Fix report analysis input paths

rust/bioscript-cli/src/main.rs

@@ -6,6 +6,7 @@ include!("cli_commands.rs");
 include!("report_options.rs");
 include!("package.rs");
 include!("report_review.rs");
+include!("report_analysis_runtime.rs");
 include!("report_execution.rs");
 include!("report_output.rs");
 include!("manifest_runner.rs");

rust/bioscript-cli/src/report_analysis_runtime.rs

@@ -0,0 +1,295 @@
+struct BioscriptAnalysisScriptInput<'a> {
+    runtime_root: &'a Path,
+    manifest_path: &'a Path,
+    interpretation: &'a PanelInterpretation,
+    script_path: &'a Path,
+    input_file: &'a Path,
+    output_file: &'a Path,
+    observations_file: &'a Path,
+    participant_id: &'a str,
+    loader: &'a GenotypeLoadOptions,
+    analysis_max_duration_ms: u64,
+}
+
+fn run_bioscript_analysis_script(input: &BioscriptAnalysisScriptInput<'_>) -> Result<(), String> {
+    let limits = ResourceLimits::new()
+        .max_duration(Duration::from_millis(input.analysis_max_duration_ms))
+        .max_memory(16 * 1024 * 1024)
+        .max_allocations(400_000)
+        .gc_interval(1000)
+        .max_recursion_depth(Some(200));
+    let observations_text = fs::read_to_string(input.observations_file).map_err(|err| {
+        format!(
+            "failed to read analysis observations {}: {err}",
+            input.observations_file.display()
+        )
+    })?;
+    let script_text = fs::read_to_string(input.script_path).map_err(|err| {
+        format!(
+            "failed to read analysis script {}: {err}",
+            input.script_path.display()
+        )
+    })?;
+    let virtual_input_file = "/input/genotypes".to_owned();
+    let virtual_observations_file = "/work/observations.tsv".to_owned();
+    let output_extension = input
+        .output_file
+        .extension()
+        .and_then(|value| value.to_str())
+        .unwrap_or("tsv");
+    let virtual_output_file = format!("/output/results.{output_extension}");
+    let (analysis_input_file, virtual_input_bytes) =
+        analysis_input_file_arg(input.runtime_root, input.input_file)?;
+    let script_virtual_path = virtual_pipeline_path(input.script_path, "analysis.py");
+    let manifest_virtual_path = virtual_pipeline_path(input.manifest_path, "manifest.yaml");
+    let AnalysisVirtualTextFiles {
+        text_files: virtual_text_files,
+        asset_paths,
+    } = collect_analysis_virtual_text_files(
+        input,
+        &script_virtual_path,
+        script_text,
+        &manifest_virtual_path,
+        &virtual_observations_file,
+        observations_text,
+    )?;
+    let mut virtual_binary_files = BTreeMap::new();
+    if let Some(input_bytes) = virtual_input_bytes {
+        virtual_binary_files.insert(virtual_input_file.clone(), input_bytes);
+    }
+    let context = analysis_context(
+        input.participant_id,
+        &analysis_input_file,
+        &script_virtual_path,
+        &manifest_virtual_path,
+        &asset_paths,
+        &virtual_observations_file,
+        &virtual_output_file,
+    );
+    let runtime = BioscriptRuntime::with_config(
+        input.runtime_root.to_path_buf(),
+        RuntimeConfig {
+            limits,
+            loader: input.loader.clone(),
+            context,
+            virtual_binary_files,
+            virtual_text_files,
+            ..RuntimeConfig::default()
+        },
+    )
+    .map_err(|err| err.to_string())?;
+    runtime
+        .run_file(
+            &script_virtual_path,
+            None,
+            vec![
+                ("input_file", monty::MontyObject::String(analysis_input_file)),
+                (
+                    "output_file",
+                    monty::MontyObject::String(virtual_output_file.clone()),
+                ),
+                (
+                    "observations_file",
+                    monty::MontyObject::String(virtual_observations_file),
+                ),
+                ("asset_paths", monty_string_dict(&asset_paths)),
+                (
+                    "participant_id",
+                    monty::MontyObject::String(input.participant_id.to_owned()),
+                ),
+            ],
+        )
+        .map_err(|err| err.to_string())?;
+    let written = runtime.virtual_written_text_files();
+    let output_text = written
+        .get(&virtual_output_file)
+        .ok_or_else(|| format!("analysis did not write {virtual_output_file}"))?;
+    if let Some(parent) = input.output_file.parent() {
+        fs::create_dir_all(parent).map_err(|err| {
+            format!(
+                "failed to create analysis output dir {}: {err}",
+                parent.display()
+            )
+        })?;
+    }
+    fs::write(input.output_file, output_text).map_err(|err| {
+        format!(
+            "failed to write analysis output {}: {err}",
+            input.output_file.display()
+        )
+    })?;
+    persist_virtual_output_files(&written, &virtual_output_file, input.output_file)
+}
+
+fn analysis_input_file_arg(
+    runtime_root: &Path,
+    input_file: &Path,
+) -> Result<(String, Option<Vec<u8>>), String> {
+    let canonical_root = runtime_root.canonicalize().map_err(|err| {
+        format!(
+            "failed to resolve runtime root {}: {err}",
+            runtime_root.display()
+        )
+    })?;
+    let canonical_input = input_file.canonicalize().map_err(|err| {
+        format!(
+            "failed to resolve analysis input {}: {err}",
+            input_file.display()
+        )
+    })?;
+    if let Ok(relative) = canonical_input.strip_prefix(&canonical_root) {
+        let relative_text = relative.display().to_string();
+        if !relative_text.is_empty() {
+            return Ok((relative_text, None));
+        }
+    }
+
+    let input_bytes = fs::read(input_file).map_err(|err| {
+        format!(
+            "failed to read analysis input {}: {err}",
+            input_file.display()
+        )
+    })?;
+    Ok(("/input/genotypes".to_owned(), Some(input_bytes)))
+}
+
+struct AnalysisVirtualTextFiles {
+    text_files: BTreeMap<String, String>,
+    asset_paths: BTreeMap<String, String>,
+}
+
+fn collect_analysis_virtual_text_files(
+    input: &BioscriptAnalysisScriptInput<'_>,
+    script_virtual_path: &str,
+    script_text: String,
+    manifest_virtual_path: &str,
+    virtual_observations_file: &str,
+    observations_text: String,
+) -> Result<AnalysisVirtualTextFiles, String> {
+    let mut virtual_text_files = BTreeMap::new();
+    virtual_text_files.insert(script_virtual_path.to_owned(), script_text);
+    virtual_text_files.insert(
+        manifest_virtual_path.to_owned(),
+        fs::read_to_string(input.manifest_path).map_err(|err| {
+            format!(
+                "failed to read analysis manifest {}: {err}",
+                input.manifest_path.display()
+            )
+        })?,
+    );
+    virtual_text_files.insert(virtual_observations_file.to_owned(), observations_text);
+    let mut asset_paths = BTreeMap::new();
+    for asset in &input.interpretation.assets {
+        let asset_path =
+            resolve_manifest_path(input.runtime_root, input.manifest_path, &asset.path)?;
+        let virtual_asset_path = virtual_pipeline_path(&asset_path, &asset.path);
+        let text = fs::read_to_string(&asset_path).map_err(|err| {
+            format!(
+                "failed to read analysis asset {}: {err}",
+                asset_path.display()
+            )
+        })?;
+        virtual_text_files.insert(virtual_asset_path.clone(), text);
+        asset_paths.insert(asset.id.clone(), virtual_asset_path);
+    }
+    Ok(AnalysisVirtualTextFiles {
+        text_files: virtual_text_files,
+        asset_paths,
+    })
+}
+
+fn persist_virtual_output_files(
+    written: &BTreeMap<String, String>,
+    primary_virtual_output_file: &str,
+    primary_output_file: &Path,
+) -> Result<(), String> {
+    let Some(output_dir) = primary_output_file.parent() else {
+        return Ok(());
+    };
+    for (virtual_path, text) in written {
+        if virtual_path == primary_virtual_output_file {
+            continue;
+        }
+        let Some(relative) = virtual_path.strip_prefix("/output/") else {
+            continue;
+        };
+        let relative_path = Path::new(relative);
+        if relative_path
+            .components()
+            .any(|component| !matches!(component, std::path::Component::Normal(_)))
+        {
+            return Err(format!("analysis wrote invalid output path {virtual_path}"));
+        }
+        let output_path = output_dir.join(relative_path);
+        if let Some(parent) = output_path.parent() {
+            fs::create_dir_all(parent).map_err(|err| {
+                format!("failed to create output dir {}: {err}", parent.display())
+            })?;
+        }
+        fs::write(&output_path, text).map_err(|err| {
+            format!(
+                "failed to write analysis output {}: {err}",
+                output_path.display()
+            )
+        })?;
+    }
+    Ok(())
+}
+
+fn virtual_pipeline_path(path: &Path, fallback: &str) -> String {
+    let name = path
+        .file_name()
+        .and_then(|value| value.to_str())
+        .unwrap_or(fallback);
+    format!("/input/pipeline/{name}")
+}
+
+fn analysis_context(
+    participant_id: &str,
+    input_file: &str,
+    script_path: &str,
+    manifest_path: &str,
+    asset_paths: &BTreeMap<String, String>,
+    observations_file: &str,
+    output_file: &str,
+) -> BTreeMap<String, monty::MontyObject> {
+    BTreeMap::from([
+        (
+            "participant_id".to_owned(),
+            monty::MontyObject::String(participant_id.to_owned()),
+        ),
+        (
+            "input_files".to_owned(),
+            monty_string_dict(&BTreeMap::from([(
+                "genotypes".to_owned(),
+                input_file.to_owned(),
+            )])),
+        ),
+        (
+            "pipeline_files".to_owned(),
+            monty_string_dict(&BTreeMap::from([
+                ("manifest".to_owned(), manifest_path.to_owned()),
+                ("analysis".to_owned(), script_path.to_owned()),
+            ])),
+        ),
+        ("assets".to_owned(), monty_string_dict(asset_paths)),
+        (
+            "observations_file".to_owned(),
+            monty::MontyObject::String(observations_file.to_owned()),
+        ),
+        (
+            "output_file".to_owned(),
+            monty::MontyObject::String(output_file.to_owned()),
+        ),
+    ])
+}
+
+fn parse_analysis_output(
+    path: &Path,
+    format: &str,
+) -> Result<(Vec<serde_json::Value>, Vec<String>), String> {
+    let text = fs::read_to_string(path)
+        .map_err(|err| format!("failed to read analysis output {}: {err}", path.display()))?;
+    bioscript_reporting::parse_analysis_output_text(&text, format)
+        .map_err(|err| format!("failed to parse analysis output {}: {err}", path.display()))
+}