Add manifest creator code.

Add manifest builder function.
Add doc strings.
Add json and h5 file manifest creation.
Hide mapmycells for now.

src/abc_atlas_access/abc_atlas_cache/manifest.py

@@ -92,7 +92,7 @@ def _list_data_in_directory(
             output_data_list.extend(list(sub_directories['metadata'].keys()))
         else:
             for sub_dir in sub_directories.keys():
-                if sub_dir == 'metadata':
+                if sub_dir == 'metadata' or sub_dir == 'mapmycells':
                     continue
                 for sub_dir_key in sub_directories[sub_dir].keys():
                     # Check for files with multiple kinds (e.g. raw and log2)

src/manifest_builder/manifest_builder.py

@@ -0,0 +1,331 @@
+import argparse
+from collections import OrderedDict
+import datetime
+import glob
+import json
+import logging
+import os
+from pathlib import Path, PurePosixPath
+from typing import List, Union
+
+from abc_atlas_access.abc_atlas_cache.utils import file_hash_from_path
+
+
+def _validate_version(version: str) -> bool:
+    try:
+        datetime.datetime.strptime(version, '%Y%m%d').date()
+        return True
+    except ValueError:
+        return False
+
+
+def find_directories(
+        base_dir: Union[str, Path],
+        version: str,
+        dirs_to_skip: List[str]
+) -> dict:
+    """Crawl ``base_dir`` to find all sub-directories with versions up to and
+    including ``version``.
+
+    Finds subdirectories of the form <project_name>/<version>/
+
+    Parameters
+    ----------
+    base_dir: str or Path
+        Base directory to look for ABC atlas release files.
+    version: str
+        String date format of the version. Should be of the form %Y%m%d (e.g.
+        20240330)
+    dirs_to_skip: list of str
+        List of projects/directories to skip. Can either be full directory
+        name or the first part of a data_set pattern to match. (e.g. SEAD will
+        exclude all directories that start with that pattern for example,
+        SEAD-taxonomy etc.)
+
+    Returns
+    -------
+    release: dict
+        Base release manifest dictionary with all directories populated.
+    """
+    find_logger = logging.getLogger("find_directories")
+
+    release = {
+        "version": version,
+        "resource_uri": "s3://allen-brain-cell-atlas/",
+        "directory_listing": {}
+    }
+    for directory in os.walk(base_dir):
+        version_list = []
+        # Find only directories with properly formated date version
+        # subdirectories
+        for subdir in directory[1]:
+            if _validate_version(subdir):
+                version_list.append(subdir)
+        # If we find a version  select either the max version
+        if version_list:
+            max_version = max(version_list)
+            split_dir = str(PurePosixPath(directory[0])).split('/')
+            data_set = split_dir[-1]
+            if any([data_set.startswith(skip) for skip in dirs_to_skip]):
+                find_logger.info(f"Skipping dataset: {data_set}")
+                continue
+            if version < max_version and version not in version_list:
+                continue
+            data_kind = split_dir[-2]
+            if data_set not in release['directory_listing']:
+                release['directory_listing'][data_set] = {}
+                release['directory_listing'][data_set]['directories'] = {}
+            release['directory_listing'][data_set]['directories'][data_kind] = {
+                'version': version if version < max_version else max_version
+            }
+    release['directory_listing'] = OrderedDict(
+        sorted(release['directory_listing'].items()))
+    return release
+
+
+def populate_directories(
+        base_dir: Union[str, Path],
+        release: dict,
+        bucket_prefix: str,
+        browse_prefix: str
+) -> dict:
+    """Populate paths and urls for each dataset/directory in the release.
+
+    Parameters
+    ----------
+    base_dir: str or Path
+        Base directory to look for ABC atlas release files.
+    release: dict
+        Base release manifest dictionary with all directories populated.
+    bucket_prefix: str
+        Prefix to add to the bucket url.
+    browse_prefix: str
+        Prefix to add to the browse url.
+
+    Returns
+    -------
+    release: dict
+        Base release manifest dictionary with all directories, links, and paths
+        populated.
+    """
+    dir_logger = logging.getLogger("populate_directories")
+    dir_logger.info('Populating paths and urls for each dataset/directory')
+    for data_set in release['directory_listing'].keys():
+
+        dir_logger.info(f'- {data_set}')
+        ds_dict = release['directory_listing'][data_set]['directories']
+
+        for data_dir in ds_dict.keys():
+
+            dir_logger.info(f'-- {data_dir}')
+            ver_dict = ds_dict[data_dir]
+            rel_path = os.path.join(data_dir, data_set, ver_dict['version'])
+            full_path = os.path.join(base_dir, rel_path)
+            bucket_url = bucket_prefix + rel_path + '/'
+            browse_url = browse_prefix + rel_path + '/'
+
+            if not os.path.isdir(full_path):
+                raise FileNotFoundError(f"{full_path} is not a directory")
+
+            dir_logger.debug(f'--- {rel_path}')
+            dir_logger.debug(f'--- {bucket_url}')
+            dir_logger.debug(f'--- {browse_url}')
+
+            ver_dict['relative_path'] = rel_path
+            ver_dict['url'] = bucket_url
+            ver_dict['view_link'] = browse_url
+    return release
+
+
+def populate_datasets(
+        base_dir: Union[str, Path],
+        release: dict,
+        bucket_prefix: str,
+) -> dict:
+    """Populate all files in the manifest by crawling the base directory.
+
+    Parameters
+    ----------
+    base_dir: str or Path
+        Staging directory of the ABC atlas release.
+    release: dict
+        Base release manifest dictionary with all directories populated, links,
+        and paths populated.
+    bucket_prefix: str
+        Prefix to add to the bucket url.
+
+    Returns
+    -------
+    release: dict
+        Base release manifest dictionary with all directories, links, paths,
+        and files populated.
+    """
+    dataset_logger = logging.getLogger("populate_datasets")
+    dataset_logger.info("Populating files and hashes for each "
+                        "dataset/directory")
+    dataset_lookup = {}
+
+    for dataset in release['directory_listing'].keys():
+
+        dataset_logger.info(f'- {dataset}')
+        ds_dict = release['directory_listing'][dataset]['directories']
+        dataset_lookup[dataset] = {}
+
+        for data_kind in ds_dict.keys():
+
+            dataset_logger.info(f'-- {data_kind}')
+            dataset_lookup[dataset][data_kind] = {}
+            ver_dict = ds_dict[data_kind]
+
+            data_dir = os.path.join(base_dir, ver_dict['relative_path'])
+
+            total_size = 0
+
+            for file_path in ['*', '*/*']:
+
+                for full_path in glob.glob(
+                        os.path.join(data_dir, file_path),
+                        recursive=True
+                ):
+                    if os.path.isdir(full_path):
+                        continue
+
+                    dataset_logger.debug(full_path)
+                    file_size = os.path.getsize(full_path)
+                    total_size += file_size
+
+                    rel_path = os.path.relpath(full_path, base_dir)
+
+                    bname = os.path.basename(full_path)
+
+                    bsplit = os.path.splitext(bname)
+                    ext = bsplit[1]
+                    ext = ext.replace('.', '')
+
+                    file_hash = file_hash_from_path(full_path)
+
+                    # Metadata for an individual file.
+                    file_dict = {
+                        'version': ds_dict[data_kind]['version'],
+                        'relative_path': rel_path,
+                        'url': bucket_prefix + rel_path,
+                        'size': file_size,
+                        'file_hash': file_hash
+                    }
+
+                    if ext in ['csv', 'json', 'h5']:
+                        tag = bsplit[0]
+                        dataset_lookup[dataset][data_kind][tag] = {}
+                        dataset_lookup[dataset][data_kind][tag]['files'] = {}
+                        dataset_lookup[dataset][data_kind][tag]['files'][
+                            ext] = file_dict
+                    elif ext == 'h5ad':
+
+                        if '-raw.h5ad' in bname:
+                            tag = bname.split('-raw.h5ad')[0]
+                            norm = 'raw'
+                        elif '-log2.h5ad' in bname:
+                            tag = bname.split('-log2.h5ad')[0]
+                            norm = 'log2'
+
+                        if tag not in dataset_lookup[dataset][data_kind].keys():
+                            dataset_lookup[dataset][data_kind][tag] = {}
+
+                        dataset_lookup[dataset][data_kind][tag][norm] = {}
+                        dataset_lookup[dataset][data_kind][tag][norm]['files'] = {}
+                        dataset_lookup[dataset][data_kind][tag][norm]['files'][
+                            ext] = file_dict
+                    elif ext == 'gz':
+                        ext = 'nii.gz'
+                        tag = bname.replace('.nii.gz', '')
+                        dataset_lookup[dataset][data_kind][tag] = {}
+                        dataset_lookup[dataset][data_kind][tag]['files'] = {}
+                        dataset_lookup[dataset][data_kind][tag]['files'][
+                            ext] = file_dict
+
+                ver_dict['total_size'] = total_size
+
+    release['file_listing'] = dataset_lookup
+    return release
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--abc_atlas_staging_path",
+        type=str,
+        required=True,
+        help="Path to the ABC Atlas staging directory.  "
+    )
+    parser.add_argument(
+        "--output_file",
+        type=str,
+        required=True,
+        help="File to output the manifest to."
+    )
+    parser.add_argument(
+        "--manifest_version",
+        type=str,
+        required=True,
+        help="Verion of the manifest to build. Should be in the format "
+             "%Y%m%d. (e.g. 20240315)"
+    )
+    parser.add_argument(
+        "--bucket_prefix",
+        type=str,
+        default="https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/",
+        help=""
+    )
+    parser.add_argument(
+        "--datasets_to_skip",
+        nargs='+',
+        type=str,
+        default=['releases', 'SEAAD', 'SEA-AD', 'Zhuang-C57BL6J'],
+        help="Skip a given project for all directories that start with the "
+             "given pattern. (e.g. SEAD will exclude all directories that "
+                "start with that pattern for example, SEAD-taxonomy etc.)"
+    )
+    parser.add_argument(
+        "--logging_level",
+        type=str,
+        choices=['INFO', 'DEBUG'],
+        default="INFO",
+        help="Set the logging level."
+    )
+    args = parser.parse_args()
+    logger = logging.getLogger(__name__)
+    if args.logging_level == "DEBUG":
+        logging.basicConfig(level=logging.DEBUG)
+    else:
+        logging.basicConfig(level=logging.INFO)
+
+    base_dir = Path(args.abc_atlas_staging_path)
+    version = args.manifest_version
+    if not _validate_version(args.manifest_version):
+        raise ValueError("Invalid version format. Please use %Y%m%d format "
+                         "(e.g. 20240315)")
+    bucket_prefix = args.bucket_prefix
+    browse_prefix = args.bucket_prefix + 'index.html#'
+    datasets_to_skip = args.datasets_to_skip
+
+    logger.info(f"Building manifest for version: {version}")
+    output_release = find_directories(
+        base_dir=base_dir,
+        version=version,
+        dirs_to_skip=datasets_to_skip
+    )
+    output_release = populate_directories(
+        base_dir=base_dir,
+        release=output_release,
+        bucket_prefix=bucket_prefix,
+        browse_prefix=browse_prefix
+    )
+    output_release = populate_datasets(
+        base_dir=base_dir,
+        release=output_release,
+        bucket_prefix=bucket_prefix
+    )
+
+    logger.info(f"Writing manifest to {args.output_file}")
+    with open(args.output_file, 'w') as jfile:
+        json.dump(output_release, jfile, indent=4)