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Fix report analysis runtime lint #80

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Merged
madhavajay merged 1 commit into from
Jun 23, 2026
Merged

Fix report analysis runtime lint #80

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147 changes: 95 additions & 52 deletions rust/bioscript-cli/src/report_analysis_runtime.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,81 @@ struct BioscriptAnalysisScriptInput<'a> {
analysis_max_duration_ms: u64,
}

struct AnalysisRuntimeInputs {
analysis_input_file: String,
script_virtual_path: String,
virtual_observations_file: String,
virtual_output_file: String,
virtual_binary_files: BTreeMap<String, Vec<u8>>,
virtual_text_files: BTreeMap<String, String>,
asset_paths: BTreeMap<String, String>,
}

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 runtime_inputs = collect_analysis_runtime_inputs(input)?;
let context = analysis_context(
input.participant_id,
&runtime_inputs.analysis_input_file,
&runtime_inputs.script_virtual_path,
input.manifest_path,
&runtime_inputs.asset_paths,
&runtime_inputs.virtual_observations_file,
&runtime_inputs.virtual_output_file,
);
let runtime = BioscriptRuntime::with_config(
input.runtime_root.to_path_buf(),
RuntimeConfig {
limits,
loader: input.loader.clone(),
context,
virtual_binary_files: runtime_inputs.virtual_binary_files,
virtual_text_files: runtime_inputs.virtual_text_files,
..RuntimeConfig::default()
},
)
.map_err(|err| err.to_string())?;
runtime
.run_file(
&runtime_inputs.script_virtual_path,
None,
vec![
(
"input_file",
monty::MontyObject::String(runtime_inputs.analysis_input_file),
),
(
"output_file",
monty::MontyObject::String(runtime_inputs.virtual_output_file.clone()),
),
(
"observations_file",
monty::MontyObject::String(runtime_inputs.virtual_observations_file),
),
(
"asset_paths",
monty_string_dict(&runtime_inputs.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();
write_primary_analysis_output(input.output_file, &written, &runtime_inputs.virtual_output_file)?;
persist_virtual_output_files(&written, &runtime_inputs.virtual_output_file, input.output_file)
}

fn collect_analysis_runtime_inputs(
input: &BioscriptAnalysisScriptInput<'_>,
) -> Result<AnalysisRuntimeInputs, String> {
let observations_text = fs::read_to_string(input.observations_file).map_err(|err| {
format!(
"failed to read analysis observations {}: {err}",
Expand Down Expand Up @@ -57,68 +125,40 @@ fn run_bioscript_analysis_script(input: &BioscriptAnalysisScriptInput<'_>) -> Re
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();

Ok(AnalysisRuntimeInputs {
analysis_input_file,
script_virtual_path,
virtual_observations_file,
virtual_output_file,
virtual_binary_files,
virtual_text_files,
asset_paths,
})
}

fn write_primary_analysis_output(
output_file: &Path,
written: &BTreeMap<String, String>,
virtual_output_file: &str,
) -> Result<(), String> {
let output_text = written
.get(&virtual_output_file)
.get(virtual_output_file)
.ok_or_else(|| format!("analysis did not write {virtual_output_file}"))?;
if let Some(parent) = input.output_file.parent() {
if let Some(parent) = 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| {
fs::write(output_file, output_text).map_err(|err| {
format!(
"failed to write analysis output {}: {err}",
input.output_file.display()
output_file.display()
)
})?;
persist_virtual_output_files(&written, &virtual_output_file, input.output_file)
})
}

fn analysis_input_file_arg(
Expand Down Expand Up @@ -248,7 +288,7 @@ fn analysis_context(
participant_id: &str,
input_file: &str,
script_path: &str,
manifest_path: &str,
manifest_path: &Path,
asset_paths: &BTreeMap<String, String>,
observations_file: &str,
output_file: &str,
Expand All @@ -268,7 +308,10 @@ fn analysis_context(
(
"pipeline_files".to_owned(),
monty_string_dict(&BTreeMap::from([
("manifest".to_owned(), manifest_path.to_owned()),
(
"manifest".to_owned(),
virtual_pipeline_path(manifest_path, "manifest.yaml"),
),
("analysis".to_owned(), script_path.to_owned()),
])),
),
Expand Down
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