Differential D8566 Diff 31014 swh/loader/package/conda/loader.py

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swh/loader/package/conda/loader.py

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# See the AUTHORS file at the top-level directory of this distribution

# License: GNU General Public License version 3, or any later version

# See top-level LICENSE file for more information

import json

from pathlib import Path

from typing import Any, Dict, Iterator, List, Optional, Sequence, Tuple

import attr

import iso8601

from packaging.version import parse as parse_version

import yaml

from swh.loader.package.loader import BasePackageInfo, PackageLoader

from swh.loader.package.utils import EMPTY_AUTHOR, Person, get_url_body, release_name

from swh.model.model import ObjectType, Release, Sha1Git, TimestampWithTimezone

from swh.storage.interface import StorageInterface

@attr.s

class CondaPackageInfo(BasePackageInfo):

name = attr.ib(type=str)

"""Name of the package"""

filename = attr.ib(type=str)

"""Archive (tar.gz) file name"""

version = attr.ib(type=str)

"""Complete version and distribution name. Ex: 'linux-64/0.1.1-py37'

"""

last_modified = attr.ib(type=str)

"""File last modified date as release date"""

def extract_intrinsic_metadata(dir_path: Path) -> Dict[str, Any]:

"""Extract intrinsic metadata from file at dir_path.

Each Conda package version may have an info/about.json file in the

archive. If missing we try to get metadata from info/recipe/meta.yaml

See https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/pkg-specs.html?highlight=meta.yaml#info-about-json # noqa: B950

for package specifications.

Args:

dir_path: A directory on disk where a metadata file can be found

Returns:

A dict mapping from yaml parser

"""

metadata: Dict[str, Any] = {}

meta_json_path = dir_path / "info" / "about.json"

if meta_json_path.exists():

metadata = json.loads(meta_json_path.read_text())

meta_yml_path = dir_path / "info" / "recipe" / "meta.yaml"

if meta_yml_path.exists():

metadata = yaml.safe_load(meta_yml_path.read_text())

anlambertUnsubmitted

Done

You should return the first metadata file content you find here:

meta_json_path = dir_path / "info" / "about.json"
meta_yml_path = dir_path / "info" / "recipe" / "meta.yaml"
if meta_json_path.exists():
    metadata = json.loads(meta_json_path.read_text())
elif meta_yml_path.exists():
    metadata = yaml.safe_load(meta_yml_path.read_text())

anlambert: You should return the first metadata file content you find here: ```lang=python meta_json_path…

return metadata

anlambertUnsubmitted

Done

We should return the first parsed metadata file and handle parsing errors here:

metadata: Dict[str, Any] = {}

meta_json_path = dir_path / "info" / "about.json"
meta_yml_path = dir_path / "info" / "recipe" / "meta.yaml"

if meta_json_path.exists():
    try:
        metadata = json.loads(meta_json_path.read_text())
    except json.JSONDecodeError:
        pass

if meta_yml_path.exists() and not metadata:
    try:
        metadata = yaml.safe_load(meta_yml_path.read_text())
    except yaml.YAMLError:
        pass

return metadata

anlambert: We should return the first parsed metadata file and handle parsing errors here: ```lang=python…

class CondaLoader(PackageLoader[CondaPackageInfo]):

visit_type = "conda"

def __init__(

self,

storage: StorageInterface,

url: str,

artifacts: List[Dict[str, Any]],

**kwargs,

super().__init__(storage=storage, url=url, **kwargs)

self.url = url

self.artifacts: Dict[str, Dict] = {

artifact["version"]: artifact for artifact in artifacts

}

def _raw_info(self, url: str, **extra_params) -> bytes:

return get_url_body(url=url, **extra_params)

def get_versions(self) -> Sequence[str]:

"""Get all released versions of a Conda package

Returns:

A sequence of versions

Example::

["0.1.1", "0.10.2"]

"""

versions = list(self.artifacts.keys())

versions.sort(key=parse_version)

return versions

def get_default_version(self) -> str:

"""Get the newest release version of a Conda package

Returns:

A string representing a version

Example::

"0.10.2"

"""

return self.get_versions()[-1]

def get_package_info(self, version: str) -> Iterator[Tuple[str, CondaPackageInfo]]:

"""Get release name and package information from version

Args:

version: Package version (e.g: "0.1.0")

Returns:

Iterator of tuple (release_name, p_info)

"""

data = self.artifacts[version]

pkgname: str = self.url.split("/")[-1]

url: str = data["url"]

filename: str = data["filename"]

last_modified = iso8601.parse_date(data["date"]).isoformat()

anlambertUnsubmitted

Done

date can be missing from listed artifacts, this needs to be handled:

[2022-10-19 13:52:59,918: ERROR/ForkPoolWorker-4] Failed to get package info for version linux-64/0.20.0-py27_0 of https://anaconda.org/main/llvmlite
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 634, in load
docker-swh-loader-1  |     for branch_name, p_info in self.get_package_info(version):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 125, in get_package_info
docker-swh-loader-1  |     last_modified = iso8601.parse_date(data["date"]).isoformat()
docker-swh-loader-1  | KeyError: 'date'
docker-swh-loader-1  | [2022-10-19 13:52:59,919: ERROR/ForkPoolWorker-4] Failed to get package info for version linux-64/0.20.0-py34_0 of https://anaconda.org/main/llvmlite
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 634, in load
docker-swh-loader-1  |     for branch_name, p_info in self.get_package_info(version):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 125, in get_package_info
docker-swh-loader-1  |     last_modified = iso8601.parse_date(data["date"]).isoformat()
docker-swh-loader-1  | KeyError: 'date'
docker-swh-loader-1  | [2022-10-19 13:52:59,919: ERROR/ForkPoolWorker-4] Failed to get package info for version linux-64/0.20.0-py35_0 of https://anaconda.org/main/llvmlite
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 634, in load
docker-swh-loader-1  |     for branch_name, p_info in self.get_package_info(version):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 125, in get_package_info
docker-swh-loader-1  |     last_modified = iso8601.parse_date(data["date"]).isoformat()
docker-swh-loader-1  | KeyError: 'date'
docker-swh-loader-1  | [2022-10-19 13:52:59,920: ERROR/ForkPoolWorker-4] Failed to get package info for version linux-64/0.20.0-py36_0 of https://anaconda.org/main/llvmlite
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 634, in load
docker-swh-loader-1  |     for branch_name, p_info in self.get_package_info(version):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 125, in get_package_info
docker-swh-loader-1  |     last_modified = iso8601.parse_date(data["date"]).isoformat()
docker-swh-loader-1  | KeyError: 'date'

anlambert: date can be missing from listed artifacts, this needs to be handled: ``` [2022-10-19 13:52:59…

# TODO: Make use of data["checksums"]

p_info = CondaPackageInfo(

name=pkgname,

filename=filename,

url=url,

version=version,

last_modified=last_modified,

)

anlambertUnsubmitted

Done

I landed D8595 about that feature, you can simply pass the checksums as parameter here to check downloaded tarball integrity:

p_info = CondaPackageInfo(
    name=pkgname,
    filename=filename,
    url=url,
    version=version,
    last_modified=last_modified,
    checksums=data["checksums"],
)

anlambert: I landed D8595 about that feature, you can simply pass the checksums as parameter here to check…

yield release_name(version), p_info

def build_release(

self, p_info: CondaPackageInfo, uncompressed_path: str, directory: Sha1Git

) -> Optional[Release]:

# Extract intrinsic metadata from archive to get description and author

metadata = extract_intrinsic_metadata(Path(uncompressed_path))

description: str = (

metadata.get("summary") or metadata.get("about", {}).get("summary") or ""

)

vlorentzUnsubmitted

Done

metadata = extract_intrinsic_metadata(Path(uncompressed_path))

- description: str = ""

- if "summary" in metadata:

- description = metadata["summary"]

- elif "about" in metadata and "summary" in metadata["about"]:

- description = metadata["about"]["summary"]

+ description = (

+ metadata.get("summary")

+ or metadata.get("about", {}).get("summary")

+ or ""

+ )

author = EMPTY_AUTHOR

that's simpler IMO

(also, it will use metadata["about"]["summary"] if metadata["summary"] is empty. I don't know if it matters for any package, but there's not harm in doing that)

vlorentz: that's simpler IMO (also, it will use `metadata["about"]["summary"]` if `metadata["summary"]`…

author = EMPTY_AUTHOR

anlambertUnsubmitted

Done

Looks like maintainers[0] can be None for some edge cases:

docker-swh-loader-1  | [2022-10-19 13:46:51,264: DEBUG/ForkPoolWorker-3] package_info: CondaPackageInfo(url='https://repo.anaconda.com/pkgs/main/linux-64/mkl-dpcpp-2021.3.0-h66538d2_521.tar.bz2', directory_extrinsic_metadata=[], checksums={'md5': 'e637920edc32a328881369008fc95203', 'sha256': '6c6e9a64ccbe997135297b5d0c59c255246d52d5f589e096a0e2db8ad73243be'}, name='mkl-dpcpp', filename='mkl-dpcpp-2021.3.0-h66538d2_521.tar.bz2', version='linux-64/2021.3.0-h66538d2_521', last_modified='2022-02-21T22:17:58.589000+00:00')
docker-swh-loader-1  | [2022-10-19 13:46:51,524: DEBUG/ForkPoolWorker-3] filename: mkl-dpcpp-2021.3.0-h66538d2_521.tar.bz2
docker-swh-loader-1  | [2022-10-19 13:46:51,524: DEBUG/ForkPoolWorker-3] filepath: /tmp/tmpdvk30qj0/mkl-dpcpp-2021.3.0-h66538d2_521.tar.bz2
docker-swh-loader-1  | [2022-10-19 13:47:13,982: DEBUG/ForkPoolWorker-3] extrinsic_metadata
docker-swh-loader-1  | [2022-10-19 13:48:08,558: DEBUG/ForkPoolWorker-3] uncompressed_path: /tmp/tmpdvk30qj0/src
docker-swh-loader-1  | [2022-10-19 13:48:18,532: DEBUG/ForkPoolWorker-3] Filtered out 1 contents, 0 skipped contents and 0 directories
docker-swh-loader-1  | [2022-10-19 13:48:18,532: DEBUG/ForkPoolWorker-3] Number of skipped contents: 1
docker-swh-loader-1  | [2022-10-19 13:48:18,532: DEBUG/ForkPoolWorker-3] Number of contents: 17
docker-swh-loader-1  | [2022-10-19 13:48:18,532: DEBUG/ForkPoolWorker-3] Number of directories: 10
docker-swh-loader-1  | [2022-10-19 13:48:18,689: ERROR/ForkPoolWorker-3] Failed to load branch releases/linux-64/2021.3.0-h66538d2_521 for https://anaconda.org/main/mkl-dpcpp
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 688, in load
docker-swh-loader-1  |     res = self._load_release(p_info, origin)
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 877, in _load_release
docker-swh-loader-1  |     p_info, uncompressed_path, directory=directory.hash
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 148, in build_release
docker-swh-loader-1  |     author = Person.from_fullname(maintainers[0].encode())
docker-swh-loader-1  | AttributeError: 'NoneType' object has no attribute 'encode'
docker-swh-loader-1  | [2022-10-19 13:48:18,692: DEBUG/ForkPoolWorker-3] package_info: CondaPackageInfo(url='https://repo.anaconda.com/pkgs/main/linux-64/mkl-dpcpp-2021.4.0-h66538d2_640.tar.bz2', directory_extrinsic_metadata=[], checksums={'md5': 'fe3fcabdefbf7fa7c6b7a603c71d3aff', 'sha256': 'b6f25a926bc6b94fb8fa38ca9c7caba894a5bd0b4d6fa948d8038f3dafc65eaa'}, name='mkl-dpcpp', filename='mkl-dpcpp-2021.4.0-h66538d2_640.tar.bz2', version='linux-64/2021.4.0-h66538d2_640', last_modified='2022-02-21T22:23:28.671000+00:00')
docker-swh-loader-1  | [2022-10-19 13:48:18,904: DEBUG/ForkPoolWorker-3] filename: mkl-dpcpp-2021.4.0-h66538d2_640.tar.bz2
docker-swh-loader-1  | [2022-10-19 13:48:18,904: DEBUG/ForkPoolWorker-3] filepath: /tmp/tmphnski1iw/mkl-dpcpp-2021.4.0-h66538d2_640.tar.bz2
docker-swh-loader-1  | [2022-10-19 13:48:36,899: DEBUG/ForkPoolWorker-3] extrinsic_metadata
docker-swh-loader-1  | [2022-10-19 13:49:26,037: DEBUG/ForkPoolWorker-3] uncompressed_path: /tmp/tmphnski1iw/src
docker-swh-loader-1  | [2022-10-19 13:49:37,059: DEBUG/ForkPoolWorker-3] Filtered out 1 contents, 0 skipped contents and 0 directories
docker-swh-loader-1  | [2022-10-19 13:49:37,059: DEBUG/ForkPoolWorker-3] Number of skipped contents: 1
docker-swh-loader-1  | [2022-10-19 13:49:37,059: DEBUG/ForkPoolWorker-3] Number of contents: 17
docker-swh-loader-1  | [2022-10-19 13:49:37,059: DEBUG/ForkPoolWorker-3] Number of directories: 10
docker-swh-loader-1  | [2022-10-19 13:49:37,272: ERROR/ForkPoolWorker-3] Failed to load branch releases/linux-64/2021.4.0-h66538d2_640 for https://anaconda.org/main/mkl-dpcpp
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 688, in load
docker-swh-loader-1  |     res = self._load_release(p_info, origin)
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 877, in _load_release
docker-swh-loader-1  |     p_info, uncompressed_path, directory=directory.hash
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 148, in build_release
docker-swh-loader-1  |     author = Person.from_fullname(maintainers[0].encode())
docker-swh-loader-1  | AttributeError: 'NoneType' object has no attribute 'encode'
docker-swh-loader-1  | [2022-10-19 13:49:37,272: DEBUG/ForkPoolWorker-3] package_info: CondaPackageInfo(url='https://repo.anaconda.com/pkgs/main/linux-64/mkl-dpcpp-2022.0.1-h66538d2_117.tar.bz2', directory_extrinsic_metadata=[], checksums={'md5': 'a858b82a575e3bc331abf2a49d3e9289', 'sha256': '8f6c3946a80e64a2ea703e97bbe1c80e50dc237021e4167feed4c061b7b5774a'}, name='mkl-dpcpp', filename='mkl-dpcpp-2022.0.1-h66538d2_117.tar.bz2', version='linux-64/2022.0.1-h66538d2_117', last_modified='2022-02-22T14:16:39.634000+00:00')
docker-swh-loader-1  | [2022-10-19 13:49:37,522: DEBUG/ForkPoolWorker-3] filename: mkl-dpcpp-2022.0.1-h66538d2_117.tar.bz2
docker-swh-loader-1  | [2022-10-19 13:49:37,522: DEBUG/ForkPoolWorker-3] filepath: /tmp/tmpuijki00g/mkl-dpcpp-2022.0.1-h66538d2_117.tar.bz2
docker-swh-loader-1  | [2022-10-19 13:49:56,567: DEBUG/ForkPoolWorker-3] extrinsic_metadata
docker-swh-loader-1  | [2022-10-19 13:50:39,400: DEBUG/ForkPoolWorker-3] uncompressed_path: /tmp/tmpuijki00g/src
docker-swh-loader-1  | [2022-10-19 13:50:49,083: DEBUG/ForkPoolWorker-3] Filtered out 1 contents, 0 skipped contents and 0 directories
docker-swh-loader-1  | [2022-10-19 13:50:49,084: DEBUG/ForkPoolWorker-3] Number of skipped contents: 1
docker-swh-loader-1  | [2022-10-19 13:50:49,084: DEBUG/ForkPoolWorker-3] Number of contents: 17
docker-swh-loader-1  | [2022-10-19 13:50:49,084: DEBUG/ForkPoolWorker-3] Number of directories: 10
docker-swh-loader-1  | [2022-10-19 13:50:49,313: ERROR/ForkPoolWorker-3] Failed to load branch releases/linux-64/2022.0.1-h66538d2_117 for https://anaconda.org/main/mkl-dpcpp
docker-swh-loader-1  | Traceback (most recent call last):
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 688, in load
docker-swh-loader-1  |     res = self._load_release(p_info, origin)
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/loader.py", line 877, in _load_release
docker-swh-loader-1  |     p_info, uncompressed_path, directory=directory.hash
docker-swh-loader-1  |   File "/tmp/tmp.0uo1le4WBL/swh-loader-core/swh/loader/package/conda/loader.py", line 148, in build_release
docker-swh-loader-1  |     author = Person.from_fullname(maintainers[0].encode())
docker-swh-loader-1  | AttributeError: 'NoneType' object has no attribute 'encode'

anlambert: Looks like `maintainers[0]` can be `None` for some edge cases: ``` docker-swh-loader-1 | [2022…

maintainers = metadata.get("extra", {}).get("recipe-maintainers")

if maintainers and isinstance(maintainers, list) and any(maintainers):

# TODO: here we have a list of author, see T3887

author = Person.from_fullname(maintainers[0].encode())

message = (

vlorentzUnsubmitted

Done

author = EMPTY_AUTHOR

- if "extra" in metadata and "recipe-maintainers" in metadata["extra"]:

- maintainer = metadata["extra"]["recipe-maintainers"][

- 0

- ] # TODO: here we have a list of author, see T3887

- author = Person.from_fullname(maintainer.encode())

+ maintainers = metadata.get("extra", {}).get("recipe-maintainers")

+ if maintainers:

+ # TODO: here we have a list of author, see T3887

+ author = Person.from_fullname(maintainers[0].encode())

message = (

Simpler.

Also, you should add a check that maintainers is indeed a list, or we will silently end up with the first character as author.

vlorentz: Simpler. Also, you should add a check that `maintainers` is indeed a list, or we will silently…

f"Synthetic release for Conda source package {p_info.name} "

f"version {p_info.version}\n\n"

f"{description}\n"

anlambertUnsubmitted

Done

if the description is empty, we do not need the two line breaks, I'll rather do:

message = (
    f"Synthetic release for Conda source package {p_info.name} "
    f"version {p_info.version}"
)

if description:
    message += f"\n\n{description}"

anlambert: if the description is empty, we do not need the two line breaks, I'll rather do…

)

return Release(

name=p_info.version.encode(),

author=author,

date=TimestampWithTimezone.from_iso8601(p_info.last_modified),

message=message.encode(),

target_type=ObjectType.DIRECTORY,

target=directory,

synthetic=True,

)