mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
fc68cb8449
The included script takes in an object store definition to write to, model store output target (e.g. tar file or directory or bagit file/directory format matching the new history exports added in 7367), and a bunch of files in defined via an upload-2.0-style YAML - and writes the physical files into the object store and writes persisted metadata into the model store. The supplied script describes the input format as do the new unit tests in test_model_discover.py. Right now datasets for a history and whole libraries (including recursive folders and library datasets) can be described this way. These concepts have been extended to collections in #7058 but only in the context of discovering job outputs and writing them to an export model store current. This script was created mostly by refactoring stuff out of output_collect.py that is used to create datasets during output discovery (i.e. parsing the same data out of galaxy.json files).
112 lines
3.0 KiB
Python
112 lines
3.0 KiB
Python
#!/usr/bin/env python
|
|
# -*- coding: utf-8 -*-
|
|
|
|
import ast
|
|
import os
|
|
import re
|
|
try:
|
|
from setuptools import setup
|
|
except ImportError:
|
|
from distutils.core import setup
|
|
|
|
SOURCE_DIR = "galaxy"
|
|
|
|
_version_re = re.compile(r'__version__\s+=\s+(.*)')
|
|
|
|
with open('%s/project_galaxy_data.py' % SOURCE_DIR, 'rb') as f:
|
|
init_contents = f.read().decode('utf-8')
|
|
|
|
def get_var(var_name):
|
|
pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
|
|
match = pattern.search(init_contents).group(1)
|
|
return str(ast.literal_eval(match))
|
|
|
|
version = get_var("__version__")
|
|
PROJECT_NAME = get_var("PROJECT_NAME")
|
|
PROJECT_URL = get_var("PROJECT_URL")
|
|
PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
|
|
PROJECT_EMAIL = get_var("PROJECT_EMAIL")
|
|
|
|
TEST_DIR = 'tests'
|
|
PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes'
|
|
PACKAGES = [
|
|
'galaxy',
|
|
'galaxy.datatypes',
|
|
'galaxy.datatypes.dataproviders',
|
|
'galaxy.datatypes.util',
|
|
'galaxy.datatypes.test',
|
|
'galaxy.model',
|
|
'galaxy.model.dataset_collections',
|
|
'galaxy.model.migrate',
|
|
'galaxy.model.orm',
|
|
'galaxy.model.store',
|
|
'galaxy.model.tool_shed_install',
|
|
'galaxy.security',
|
|
]
|
|
ENTRY_POINTS = '''
|
|
[console_scripts]
|
|
gx-build-objects=galaxy.model.store.build_objects:main
|
|
'''
|
|
PACKAGE_DATA = {
|
|
# Be sure to update MANIFEST.in for source dist.
|
|
'galaxy': [
|
|
'datatypes/test/*',
|
|
],
|
|
}
|
|
PACKAGE_DIR = {
|
|
SOURCE_DIR: SOURCE_DIR,
|
|
}
|
|
|
|
readme = open('README.rst').read()
|
|
history = open('HISTORY.rst').read().replace('.. :changelog:', '')
|
|
|
|
if os.path.exists("requirements.txt"):
|
|
requirements = open("requirements.txt").read().split("\n")
|
|
else:
|
|
# In tox, it will cover them anyway.
|
|
requirements = []
|
|
|
|
|
|
test_requirements = [
|
|
# TODO: put package test requirements here
|
|
]
|
|
|
|
|
|
setup(
|
|
name=PROJECT_NAME,
|
|
version=version,
|
|
description=PROJECT_DESCRIPTION,
|
|
long_description=readme + '\n\n' + history,
|
|
author=PROJECT_AUTHOR,
|
|
author_email=PROJECT_EMAIL,
|
|
url=PROJECT_URL,
|
|
packages=PACKAGES,
|
|
entry_points=ENTRY_POINTS,
|
|
package_data=PACKAGE_DATA,
|
|
package_dir=PACKAGE_DIR,
|
|
include_package_data=True,
|
|
install_requires=requirements,
|
|
license="AFL",
|
|
zip_safe=False,
|
|
keywords='galaxy',
|
|
classifiers=[
|
|
'Development Status :: 5 - Production/Stable',
|
|
'Intended Audience :: Developers',
|
|
'Environment :: Console',
|
|
'License :: OSI Approved :: Academic Free License (AFL)',
|
|
'Operating System :: POSIX',
|
|
'Topic :: Software Development',
|
|
'Topic :: Software Development :: Code Generators',
|
|
'Topic :: Software Development :: Testing',
|
|
'Natural Language :: English',
|
|
"Programming Language :: Python :: 2",
|
|
'Programming Language :: Python :: 2.7',
|
|
'Programming Language :: Python :: 3.4',
|
|
'Programming Language :: Python :: 3.5',
|
|
'Programming Language :: Python :: 3.6',
|
|
'Programming Language :: Python :: 3.7',
|
|
],
|
|
test_suite=TEST_DIR,
|
|
tests_require=test_requirements
|
|
)
|