Create pkg_archiver.py

pkg_archiver.py

@@ -0,0 +1,113 @@
+#!/usr/bin/python
+
+'''
+Update the PKGBUILD and lilac.yaml of archived pkgs in `pkgname.txt`
+'''
+import os
+import fileinput
+import re
+import yaml
+import argparse
+
+
+def archive_pkg_by_file_list(file, bioarch_path="BioArchLinux", biconductor_version=3.15, step=1):
+    current_dir = os.getcwd()
+    # where the name are _pkgname (May have upper letters) or pkgname (r-xxx)
+    case = "_pkgname"
+    with open(file, "r") as f:
+        for pkgname in f:
+            pkgname = pkgname.strip()
+            if pkgname.startswith("r-"):
+                case = "pkgname"
+                break
+    with open(file, "r") as f:
+        for pkgname in f:
+            pkgname = pkgname.strip()
+            if case == '_pkgname':
+                pkgname = 'r-'+pkgname.lower()
+
+            os.chdir(f"{bioarch_path}/{pkgname}")
+            bump_pkgrel(step)
+            archive_pkg_yaml(biconductor_version)
+            archive_pkg_pkgbuild(biconductor_version)
+            os.chdir(current_dir)
+
+
+def bump_pkgrel(step=1):
+    with fileinput.input(r"PKGBUILD", inplace=True) as f:
+        for line in f:
+            if line.startswith("pkgrel="):
+                new_pkgrel = int(line.split("=")[1])+step
+                line = re.sub(
+                    r'pkgrel=\d+', f'pkgrel={new_pkgrel}', line)
+                break
+            print(line.rstrip())
+
+
+def archive_pkg_yaml(bioconductor_version=3.15, yaml_file="lilac.yaml"):
+  '''
+  archive pkg in CRAN and bioconductor (the latest bioconductor_version that contains the pkg  needed)
+  '''
+    with open(yaml_file, "r") as f:
+        docs = yaml.load(f, Loader=yaml.FullLoader)
+        print(docs)
+    url_idx = -1
+    for i in range(len(docs['update_on'])):
+        if "url" in docs['update_on'][i].keys():
+            url = docs['update_on'][i]['url']
+            url_idx = i
+            break
+
+    pkg = url.rstrip('/').split('/')[-1]
+    # CRAN ARCHIVE
+    if 'cran.r-project.org' in url:
+        archive_url = f"https://cran.r-project.org/src/contrib/Archive/{pkg}"
+    # Bioconductor ARCHIVE
+    elif 'bioconductor.org' in url:
+        archive_url = f"https://bioconductor.org/packages/{bioconductor_version}/{pkg}"
+
+    docs['update_on'][url_idx]['url'] = archive_url
+    with open(yaml_file, 'w') as f:
+        yaml.dump(docs, f)
+
+
+def archive_pkg_pkgbuild(bioconductor_version=3.15, _pkgname="_pkgname"):
+    '''
+    Under some cases, _pkgname maybe _cranname
+    '''
+    with open("PKGBUILD", "r") as f:
+        lines = f.readlines()
+
+    flag = False
+    for i in range(len(lines)):
+        if lines[i].startswith("source="):
+            flag = True
+        if flag:
+            if 'cran.r-project.org' in lines[i] and "src/contrib/Archive" not in lines[i]:
+                # https://cran.r-project.org/src/contrib/${_pkgname}_${pkgver}.tar.gz
+                # to
+                # https://cran.r-project.org/src/contrib/Archive/${_pkgname}/${_pkgname}_${pkgver}.tar.gz
+                lines[i] = lines[i].replace(
+                    "src/contrib", r"src/contrib/Archive/${" + _pkgname + '}')
+            elif '//bioconductor.org' in lines[i]:
+                # https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz
+                # to
+                # https://bioconductor.org/packages/3.14/bioc/src/contrib/ABAEnrichment_1.24.0.tar.gz
+                lines[i] = lines[i].replace(
+                    "packages/release/bioc", f"packages/{bioconductor_version}/bioc")
+    with open("PKGBUILD", "w") as f:
+        f.writelines(lines)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '--file', help='The file that contains the pkgname to be archived, one pkgname per line')
+    parser.add_argument('--bioarch_path', help='The path of BioArchLinux repo')
+    parser.add_argument(
+        '--bico_ver', help='The Bioconductor version to be used in archived url, default 3.15')
+    args = parser.parse_args()
+    if args.file:
+        archive_pkg_by_file_list(args.file, args.bioarch_path, args.bico_ver)
+    else:
+        parser.print_help()