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support precise archived bioc version

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This commit is contained in:
sukanka 2022-11-26 19:34:21 +08:00
parent 5b9e7fabd2
commit c05084518c
1 changed files with 33 additions and 5 deletions
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38
updater/depends_updater.py
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@ -17,6 +17,7 @@ import sqlite3
from dbmanager import get_bioc_versions, EXCLUDED_PKGS
from pkg_archiver import archive_pkg_yaml, archive_pkg_pkgbuild, unarchive_cran
import re
import requests
class PkgInfo:
@ -106,14 +107,15 @@ class PkgInfo:
else:
return None
def is_archived(self) -> bool:
def is_archived(self, release_ver) -> bool:
'''
Check if the package is archived in CRAN or BIOC
release_ver: current release of BIOC, should be a Version e.g., "3.16"
'''
if not self.desc: # not in database, archived in CRAN
return True
# not in the latest BIOC version, archived in BIOC
elif self.bioc_ver and self.bioc_ver != max(self.bioc_versions):
elif self.bioc_ver and self.bioc_ver < release_ver:
return True
return False
@ -273,6 +275,21 @@ class PkgInfo:
change_arch(self.desc)
return self.added_depends
def get_web_bioc_version(self) -> version.Version:
'''
get bioc version from BIOC website, usually newer than the one in BIOC metadata
'''
if self.bioc_ver is None or self.bioc_ver == max(self.bioc_versions):
return self.bioc_ver
for ver in self.bioc_versions:
if ver > self.bioc_ver:
url = f"{self.bioc_meta_mirror}/packages/{ver}/{self.pkgname}"
r = requests.get(url)
if r.status_code == 200:
if not 'packages-removed-with-bioconductor' in r.text:
return ver
return self.bioc_ver
def update_yaml(self, yaml_file='lilac.yaml'):
'''
update the `repo_depends` part of pkg, repo_depends will be sorted (systemlibs first, then r-pkgs)
@ -294,12 +311,18 @@ class PkgInfo:
def create_temporary_copy(path):
'''
create temporary copy of path, remember to manually delete it.
'''
tmp = tempfile.NamedTemporaryFile(delete=False)
shutil.copy2(path, tmp.name)
return tmp.name
def change_arch(desc: str):
'''
change `arch` to `any` if NeedsCompilation is No, and change it to x86_64 if it is Yes
'''
# change any to x86_64 in PKGBUILD or vice versa
need_compile = re.search("NeedsCompilation: (.*)", desc)
if not need_compile:
@ -338,6 +361,7 @@ def update_depends_by_file(file, bioarch_path="BioArchLinux", db="sqlite.db",
output_file: file to write the added depends to.
'''
bioc_versions = get_bioc_versions(bioc_meta_mirror)
MAX_BIOC_VERSION = max(bioc_versions)
current_dir = os.getcwd()
# where the name are _pkgname (May have upper letters) or pkgname (r-xxx)
conn = sqlite3.connect(db)
@ -357,9 +381,13 @@ def update_depends_by_file(file, bioarch_path="BioArchLinux", db="sqlite.db",
pkginfo.build_body(cursor)
pkginfo.update_pkgbuild()
pkginfo.update_yaml()
if auto_archive and pkginfo.is_archived():
archive_pkg_yaml(bioconductor_version=pkginfo.bioc_ver)
archive_pkg_pkgbuild(bioconductor_version=pkginfo.bioc_ver)
if auto_archive and pkginfo.is_archived(MAX_BIOC_VERSION):
temp_bioc_ver = pkginfo.bioc_ver
if pkginfo.bioc_ver != None and pkginfo.bioc_ver < MAX_BIOC_VERSION:
temp_bioc_ver = pkginfo.get_web_bioc_version()
if temp_bioc_ver == None or temp_bioc_ver < MAX_BIOC_VERSION:
archive_pkg_yaml(bioconductor_version=temp_bioc_ver)
archive_pkg_pkgbuild(bioconductor_version=temp_bioc_ver)
# if PKGBUILD changed, bump pkgrel
if auto_unarchive and pkginfo.desc:
unarchive_cran()