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+ "name": "hdmf-common", + "total_count": 131, + "versions": { + "1.8.0": 131 + } + }, + { + "name": "hdmf-experimental", + "total_count": 131, + "versions": { + "0.5.0": 131 + } + } + ], + "001359": [], + "001360": [], + "001362": [] +} \ No newline at end of file diff --git a/sandbox/ndx-stats/ndx-stats.py b/sandbox/ndx-stats/ndx-stats.py new file mode 100755 index 000000000..5968a867b --- /dev/null +++ b/sandbox/ndx-stats/ndx-stats.py @@ -0,0 +1,213 @@ +#!/usr/bin/env python3 +""" +A Python script to extract extension specifications and versions from NWB files. +Supports both local files and remote URLs, and outputs statistics on extension usage. +""" + +import argparse +from collections import defaultdict +from dataclasses import asdict, dataclass, field, is_dataclass +import json +import sys +from typing import Dict, List + +import h5py +from nwbinspector.tools import get_s3_urls_and_dandi_paths +from packaging import version +from tqdm import tqdm + +from dandi.dandiapi import DandiAPIClient + +# For remote file access +try: + import remfile + + REMOTE_ACCESS_AVAILABLE = True +except ImportError: + REMOTE_ACCESS_AVAILABLE = False + + +@dataclass +class ExtensionStats: + """Data class to store statistics about an NWB extension.""" + + name: str + total_count: int = 0 + versions: Dict[str, int] = field(default_factory=lambda: defaultdict(int)) + + +class EnhancedJSONEncoder(json.JSONEncoder): + def default(self, obj): + if is_dataclass(obj): + return asdict(obj) + return super().default(obj) + + +def get_nwb_specifications(file_path: str, is_url: bool = False) -> Dict[str, str]: + """ + Extract all specification names and versions from an NWB file. + + Args: + file_path: URL to the NWB file + is_url: Whether the file_path is a URL + + Returns: + Dictionary containing the specification names and versions + """ + specifications = {} + + try: + if is_url: + if not REMOTE_ACCESS_AVAILABLE: + raise ImportError("remfile is required for remote file access") + + # Open remote file using remfile + f = remfile.File(file_path) + try: + h5_file = h5py.File(f, "r") + # Need to use a context manager for the h5py file + with h5_file as h5f: + specifications = _extract_specifications(h5f) + finally: + f.close() + else: + # Local file + with h5py.File(file_path, "r") as f: + specifications = _extract_specifications(f) + + except Exception as e: + print(f"Error processing file {file_path}: {str(e)}", file=sys.stderr) + + return specifications + + +def _extract_specifications(h5_file) -> Dict[str, str]: + """Extract specifications from an opened h5py File object.""" + specifications = {} + + if "specifications" in h5_file: + specs_group = h5_file["specifications"] + if len(specs_group) > 0: + for name in specs_group: + extension_group = specs_group[name] + if not isinstance(extension_group, h5py.Group): + continue + + try: + sorted_versions = sorted(extension_group, key=version.parse) + if len(sorted_versions) > 0: + # Use only the latest version + latest_version = sorted_versions[-1] + specifications[name] = latest_version + except Exception as e: + print( + f"Error processing extension {name}: {str(e)}", file=sys.stderr + ) + + return specifications + + +def analyze_extensions( + file_paths: List[str], is_url: bool = False +) -> List[ExtensionStats]: + """ + Analyze extensions across multiple NWB files. + + Args: + file_paths: List of paths or URLs to NWB files + is_url: Whether the file_paths are URLs + + Returns: + List of ExtensionStats objects + """ + # Dictionary to store extension statistics + extension_stats = {} + + # Process each file + for file_path in tqdm(file_paths, desc="Processing NWB files"): + specifications = get_nwb_specifications(file_path, is_url) + + # Filter out core specifications that are not extensions + extensions = { + k: v + for k, v in specifications.items() + # if k not in ["core", "hdmf-common", "hdmf-experimental"] + } + + # Update statistics + for ext_name, ext_version in extensions.items(): + if ext_name not in extension_stats: + extension_stats[ext_name] = ExtensionStats(name=ext_name) + + extension_stats[ext_name].total_count += 1 + extension_stats[ext_name].versions[ext_version] += 1 + + # Convert to list for output + return list(extension_stats.values()) + +def snapshot_result(result, output): + out = json.dumps(result, indent=2, cls=EnhancedJSONEncoder) + if output: + with open(output, "w") as f: + f.write(out) + return out + +def main(): + parser = argparse.ArgumentParser(description="Analyze NWB file extensions") + + # Input source group (mutually exclusive) + input_group = parser.add_mutually_exclusive_group(required=True) + input_group.add_argument("-f", "--files", nargs="+", help="Local NWB file path(s)") + input_group.add_argument("-u", "--urls", nargs="+", help="URL(s) to NWB file(s)") + input_group.add_argument( + "-d", + "--dandisets", + default=None, + nargs="*", + help="Dandisets to work on. If none specified but option is given, will process all", + ) + + # Output options + parser.add_argument( + "-o", "--output", help="Output JSON file path (default: stdout)" + ) + + args = parser.parse_args() + + # Determine input source + if args.dandisets is not None: + if not args.dandisets: # specified but none specifically + client = DandiAPIClient() + dandisets = list(client.get_dandisets()) + args.dandisets = [d.identifier for d in dandisets] + print(f"Analyzing {len(args.dandisets)} dandisets", file=sys.stderr) + result = {} + for d in tqdm(args.dandisets): + urls = get_s3_urls_and_dandi_paths(dandiset_id=d) + nwb_urls = [url for url, path in urls.items() if path.endswith(".nwb")] + result[d] = analyze_extensions(nwb_urls, True) + snapshot_result(result, args.output) + else: + if args.files: + file_paths = args.files + is_url = False + else: # args.urls + file_paths = args.urls + is_url = True + if not REMOTE_ACCESS_AVAILABLE: + parser.error("remfile is required for URL access. ") + + # Analyze extensions + extension_stats = analyze_extensions(file_paths, is_url) + + # Convert to serializable format + result = [asdict(stat) for stat in extension_stats] + + # Output results + out = snapshot_result(result, args.output) + if not args.output: + print(out) + + +if __name__ == "__main__": + main() diff --git a/sandbox/ndx-stats/requirements.txt b/sandbox/ndx-stats/requirements.txt new file mode 100644 index 000000000..8c06abfb0 --- /dev/null +++ b/sandbox/ndx-stats/requirements.txt @@ -0,0 +1,6 @@ +h5py +packaging +tqdm +remfile +fsspec +nwbinspector