Decompose Galaxy into Python libraries in-tree.

Alternative to galaxy-lib codebase sychronziation.
2026-09-24 16:30:27 +08:00 · 2019-03-28 09:16:59 -04:00
parent 9f344cf893
commit 9964753b0b
42 changed files with 486 additions and 2 deletions
@@ -150,6 +150,11 @@ client/styleguide
 # webpack stats
 client/webpack-stats.json

+# Projects
+projects/*/build
+projects/*/dist
+projects/*/*.egg-info
+
 # Misc
 *.orig
 .DS_Store
@@ -1524,7 +1524,10 @@ galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")


 def galaxy_directory():
-    return os.path.abspath(galaxy_root_path)
+    root_path = os.path.abspath(galaxy_root_path)
+    if os.path.basename(root_path) == "projects":
+        root_path = os.path.abspath(os.path.join(root_path, ".."))
+    return root_path


 def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root_path):
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.5.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.05 release cycle.
@@ -0,0 +1 @@
+../../LICENSE.txt
@@ -0,0 +1,3 @@
+include *.rst LICENSE
+include galaxy/datatypes/test/*
+
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-datatypes.svg
+   :target: https://pypi.python.org/pypi/galaxy-datatypes/
+
+
+Overview
+--------
+
+The Galaxy_ models, datatype framework, and datatype implementations.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
@@ -0,0 +1 @@
+../../../lib/galaxy/datatypes
@@ -0,0 +1 @@
+../../../lib/galaxy/model
@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.5.0.dev0'
+
+PROJECT_NAME = "galaxy-data"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
@@ -0,0 +1 @@
+../../../lib/galaxy/security
@@ -0,0 +1,12 @@
+galaxy-objectstore
+galaxy-util
+bx
+h5py
+isa-rwval
+numpy
+pycryptodome
+pysam
+social_auth_core
+SQLAlchemy==1.2
+sqlalchemy-migrate
+WebOb
@@ -0,0 +1 @@
+../../setup.cfg
@@ -0,0 +1,108 @@
+#!/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.migrate',
+    'galaxy.model.orm',
+    'galaxy.model.tool_shed_install',
+    'galaxy.security',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+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
+)
@@ -0,0 +1 @@
+../../../test/unit/datatypes
@@ -0,0 +1 @@
+../../../test/unit/test_galaxy_mapping.py
@@ -0,0 +1 @@
+../../../test/unit/unittest_utils
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.5.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.05 release cycle.
@@ -0,0 +1 @@
+../../LICENSE.txt
@@ -0,0 +1,2 @@
+include *.rst LICENSE
+
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-objectstore.svg
+   :target: https://pypi.python.org/pypi/galaxy-objectstore/
+
+
+Overview
+--------
+
+The Galaxy_ object store framework and default implementations.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
@@ -0,0 +1 @@
+../../../lib/galaxy/objectstore
@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.5.0.dev0'
+
+PROJECT_NAME = "galaxy-objectstore"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
@@ -0,0 +1 @@
+galaxy-util
@@ -0,0 +1 @@
+../../setup.cfg
@@ -0,0 +1,99 @@
+#!/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_objectstore.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.objectstore',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+    ],
+}
+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
+)
@@ -0,0 +1 @@
+../../../test/unit/test_objectstore.py
@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.5.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.05 release cycle.
@@ -0,0 +1 @@
+../../LICENSE.txt
@@ -0,0 +1,3 @@
+include *.rst LICENSE
+include galaxy/util/docutils_template.txt
+include galaxy/exceptions/error_codes.json
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-util.svg
+   :target: https://pypi.python.org/pypi/galaxy-util/
+
+
+Overview
+--------
+
+The Galaxy_ utilities module.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
@@ -0,0 +1 @@
+../../../lib/galaxy/exceptions
@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.5.0.dev0'
+
+PROJECT_NAME = "galaxy-util"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
@@ -0,0 +1 @@
+../../../lib/galaxy/util
@@ -0,0 +1,9 @@
+bleach
+boltons
+bz2file; python_version < '3.3'
+Cheetah3
+docutils
+markupsafe
+packaging
+pyyaml
+six>=1.9.0
@@ -0,0 +1 @@
+../../setup.cfg
@@ -0,0 +1,103 @@
+#!/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_util.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.util',
+    'galaxy.util.logging',
+    'galaxy.util.path',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+        'util/docutils_template.txt',
+        'exceptions/error_codes.json',
+    ],
+}
+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
+)
@@ -0,0 +1 @@
+../../../test/unit/test_utils.py
@@ -2,10 +2,12 @@
 Unit tests for base DataTypes.
 .. seealso:: galaxy.datatypes.data
 """
+import os

 from galaxy.datatypes.data import get_file_peek
+from galaxy.util import galaxy_directory


 def test_get_file_peek():
    # should get the first 5 lines of the file without a trailing newline character
-    assert get_file_peek('test-data/1.tabular', line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'
+    assert get_file_peek(os.path.join(galaxy_directory(), 'test-data/1.tabular'), line_wrap=False) == 'chr22\t1000\tNM_17\nchr22\t2000\tNM_18\nchr10\t2200\tNM_10\nchr10\thap\ttest\nchr10\t1200\tNM_11'
				`@@ -0,0 +1 @@`
				`__path__ = __import__('pkgutil').extend_path(__path__, __name__)`