Merge pull request #7992 from jmchilton/more_packages

Add galaxy-tool-util and galaxy-job-metrics packages.

test/base/integration_util.py

@@ -9,7 +9,7 @@ from unittest import skip, SkipTest, TestCase
 
 import pytest
 
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 from galaxy.tools.verify.test_data import TestDataResolver
 from .api import UsesApiTestCaseMixin
 from .driver_util import GalaxyTestDriver

test/integration/test_containerized_jobs.py

@@ -8,7 +8,7 @@ from base.populators import (
     DatasetPopulator,
 )
 
-from galaxy.tools.deps.commands import which
+from galaxy.tool_util.deps.commands import which
 from .test_job_environments import RunsEnvironmentJobs
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))

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_job_output_checker.py

@@ -1,8 +1,8 @@
 from unittest import TestCase
 
 from galaxy.jobs.output_checker import check_output, DETECTED_JOB_STATE
-from galaxy.tools.parser.error_level import StdioErrorLevel
-from galaxy.tools.parser.interface import ToolStdioRegex
+from galaxy.tool_util.parser.error_level import StdioErrorLevel
+from galaxy.tool_util.parser.interface import ToolStdioRegex
 from galaxy.util.bunch import Bunch
 
 

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):

test/unit/tools/test_actions.py

@@ -4,12 +4,12 @@ from xml.etree.ElementTree import XML
 
 from galaxy import model
 from galaxy.exceptions import UserActivationRequiredException
+from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.actions import (
     DefaultToolAction,
     determine_output_format,
     on_text_for_names
 )
-from galaxy.tools.parser.output_objects import ToolOutput
 from .. import tools_support
 
 

test/unit/tools/test_collect_primary_datasets.py

@@ -6,7 +6,7 @@ from galaxy import (
     model,
     util
 )
-from galaxy.tools.parser import output_collection_def
+from galaxy.tool_util.parser import output_collection_def
 from galaxy.tools.provided_metadata import LegacyToolProvidedMetadata, NullToolProvidedMetadata
 from .. import tools_support
 

test/unit/tools/test_conda_resolution.py

@@ -3,12 +3,12 @@ import shutil
 import unittest
 from tempfile import mkdtemp
 
-from galaxy.tools.deps import (
+from galaxy.tool_util.deps import (
     conda_util,
     DependencyManager
 )
-from galaxy.tools.deps.requirements import ToolRequirement
-from galaxy.tools.deps.resolvers.conda import CondaDependencyResolver
+from galaxy.tool_util.deps.requirements import ToolRequirement
+from galaxy.tool_util.deps.resolvers.conda import CondaDependencyResolver
 
 
 def skip_unless_environ(var):

test/unit/tools/test_evaluation.py

@@ -12,6 +12,7 @@ from galaxy.model import (
     JobParameter,
     JobToInputDatasetAssociation
 )
+from galaxy.tool_util.parser.output_objects import ToolOutput
 from galaxy.tools.evaluation import ToolEvaluator
 # For MockTool
 from galaxy.tools.parameters import params_from_strings
@@ -25,7 +26,6 @@ from galaxy.tools.parameters.grouping import (
     ConditionalWhen,
     Repeat
 )
-from galaxy.tools.parser.output_objects import ToolOutput
 from galaxy.util.bunch import Bunch
 # Test fixtures for Galaxy infrastructure.
 from ..tools_support import UsesApp

test/unit/tools/test_parsing.py

@@ -5,7 +5,8 @@ import tempfile
 import unittest
 from math import isinf
 
-from galaxy.tools.parser.factory import get_tool_source
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.util import galaxy_directory
 
 
 TOOL_XML_1 = """
@@ -521,7 +522,7 @@ class DataSourceLoaderTestCase(BaseLoaderTestCase):
 
 
 class ApplyRulesToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/apply_rules.xml")
+    source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/apply_rules.xml")
     source_contents = None
 
     def test_tool_type(self):
@@ -537,7 +538,7 @@ class ApplyRulesToolLoaderTestCase(BaseLoaderTestCase):
 
 
 class BuildListToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/build_list.xml")
+    source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/build_list.xml")
     source_contents = None
 
     def test_tool_type(self):
@@ -547,7 +548,7 @@ class BuildListToolLoaderTestCase(BaseLoaderTestCase):
 
 
 class SpecialToolLoaderTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "lib/galaxy/tools/imp_exp/exp_history_to_archive.xml")
+    source_file_name = os.path.join(galaxy_directory(), "lib/galaxy/tools/imp_exp/exp_history_to_archive.xml")
     source_contents = None
 
     def test_tool_type(self):
@@ -572,7 +573,7 @@ class SpecialToolLoaderTestCase(BaseLoaderTestCase):
 
 
 class CollectionTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_two_paired.xml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_two_paired.xml")
     source_contents = None
 
     def test_tests(self):
@@ -586,7 +587,7 @@ class CollectionTestCase(BaseLoaderTestCase):
 
 
 class CollectionOutputXmlTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_creates_pair.xml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_creates_pair.xml")
     source_contents = None
 
     def test_tests(self):
@@ -595,7 +596,7 @@ class CollectionOutputXmlTestCase(BaseLoaderTestCase):
 
 
 class CollectionOutputYamlTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/collection_creates_pair_y.yml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/collection_creates_pair_y.yml")
     source_contents = None
 
     def test_tests(self):
@@ -604,7 +605,7 @@ class CollectionOutputYamlTestCase(BaseLoaderTestCase):
 
 
 class ExpectationsTestCase(BaseLoaderTestCase):
-    source_file_name = os.path.join(os.getcwd(), "test/functional/tools/detect_errors.xml")
+    source_file_name = os.path.join(galaxy_directory(), "test/functional/tools/detect_errors.xml")
     source_contents = None
 
     def test_tests(self):

test/unit/tools/test_tool_dependency_description.py

@@ -1,5 +1,5 @@
 from galaxy.model import tool_shed_install
-from galaxy.tools.deps import (
+from galaxy.tool_util.deps import (
     dependencies,
     requirements
 )

test/unit/tools/test_tool_deps.py

@@ -12,15 +12,15 @@ from shutil import rmtree
 from stat import S_IXUSR
 from subprocess import PIPE, Popen
 
-from galaxy.tools.deps import DependencyManager
-from galaxy.tools.deps.requirements import (
+from galaxy.tool_util.deps import DependencyManager
+from galaxy.tool_util.deps.requirements import (
     ToolRequirement,
     ToolRequirements
 )
-from galaxy.tools.deps.resolvers import NullDependency
-from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency
-from galaxy.tools.deps.resolvers.lmod import LmodDependency, LmodDependencyResolver
-from galaxy.tools.deps.resolvers.modules import ModuleDependency, ModuleDependencyResolver
+from galaxy.tool_util.deps.resolvers import NullDependency
+from galaxy.tool_util.deps.resolvers.galaxy_packages import GalaxyPackageDependency
+from galaxy.tool_util.deps.resolvers.lmod import LmodDependency, LmodDependencyResolver
+from galaxy.tool_util.deps.resolvers.modules import ModuleDependency, ModuleDependencyResolver
 from galaxy.util.bunch import Bunch
 
 

test/unit/tools/test_tool_loader.py

@@ -3,7 +3,7 @@ from shutil import rmtree
 from string import Template
 from tempfile import mkdtemp
 
-from galaxy.tools.loader import load_tool, template_macro_params
+from galaxy.tool_util.loader import load_tool, template_macro_params
 from galaxy.util import parse_xml
 
 

test/unit/tools_support.py

@@ -11,8 +11,8 @@ from collections import defaultdict
 
 import galaxy.datatypes.registry
 import galaxy.model
+from galaxy.tool_util.parser import get_tool_source
 from galaxy.tools import create_tool_from_source
-from galaxy.tools.parser import get_tool_source
 from galaxy.util.bunch import Bunch
 from .unittest_utils import galaxy_mock
 

test/unit/unittest_utils/galaxy_mock.py

@@ -15,7 +15,7 @@ from galaxy.datatypes import registry
 from galaxy.jobs.manager import NoopManager
 from galaxy.model import mapping, tags
 from galaxy.security import idencoding
-from galaxy.tools.deps.containers import NullContainerFinder
+from galaxy.tool_util.deps.containers import NullContainerFinder
 from galaxy.util.bunch import Bunch
 from galaxy.util.dbkeys import GenomeBuilds
 from galaxy.web.stack import ApplicationStack