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hmftools-build.py
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hmftools-build.py
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"""
This script does the following:
- Whenever a user pushes a git tag in the format '<tool>-<version>' this script will parse that tag.
The 'v' character prefixing the version will be stripped.
- The script will build the tool with the given version and deploy it using Maven with version equal to the 'version'
part of the tag.
- The script will build all direct hmf-tools dependencies of the given tool (i.e. 'hmf-common') and deploy those with
the version set equal to '<tool>-<version>'.
By building and deploying each tool together with their dependencies, we ensure each deployment is isolated.
Example:
- 'git tag neo-v1.0.0' will start building the 'neo' tool and deploy it with version '1.0.0'.
- 'neo' has a dependency on 'hmf-common', so it will deploy 'hmf-common' with version 'neo-1.0.0'.
- The pom of the deployed 'neo' will be updated such that the 'hmf-common' dependency will point towards the correct
version.
"""
import re
import subprocess
import requests
import os.path
import sys
import time
import jwt
from xml.etree import ElementTree
from argparse import ArgumentParser
SEMVER_REGEX = re.compile(
r'^([a-z-]+)-v([0-9]+\.[0-9]+(?:\.[0-9]+)?(?:-(?:alpha|beta)\.[0-9]+)?(?:_(?:[0-9a-zA-Z-]+(\.[0-9a-zA-Z-]+)*))?)$')
class Maven:
def __init__(self, pom_path, name=''):
self.pom_path = pom_path
self.name = name
def set_property(self, property, value):
subprocess.run(['mvn', '-f', self.pom_path, 'versions:set-property',
'-DgenerateBackupPoms=false', f'-Dproperty={property}', f'-DnewVersion={value}'], check=True)
def set_version(self, version):
subprocess.run(['mvn', '-f', self.pom_path, 'versions:set',
'-DgenerateBackupPoms=false', f'-DnewVersion={version}'], check=True)
@staticmethod
def deploy_all(*modules):
module_str = ','.join([m.name for m in modules])
subprocess.run(['mvn', 'deploy', '-B', '-pl', module_str, '-am', '-DdeployAtEnd=true'], check=True)
class Docker:
def __init__(self, module, version):
self.module = module
self.version = version
self.internal_image = f'europe-west4-docker.pkg.dev/hmf-build/hmf-docker/{self.module}:{self.version}'
self.external_image = f'hartwigmedicalfoundation/{self.module}:{self.version}'
def build(self):
with open("/workspace/docker.sh", "w") as output:
output.write(f'[ ! -f {self.module}/Dockerfile ] && echo "No Dockerfile for {self.module}" && exit 0\n')
output.write(f'docker build {self.module} -t {self.internal_image} -t {self.external_image} --build-arg VERSION={self.version}\n')
output.write(f'docker push {self.internal_image}\n')
output.write(f'docker login -u hartwigmedicalfoundation -p $(cat /workspace/dockerhub.password)\n')
output.write(f'docker push {self.external_image}\n')
class GithubRelease:
def __init__(self, tag_name: str, module: str, version: str, artifact_file: str, private_key: str, github_client_id: str,
github_installation_id: str):
self.tag_name = tag_name
self.module = module
self.version = version
self.artifact_file = artifact_file
self.private_key = private_key
self.github_client_id = github_client_id
self.github_installation_id = github_installation_id
self.release_name = f"{module} v{version}"
def create(self):
jwt = self._construct_jwt()
token = self._refresh_token(jwt)
print("Successfully refreshed token")
id = self._create_release(token)
print(f"Created release with id {id}")
self._upload_artifacts(id, token)
def _create_release(self, token: str):
print(f"Creating release [{self.release_name}]")
request = {"tag_name": self.tag_name,
"target_commitish": "master",
"name": self.release_name,
"body": f"Description of release {self.release_name}",
"prerelease": True,
"generate_release_notes": True
}
response = requests.post(self._construct_url("api"),
json = request,
headers = self._headers(token))
print(f"Response: {response.text}")
response.raise_for_status()
return response.json()["id"]
def _upload_artifacts(self, id: str, token: str):
print(f"Uploading artifact to release {id}")
headers = self._headers(token)
headers["Content-Type"] = "application/octet-stream"
base_url="{}/{}/assets?name".format(self._construct_url("uploads"), id)
response = requests.post(f"{base_url}={self.module}_v{self.version}.jar",
headers = headers,
data = self.artifact_file.read())
response.raise_for_status()
print(f"Uploaded {self.artifact_file.name}")
def _construct_url(self, prefix):
return f"https://{prefix}.github.com/repos/hartwigmedical/hmftools/releases"
# This method gleaned from Github docs/examples
def _construct_jwt(self):
payload = {
'iat': int(time.time()),
# JWT expiration time (10 minutes maximum)
'exp': int(time.time()) + 600,
'iss': self.github_client_id
}
return jwt.encode(payload, self.private_key, algorithm='RS256')
def _refresh_token(self, jwt: str):
response = requests.post(f"https://api.github.com/app/installations/{self.github_installation_id}/access_tokens",
headers = self._headers(jwt))
response.raise_for_status()
return response.json()["token"]
def _headers(self, token: str):
return {"Accept": "application/vnd.github+json",
"Authorization": f"Bearer {token}",
"X-GitHub-Api-Version": "2022-11-28"
}
def extract_hmftools_dependencies(pom_path):
namespace = {'ns': 'http://maven.apache.org/POM/4.0.0'}
# First, obtain a list of all modules defined in the parent
parsed_parent_pom = ElementTree.parse('pom.xml')
modules = parsed_parent_pom.getroot().findall('.//ns:modules/ns:module', namespace)
module_set = {module.text for module in modules}
# Then, obtain dependencies on these modules from target module
parsed_module_pom = ElementTree.parse(pom_path)
dependencies = parsed_module_pom.getroot().findall('.//ns:dependencies/ns:dependency', namespace)
hmftools_dependencies = set()
for dep in dependencies:
group_id = dep.find('ns:groupId', namespace).text
artifact_id = dep.find('ns:artifactId', namespace).text
if group_id == "com.hartwig" and artifact_id in module_set:
hmftools_dependencies.add(artifact_id)
return hmftools_dependencies
def main():
parser = ArgumentParser(
description="A tool for automatically building and deploying individual modules in HMF-tools.")
parser.add_argument('tag', help="The semantic versioning tag in the following format: <tool-name>-<version>")
parser.add_argument('github_key_path', help="Path to private key for the Github deployment bot")
parser.add_argument('github_client_id', help="Client id for the deployment bot")
parser.add_argument('github_installation_id', help="Installation id of the deployment bot")
args = parser.parse_args()
build_and_release(args.tag, args.github_key_path, args.github_client_id, args.github_installation_id)
def build_and_release(raw_tag: str, github_key: str, github_client_id: str, github_installation_id: str):
match = SEMVER_REGEX.match(raw_tag)
if not match:
print(f"Invalid tag: '{raw_tag}' (it does not match the regex pattern: '{SEMVER_REGEX.pattern}')")
exit(1)
module = match.group(1)
version = match.group(2)
# Clean the raw_tag such that it only includes the groups captured by the regex
# For example: raw_tag = orange-v1.0.0 then tag = orange-1.1.0
tag = f'{module}-{version}'
# parse all the hmftools modules the project depends on from the pom.xml
hmftools_dependencies = extract_hmftools_dependencies(f'{module}/pom.xml')
parent_pom = Maven('pom.xml')
module_pom = Maven(f'{module}/pom.xml', name=module)
dependencies_pom = [Maven(f'{hmf_dep}/pom.xml', name=hmf_dep) for hmf_dep in hmftools_dependencies]
# Set versions in appropriate poms
# For the module we are targeting, we will use only the version part of the semver tag
# For all dependencies, we will use the entire semver tag
parent_pom.set_property(f'{module}.version', version)
for hmf_dep in hmftools_dependencies:
parent_pom.set_property(f'{hmf_dep}.version', tag)
parent_pom.set_version(tag)
module_pom.set_version(version)
Maven.deploy_all(module_pom, *dependencies_pom)
Docker(module, version).build()
GithubRelease(raw_tag, module, version, open(f"/workspace/{module}/target/{module}-{version}-jar-with-dependencies.jar", "rb"),
open(github_key, "r").read(), github_client_id, github_installation_id).create()
if __name__ == '__main__':
main()