Stub out job_exection package for remote job finish code.

lib/galaxy/tools/__init__.py

@@ -25,11 +25,11 @@ from galaxy import (
     exceptions,
     model
 )
+from galaxy.job_execution import output_collect
 from galaxy.managers.jobs import JobSearch
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.model.tags import GalaxyTagHandler
 from galaxy.queue_worker import send_control_task
-from galaxy.tool_util import output_collect
 from galaxy.tool_util.deps import (
     CachedDependencyManager,
 )
@@ -1737,6 +1737,8 @@ class Tool(Dictifiable):
         Find any additional datasets generated by a tool and attach (for
         cases where number of outputs is not known in advance).
         """
+        # given the job_execution import is the only one, probably makes sense to refactor this out
+        # into job_wrapper.
         tool = self
         permission_provider = output_collect.PermissionProvider(inp_data, tool.app.security_agent, job)
         metadata_source_provider = output_collect.MetadataSourceProvider(inp_data)

packages/job_execution/HISTORY.rst

@@ -0,0 +1,12 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+19.9.0.dev0
+---------------------
+
+* Initial import from dev branch of Galaxy during 19.09 development cycle.

packages/job_execution/LICENSE

@@ -0,0 +1 @@
+../../LICENSE.txt

packages/job_execution/MANIFEST.in

@@ -0,0 +1,2 @@
+include *.rst LICENSE
+

packages/job_execution/Makefile

@@ -0,0 +1 @@
+../package.Makefile

packages/job_execution/README.rst

@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-util.svg
+   :target: https://pypi.python.org/pypi/galaxy-util/
+
+
+Overview
+--------
+
+The Galaxy_ job execution runtime module.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/

packages/job_execution/dev-requirements.txt

@@ -0,0 +1 @@
+../package-dev-requirements.txt

packages/job_execution/galaxy/__init__.py

@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)

packages/job_execution/galaxy/job_execution

@@ -0,0 +1 @@
+../../../lib/galaxy/job_execution

packages/job_execution/galaxy/project_galaxy_job_execution.py

@@ -0,0 +1,13 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-job-execution"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Job Execution Runtime Utilities'
+PROJECT_EMAIL = 'jmchilton@gmail.com'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)

packages/job_execution/requirements.txt

@@ -0,0 +1,2 @@
+galaxy-data
+

packages/job_execution/scripts

@@ -0,0 +1 @@
+../build_scripts

packages/job_execution/setup.cfg

@@ -0,0 +1 @@
+../../setup.cfg

packages/job_execution/setup.py

@@ -0,0 +1,100 @@
+#!/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_job_execution.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")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.job_execution',
+]
+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,
+    long_description_content_type='text/x-rst',
+    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,
+    extras_require={},
+    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 :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)

packages/test.sh

@@ -20,10 +20,11 @@ PACKAGE_DIRS=(
     containers
     tool_util
     data
+    job_execution
 )
 # containers has no tests, tool_util not yet working 100%,
 # data has many problems quota, tool shed install database, etc..
-RUN_TESTS=(1 1 1 0 0 0 0)
+RUN_TESTS=(1 1 1 0 0 0 0 0)
 
 for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
     package_dir=${PACKAGE_DIRS[$i]}