ['fq', 'fastq']}]
-    });
-    return selected
-};
-
-```
 
 ```js
+import {getFastaStats} from "../components/fasta_processing.js";
 
 const fasta_stats = view(
-  Inputs.button("Get Fasta Stats", {
-    value: null,
-    reduce: () => choosefasta().then((fname) => {
-      console.log('Selected file:', fname);
-      return invoke("get_stats", { filename: fname });
-    })
-  }),
-);
-
-let fasta_stats_realized =
-  fasta_stats == null ? "Click Above to Get Fasta Statistics" : fasta_stats;
+Inputs.button("Get Fasta Stats: Part 2 ", {
+  value: null,
+  reduce: () => getFastaStats()
+}));
 
 ```
 
-
 ```js
-display(fasta_stats_realized)
+if (fasta_stats != null) {
+  display(fasta_stats)
+}
+
 ```

src/fastx/fastq_to_fasta.md

@@ -6,12 +6,8 @@ This function will take a fasq file and convert it to a fasta file.
 
 
 ```js
-let open = window.__TAURI__.dialog.open;
-let invoke = window.__TAURI__.core.invoke;
-```
-
-
-```js
+import { open } from "@tauri-apps/plugin-dialog";
+import { invoke } from "npm:@tauri-apps/api/core";
 
 async function choosefastq(){
     const selected = open({
@@ -24,9 +20,9 @@ async function choosefastq(){
 };
 
 const convert_stats = view(Inputs.button(
-    "Convert FastQ to Fasta", 
-    { 
-        value: null, 
+    "Convert FastQ to Fasta",
+    {
+        value: null,
         reduce: () => choosefastq()
             .then( function (fqname) {
                 // console.log(fqname);

src/fastx/fastx_stats.md

@@ -4,8 +4,9 @@ title: "Fastx stats"
 
 
 ```js
-let open = window.__TAURI__.dialog.open;
-let invoke = window.__TAURI__.core.invoke;
+import { open } from "@tauri-apps/plugin-dialog";
+import { invoke } from "npm:@tauri-apps/api/core";
+
 
 // use the tauri open to get absolute file paths
 async function choosefasta(){

src/rna/rna_rnapkin_viz.md

@@ -2,7 +2,8 @@
 
 ```js
 import {svg, html} from "npm:htl";
-let invoke = window.__TAURI__.core.invoke;
+import { invoke } from "npm:@tauri-apps/api/core";
+
 
 function unsafe_html() {
   const span = document.createElement("span");
@@ -60,13 +61,12 @@ if (rnapkin_params.rna != "") {
   // retunrs text. I need a propr DOM element
   rna_text_realized = await invoke("rnapkin_fn", {
   sequence: rnapkin_params.rna,
-  height: rnapkin_params.height, 
+  height: rnapkin_params.height,
   color_theme:  rnapkin_params.color_theme,
-   mirror_x: rnapkin_params.mirror_x, 
-   mirror_y: rnapkin_params.mirror_y, 
-   rotation_angle:rnapkin_params.angle, 
-   bubble_radius: rnapkin_params.bubble_radius});    
+   mirror_x: rnapkin_params.mirror_x,
+   mirror_y: rnapkin_params.mirror_y,
+   rotation_angle:rnapkin_params.angle,
+   bubble_radius: rnapkin_params.bubble_radius});
   console.log(rna_text_realized);
   display(unsafe_html`${rna_text_realized}`);
 }
-