pyobo 0.11.2__py3-none-any.whl → 0.12.1__py3-none-any.whl

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+pyobo/reader_utils.py,sha256=5324154d08576e167d7c28b3660dbaa394e67878acf7ea9930abd0170201460a,4423
+pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15e56d72,2440
+pyobo-0.12.1.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+pyobo-0.12.1.dist-info/WHEEL,sha256=1c77bbda0b527f376a68ced20cbc1aac3efc7bc4d7c10cc4323a905ef79ae8db,78
+pyobo-0.12.1.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
+pyobo-0.12.1.dist-info/METADATA,sha256=891eda0af949aecf1dc5064aaba32edf807fc6ec4d43d7eebd8b0af65dc3b388,22299
+pyobo-0.12.1.dist-info/RECORD,,

pyobo-0.12.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: uv 0.7.2
+Root-Is-Purelib: true
+Tag: py3-none-any

{pyobo-0.11.2.dist-info → pyobo-0.12.1.dist-info}/entry_points.txt

@@ -1,2 +1,3 @@
 [console_scripts]
 pyobo = pyobo.cli:main
+

pyobo-0.12.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Charles Tapley Hoyt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyobo/aws.py

@@ -1,162 +0,0 @@
-"""Interface for caching data on AWS S3."""
-
-import logging
-import os
-from typing import Optional
-
-import boto3
-import humanize
-from tabulate import tabulate
-
-from pyobo import (
-    get_id_name_mapping,
-    get_id_synonyms_mapping,
-    get_id_to_alts,
-    get_properties_df,
-    get_relations_df,
-    get_xrefs_df,
-)
-from pyobo.api.utils import get_version
-from pyobo.constants import RAW_DIRECTORY
-from pyobo.registries import iter_cached_obo
-from pyobo.utils.path import prefix_cache_join
-
-__all__ = [
-    "download_artifacts",
-    "upload_artifacts",
-    "upload_artifacts_for_prefix",
-    "list_artifacts",
-]
-
-logger = logging.getLogger(__name__)
-
-
-def download_artifacts(bucket: str, suffix: Optional[str] = None) -> None:
-    """Download compiled parts from AWS.
-
-    :param bucket: The name of the S3 bucket to download
-    :param suffix: If specified, only download files with this suffix. Might
-     be useful to specify ``suffix='names.tsv`` if you just want to run the
-     name resolution service.
-    """
-    s3_client = boto3.client("s3")
-    all_objects = s3_client.list_objects(Bucket=bucket)
-    for entry in all_objects["Contents"]:
-        key = entry["Key"]
-        if suffix and not key.endswith(suffix):
-            pass
-        path = os.path.join(RAW_DIRECTORY, key)
-        os.makedirs(os.path.dirname(path), exist_ok=True)
-        if os.path.exists(path):
-            continue  # no need to download again
-        logging.warning("downloading %s to %s", key, path)
-        s3_client.download_file(bucket, key, path)
-
-
-def upload_artifacts(
-    bucket: str,
-    whitelist: Optional[set[str]] = None,
-    blacklist: Optional[set[str]] = None,
-    s3_client=None,
-) -> None:
-    """Upload all artifacts to AWS."""
-    if s3_client is None:
-        s3_client = boto3.client("s3")
-    all_objects = s3_client.list_objects(Bucket=bucket)
-    uploaded_prefixes = {entry["Key"].split("/")[0] for entry in all_objects["Contents"]}
-
-    for prefix, _ in sorted(iter_cached_obo()):
-        if prefix in uploaded_prefixes:
-            continue
-        if whitelist and prefix not in whitelist:
-            continue
-        if blacklist and prefix in blacklist:
-            continue
-        upload_artifacts_for_prefix(prefix=prefix, bucket=bucket, s3_client=s3_client)
-
-
-def upload_artifacts_for_prefix(
-    *, prefix: str, bucket: str, s3_client=None, version: Optional[str] = None
-):
-    """Upload compiled parts for the given prefix to AWS."""
-    if s3_client is None:
-        s3_client = boto3.client("s3")
-
-    if version is None:
-        version = get_version(prefix)
-
-    logger.info("[%s] getting id->name mapping", prefix)
-    get_id_name_mapping(prefix)
-    id_name_path = prefix_cache_join(prefix, name="names.tsv", version=version)
-    if not id_name_path.exists():
-        raise FileNotFoundError
-    id_name_key = os.path.join(prefix, "cache", "names.tsv")
-    logger.info("[%s] uploading id->name mapping", prefix)
-    upload_file(path=id_name_path, bucket=bucket, key=id_name_key, s3_client=s3_client)
-
-    logger.info("[%s] getting id->synonyms mapping", prefix)
-    get_id_synonyms_mapping(prefix)
-    id_synonyms_path = prefix_cache_join(prefix, name="synonyms.tsv", version=version)
-    if not id_synonyms_path.exists():
-        raise FileNotFoundError
-    id_synonyms_key = os.path.join(prefix, "cache", "synonyms.tsv")
-    logger.info("[%s] uploading id->synonyms mapping", prefix)
-    upload_file(path=id_synonyms_path, bucket=bucket, key=id_synonyms_key, s3_client=s3_client)
-
-    logger.info("[%s] getting xrefs", prefix)
-    get_xrefs_df(prefix)
-    xrefs_path = prefix_cache_join(prefix, name="xrefs.tsv", version=version)
-    if not xrefs_path.exists():
-        raise FileNotFoundError
-    xrefs_key = os.path.join(prefix, "cache", "xrefs.tsv")
-    logger.info("[%s] uploading xrefs", prefix)
-    upload_file(path=xrefs_path, bucket=bucket, key=xrefs_key, s3_client=s3_client)
-
-    logger.info("[%s] getting relations", prefix)
-    get_relations_df(prefix)
-    relations_path = prefix_cache_join(prefix, name="relations.tsv", version=version)
-    if not relations_path.exists():
-        raise FileNotFoundError
-    relations_key = os.path.join(prefix, "cache", "relations.tsv")
-    logger.info("[%s] uploading relations", prefix)
-    upload_file(path=relations_path, bucket=bucket, key=relations_key, s3_client=s3_client)
-
-    logger.info("[%s] getting properties", prefix)
-    get_properties_df(prefix)
-    properties_path = prefix_cache_join(prefix, name="properties.tsv", version=version)
-    if not properties_path.exists():
-        raise FileNotFoundError
-    properties_key = os.path.join(prefix, "cache", "properties.tsv")
-    logger.info("[%s] uploading properties", prefix)
-    upload_file(path=properties_path, bucket=bucket, key=properties_key, s3_client=s3_client)
-
-    logger.info("[%s] getting alternative identifiers", prefix)
-    get_id_to_alts(prefix)
-    alts_path = prefix_cache_join(prefix, name="alt_ids.tsv", version=version)
-    if not alts_path.exists():
-        raise FileNotFoundError
-    alts_key = os.path.join(prefix, "cache", "alt_ids.tsv")
-    logger.info("[%s] uploading alternative identifiers", prefix)
-    upload_file(path=alts_path, bucket=bucket, key=alts_key)
-
-
-def upload_file(*, path, bucket, key, s3_client=None):
-    """Upload a file to an S3 bucket.
-
-    :param path: The local file path
-    :param bucket: The name of the S3 bucket
-    :param key: The relative file path to put on the S3 bucket
-    """
-    if s3_client is None:
-        s3_client = boto3.client("s3")
-    s3_client.upload_file(path, bucket, key)
-
-
-def list_artifacts(bucket: str) -> str:
-    """List the files in a given bucket."""
-    s3_client = boto3.client("s3")
-    all_objects = s3_client.list_objects(Bucket=bucket)
-    rows = [
-        (entry["Key"], humanize.naturalsize(entry["Size"])) for entry in all_objects["Contents"]
-    ]
-    return tabulate(rows, headers=["File", "Size"])

pyobo/cli/aws.py

@@ -1,47 +0,0 @@
-"""CLI for PyOBO's interface to S3."""
-
-import click
-from more_click import verbose_option
-
-from ..aws import download_artifacts, list_artifacts, upload_artifacts
-
-__all__ = [
-    "main",
-]
-
-bucket_argument = click.argument("bucket")
-
-
-@click.group(name="aws")
-def main():
-    """S3 utilities."""
-
-
-@main.command()
-@bucket_argument
-@verbose_option
-def download(bucket):
-    """Download all artifacts from the S3 bucket."""
-    download_artifacts(bucket)
-
-
-@main.command()
-@bucket_argument
-@verbose_option
-@click.option("-w", "--whitelist", multiple=True)
-@click.option("-b", "--blacklist", multiple=True)
-def upload(bucket, whitelist, blacklist):
-    """Download all artifacts from the S3 bucket."""
-    upload_artifacts(bucket, whitelist=whitelist, blacklist=blacklist)
-
-
-@main.command()
-@bucket_argument
-@verbose_option
-def ls(bucket):
-    """List all artifacts on the S3 bucket."""
-    click.echo(list_artifacts(bucket))
-
-
-if __name__ == "__main__":
-    main()

pyobo/identifier_utils.py

@@ -1,142 +0,0 @@
-"""Utilities for handling prefixes."""
-
-from __future__ import annotations
-
-import logging
-from functools import wraps
-
-import bioregistry
-from curies import Reference, ReferenceTuple
-
-from .registries import (
-    curie_has_blacklisted_prefix,
-    curie_has_blacklisted_suffix,
-    curie_is_blacklisted,
-    remap_full,
-    remap_prefix,
-)
-
-__all__ = [
-    "normalize_curie",
-    "wrap_norm_prefix",
-    "standardize_ec",
-]
-
-logger = logging.getLogger(__name__)
-
-
-class MissingPrefixError(ValueError):
-    """Raised on a missing prefix."""
-
-    reference: Reference | None
-
-    def __init__(
-        self, prefix: str, curie: str, xref: str | None = None, ontology: str | None = None
-    ):
-        """Initialize the error."""
-        self.prefix = prefix
-        self.curie = curie
-        self.xref = xref
-        self.ontology = ontology
-        self.reference = None
-
-    def __str__(self) -> str:
-        s = ""
-        if self.ontology:
-            s += f"[{self.ontology}] "
-        s += f"unhandled prefix {self.prefix} found in curie {self.curie}"
-        if self.xref:
-            s += f"/xref {self.xref}"
-        if self.reference is not None:
-            s += f" from {self.reference.curie}"
-        return s
-
-
-def _normalize_prefix(prefix: str, *, curie=None, xref=None, strict: bool = True) -> str | None:
-    """Normalize a namespace and return, if possible."""
-    norm_prefix = bioregistry.normalize_prefix(prefix)
-    if norm_prefix is not None:
-        return norm_prefix
-    elif strict:
-        raise MissingPrefixError(prefix=prefix, curie=curie, xref=xref)
-    else:
-        return None
-
-
-BAD_CURIES = set()
-
-
-def normalize_curie(curie: str, *, strict: bool = True) -> tuple[str, str] | tuple[None, None]:
-    """Parse a string that looks like a CURIE.
-
-    :param curie: A compact uniform resource identifier (CURIE)
-    :param strict: Should an exception be thrown if the CURIE can not be parsed w.r.t. the Bioregistry?
-    :return: A parse tuple or a tuple of None, None if not able to parse and not strict
-
-    - Normalizes the namespace
-    - Checks against a blacklist for the entire curie, for the namespace, and for suffixes.
-    """
-    if curie_is_blacklisted(curie):
-        return None, None
-    if curie_has_blacklisted_prefix(curie):
-        return None, None
-    if curie_has_blacklisted_suffix(curie):
-        return None, None
-
-    # Remap the curie with the full list
-    curie = remap_full(curie)
-
-    # Remap node's prefix (if necessary)
-    curie = remap_prefix(curie)
-
-    try:
-        head_ns, identifier = curie.split(":", 1)
-    except ValueError:  # skip nodes that don't look like normal CURIEs
-        if curie not in BAD_CURIES:
-            BAD_CURIES.add(curie)
-            logger.debug(f"could not split CURIE on colon: {curie}")
-        return None, None
-
-    # remove redundant prefix
-    if identifier.casefold().startswith(f"{head_ns.casefold()}:"):
-        identifier = identifier[len(head_ns) + 1 :]
-
-    norm_node_prefix = _normalize_prefix(head_ns, curie=curie, strict=strict)
-    if not norm_node_prefix:
-        return None, None
-    return norm_node_prefix, identifier
-
-
-def wrap_norm_prefix(f):
-    """Decorate a function that take in a prefix to auto-normalize, or return None if it can't be normalized."""
-
-    @wraps(f)
-    def _wrapped(prefix: str | Reference | ReferenceTuple, *args, **kwargs):
-        if isinstance(prefix, str):
-            norm_prefix = bioregistry.normalize_prefix(prefix)
-            if norm_prefix is None:
-                raise ValueError(f"Invalid prefix: {prefix}")
-            prefix = norm_prefix
-        elif isinstance(prefix, Reference):
-            norm_prefix = bioregistry.normalize_prefix(prefix.prefix)
-            if norm_prefix is None:
-                raise ValueError(f"Invalid prefix: {prefix.prefix}")
-            prefix = Reference(prefix=norm_prefix, identifier=prefix.identifier)
-        elif isinstance(prefix, ReferenceTuple):
-            norm_prefix = bioregistry.normalize_prefix(prefix.prefix)
-            if norm_prefix is None:
-                raise ValueError(f"Invalid prefix: {prefix.prefix}")
-            prefix = ReferenceTuple(norm_prefix, prefix.identifier)
-        else:
-            raise TypeError
-        return f(prefix, *args, **kwargs)
-
-    return _wrapped
-
-
-def standardize_ec(ec: str) -> str:
-    """Standardize an EC code identifier by removing all trailing dashes and dots."""
-    ec = ec.strip().replace(" ", "")
-    for _ in range(4):
-        ec = ec.rstrip("-").rstrip(".")
-    return ec