chore(dev): fix navigation; add report template appendices

.gitignore

@@ -2,6 +2,7 @@
 testing/
 .nextflow/
 templates/report/report.pdf
+cerebro/stack/report-wasm/tests/
 
 # Triggered dev builds
 trigger

app/src/lib/components/data/sample/Test.svelte

@@ -120,6 +120,8 @@
   let reportTemplateSchema: ReportTemplateSchema = {
     template_id: "",
     template_name: "",
+    preamble: "",
+    introduction: "",
     contact_name: "",
     contact_email: "",
     legal_disclaimer: "",
@@ -128,11 +130,7 @@
     signatures: []
   }
 
-  $: {
-    if (compiler) {
-      compileSVG(reportSchema);
-    }
-  }
+  $: if (compiler) compileSVG(reportSchema);
   
 </script>
 
@@ -145,10 +143,23 @@
           <form>
             <div class="p-4">
 
+
+              <div id="reportIntroduction" class="py-8"> 
+                <p class="opacity-40 text-regular">Prelude text</p>
+                <div class="grid grid-cols-1 sm:grid-cols-1 md:grid-cols-1 gap-6 w-3/4 pt-4">
+                  <label class="label">
+                    <span class="text-xs opacity-60">Preamble</span>
+                    <textarea class="textarea text-xs" rows="4" bind:value={reportTemplateSchema.preamble} placeholder="Preamble" required={false} />
+                  </label>
+                  <label class="label">
+                    <span class="text-xs opacity-60">Introduction</span>
+                    <textarea class="textarea text-xs" rows="4" bind:value={reportTemplateSchema.introduction} placeholder="Introduction" required={false} />
+                  </label>
+                </div>
+              </div>
+
               <div id="reportConfigurationAuthorisation" class="py-8"> 
-
                 <p class="opacity-40 text-regular">Contact details</p>
-
                 <div class="grid grid-cols-1 sm:grid-cols-1 md:grid-cols-2 gap-6 w-3/4 pb-12 pt-4">
                   <label class="label">
                     <span class="text-xs opacity-60">Name</span>
@@ -159,7 +170,6 @@
                     <input class="input text-xs" bind:value={reportTemplateSchema.contact_email}  placeholder="Contact email" required={true} />
                   </label>
                 </div>
-
               </div>
 
               <div id="reportConfigurationAuthorisation" class="py-8"> 

app/src/lib/utils/types.ts

@@ -1867,6 +1867,8 @@ export type PatientResult = {
 export type ReportTemplateSchema = {
     template_id: string;
     template_name: string;
+    preamble: string;
+    introduction: string;
     contact_name: string;
     contact_email: string;
     legal_disclaimer: string;

cerebro/stack/report-wasm/Cargo.toml

@@ -39,11 +39,13 @@ typst-svg = "0.12.0"
 wasm-bindgen = "0.2.99"
 serde-wasm-bindgen = "0.6.5"
 
-# CLI feature
+# Command-line interface feature
 clap = { version = "4", optional = true, features = ["derive", "env", "unstable-styles", "wrap_help"] }
 anstyle = { version = "1", optional = true }
+toml = { version = "0.8.20", optional = true}
+uuid = { version = "1.13.1", features = ["v4"] }
 
 
 [features]
 default = []
-cli = ["clap", "anstyle"]
+cli = ["clap", "anstyle", "toml"]

cerebro/stack/report-wasm/src/compiler.rs

@@ -1,4 +1,5 @@
 use chrono::{Datelike, Timelike};
+use typst::layout::Abs;
 use typst_pdf::PdfStandards;
 
 #[cfg(feature = "cli")]
@@ -10,7 +11,7 @@ use wasm_bindgen::prelude::*;
 use crate::report::ReportConfig;
 
 use crate::world::SystemWorld;
-use crate::report::{PathogenDetectionReport, ReportType, TemplateManager};
+use crate::report::{PathogenDetectionReport, ReportType, TemplateFormat, TemplateManager};
 
 
 #[cfg(feature = "cli")]
@@ -29,10 +30,16 @@ impl CommandLineReportCompiler {
             report_type,
         })
     }
-    pub fn report(&mut self, config: &Path) -> anyhow::Result<String>  {
+    pub fn report(&mut self, config: &Path, format: TemplateFormat) -> anyhow::Result<String>  {
 
         let report = match self.report_type {
-            ReportType::PathogenDetection => PathogenDetectionReport::from_json(config)?
+            ReportType::PathogenDetection => {
+                match format {
+                    TemplateFormat::Json => PathogenDetectionReport::from_json(config)?,
+                    TemplateFormat::Toml => PathogenDetectionReport::from_toml(config)?
+                }
+
+            }
         };
 
         // Render the template for the selected report type
@@ -41,10 +48,19 @@ impl CommandLineReportCompiler {
                 anyhow::anyhow!("failed to render report template: {}", e.to_string())
             })
     }
-    pub fn template(&self, text: &str, output: &Path) -> anyhow::Result<()>  {
-        std::fs::write(output, text).map_err(|e| {
-            anyhow::anyhow!("failed to write template to file: {:?}", e)
-        })
+    pub fn typst(&mut self, text: &str, output: &Path) -> anyhow::Result<()> {
+
+        std::fs::write(output, text).map_err(|e| anyhow::anyhow!("Failed to write Typst file: {:?}", e))
+    }
+    pub fn svg(&mut self, text: &str, vpath: String, output: &Path) -> anyhow::Result<()> {
+
+        let document = self.world.compile(text.to_string(), vpath, None)?;
+
+        let padding = Abs::pt(12.0);
+
+        let svg_data = typst_svg::svg_merged(&document, padding);
+
+        std::fs::write(output, svg_data).map_err(|e| anyhow::anyhow!("Failed to write SVG file: {:?}", e))
     }
     pub fn pdf(&mut self, text: &str, vpath: String, output: &Path) -> anyhow::Result<()> {
 
@@ -67,7 +83,7 @@ impl CommandLineReportCompiler {
             let pdf_data = typst_pdf::pdf(&document, &options)
                 .map_err(|_| anyhow::anyhow!("failed to create PDF with Typst"))?;
 
-            std::fs::write(output, pdf_data).map_err(|e| anyhow::anyhow!("Failed to write PDF: {:?}", e))
+            std::fs::write(output, pdf_data).map_err(|e| anyhow::anyhow!("Failed to write PDF file: {:?}", e))
         }
     }
 }

cerebro/stack/report-wasm/src/main.rs

@@ -6,15 +6,15 @@ mod report;
 #[cfg(feature = "cli")]
 mod world;
 
-
 #[cfg(feature = "cli")]
 use std::path::PathBuf;
-
 #[cfg(feature = "cli")]
 use clap::{Args, Parser, Subcommand};
+use report::TemplateFormat;
 #[cfg(feature = "cli")]
-use report::ReportType;
-
+use report::{ReportFormat, ReportType, PathogenDetectionReport};
+#[cfg(feature = "cli")]
+use compiler::CommandLineReportCompiler;
 
 #[cfg(feature = "cli")]
 /// Cerebro: clinical report compiler for production
@@ -31,37 +31,44 @@ pub struct Cli {
 #[cfg(feature = "cli")]
 #[derive(Debug, Subcommand)]
 pub enum Commands {
-    /// Compile a report from configuration file (.json)
+    /// Compile a report (JSON | TOML)
     Compile(CompileArgs),
-    /// Compile a report from configuration file (.json)
+    /// Output a report template (JSON | TOML)
     Template(TemplateArgs),
 }
+
 #[cfg(feature = "cli")]
 #[derive(Debug, Args)]
 pub struct CompileArgs {
-    /// Report template
-    #[clap(long, short = 'r')]
-    pub report: ReportType,
-    /// Report template configuration (.json)
+    /// Report output file
+    #[clap(long, short = 'o')]
+    pub output: PathBuf,
+    /// Report configuration
     #[clap(long, short = 'c')]
     pub config: PathBuf,
-    /// Compile report to PDF (.pdf)
-    #[clap(long, short = 'p')]
-    pub pdf: Option<PathBuf>,
-    /// Compile report to template (.typ)
-    #[clap(long, short = 'o')]
-    pub template: Option<PathBuf>,
+    /// Report template format
+    #[clap(long, short = 't', default_value="json")]
+    pub template: TemplateFormat,
+    /// Output format
+    #[clap(long, short = 'f', default_value="pdf")]
+    pub format: ReportFormat,
+    /// Report type 
+    #[clap(long, short = 'r', default_value="pathogen-detection")]
+    pub report: ReportType,
 }
 
 #[cfg(feature = "cli")]
 #[derive(Debug, Args)]
 pub struct TemplateArgs {
-    /// Report template
-    #[clap(long, short = 'r')]
+    /// Report template output (.json | .toml)
+    #[clap(long, short = 'o')]
+    pub output: PathBuf,
+    /// Report template format
+    #[clap(long, short = 't', default_value="json")]
+    pub template: TemplateFormat,
+    /// Report type
+    #[clap(long, short = 'r', default_value="pathogen-detection")]
     pub report: ReportType,
-    /// Report configuration template (.json)
-    #[clap(long, short = 'c')]
-    pub config: PathBuf,
 }
 
 #[cfg(feature = "cli")]
@@ -88,23 +95,32 @@ fn main() -> anyhow::Result<()> {
 
     match cli.command {
         Commands::Compile( args ) => {
-            let mut compiler = crate::compiler::CommandLineReportCompiler::new(
+
+            let mut compiler = CommandLineReportCompiler::new(
                 String::from("/"), args.report
             )?;
 
-            let report = compiler.report(&args.config)?;
-
-            if let Some(ref path) = args.pdf {
-                compiler.pdf(&report, "pdf.typ".to_string(), &path)?;
-            }
-            if let Some(ref path) = args.template {
-                compiler.template(&report, path)?;
+            let report = compiler.report(&args.config, args.template)?;
+
+            match args.format {
+                ReportFormat::Pdf => {
+                    compiler.pdf(&report, String::from("/report"), &args.output)?;
+                },
+                ReportFormat::Svg => {
+                    compiler.svg(&report, String::from("/report"), &args.output)?;
+                },
+                ReportFormat::Typst => {
+                    compiler.typst(&report, &args.output)?;
+                },
             }
         },
         Commands::Template( args ) => {
             match args.report {
                 ReportType::PathogenDetection => {
-                    crate::report::PathogenDetectionReport::default().to_json_file(&args.config)?;
+                    match args.template {
+                        TemplateFormat::Json => PathogenDetectionReport::default().to_json(&args.output)?,
+                        TemplateFormat::Toml => PathogenDetectionReport::default().to_toml(&args.output)?,
+                    }
                 }
             }
         }
@@ -116,4 +132,4 @@ fn main() -> anyhow::Result<()> {
 #[cfg(not(feature = "cli"))]
 fn main() {
     eprintln!("Command-line interface feature is not enabled. You can enable it with: `--features cli`.");
-}
+}