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Hack for updating Galaxy tool_dependencies.xml files with depot.galaxyproject.org URLs
# Copyright 2016 Peter Cock, James Hutton Institute.
# All Rights Reserved.
# Released as open source under the MIT license.
"""Update URLs in Galaxy tool_dependencies.xml files
Assumes have a copy of the urls.tsv file from
https://github.com/galaxyproject/cargo-port/blob/master/urls.tsv
This file defines the https://depot.galaxyproject.org/software/
URL naming used for caching Galaxy dependencies.
The script will check or insert the SHA256 checksum, and will
preserve the download filename (since the depot renames things).
Sample usage:
$ python update_tool_dependencies.py ../galaxy_blast/packages/*/tool_dependencies.xml
WARNING: Edits files in place!
"""
import os
import sys
def load_urls(filename):
mapping = dict()
for line in open(filename):
if line.startswith("#"):
continue
parts = line.rstrip("\n").split("\t")
id, version, platform, arch, old_url, ext, sha256sum, _ = line.rstrip("\n").split("\t", 7)
if ext:
assert ext.startswith("."), line
new_url = "https://depot.galaxyproject.org/software/%s/%s_%s_%s_%s%s" % (id, id, version, platform, arch, ext)
mapping[old_url] = new_url, sha256sum
return mapping
def update_tool_dependency(filename, mapping):
print("Updating %s" % filename)
lines = list(open(filename))
with open(filename, "w") as handle:
for line in lines:
if "<action " in line and "download" in line:
indent = " " * line.index("<action ")
assert not indent.strip(), line
for old, (new, checksum) in mapping.items():
if old in line:
base = os.path.basename(old)
# TODO - escape URLs, e.g. ampersand
assert '>%s</action>' % old in line
if 'target_filename=' not in line and not new.endswith("/" + base):
# Preserve the original filename
line = line.replace('>%s</action>' % old,
' target_filename="%s">%s</action>' % (base, old))
if 'sha256sum=' in line:
# Check checksum matches
assert 'sha256sum="%s"' % checksum in line
else:
# Record the checksum
line = line.replace('>%s</action>' % old,
' sha256sum="%s">%s</action>' % (checksum, old))
# Finally, replace the URL
line = line.replace('>%s</action>' % old,
'>%s</action>' % new)
print("Updated %s --> %s" % (old, new))
handle.write("%s<!-- Original URL %s -->\n" % (indent, old))
handle.write(line)
mapping = load_urls("urls.tsv")
for filename in sys.argv[1:]:
update_tool_dependency(filename, mapping)
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