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Look for sha256sum checksums during shed_lint #539

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Aug 17, 2016
Merged

Look for sha256sum checksums during shed_lint #539

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bc60e12
Look for sha256sum checksums during shed_lint
peterjc Aug 17, 2016
ea4ba2c
Fill in missing SHA256 checksums in good test case
peterjc Aug 17, 2016
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32 changes: 32 additions & 0 deletions planemo/shed_lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,11 @@ def lint_repository(ctx, realized_repository, **kwds):
lint_tool_dependencies_xsd,
path,
)
lint_ctx.lint(
"lint_tool_dependencies_sha256sum",
lint_tool_dependencies_sha256sum,
path,
)
lint_ctx.lint(
"lint_tool_dependencies_actions",
lint_tool_dependencies_actions,
Expand Down Expand Up @@ -190,6 +195,33 @@ def lint_tool_dependencies_urls(path, lint_ctx):
lint_urls(root, lint_ctx)


def lint_tool_dependencies_sha256sum(path, lint_ctx):
tool_dependencies = os.path.join(path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
lint_ctx.info("No tool_dependencies.xml, skipping.")
return

root = ET.parse(tool_dependencies).getroot()

count = 0
for action in root.findall(".//action"):
assert action.tag == "action"
if action.attrib.get('type', '') not in ['download_by_url', 'download_file']:
continue
url = action.text.strip()
checksum = action.attrib.get('sha256sum', '')
if not checksum:
lint_ctx.warn("Missing checksum for %s" % url)
elif len(checksum) != 64 or not set("0123456789abcdef").issuperset(checksum.lower()):
lint_ctx.error("Invalid checksum %r for %s" % (checksum, url))
else:
# TODO - See planned --verify option to check it matches
# lint_ctx.info("SHA256 checkum listed for %s" % url)
count += 1
if count:
lint_ctx.info("Found %i download action(s) with SHA256 checksums" % count)


def lint_tool_dependencies_xsd(path, lint_ctx):
tool_dependencies = os.path.join(path, "tool_dependencies.xml")
if not os.path.exists(tool_dependencies):
Expand Down
10 changes: 5 additions & 5 deletions tests/data/repos/package_1/tool_dependencies.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,35 +4,35 @@
<install version="1.0">
<actions_group>
<actions os="linux" architecture="i386">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="7090bd62142df0ed3a2b4000292fc0edc917e773d0269c2f3f5b0d36b7888c22">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions os="linux" architecture="x86_64">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="1d050e70fb6570117f282e3ab827f1f37fd453a0558c55ea565092ec3b2b9db2">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions os="darwin" architecture="i386">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="4b89dd5542809098269939f6eb913abcf0011c746e02085221d171e3942b6e1f">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions os="darwin" architecture="x86_64">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="4e74d7ce4eb5d26166ff6f9bb5939d9a0110d9bdb0baf9ff08cc9522a49e09cb">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions>
<action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
<action type="download_by_url" sha256sum="ae37c49f2414d1fabe597f68f2351f6cce4b6c0a1a512a5d739bbf759f80a726">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
<action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
<action type="shell_command">make</action>
<action type="move_file">
Expand Down
10 changes: 5 additions & 5 deletions tests/tool_dependencies_good_1.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,35 +4,35 @@
<install version="1.0">
<actions_group>
<actions os="linux" architecture="i386">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="7090bd62142df0ed3a2b4000292fc0edc917e773d0269c2f3f5b0d36b7888c22">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions os="linux" architecture="x86_64">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="1d050e70fb6570117f282e3ab827f1f37fd453a0558c55ea565092ec3b2b9db2">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions os="darwin" architecture="i386">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="4b89dd5542809098269939f6eb913abcf0011c746e02085221d171e3942b6e1f">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions os="darwin" architecture="x86_64">
<action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
<action type="download_by_url" target_filename="samtools-0.1.16.tgz" sha256sum="4e74d7ce4eb5d26166ff6f9bb5939d9a0110d9bdb0baf9ff08cc9522a49e09cb">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions>
<action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
<action type="download_by_url" sha256sum="ae37c49f2414d1fabe597f68f2351f6cce4b6c0a1a512a5d739bbf759f80a726">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
<action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
<action type="shell_command">make</action>
<action type="move_file">
Expand Down