Fix issue with initialization of mock_galaxy object

galaxyproject · Feb 18, 2023 · 62063de · 62063de
1 parent 19113a9
commit 62063de
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Showing 24 changed files with 68 additions and 21 deletions.
diff --git a/docs/topics/shell_commands.rst b/docs/topics/shell_commands.rst
@@ -30,7 +30,7 @@ example:
         rules: []
     EOF
     $ tpv lint good.yml
-    INFO : tpv.core.shell: lint successful.
+    INFO : tpv.commands.shell: lint successful.
     $ echo $?
     0
 
@@ -40,7 +40,7 @@ example:
           cores: 1
     EOF
     $ tpv lint bad.yml
-    INFO : tpv.core.shell: lint failed.
+    INFO : tpv.commands.shell: lint failed.
     $ echo $?
     1
     

diff --git a/requirements_test.txt b/requirements_test.txt
@@ -5,6 +5,7 @@ galaxy-files@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdi
 galaxy-data@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/data
 galaxy-auth@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/auth
 galaxy-selenium@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/selenium
+galaxy-data@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/data
 galaxy-job-execution@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/job_execution
 galaxy-job-metrics@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/job_metrics
 galaxy-tool-util@git+https://github.com/galaxyproject/galaxy.git@release_22.05#subdirectory=packages/tool_util

diff --git a/setup.py b/setup.py
@@ -55,7 +55,7 @@
     },
     entry_points={
         'console_scripts': [
-            'tpv = tpv.core.shell:main'
+            'tpv = tpv.commands.shell:main'
         ]
     },
     classifiers=[

diff --git a/tests/test_entity.py b/tests/test_entity.py
@@ -3,7 +3,7 @@
 from tpv.rules import gateway
 from tpv.core.entities import Tag
 from tpv.core.entities import TagType
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestEntity(unittest.TestCase):

diff --git a/tests/test_mapper_basic.py b/tests/test_mapper_basic.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 from galaxy.jobs.mapper import JobMappingException
 
 

diff --git a/tests/test_mapper_context.py b/tests/test_mapper_context.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestMapperContext(unittest.TestCase):

diff --git a/tests/test_mapper_destinations.py b/tests/test_mapper_destinations.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 from galaxy.jobs.mapper import JobMappingException
 
 

diff --git a/tests/test_mapper_inheritance.py b/tests/test_mapper_inheritance.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 from tpv.core.loader import InvalidParentException
 
 

diff --git a/tests/test_mapper_merge_multiple.py b/tests/test_mapper_merge_multiple.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 from galaxy.jobs.mapper import JobMappingException
 
 

diff --git a/tests/test_mapper_params_specific.py b/tests/test_mapper_params_specific.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestParamsSpecific(unittest.TestCase):

diff --git a/tests/test_mapper_rank.py b/tests/test_mapper_rank.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestMapperRank(unittest.TestCase):

diff --git a/tests/test_mapper_role.py b/tests/test_mapper_role.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 from galaxy.jobs.mapper import JobMappingException
 
 

diff --git a/tests/test_mapper_rules.py b/tests/test_mapper_rules.py
@@ -4,7 +4,7 @@
 import shutil
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 from galaxy.jobs.mapper import JobMappingException
 from galaxy.jobs.mapper import JobNotReadyException
 

diff --git a/tests/test_mapper_sample.py b/tests/test_mapper_sample.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestMapperSample(unittest.TestCase):

diff --git a/tests/test_mapper_user.py b/tests/test_mapper_user.py
@@ -2,7 +2,7 @@
 import unittest
 from tpv.rules import gateway
 from tpv.core.entities import IncompatibleTagsException
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestMapperUser(unittest.TestCase):

diff --git a/tests/test_scenarios.py b/tests/test_scenarios.py
@@ -7,7 +7,7 @@
 import unittest
 from galaxy.jobs.mapper import JobMappingException
 from tpv.rules import gateway
-from tpv.core.test import mock_galaxy
+from tpv.commands.test import mock_galaxy
 
 
 class TestScenarios(unittest.TestCase):

diff --git a/tests/test_shell.py b/tests/test_shell.py
@@ -9,7 +9,7 @@
 import yaml
 from galaxy.jobs.mapper import JobMappingException
 
-from tpv.core.shell import main
+from tpv.commands.shell import main
 
 
 @pytest.fixture

diff --git a/tpv/core/test/__init__.py → tpv/commands/__init__.py b/tpv/core/test/__init__.py → tpv/commands/__init__.py
diff --git a/tpv/commands/dryrunner.py b/tpv/commands/dryrunner.py
@@ -0,0 +1,46 @@
+from .test import mock_galaxy
+from tpv.rules import gateway
+
+
+class TPVDryRunner():
+
+    def __init__(self, job_conf, tpv_confs=None, user=None, tool=None, job=None):
+        self.galaxy_app = mock_galaxy.App(job_conf=job_conf, create_model=True)
+        self.user = user
+        self.tool = tool
+        self.job = job
+        if tpv_confs:
+            self.tpv_config_files = tpv_confs
+        else:
+            self.tpv_config_files = self.galaxy_app.job_config.get_destination(
+                'tpv_dispatcher').params['tpv_config_files']
+
+    def run(self):
+        gateway.ACTIVE_DESTINATION_MAPPER = None
+        return gateway.map_tool_to_destination(self.galaxy_app, self.job, self.tool, self.user,
+                                               tpv_config_files=self.tpv_config_files)
+
+    @staticmethod
+    def from_params(job_conf, user=None, tool=None, tpv_confs=None, input_size=None):
+        if user is not None:
+            if '@' in user:
+                username, email = user.split('@', 1)
+            else:
+                username, email = (user, 'example.org')
+            user = mock_galaxy.User(username, email)
+        else:
+            user = None
+
+        if tool:
+            tool = mock_galaxy.Tool(tool)
+        else:
+            tool = None
+
+        job = mock_galaxy.Job()
+        if input_size:
+            dataset = mock_galaxy.DatasetAssociation(
+                "test",
+                mock_galaxy.Dataset("test.txt", file_size=input_size*1024**3))
+            job.add_input_dataset(dataset)
+
+        return TPVDryRunner(job_conf=job_conf, tpv_confs=tpv_confs, user=user, tool=tool, job=job)
diff --git a/tpv/core/formatter.py → tpv/commands/formatter.py b/tpv/core/formatter.py → tpv/commands/formatter.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 import logging
 
-from . import util
+from tpv.core import util
 
 log = logging.getLogger(__name__)
 

diff --git a/tpv/core/linter.py → tpv/commands/linter.py b/tpv/core/linter.py → tpv/commands/linter.py
@@ -1,6 +1,6 @@
 import logging
 
-from .loader import TPVConfigLoader
+from tpv.core.loader import TPVConfigLoader
 
 log = logging.getLogger(__name__)
 

diff --git a/tpv/core/shell.py → tpv/commands/shell.py b/tpv/core/shell.py → tpv/commands/shell.py
diff --git a/tpv/commands/test/__init__.py b/tpv/commands/test/__init__.py
diff --git a/tpv/core/test/mock_galaxy.py → tpv/commands/test/mock_galaxy.py b/tpv/core/test/mock_galaxy.py → tpv/commands/test/mock_galaxy.py
@@ -63,15 +63,15 @@ def __init__(self, job_conf=None, create_model=False):
             server_name="main",
             is_set=lambda x: True,
         )
-        self.application_stack = ApplicationStack()
         self.job_metrics = JobMetrics()
-        self.job_config = JobConfiguration(self)
         if create_model:
             self.model = mapping.init(
                 "/tmp",
                 "sqlite:///:memory:",
                 create_tables=True
             )
+        self.application_stack = ApplicationStack(app=self)
+        self.job_config = JobConfiguration(self)
 
 
 class User: