Introduce bioconductor lister
This commit is contained in:
Kumar Shivendu
Antoine R. Dumont
parent
a04975571c
commit
88611642fc
13 changed files with 1845 additions and 0 deletions
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@ -28,6 +28,7 @@ following Python modules:
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- `swh.lister.pypi`
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- `swh.lister.rpm`
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- `swh.lister.tuleap`
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- `swh.lister.bioconductor`
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Dependencies
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------------
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1
setup.py
1
setup.py
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@ -93,6 +93,7 @@ setup(
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lister.stagit=swh.lister.stagit:register
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lister.tuleap=swh.lister.tuleap:register
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lister.maven=swh.lister.maven:register
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lister.bioconductor=swh.lister.bioconductor:register
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""",
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classifiers=[
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"Programming Language :: Python :: 3",
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13
swh/lister/bioconductor/__init__.py
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13
swh/lister/bioconductor/__init__.py
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@ -0,0 +1,13 @@
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# Copyright (C) 2022 The Software Heritage developers
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# See the AUTHORS file at the top-level directory of this distribution
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# License: GNU General Public License version 3, or any later version
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# See top-level LICENSE file for more information
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def register():
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from .lister import BioconductorLister
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return {
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"lister": BioconductorLister,
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"task_modules": [f"{__name__}.tasks"],
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}
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314
swh/lister/bioconductor/lister.py
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314
swh/lister/bioconductor/lister.py
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@ -0,0 +1,314 @@
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# Copyright (C) 2023 The Software Heritage developers
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# See the AUTHORS file at the top-level directory of this distribution
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# License: GNU General Public License version 3, or any later version
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# See top-level LICENSE file for more information
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from dataclasses import dataclass, field
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import json
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import logging
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from typing import Any, Dict, Iterator, List, Optional, Set, Tuple
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from urllib.parse import urljoin
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from bs4 import BeautifulSoup
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from debian.deb822 import Sources
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import iso8601
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from packaging import version
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from requests import HTTPError
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from swh.scheduler.interface import SchedulerInterface
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from swh.scheduler.model import ListedOrigin
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from ..pattern import CredentialsType, Lister
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logger = logging.getLogger(__name__)
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Release = str
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Category = str
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BioconductorListerPage = Optional[Tuple[Release, Category, Dict[str, Any]]]
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@dataclass
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class BioconductorListerState:
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"""State of the Bioconductor lister"""
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package_versions: Dict[str, Set[str]] = field(default_factory=dict)
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"""Dictionary mapping a package name to all the versions found during
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last listing"""
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class BioconductorLister(Lister[BioconductorListerState, BioconductorListerPage]):
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"""List origins from Bioconductor, a collection of open source software
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for bioinformatics based on the R statistical programming language."""
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LISTER_NAME = "bioconductor"
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VISIT_TYPE = "bioconductor"
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INSTANCE = "bioconductor"
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BIOCONDUCTOR_HOMEPAGE = "https://www.bioconductor.org"
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def __init__(
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self,
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scheduler: SchedulerInterface,
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url: str = BIOCONDUCTOR_HOMEPAGE,
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instance: str = INSTANCE,
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credentials: Optional[CredentialsType] = None,
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releases: Optional[List[Release]] = None,
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categories: Optional[List[Category]] = None,
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incremental: bool = False,
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max_origins_per_page: Optional[int] = None,
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max_pages: Optional[int] = None,
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enable_origins: bool = True,
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record_batch_size: int = 1000,
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):
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super().__init__(
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scheduler=scheduler,
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url=url,
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instance=instance,
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credentials=credentials,
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max_origins_per_page=max_origins_per_page,
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max_pages=max_pages,
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enable_origins=enable_origins,
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record_batch_size=record_batch_size,
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)
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if releases is None:
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self.releases = self.fetch_versions()
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else:
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self.releases = releases
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self.categories = categories or [
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"bioc",
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"workflows",
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"data/annotation",
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"data/experiment",
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]
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self.incremental = incremental
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self.listed_origins: Dict[str, ListedOrigin] = {}
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self.origins_to_send: Set[str] = set()
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self.package_versions: Dict[str, Set[str]] = {}
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def state_from_dict(self, d: Dict[str, Any]) -> BioconductorListerState:
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return BioconductorListerState(
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package_versions={k: set(v) for k, v in d.items()}
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)
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def state_to_dict(self, state: BioconductorListerState) -> Dict[str, Any]:
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return {k: list(v) for k, v in state.package_versions.items()}
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def origin_url_for_package(self, package_name: str) -> str:
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return f"{self.BIOCONDUCTOR_HOMEPAGE}/packages/{package_name}"
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def get_pages(self) -> Iterator[BioconductorListerPage]:
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"""Return an iterator for each page. Every page is a (release, category) pair."""
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for release in self.releases:
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if version.parse(release) < version.parse("1.8"):
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# only bioc category existed before 1.8
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url_template = urljoin(
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self.url, "/packages/{category}/{release}/src/contrib/PACKAGES"
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)
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categories = {"bioc"}
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elif version.parse(release) < version.parse("2.5"):
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# workflows category won't exist for these
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url_template = urljoin(
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self.url, "/packages/{release}/{category}/src/contrib/PACKAGES"
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)
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categories = {"bioc", "data/annotation", "data/experiment"}
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else:
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url_template = urljoin(
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self.url, "/packages/json/{release}/{category}/packages.json"
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)
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categories = set(self.categories)
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for category in categories:
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url = url_template.format(release=release, category=category)
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try:
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packages_txt = self.http_request(url).text
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packages = self.parse_packages(packages_txt)
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except HTTPError as e:
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logger.debug(
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"Skipping page since got %s response for %s",
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e.response.status_code,
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url,
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)
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continue
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yield (release, category, packages)
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# Yield extra none to signal get_origins_from_page()
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# to stop iterating and yield the extracted origins
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yield None
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def fetch_versions(self) -> List[str]:
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html = self.http_request(
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f"{self.BIOCONDUCTOR_HOMEPAGE}/about/release-announcements"
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).text
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bs = BeautifulSoup(html, "html.parser")
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return [
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tr.find_all("td")[0].text
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for tr in reversed(bs.find("table").find("tbody").find_all("tr"))
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if tr.find_all("td")[2].find("a")
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]
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def parse_packages(self, text: str) -> Dict[str, Any]:
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"""Parses packages.json and PACKAGES files"""
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try:
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return json.loads(text)
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except json.JSONDecodeError:
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pass
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sources = Sources.iter_paragraphs(text)
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return {s["Package"]: dict(s) for s in sources}
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def get_origins_from_page(
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self, page: BioconductorListerPage
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) -> Iterator[ListedOrigin]:
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"""Convert a page of BioconductorLister PACKAGES/packages.json
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metadata into a list of ListedOrigins"""
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assert self.lister_obj.id is not None
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if page is None:
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for origin_url in self.origins_to_send:
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yield self.listed_origins[origin_url]
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return
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release, category, packages = page
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origins_to_send = set()
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for pkg_name, pkg_metadata in packages.items():
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pkg_version = pkg_metadata["Version"]
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last_update_date = None
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last_update_str = ""
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if version.parse(release) < version.parse("1.8"):
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tar_url = urljoin(
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self.url,
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f"/packages/{category}/{release}/src/contrib/Source/{pkg_name}_{pkg_metadata['Version']}.tar.gz",
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)
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elif version.parse(release) < version.parse("2.5"):
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tar_url = urljoin(
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self.url,
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f"/packages/{release}/{category}/src/contrib/{pkg_name}_{pkg_metadata['Version']}.tar.gz",
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)
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else:
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# Some packages don't have don't have a download URL (based on source.ver)
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# and hence can't be archived. For example see the package
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# maEndToEnd at the end of
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# https://bioconductor.org/packages/json/3.17/workflows/packages.json
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# Even guessing tar url path based on the expected url format doesn't work. i.e.
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# https://bioconductor.org/packages/3.17/workflows/src/contrib/maEndToEnd_2.20.0.tar.gz
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# doesn't respond with a tar file. Plus, the mirror clearly shows
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# that maEndToEnd tar is missing.
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# https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.17/workflows/src/contrib/
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# So skipping such packages
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if "source.ver" not in pkg_metadata:
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logger.info(
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(
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"Skipping package %s listed in release %s "
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"category %s since it doesn't have a download URL"
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),
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pkg_name,
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release,
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category,
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)
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continue
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if "git_url" in pkg_metadata:
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# Along with the .tar.gz files grab the git repo as well
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git_origin_url = pkg_metadata["git_url"]
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git_last_update_str = pkg_metadata.get("git_last_commit_date")
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self.listed_origins[git_origin_url] = ListedOrigin(
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lister_id=self.lister_obj.id,
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visit_type="git",
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url=git_origin_url,
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last_update=(
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iso8601.parse_date(git_last_update_str)
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if git_last_update_str
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else None
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),
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)
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origins_to_send.add(git_origin_url)
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tar_url = urljoin(
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self.url,
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f"/packages/{release}/{category}/{pkg_metadata['source.ver']}",
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)
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last_update_str = pkg_metadata.get(
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"Date/Publication", pkg_metadata.get("git_last_commit_date")
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)
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last_update_date = (
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iso8601.parse_date(last_update_str) if last_update_str else None
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)
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# For some packages in releases >= 2.5, last_update can still
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# remain None. Example: See "adme16cod.db" entry in
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# https://bioconductor.org/packages/json/3.17/data/annotation/packages.json
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origin_url = self.origin_url_for_package(pkg_name)
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package_version_key = f"{release}/{category}/{pkg_version}"
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if origin_url not in self.listed_origins:
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self.listed_origins[origin_url] = ListedOrigin(
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lister_id=self.lister_obj.id,
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visit_type=self.VISIT_TYPE,
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url=origin_url,
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last_update=last_update_date,
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extra_loader_arguments={"packages": {}},
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)
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self.package_versions[pkg_name] = set()
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origins_to_send.add(origin_url)
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optional_fields: Dict[str, Any] = {}
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if "MD5sum" in pkg_metadata:
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optional_fields["checksums"] = {"md5": pkg_metadata["MD5sum"]}
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if last_update_str:
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optional_fields["last_update_date"] = last_update_str
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self.listed_origins[origin_url].extra_loader_arguments["packages"][
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package_version_key
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] = {
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"release": release,
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"version": pkg_version,
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"category": category,
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"package": pkg_name,
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"tar_url": tar_url,
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}
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self.listed_origins[origin_url].extra_loader_arguments["packages"][
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package_version_key
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].update(optional_fields)
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last_update = self.listed_origins[origin_url].last_update
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if (
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last_update is not None
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and last_update_date is not None
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and last_update_date > last_update
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):
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self.listed_origins[origin_url].last_update = last_update_date
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self.package_versions[pkg_name].add(package_version_key)
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# package has been listed during a previous listing
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if self.incremental and pkg_name in self.state.package_versions:
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new_versions = (
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self.package_versions[pkg_name]
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- self.state.package_versions[pkg_name]
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)
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# no new versions, no need to send the origin to the scheduler
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if not new_versions:
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origins_to_send.remove(origin_url)
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self.origins_to_send.update(origins_to_send)
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def finalize(self) -> None:
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if self.incremental:
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self.state.package_versions = self.package_versions
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self.updated = len(self.listed_origins) > 0
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28
swh/lister/bioconductor/tasks.py
Normal file
28
swh/lister/bioconductor/tasks.py
Normal file
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@ -0,0 +1,28 @@
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# Copyright (C) 2022-2023 the Software Heritage developers
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# License: GNU General Public License version 3, or any later version
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# See top-level LICENSE file for more information
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from typing import Dict
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from celery import shared_task
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from .lister import BioconductorLister
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@shared_task(name=__name__ + ".BioconductorListerTask")
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def list_bioconductor_full(**lister_args) -> Dict[str, int]:
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"""Full listing of Bioconductor packages"""
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lister = BioconductorLister.from_configfile(**lister_args)
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return lister.run().dict()
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@shared_task(name=__name__ + ".BioconductorIncrementalListerTask")
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def list_bioconductor_incremental(**lister_args) -> Dict[str, int]:
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"""Incremental listing of Bioconductor packages"""
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lister = BioconductorLister.from_configfile(**lister_args, incremental=True)
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return lister.run().dict()
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@shared_task(name=__name__ + ".ping")
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def _ping() -> str:
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return "OK"
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0
swh/lister/bioconductor/tests/__init__.py
Normal file
0
swh/lister/bioconductor/tests/__init__.py
Normal file
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Package: affylmGUI
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Version: 1.4.0
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Depends: limma, tcltk, affy
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Suggests: tkrplot, affyPLM, R2HTML, xtable
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Package: affypdnn
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Version: 1.4.0
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Depends: R (>= 1.9.0), affy (>= 1.5), affydata, hgu95av2probe
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Package: affyPLM
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Version: 1.6.0
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Depends: R (>= 2.0.0), affy (>= 1.5.0), affydata, Biobase, methods,
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gcrma
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@ -0,0 +1,12 @@
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Package: ABarray
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Version: 1.8.0
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Depends: Biobase, multtest, tcltk
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Suggests: limma, LPE
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Package: AnnotationDbi
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Version: 1.2.2
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Depends: R (>= 2.7.0), methods, utils, Biobase (>= 1.17.0), DBI (>=
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0.2-4), RSQLite (>= 0.6-4)
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Imports: methods, utils, Biobase, DBI, RSQLite
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Suggests: hgu95av2.db, hgu95av2, GO.db, GO, human.db0, mouse.db0,
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rat.db0, fly.db0, yeast.db0, arabidopsis.db0
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{
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"annotation": {
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"Package": "annotation",
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"Version": "1.24.1",
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"Depends": [
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"R (>= 3.3.0)",
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"VariantAnnotation",
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"AnnotationHub",
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"Organism.dplyr",
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"TxDb.Hsapiens.UCSC.hg19.knownGene",
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"TxDb.Hsapiens.UCSC.hg38.knownGene",
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"TxDb.Mmusculus.UCSC.mm10.ensGene",
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"org.Hs.eg.db",
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"org.Mm.eg.db",
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"Homo.sapiens",
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"BSgenome.Hsapiens.UCSC.hg19",
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"biomaRt",
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"BSgenome",
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"TxDb.Athaliana.BioMart.plantsmart22"
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],
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"Suggests": [
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"knitr",
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"rmarkdown",
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"BiocStyle"
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],
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"License": "Artistic-2.0",
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"MD5sum": "4cb4db8807acb2e164985636091faa93",
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"NeedsCompilation": "no",
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"Title": "Genomic Annotation Resources",
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"Description": "Annotation resources make up a significant proportion of the Bioconductor project. And there are also a diverse set of online resources available which are accessed using specific packages. This walkthrough will describe the most popular of these resources and give some high level examples on how to use them.",
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"biocViews": [
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"AnnotationWorkflow",
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"Workflow"
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],
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"Author": "Marc RJ Carlson [aut], Herve Pages [aut], Sonali Arora [aut], Valerie Obenchain [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre]",
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"Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
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"URL": "http://bioconductor.org/help/workflows/annotation/Annotation_Resources/",
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"VignetteBuilder": "knitr",
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"git_url": "https://git.bioconductor.org/packages/annotation",
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"git_branch": "RELEASE_3_17",
|
||||
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<h1 id="bioconductor-releases">Bioconductor releases</h1>
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|
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<p>Each <em>Bioconductor</em> release is designed to work with a specific
|
||||
version of <em>R</em>. The following table summarizes the relationship, and
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||||
<td style="text-align: left"><a href="/news/bioc_3_17_release">3.17</a></td>
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<td style="text-align: left">April 26, 2023</td>
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<td style="text-align: right"><a href="/packages/3.17/">2230</a></td>
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<td style="text-align: left">4.3</td>
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</tr>
|
||||
<tr>
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||||
<td style="text-align: left"><a href="/news/bioc_3_16_release">3.16</a></td>
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<td style="text-align: left">November 2, 2022</td>
|
||||
<td style="text-align: right"><a href="/packages/3.16/">2183</a></td>
|
||||
<td style="text-align: left">4.2</td>
|
||||
</tr>
|
||||
<tr>
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||||
<td style="text-align: left"><a href="/news/bioc_3_15_release">3.15</a></td>
|
||||
<td style="text-align: left">April 27, 2022</td>
|
||||
<td style="text-align: right"><a href="/packages/3.15/">2140</a></td>
|
||||
<td style="text-align: left">4.2</td>
|
||||
</tr>
|
||||
<tr>
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||||
<td style="text-align: left"><a href="/news/bioc_3_14_release">3.14</a></td>
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<td style="text-align: left">October 27, 2021</td>
|
||||
<td style="text-align: right"><a href="/packages/3.14/">2083</a></td>
|
||||
<td style="text-align: left">4.1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_13_release">3.13</a></td>
|
||||
<td style="text-align: left">May 20, 2021</td>
|
||||
<td style="text-align: right"><a href="/packages/3.13/">2042</a></td>
|
||||
<td style="text-align: left">4.1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_12_release">3.12</a></td>
|
||||
<td style="text-align: left">October 28, 2020</td>
|
||||
<td style="text-align: right"><a href="/packages/3.12/">1974</a></td>
|
||||
<td style="text-align: left">4.0</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_11_release">3.11</a></td>
|
||||
<td style="text-align: left">April 28, 2020</td>
|
||||
<td style="text-align: right"><a href="/packages/3.11/">1903</a></td>
|
||||
<td style="text-align: left">4.0</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_10_release">3.10</a></td>
|
||||
<td style="text-align: left">October 30, 2019</td>
|
||||
<td style="text-align: right"><a href="/packages/3.10/">1823</a></td>
|
||||
<td style="text-align: left">3.6</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_9_release">3.9</a></td>
|
||||
<td style="text-align: left">May 3, 2019</td>
|
||||
<td style="text-align: right"><a href="/packages/3.9/">1741</a></td>
|
||||
<td style="text-align: left">3.6</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_8_release">3.8</a></td>
|
||||
<td style="text-align: left">October 31, 2018</td>
|
||||
<td style="text-align: right"><a href="/packages/3.8/">1649</a></td>
|
||||
<td style="text-align: left">3.5</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_7_release">3.7</a></td>
|
||||
<td style="text-align: left">May 1, 2018</td>
|
||||
<td style="text-align: right"><a href="/packages/3.7/">1560</a></td>
|
||||
<td style="text-align: left">3.5</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_6_release">3.6</a></td>
|
||||
<td style="text-align: left">October 31, 2017</td>
|
||||
<td style="text-align: right"><a href="/packages/3.6/">1473</a></td>
|
||||
<td style="text-align: left">3.4</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_5_release">3.5</a></td>
|
||||
<td style="text-align: left">April 25, 2017</td>
|
||||
<td style="text-align: right"><a href="/packages/3.5/">1383</a></td>
|
||||
<td style="text-align: left">3.4</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_4_release">3.4</a></td>
|
||||
<td style="text-align: left">October 18, 2016</td>
|
||||
<td style="text-align: right"><a href="/packages/3.4/">1296</a></td>
|
||||
<td style="text-align: left">3.3</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_3_release">3.3</a></td>
|
||||
<td style="text-align: left">May 4, 2016</td>
|
||||
<td style="text-align: right"><a href="/packages/3.3/">1211</a></td>
|
||||
<td style="text-align: left">3.3</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_2_release">3.2</a></td>
|
||||
<td style="text-align: left">October 14, 2015</td>
|
||||
<td style="text-align: right"><a href="/packages/3.2/">1104</a></td>
|
||||
<td style="text-align: left">3.2</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_1_release">3.1</a></td>
|
||||
<td style="text-align: left">April 17, 2015</td>
|
||||
<td style="text-align: right"><a href="/packages/3.1/">1024</a></td>
|
||||
<td style="text-align: left">3.2</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_3_0_release">3.0</a></td>
|
||||
<td style="text-align: left">October 14, 2014</td>
|
||||
<td style="text-align: right"><a href="/packages/3.0/">934</a></td>
|
||||
<td style="text-align: left">3.1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_14_release">2.14</a></td>
|
||||
<td style="text-align: left">April 14, 2014</td>
|
||||
<td style="text-align: right"><a href="/packages/2.14/">824</a></td>
|
||||
<td style="text-align: left">3.1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_13_release">2.13</a></td>
|
||||
<td style="text-align: left">October 15, 2013</td>
|
||||
<td style="text-align: right"><a href="/packages/2.13/">749</a></td>
|
||||
<td style="text-align: left">3.0</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_12_release">2.12</a></td>
|
||||
<td style="text-align: left">April 4, 2013</td>
|
||||
<td style="text-align: right"><a href="/packages/2.12/">671</a></td>
|
||||
<td style="text-align: left">3.0</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_11_release">2.11</a></td>
|
||||
<td style="text-align: left">October 3, 2012</td>
|
||||
<td style="text-align: right"><a href="/packages/2.11/">610</a></td>
|
||||
<td style="text-align: left">2.15</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_10_release">2.10</a></td>
|
||||
<td style="text-align: left">April 2, 2012</td>
|
||||
<td style="text-align: right"><a href="/packages/2.10/">554</a></td>
|
||||
<td style="text-align: left">2.15</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_9_release">2.9</a></td>
|
||||
<td style="text-align: left">November 1, 2011</td>
|
||||
<td style="text-align: right"><a href="/packages/2.9/">517</a></td>
|
||||
<td style="text-align: left">2.14</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_8_release">2.8</a></td>
|
||||
<td style="text-align: left">April 14, 2011</td>
|
||||
<td style="text-align: right"><a href="/packages/2.8/">466</a></td>
|
||||
<td style="text-align: left">2.13</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_7_release">2.7</a></td>
|
||||
<td style="text-align: left">October 18, 2010</td>
|
||||
<td style="text-align: right"><a href="/packages/2.7/">418</a></td>
|
||||
<td style="text-align: left">2.12</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_6_release">2.6</a></td>
|
||||
<td style="text-align: left">April 23, 2010</td>
|
||||
<td style="text-align: right"><a href="/packages/2.6/">389</a></td>
|
||||
<td style="text-align: left">2.11</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left"><a href="/news/bioc_2_5_release">2.5</a></td>
|
||||
<td style="text-align: left">October 28, 2009</td>
|
||||
<td style="text-align: right"><a href="/packages/2.5/">352</a></td>
|
||||
<td style="text-align: left">2.10</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">2.4</td>
|
||||
<td style="text-align: left">April 21, 2009</td>
|
||||
<td style="text-align: right"><a href="/packages/2.4/BiocViews.html">320</a></td>
|
||||
<td style="text-align: left">2.9</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">2.3</td>
|
||||
<td style="text-align: left">October 22, 2008</td>
|
||||
<td style="text-align: right"><a href="/packages/2.3/BiocViews.html">294</a></td>
|
||||
<td style="text-align: left">2.8</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">2.2</td>
|
||||
<td style="text-align: left">May 1, 2008</td>
|
||||
<td style="text-align: right"><a href="/packages/2.2/BiocViews.html">260</a></td>
|
||||
<td style="text-align: left">2.7</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">2.1</td>
|
||||
<td style="text-align: left">October 8, 2007</td>
|
||||
<td style="text-align: right"><a href="/packages/2.1/BiocViews.html">233</a></td>
|
||||
<td style="text-align: left">2.6</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">2.0</td>
|
||||
<td style="text-align: left">April 26, 2007</td>
|
||||
<td style="text-align: right"><a href="/packages/2.0/BiocViews.html">214</a></td>
|
||||
<td style="text-align: left">2.5</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.9</td>
|
||||
<td style="text-align: left">October 4, 2006</td>
|
||||
<td style="text-align: right"><a href="/packages/1.9/BiocViews.html">188</a></td>
|
||||
<td style="text-align: left">2.4</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.8</td>
|
||||
<td style="text-align: left">April 27, 2006</td>
|
||||
<td style="text-align: right"><a href="/packages/1.8/BiocViews.html">172</a></td>
|
||||
<td style="text-align: left">2.3</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.7</td>
|
||||
<td style="text-align: left">October 14, 2005</td>
|
||||
<td style="text-align: right"><a href="/packages/bioc/1.7/src/contrib/html/">141</a></td>
|
||||
<td style="text-align: left">2.2</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.6</td>
|
||||
<td style="text-align: left">May 18, 2005</td>
|
||||
<td style="text-align: right"><a href="/packages/bioc/1.6/src/contrib/html/">123</a></td>
|
||||
<td style="text-align: left">2.1</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.5</td>
|
||||
<td style="text-align: left">October 25, 2004</td>
|
||||
<td style="text-align: right"><a href="/packages/bioc/1.5/src/contrib/html/">100</a></td>
|
||||
<td style="text-align: left">2.0</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.4</td>
|
||||
<td style="text-align: left">May 17, 2004</td>
|
||||
<td style="text-align: right">81</td>
|
||||
<td style="text-align: left">1.9</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.3</td>
|
||||
<td style="text-align: left">October 30, 2003</td>
|
||||
<td style="text-align: right">49</td>
|
||||
<td style="text-align: left">1.8</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.2</td>
|
||||
<td style="text-align: left">May 29, 2003</td>
|
||||
<td style="text-align: right">30</td>
|
||||
<td style="text-align: left">1.7</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.1</td>
|
||||
<td style="text-align: left">November 19, 2002</td>
|
||||
<td style="text-align: right">20</td>
|
||||
<td style="text-align: left">1.6</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align: left">1.0</td>
|
||||
<td style="text-align: left">May 1, 2002</td>
|
||||
<td style="text-align: right">15</td>
|
||||
<td style="text-align: left">1.5</td>
|
||||
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<div id="SiteMastheadRightBackground" class="SiteMastheadRightBackground">
|
||||
|
||||
<a name="site-search"></a> <!-- accessibility anchor -->
|
||||
<form class="site_search" id="search_form" method="GET"
|
||||
action="/help/search/index.html">
|
||||
Search: <input id="q" name="q" />
|
||||
</form>
|
||||
|
||||
<ul class="masthead_nav noprint">
|
||||
<li class="masthead_nav_element" id="masthead_nav_element_1">
|
||||
<a href="/">Home</a>
|
||||
</li>
|
||||
<li class="masthead_nav_element" id="masthead_nav_element_2">
|
||||
<a href="/install/">Install</a>
|
||||
</li>
|
||||
<li class="masthead_nav_element" id="masthead_nav_element_3">
|
||||
<a href="/help/">Help</a>
|
||||
</li>
|
||||
<li class="masthead_nav_element" id="masthead_nav_element_4">
|
||||
<a href="/developers/">Developers</a>
|
||||
</li>
|
||||
<li class="masthead_nav_element" id="masthead_nav_element_5">
|
||||
<a href="/about/">About</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
</div>
|
||||
</body>
|
||||
</html>
|
||||
501
swh/lister/bioconductor/tests/test_lister.py
Normal file
501
swh/lister/bioconductor/tests/test_lister.py
Normal file
|
|
@ -0,0 +1,501 @@
|
|||
# Copyright (C) 2022-2023 The Software Heritage developers
|
||||
# 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
|
||||
|
||||
from pathlib import Path
|
||||
from unittest.mock import Mock
|
||||
|
||||
import pytest
|
||||
from requests_mock.mocker import Mocker as RequestsMocker
|
||||
|
||||
from swh.lister.bioconductor.lister import BioconductorLister
|
||||
from swh.scheduler.interface import SchedulerInterface
|
||||
|
||||
BIOCONDUCTOR_URL = "https://www.bioconductor.org"
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def packages_json1(datadir):
|
||||
text = Path(
|
||||
datadir, "https_bioconductor.org", "3.17-bioc-packages.json"
|
||||
).read_text()
|
||||
return text, {}
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def packages_json2(datadir):
|
||||
text = Path(
|
||||
datadir, "https_bioconductor.org", "3.17-workflows-packages.json"
|
||||
).read_text()
|
||||
return text, {}
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def packages_txt1(datadir):
|
||||
text = Path(datadir, "https_bioconductor.org", "1.17-PACKAGES").read_text()
|
||||
return text, {}
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
def packages_txt2(datadir):
|
||||
text = Path(datadir, "https_bioconductor.org", "2.2-PACKAGES").read_text()
|
||||
return text, {}
|
||||
|
||||
|
||||
@pytest.fixture(autouse=True)
|
||||
def mock_release_announcements(datadir, requests_mock):
|
||||
text = Path(
|
||||
datadir, "https_bioconductor.org", "about", "release-announcements"
|
||||
).read_text()
|
||||
requests_mock.get(
|
||||
"https://www.bioconductor.org/about/release-announcements",
|
||||
text=text,
|
||||
headers={},
|
||||
)
|
||||
|
||||
|
||||
def test_bioconductor_incremental_listing(
|
||||
swh_scheduler, requests_mock, mocker, packages_json1, packages_json2
|
||||
):
|
||||
kwargs = dict()
|
||||
lister = BioconductorLister(
|
||||
scheduler=swh_scheduler,
|
||||
releases=["3.17"],
|
||||
categories=["bioc", "workflows"],
|
||||
incremental=True,
|
||||
**kwargs,
|
||||
)
|
||||
assert lister.url == BIOCONDUCTOR_URL
|
||||
|
||||
lister.get_origins_from_page: Mock = mocker.spy(lister, "get_origins_from_page")
|
||||
|
||||
for category, packages_json in [
|
||||
("bioc", packages_json1),
|
||||
("workflows", packages_json2),
|
||||
]:
|
||||
text, headers = packages_json
|
||||
requests_mock.get(
|
||||
(
|
||||
"https://www.bioconductor.org/packages/"
|
||||
f"json/3.17/{category}/packages.json"
|
||||
),
|
||||
text=text,
|
||||
headers=headers,
|
||||
)
|
||||
|
||||
status = lister.run()
|
||||
scheduler_origins = swh_scheduler.get_listed_origins(lister.lister_obj.id).results
|
||||
lister_state = lister.get_state_from_scheduler()
|
||||
|
||||
assert status.pages == 3 # 2 categories for 3.17 + 1 None page
|
||||
# annotation pkg origin is in 2 categories
|
||||
# and we collect git origins as well
|
||||
assert status.origins == 6
|
||||
|
||||
assert lister.get_origins_from_page.call_count == 3
|
||||
|
||||
assert [o.url for o in scheduler_origins] == [
|
||||
"https://git.bioconductor.org/packages/annotation",
|
||||
"https://git.bioconductor.org/packages/arrays",
|
||||
"https://git.bioconductor.org/packages/variants",
|
||||
"https://www.bioconductor.org/packages/annotation",
|
||||
"https://www.bioconductor.org/packages/arrays",
|
||||
"https://www.bioconductor.org/packages/variants",
|
||||
]
|
||||
|
||||
assert [
|
||||
o.extra_loader_arguments["packages"]
|
||||
for o in scheduler_origins
|
||||
if "packages" in o.extra_loader_arguments
|
||||
] == [
|
||||
{
|
||||
"3.17/bioc/1.24.1": {
|
||||
"package": "annotation",
|
||||
"release": "3.17",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/3.17/"
|
||||
"bioc/src/contrib/annotation_1.24.1.tar.gz"
|
||||
),
|
||||
"version": "1.24.1",
|
||||
"category": "bioc",
|
||||
"checksums": {"md5": "4cb4db8807acb2e164985636091faa93"},
|
||||
"last_update_date": "2023-06-30",
|
||||
},
|
||||
"3.17/workflows/1.24.1": {
|
||||
"package": "annotation",
|
||||
"release": "3.17",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/3.17/"
|
||||
"workflows/src/contrib/annotation_1.24.1.tar.gz"
|
||||
),
|
||||
"version": "1.24.1",
|
||||
"category": "workflows",
|
||||
"checksums": {"md5": "4cb4db8807acb2e164985636091faa93"},
|
||||
"last_update_date": "2023-06-30",
|
||||
},
|
||||
},
|
||||
{
|
||||
"3.17/workflows/1.26.0": {
|
||||
"package": "arrays",
|
||||
"release": "3.17",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/3.17/"
|
||||
"workflows/src/contrib/arrays_1.26.0.tar.gz"
|
||||
),
|
||||
"version": "1.26.0",
|
||||
"category": "workflows",
|
||||
"checksums": {"md5": "009ef917ebc047246b8c62c48e02a237"},
|
||||
"last_update_date": "2023-04-28",
|
||||
}
|
||||
},
|
||||
{
|
||||
"3.17/bioc/1.24.0": {
|
||||
"package": "variants",
|
||||
"release": "3.17",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/3.17/"
|
||||
"bioc/src/contrib/variants_1.24.0.tar.gz"
|
||||
),
|
||||
"version": "1.24.0",
|
||||
"category": "bioc",
|
||||
"checksums": {"md5": "38f2c00b73e1a695f5ef4c9b4a728923"},
|
||||
"last_update_date": "2023-04-28",
|
||||
}
|
||||
},
|
||||
]
|
||||
|
||||
assert lister_state.package_versions == {
|
||||
"annotation": {"3.17/workflows/1.24.1", "3.17/bioc/1.24.1"},
|
||||
"arrays": {"3.17/workflows/1.26.0"},
|
||||
"variants": {"3.17/bioc/1.24.0"},
|
||||
}
|
||||
|
||||
|
||||
@pytest.mark.parametrize("status_code", [400, 500, 404])
|
||||
def test_bioconductor_lister_http_error(
|
||||
swh_scheduler: SchedulerInterface,
|
||||
requests_mock: RequestsMocker,
|
||||
packages_json1,
|
||||
status_code: int,
|
||||
):
|
||||
"""
|
||||
Simulates handling of HTTP Errors while fetching of packages for bioconductor releases.
|
||||
"""
|
||||
releases = ["3.8"]
|
||||
categories = ["workflows", "bioc"]
|
||||
|
||||
requests_mock.get(
|
||||
"https://www.bioconductor.org/packages/json/3.8/workflows/packages.json",
|
||||
status_code=status_code,
|
||||
text="Something went wrong",
|
||||
)
|
||||
|
||||
text, headers = packages_json1
|
||||
requests_mock.get(
|
||||
"https://www.bioconductor.org/packages/json/3.8/bioc/packages.json",
|
||||
text=text,
|
||||
headers=headers,
|
||||
)
|
||||
|
||||
lister = BioconductorLister(
|
||||
scheduler=swh_scheduler,
|
||||
releases=releases,
|
||||
categories=categories,
|
||||
incremental=True,
|
||||
)
|
||||
|
||||
# On facing HTTP errors, it should continue
|
||||
# to crawl other releases/categories
|
||||
stats = lister.run()
|
||||
# 1 None page + 3.8 bioc page
|
||||
assert stats.pages == 2
|
||||
# Both packages have git and bioconductor urls.
|
||||
assert stats.origins == 4
|
||||
scheduler_origins = swh_scheduler.get_listed_origins(lister.lister_obj.id).results
|
||||
assert [o.url for o in scheduler_origins] == [
|
||||
"https://git.bioconductor.org/packages/annotation",
|
||||
"https://git.bioconductor.org/packages/variants",
|
||||
"https://www.bioconductor.org/packages/annotation",
|
||||
"https://www.bioconductor.org/packages/variants",
|
||||
]
|
||||
assert [
|
||||
o.extra_loader_arguments["packages"]
|
||||
for o in scheduler_origins
|
||||
if "packages" in o.extra_loader_arguments
|
||||
] == [
|
||||
{
|
||||
"3.8/bioc/1.24.1": {
|
||||
"package": "annotation",
|
||||
"release": "3.8",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"3.8/bioc/src/contrib/annotation_1.24.1.tar.gz"
|
||||
),
|
||||
"version": "1.24.1",
|
||||
"category": "bioc",
|
||||
"checksums": {"md5": "4cb4db8807acb2e164985636091faa93"},
|
||||
"last_update_date": "2023-06-30",
|
||||
}
|
||||
},
|
||||
{
|
||||
"3.8/bioc/1.24.0": {
|
||||
"package": "variants",
|
||||
"release": "3.8",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"3.8/bioc/src/contrib/variants_1.24.0.tar.gz"
|
||||
),
|
||||
"version": "1.24.0",
|
||||
"category": "bioc",
|
||||
"checksums": {"md5": "38f2c00b73e1a695f5ef4c9b4a728923"},
|
||||
"last_update_date": "2023-04-28",
|
||||
}
|
||||
},
|
||||
]
|
||||
|
||||
lister_state = lister.get_state_from_scheduler()
|
||||
assert lister_state.package_versions == {
|
||||
"annotation": {"3.8/bioc/1.24.1"},
|
||||
"variants": {"3.8/bioc/1.24.0"},
|
||||
}
|
||||
|
||||
|
||||
def test_bioconductor_fetch_versions(swh_scheduler: SchedulerInterface):
|
||||
lister = BioconductorLister(scheduler=swh_scheduler)
|
||||
assert lister.releases == [
|
||||
"1.5",
|
||||
"1.6",
|
||||
"1.7",
|
||||
"1.8",
|
||||
"1.9",
|
||||
"2.0",
|
||||
"2.1",
|
||||
"2.2",
|
||||
"2.3",
|
||||
"2.4",
|
||||
"2.5",
|
||||
"2.6",
|
||||
"2.7",
|
||||
"2.8",
|
||||
"2.9",
|
||||
"2.10",
|
||||
"2.11",
|
||||
"2.12",
|
||||
"2.13",
|
||||
"2.14",
|
||||
"3.0",
|
||||
"3.1",
|
||||
"3.2",
|
||||
"3.3",
|
||||
"3.4",
|
||||
"3.5",
|
||||
"3.6",
|
||||
"3.7",
|
||||
"3.8",
|
||||
"3.9",
|
||||
"3.10",
|
||||
"3.11",
|
||||
"3.12",
|
||||
"3.13",
|
||||
"3.14",
|
||||
"3.15",
|
||||
"3.16",
|
||||
"3.17",
|
||||
]
|
||||
|
||||
|
||||
def test_bioconductor_lister_parse_packages_txt(
|
||||
swh_scheduler: SchedulerInterface, packages_json1, packages_txt1
|
||||
):
|
||||
lister = BioconductorLister(
|
||||
scheduler=swh_scheduler, releases=["3.8"], categories=["bioc"]
|
||||
)
|
||||
|
||||
text, _ = packages_json1
|
||||
res = lister.parse_packages(text)
|
||||
assert {
|
||||
pkg_name: pkg_metadata["Version"] for pkg_name, pkg_metadata in res.items()
|
||||
} == {"annotation": "1.24.1", "maEndToEnd": "2.20.0", "variants": "1.24.0"}
|
||||
|
||||
text, _ = packages_txt1
|
||||
|
||||
res = lister.parse_packages(text)
|
||||
assert res == {
|
||||
"affylmGUI": {
|
||||
"Package": "affylmGUI",
|
||||
"Version": "1.4.0",
|
||||
"Depends": "limma, tcltk, affy",
|
||||
"Suggests": "tkrplot, affyPLM, R2HTML, xtable",
|
||||
},
|
||||
"affypdnn": {
|
||||
"Package": "affypdnn",
|
||||
"Version": "1.4.0",
|
||||
"Depends": "R (>= 1.9.0), affy (>= 1.5), affydata, hgu95av2probe",
|
||||
},
|
||||
"affyPLM": {
|
||||
"Package": "affyPLM",
|
||||
"Version": "1.6.0",
|
||||
"Depends": (
|
||||
"R (>= 2.0.0), affy (>= 1.5.0), affydata, "
|
||||
"Biobase, methods,\n gcrma"
|
||||
),
|
||||
},
|
||||
}
|
||||
|
||||
|
||||
def test_bioconductor_lister_old_releases(
|
||||
swh_scheduler, mocker, requests_mock, packages_txt1, packages_txt2
|
||||
):
|
||||
releases = ["1.7"]
|
||||
categories = ["workflows", "bioc"]
|
||||
|
||||
text, headers = packages_txt1
|
||||
requests_mock.get(
|
||||
("https://www.bioconductor.org/packages/" "bioc/1.7/src/contrib/PACKAGES"),
|
||||
text=text,
|
||||
headers=headers,
|
||||
)
|
||||
|
||||
text, headers = packages_txt2
|
||||
requests_mock.get(
|
||||
"/packages/2.2/bioc/src/contrib/PACKAGES",
|
||||
text=text,
|
||||
headers=headers,
|
||||
)
|
||||
|
||||
requests_mock.get(
|
||||
"/packages/2.2/data/experiment/src/contrib/PACKAGES", status_code=404
|
||||
)
|
||||
requests_mock.get(
|
||||
"/packages/2.2/data/annotation/src/contrib/PACKAGES", status_code=404
|
||||
)
|
||||
|
||||
lister = BioconductorLister(
|
||||
scheduler=swh_scheduler,
|
||||
releases=releases,
|
||||
categories=categories,
|
||||
incremental=True,
|
||||
)
|
||||
|
||||
lister.get_origins_from_page: Mock = mocker.spy(lister, "get_origins_from_page")
|
||||
|
||||
stats = lister.run()
|
||||
scheduler_origins = swh_scheduler.get_listed_origins(lister.lister_obj.id).results
|
||||
lister_state = lister.get_state_from_scheduler()
|
||||
|
||||
assert stats.pages == 2 # 1.7 'bioc' + None page
|
||||
assert stats.origins == 3
|
||||
|
||||
assert lister.get_origins_from_page.call_count == 2
|
||||
|
||||
expected_origins = [
|
||||
"https://www.bioconductor.org/packages/affyPLM",
|
||||
"https://www.bioconductor.org/packages/affylmGUI",
|
||||
"https://www.bioconductor.org/packages/affypdnn",
|
||||
]
|
||||
|
||||
assert [o.url for o in scheduler_origins] == expected_origins
|
||||
|
||||
expected_loader_packages = [
|
||||
{
|
||||
"1.7/bioc/1.6.0": {
|
||||
"package": "affyPLM",
|
||||
"release": "1.7",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"bioc/1.7/src/contrib/Source/affyPLM_1.6.0.tar.gz"
|
||||
),
|
||||
"version": "1.6.0",
|
||||
"category": "bioc",
|
||||
}
|
||||
},
|
||||
{
|
||||
"1.7/bioc/1.4.0": {
|
||||
"package": "affylmGUI",
|
||||
"release": "1.7",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"bioc/1.7/src/contrib/Source/affylmGUI_1.4.0.tar.gz"
|
||||
),
|
||||
"version": "1.4.0",
|
||||
"category": "bioc",
|
||||
}
|
||||
},
|
||||
{
|
||||
"1.7/bioc/1.4.0": {
|
||||
"package": "affypdnn",
|
||||
"release": "1.7",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"bioc/1.7/src/contrib/Source/affypdnn_1.4.0.tar.gz"
|
||||
),
|
||||
"version": "1.4.0",
|
||||
"category": "bioc",
|
||||
}
|
||||
},
|
||||
]
|
||||
|
||||
assert [
|
||||
o.extra_loader_arguments["packages"] for o in scheduler_origins
|
||||
] == expected_loader_packages
|
||||
|
||||
assert lister_state.package_versions == {
|
||||
"affyPLM": {"1.7/bioc/1.6.0"},
|
||||
"affylmGUI": {"1.7/bioc/1.4.0"},
|
||||
"affypdnn": {"1.7/bioc/1.4.0"},
|
||||
}
|
||||
|
||||
releases.append("2.2")
|
||||
|
||||
lister = BioconductorLister(
|
||||
scheduler=swh_scheduler, releases=releases, categories=categories
|
||||
)
|
||||
|
||||
stats = lister.run()
|
||||
scheduler_origins = swh_scheduler.get_listed_origins(lister.lister_obj.id).results
|
||||
lister_state = lister.get_state_from_scheduler()
|
||||
|
||||
expected_origins = [
|
||||
"https://www.bioconductor.org/packages/ABarray",
|
||||
"https://www.bioconductor.org/packages/AnnotationDbi",
|
||||
] + expected_origins
|
||||
|
||||
assert [o.url for o in scheduler_origins] == expected_origins
|
||||
|
||||
expected_loader_packages = [
|
||||
{
|
||||
"2.2/bioc/1.8.0": {
|
||||
"package": "ABarray",
|
||||
"release": "2.2",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"2.2/bioc/src/contrib/ABarray_1.8.0.tar.gz"
|
||||
),
|
||||
"version": "1.8.0",
|
||||
"category": "bioc",
|
||||
}
|
||||
},
|
||||
{
|
||||
"2.2/bioc/1.2.2": {
|
||||
"package": "AnnotationDbi",
|
||||
"release": "2.2",
|
||||
"tar_url": (
|
||||
"https://www.bioconductor.org/packages/"
|
||||
"2.2/bioc/src/contrib/AnnotationDbi_1.2.2.tar.gz"
|
||||
),
|
||||
"version": "1.2.2",
|
||||
"category": "bioc",
|
||||
}
|
||||
},
|
||||
] + expected_loader_packages
|
||||
|
||||
assert [
|
||||
o.extra_loader_arguments["packages"] for o in scheduler_origins
|
||||
] == expected_loader_packages
|
||||
|
||||
assert lister_state.package_versions == {
|
||||
"affyPLM": {"1.7/bioc/1.6.0"},
|
||||
"affypdnn": {"1.7/bioc/1.4.0"},
|
||||
"affylmGUI": {"1.7/bioc/1.4.0"},
|
||||
}
|
||||
81
swh/lister/bioconductor/tests/test_tasks.py
Normal file
81
swh/lister/bioconductor/tests/test_tasks.py
Normal file
|
|
@ -0,0 +1,81 @@
|
|||
# Copyright (C) 2022 The Software Heritage developers
|
||||
# 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
|
||||
|
||||
from unittest.mock import patch
|
||||
|
||||
from swh.lister.pattern import ListerStats
|
||||
|
||||
|
||||
def test_ping(swh_scheduler_celery_app, swh_scheduler_celery_worker):
|
||||
res = swh_scheduler_celery_app.send_task("swh.lister.bioconductor.tasks.ping")
|
||||
assert res
|
||||
res.wait()
|
||||
assert res.successful()
|
||||
assert res.result == "OK"
|
||||
|
||||
|
||||
@patch("swh.lister.bioconductor.tasks.BioconductorLister")
|
||||
def test_full_listing(lister, swh_scheduler_celery_app, swh_scheduler_celery_worker):
|
||||
lister.from_configfile.return_value = lister
|
||||
lister.run.return_value = ListerStats(pages=10, origins=500)
|
||||
|
||||
kwargs = dict(url="https://www.bioconductor.org")
|
||||
res = swh_scheduler_celery_app.send_task(
|
||||
"swh.lister.bioconductor.tasks.BioconductorListerTask",
|
||||
kwargs=kwargs,
|
||||
)
|
||||
assert res
|
||||
res.wait()
|
||||
assert res.successful()
|
||||
|
||||
lister.from_configfile.assert_called_once_with(**kwargs)
|
||||
lister.run.assert_called_once_with()
|
||||
|
||||
|
||||
@patch("swh.lister.bioconductor.tasks.BioconductorLister")
|
||||
def test_incremental_listing(
|
||||
lister, swh_scheduler_celery_app, swh_scheduler_celery_worker
|
||||
):
|
||||
lister.from_configfile.return_value = lister
|
||||
lister.run.return_value = ListerStats(pages=10, origins=500)
|
||||
|
||||
kwargs = dict(url="https://www.bioconductor.org")
|
||||
res = swh_scheduler_celery_app.send_task(
|
||||
"swh.lister.bioconductor.tasks.BioconductorIncrementalListerTask",
|
||||
kwargs=kwargs,
|
||||
)
|
||||
assert res
|
||||
res.wait()
|
||||
assert res.successful()
|
||||
|
||||
kwargs["incremental"] = True
|
||||
|
||||
lister.from_configfile.assert_called_once_with(**kwargs)
|
||||
lister.run.assert_called_once_with()
|
||||
|
||||
|
||||
@patch("swh.lister.bioconductor.tasks.BioconductorLister")
|
||||
def test_full_listing_with_params(
|
||||
lister, swh_scheduler_celery_app, swh_scheduler_celery_worker
|
||||
):
|
||||
lister.from_configfile.return_value = lister
|
||||
lister.run.return_value = ListerStats(pages=10, origins=500)
|
||||
|
||||
kwargs = dict(
|
||||
url="https://www.bioconductor.org",
|
||||
instance="bioconductor-test",
|
||||
releases=["3.7"],
|
||||
categories=["bioc", "workflows"],
|
||||
)
|
||||
res = swh_scheduler_celery_app.send_task(
|
||||
"swh.lister.bioconductor.tasks.BioconductorListerTask",
|
||||
kwargs=kwargs,
|
||||
)
|
||||
assert res
|
||||
res.wait()
|
||||
assert res.successful()
|
||||
|
||||
lister.from_configfile.assert_called_once_with(**kwargs)
|
||||
lister.run.assert_called_once_with()
|
||||
Loading…
Add table
Add a link
Reference in a new issue