mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
22ddea4337
clean_multiline_string was used in multiple places across modules in different packages so I simply refactored it into galaxy.util and added a test case (used in multiple places and has tests a lower bar then some other code in galaxy.util). The tempfilecache abstraction was only used in one place, so I've refactored it right into that file. Together these should simplify the package tests for galaxy-data (and hopefully other packages also).
262 lines
10 KiB
Python
262 lines
10 KiB
Python
"""
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Test lib/galaxy/visualization/plugins/registry.
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"""
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import os
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import re
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import unittest
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from six import text_type
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from galaxy import model
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from galaxy.util import clean_multiline_string
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from galaxy.visualization.plugins import plugin
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from galaxy.visualization.plugins.registry import VisualizationsRegistry
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from ...unittest_utils import galaxy_mock
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glx_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, os.pardir))
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template_cache_dir = os.path.join(glx_dir, 'database', 'compiled_templates')
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addtional_templates_dir = os.path.join(glx_dir, 'config', 'plugins', 'visualizations', 'common', 'templates')
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vis_reg_path = 'config/plugins/visualizations'
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config1 = """\
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
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<visualization name="scatterplot">
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<data_sources>
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<data_source>
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<model_class>HistoryDatasetAssociation</model_class>
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<test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
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<to_param param_attr="id">dataset_id</to_param>
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</data_source>
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</data_sources>
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<params>
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<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
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</params>
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<template>scatterplot.mako</template>
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</visualization>
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"""
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class VisualizationsRegistry_TestCase(unittest.TestCase):
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def test_plugin_load_from_repo(self):
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"""should attempt load if criteria met"""
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mock_app = galaxy_mock.MockApp(root=glx_dir)
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plugin_mgr = VisualizationsRegistry(mock_app,
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directories_setting=vis_reg_path,
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template_cache_dir=None)
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expected_plugins_path = os.path.join(glx_dir, vis_reg_path)
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self.assertEqual(plugin_mgr.base_url, 'visualizations')
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self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
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scatterplot = plugin_mgr.plugins['scatterplot']
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self.assertEqual(scatterplot.name, 'scatterplot')
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self.assertEqual(scatterplot.path, os.path.join(expected_plugins_path, 'scatterplot'))
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self.assertEqual(scatterplot.base_url, '/'.join((plugin_mgr.base_url, scatterplot.name)))
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self.assertTrue(scatterplot.serves_templates)
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self.assertEqual(scatterplot.template_path, os.path.join(scatterplot.path, 'templates'))
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self.assertEqual(scatterplot.template_lookup.__class__.__name__, 'TemplateLookup')
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trackster = plugin_mgr.plugins['trackster']
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self.assertEqual(trackster.name, 'trackster')
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self.assertEqual(trackster.path, os.path.join(expected_plugins_path, 'trackster'))
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self.assertEqual(trackster.base_url, '/'.join((plugin_mgr.base_url, trackster.name)))
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self.assertFalse(trackster.serves_templates)
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def test_plugin_load(self):
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""""""
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mock_app_dir = galaxy_mock.MockDir({
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'plugins': {
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'vis1': {
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'config': {
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'vis1.xml': config1
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},
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'static': {},
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'templates': {},
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},
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'vis2': {
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'config': {
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'vis2.xml': config1
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}
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},
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'not_a_vis1': {
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'config': {
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'vis1.xml': 'blerbler'
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},
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},
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# empty
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'not_a_vis2': {},
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'not_a_vis3': 'blerbler',
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# bad config
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'not_a_vis4': {
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'config': {
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'not_a_vis4.xml': 'blerbler'
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}
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},
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'not_a_vis5': {
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# no config
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'static': {},
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'templates': {},
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},
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}
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})
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mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
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plugin_mgr = VisualizationsRegistry(mock_app,
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directories_setting='plugins',
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template_cache_dir=template_cache_dir)
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expected_plugins_path = os.path.join(mock_app_dir.root_path, 'plugins')
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expected_plugin_names = ['vis1', 'vis2']
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self.assertEqual(plugin_mgr.base_url, 'visualizations')
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self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
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self.assertEqual(sorted(plugin_mgr.plugins.keys()), expected_plugin_names)
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vis1 = plugin_mgr.plugins['vis1']
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self.assertEqual(vis1.name, 'vis1')
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self.assertEqual(vis1.path, os.path.join(expected_plugins_path, 'vis1'))
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self.assertEqual(vis1.base_url, '/'.join((plugin_mgr.base_url, vis1.name)))
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self.assertTrue(vis1.serves_templates)
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self.assertEqual(vis1.template_path, os.path.join(vis1.path, 'templates'))
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self.assertEqual(vis1.template_lookup.__class__.__name__, 'TemplateLookup')
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vis2 = plugin_mgr.plugins['vis2']
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self.assertEqual(vis2.name, 'vis2')
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self.assertEqual(vis2.path, os.path.join(expected_plugins_path, 'vis2'))
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self.assertEqual(vis2.base_url, '/'.join((plugin_mgr.base_url, vis2.name)))
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self.assertFalse(vis2.serves_templates)
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mock_app_dir.remove()
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template_cache_dir
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def test_interactive_environ_plugin_load(self):
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"""
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"""
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jupyter_config = clean_multiline_string("""\
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
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<interactive_environment name="Jupyter">
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<data_sources>
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<data_source>
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<model_class>HistoryDatasetAssociation</model_class>
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<test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
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<test type="isinstance" test_attr="datatype" result_type="datatype">data.Text</test>
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<to_param param_attr="id">dataset_id</to_param>
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</data_source>
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</data_sources>
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<params>
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<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
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</params>
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<template>jupyter.mako</template>
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</interactive_environment>
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""")
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mock_app_dir = {
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'plugins': {
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'jupyter': {
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'config': {
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'jupyter.xml': jupyter_config
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},
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'templates': {}
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},
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},
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}
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# going to use a fake template here to simplify testing
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jupyter_template = "${ ie_request }-${ get_api_key() }"
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mock_app_dir['plugins']['jupyter']['templates']['jupyter.mako'] = jupyter_template
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# so that we don't create a cached version of that fake template in the real mako caches
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# we'll set up a cache in the temp dir
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mock_app_dir['caches'] = {}
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# and make sure the vis reg uses that
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mock_app_dir = galaxy_mock.MockDir(mock_app_dir)
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mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
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plugin_mgr = VisualizationsRegistry(mock_app,
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directories_setting='plugins',
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template_cache_dir=os.path.join(mock_app_dir.root_path, 'caches'))
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# ...then start testing
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expected_plugins_path = os.path.join(mock_app_dir.root_path, 'plugins')
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expected_plugin_names = ['jupyter']
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self.assertEqual(plugin_mgr.base_url, 'visualizations')
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self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
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self.assertEqual(sorted(plugin_mgr.plugins.keys()), expected_plugin_names)
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jupyter = plugin_mgr.plugins['jupyter']
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config = jupyter.config
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self.assertEqual(jupyter.name, 'jupyter')
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self.assertEqual(config.get('plugin_type'), 'interactive_environment')
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# get_api_key needs a user, fill_template a trans
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user = model.User(email="blah@bler.blah", password="dockerDockerDOCKER")
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trans = galaxy_mock.MockTrans(user=user)
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# use a mock request factory - this will be written into the filled template to show it was used
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jupyter.INTENV_REQUEST_FACTORY = lambda t, p: 'mock'
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# should return the (new) api key for the above user (see the template above)
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response = jupyter._render({}, trans=trans)
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response.strip()
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self.assertIsInstance(response, text_type)
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self.assertTrue('-' in response)
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ie_request, api_key = response.split('-')
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self.assertEqual(ie_request, 'mock')
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match = re.match(r'[a-f0-9]{32}', api_key)
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self.assertIsNotNone(match)
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self.assertEqual(match.span(), (0, 32))
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mock_app_dir.remove()
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def test_script_entry(self):
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""""""
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script_entry_config = clean_multiline_string("""\
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<?xml version="1.0" encoding="UTF-8"?>
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<visualization name="js-test">
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<data_sources>
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<data_source>
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<model_class>HistoryDatasetAssociation</model_class>
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</data_source>
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</data_sources>
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<entry_point entry_point_type="script" data-main="one" src="bler"></entry_point>
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</visualization>
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""")
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mock_app_dir = galaxy_mock.MockDir({
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'plugins': {
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'jstest': {
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'config': {
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'jstest.xml': script_entry_config
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},
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'static': {}
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},
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}
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})
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mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
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plugin_mgr = VisualizationsRegistry(mock_app,
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directories_setting='plugins',
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template_cache_dir=template_cache_dir)
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script_entry = plugin_mgr.plugins['jstest']
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self.assertIsInstance(script_entry, plugin.ScriptVisualizationPlugin)
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self.assertEqual(script_entry.name, 'jstest')
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self.assertTrue(script_entry.serves_templates)
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trans = galaxy_mock.MockTrans()
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script_entry._set_up_template_plugin(mock_app_dir.root_path, [addtional_templates_dir])
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response = script_entry._render({}, trans=trans, embedded=True)
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self.assertTrue('src="bler"' in response)
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self.assertTrue('type="text/javascript"' in response)
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self.assertTrue('data-main="one"' in response)
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mock_app_dir.remove()
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# -----------------------------------------------------------------------------
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# TODO: config parser tests (in separate file)
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if __name__ == '__main__':
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unittest.main()
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