"""Build portable StrandMD analysis packages for browser downloads.""" from __future__ import annotations import io import json import re import zipfile from dataclasses import asdict from datetime import datetime, timezone from pathlib import Path from typing import Mapping from casmd import __version__ from casmd.project import Project from casmd.report.comparison import ComparisonData from casmd.report.data import AnalysisResult, AnalysisSummary from casmd.report.stats import StatTest _README = """# StrandMD analysis package This archive contains the numerical data, available figures, and provenance shown in the StrandMD web dashboard. ## Interpretation limits - Molecular dynamics frames are autocorrelated and are not independent biological replicates. - Descriptive differences between single trajectories do not establish statistical significance. - Structure prediction and simulation results prioritize hypotheses for experimental testing; they do not prove binding affinity or activity. - Inspect `manifest.json` and `summary.json` before reusing a figure. """ def _slug(value: str) -> str: value = re.sub(r"[^A-Za-z0-9._-]+", "_", value.strip()) return value.strip("._") or "run" def _json_bytes(value: object) -> bytes: return json.dumps(value, indent=2, allow_nan=False).encode("utf-8") def _summary_dict(summary: AnalysisSummary) -> dict: data = asdict(summary) # JSON has no portable NaN representation. Missing/non-finite values are # exported as null instead of implementation-specific NaN tokens. for key, value in list(data.items()): if isinstance(value, float) and value != value: data[key] = None return data def build_descriptive_comparison( *, summary_a: AnalysisSummary, summary_b: AnalysisSummary, label_a: str, label_b: str, figures_a: Mapping[str, Path] | None = None, figures_b: Mapping[str, Path] | None = None, ) -> ComparisonData: """Build scalar, descriptive comparison data without frame-wise tests.""" scalar_fields = { "rmsd": "protein_rmsd_equil_mean_A", "rmsf": "protein_rmsf_mean_A", "rg": "protein_rg_equil_mean_A", } stats = {} for metric, field in scalar_fields.items(): value_a = getattr(summary_a, field) value_b = getattr(summary_b, field) if value_a is None or value_b is None: continue stats[metric] = StatTest( metric=metric, mean_a=float(value_a), mean_b=float(value_b), delta=float(value_b) - float(value_a), test_name="descriptive difference", pvalue=float("nan"), significant=False, ) def _result(summary: AnalysisSummary) -> AnalysisResult: return AnalysisResult( n_frames=summary.n_frames, equil_skip=summary.equil_skip, protein_rmsd_equil_mean_A=summary.protein_rmsd_equil_mean_A, protein_rmsf_mean_A=summary.protein_rmsf_mean_A, protein_rg_equil_mean_A=summary.protein_rg_equil_mean_A, ) return ComparisonData( label_a=label_a, label_b=label_b, analysis_a=_result(summary_a), analysis_b=_result(summary_b), figures_a=dict(figures_a or {}), figures_b=dict(figures_b or {}), stats=stats, interpretation=( "Descriptive trajectory differences only; independent replicates " "are required for inferential analysis." ), ) def _write_run_files( zf: zipfile.ZipFile, *, root: str, summary: AnalysisSummary, dat_files: Mapping[str, Path], fig_files: Mapping[str, Path], ) -> list[str]: written = [] summary_name = f"{root}/summary.json" zf.writestr(summary_name, _json_bytes(_summary_dict(summary))) written.append(summary_name) for key, path in sorted(dat_files.items()): path = Path(path) if path.exists(): name = f"{root}/data/{_slug(key)}{path.suffix or '.dat'}" zf.writestr(name, path.read_bytes()) written.append(name) for key, path in sorted(fig_files.items()): path = Path(path) if path.exists(): name = f"{root}/figures/{_slug(key)}{path.suffix or '.png'}" zf.writestr(name, path.read_bytes()) written.append(name) return written def build_single_analysis_package( *, label: str, summary: AnalysisSummary, dat_files: Mapping[str, Path], fig_files: Mapping[str, Path], project: Project | None = None, condition_id: str | None = None, replicate_id: str | None = None, ) -> bytes: """Return a ZIP containing one run's dashboard data and provenance.""" output = io.BytesIO() root = f"runs/{_slug(label)}" with zipfile.ZipFile(output, "w", compression=zipfile.ZIP_DEFLATED) as zf: written = _write_run_files( zf, root=root, summary=summary, dat_files=dat_files, fig_files=fig_files, ) manifest = { "schema_version": 1, "application": "StrandMD", "application_version": __version__, "package_type": "single_analysis", "created_utc": datetime.now(timezone.utc).isoformat(), "label": label, "project_id": project.project_id if project else None, "condition_id": condition_id, "replicate_id": replicate_id, "files": written, } if project is not None: zf.writestr("project.json", _json_bytes(project.to_manifest())) written.append("project.json") zf.writestr("manifest.json", _json_bytes(manifest)) zf.writestr("README.md", _README.encode("utf-8")) return output.getvalue() def build_comparison_analysis_package( *, comparison: ComparisonData, summary_a: AnalysisSummary, summary_b: AnalysisSummary, dat_a: Mapping[str, Path], dat_b: Mapping[str, Path], fig_a: Mapping[str, Path], fig_b: Mapping[str, Path], project: Project | None = None, ) -> bytes: """Return a ZIP for a descriptive two-run comparison. Inferential p-values are deliberately excluded: a pair of autocorrelated trajectories does not provide independent replicate-level evidence. """ output = io.BytesIO() with zipfile.ZipFile(output, "w", compression=zipfile.ZIP_DEFLATED) as zf: written = [] written += _write_run_files( zf, root=f"runs/{_slug(comparison.label_a)}", summary=summary_a, dat_files=dat_a, fig_files=fig_a, ) written += _write_run_files( zf, root=f"runs/{_slug(comparison.label_b)}", summary=summary_b, dat_files=dat_b, fig_files=fig_b, ) descriptive = { "label_a": comparison.label_a, "label_b": comparison.label_b, "note": ( "Descriptive trajectory differences only. Add independent " "replicates before inferential analysis." ), "metrics": { key: { "mean_a": stat.mean_a, "mean_b": stat.mean_b, "delta_b_minus_a": stat.delta, } for key, stat in comparison.stats.items() }, } zf.writestr("comparison_summary.json", _json_bytes(descriptive)) written.append("comparison_summary.json") if project is not None: zf.writestr("project.json", _json_bytes(project.to_manifest())) written.append("project.json") manifest = { "schema_version": 1, "application": "StrandMD", "application_version": __version__, "package_type": "descriptive_comparison", "created_utc": datetime.now(timezone.utc).isoformat(), "labels": [comparison.label_a, comparison.label_b], "project_id": project.project_id if project else None, "files": written, } zf.writestr("manifest.json", _json_bytes(manifest)) zf.writestr("README.md", _README.encode("utf-8")) return output.getvalue()