Create galaxy-job-metrics package to share with Pulsar.

lib/galaxy/app.py

@@ -10,9 +10,8 @@ import galaxy.model.security
 import galaxy.queues
 import galaxy.quota
 import galaxy.security
-from galaxy import config, jobs
+from galaxy import config, job_metrics, jobs
 from galaxy.containers import build_container_interfaces
-from galaxy.jobs import metrics as job_metrics
 from galaxy.managers.collections import DatasetCollectionManager
 from galaxy.managers.folders import FolderManager
 from galaxy.managers.histories import HistoryManager

lib/galaxy/job_metrics/__init__.py

@@ -16,7 +16,7 @@ import os
 
 from galaxy import util
 from galaxy.util import plugin_config
-from ..metrics import formatting
+from ..job_metrics import formatting
 
 log = logging.getLogger(__name__)
 
@@ -59,8 +59,8 @@ class JobMetrics(object):
         return self.job_instrumenters[destination_id].collect_properties(job_id, job_directory)
 
     def __plugins_dict(self):
-        import galaxy.jobs.metrics.instrumenters
-        return plugin_config.plugins_dict(galaxy.jobs.metrics.instrumenters, 'plugin_type')
+        import galaxy.job_metrics.instrumenters
+        return plugin_config.plugins_dict(galaxy.job_metrics.instrumenters, 'plugin_type')
 
 
 class NullJobInstrumenter(object):

lib/galaxy/job_metrics/instrumenters/__init__.py

@@ -10,7 +10,7 @@ from abc import (
 
 import six
 
-from ...metrics import formatting
+from .. import formatting
 
 INSTRUMENT_FILE_PREFIX = "__instrument"
 

packages/job_metrics/HISTORY.rst

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

packages/job_metrics/LICENSE

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

packages/job_metrics/MANIFEST.in

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

packages/job_metrics/README.rst

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

packages/job_metrics/galaxy/__init__.py

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

packages/job_metrics/galaxy/job_metrics

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

packages/job_metrics/galaxy/project_galaxy_job_metrics.py

@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+
+__version__ = '19.9.0.dev0'
+
+PROJECT_NAME = "galaxy-job-metrics"
+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
+)

packages/job_metrics/requirements.txt

@@ -0,0 +1 @@
+galaxy-util

packages/job_metrics/setup.cfg

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

packages/job_metrics/setup.py

@@ -0,0 +1,101 @@
+#!/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_metrics.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 Job Metrics'
+PACKAGES = [
+    'galaxy',
+    'galaxy.job_metrics',
+    'galaxy.job_metrics.instrumers',
+    'galaxy.job_metrics.collectl',
+]
+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
+)

packages/job_metrics/tests/test_job_metrics.py

@@ -0,0 +1 @@
+../../../test/unit/jobs/test_job_metrics.py

test/unit/jobs/test_job_metrics.py

@@ -0,0 +1,7 @@
+from galaxy.job_metrics import JobMetrics
+
+
+def test_job_metrics_load():
+    # Just construct the manager to make sure all the plugin classes load fine
+    # and package is configured properly.
+    JobMetrics()

test/unit/jobs/test_runner_local.py

@@ -5,8 +5,8 @@ from unittest import TestCase
 
 import psutil
 
+from galaxy import job_metrics
 from galaxy import model
-from galaxy.jobs import metrics
 from galaxy.jobs.runners import local
 from galaxy.util import bunch
 from ..tools_support import (
@@ -20,7 +20,7 @@ class TestLocalJobRunner(TestCase, UsesApp, UsesTools):
     def setUp(self):
         self.setup_app()
         self._init_tool()
-        self.app.job_metrics = metrics.JobMetrics()
+        self.app.job_metrics = job_metrics.JobMetrics()
         self.job_wrapper = MockJobWrapper(self.app, self.test_directory, self.tool)
 
     def tearDown(self):