mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Anne Fouilloux
93da60c48e
not only for converting jupyter notebook to HTML (with nbconvert) but also where ipython/IPython was referenced. Some files still contain ipython but this is mostly related to documentation or to the IE docker container itself.
278 lines
12 KiB
Python
278 lines
12 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 sys
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import unittest
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from six import string_types
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from galaxy import model
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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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unit_root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir ) )
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sys.path.insert( 1, unit_root )
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from unittest_utils import galaxy_mock, utility
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# -----------------------------------------------------------------------------
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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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# -----------------------------------------------------------------------------
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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_static )
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self.assertEqual( scatterplot.static_path, os.path.join( scatterplot.path, 'static' ) )
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self.assertEqual( scatterplot.static_url, '/'.join([ scatterplot.base_url, 'static' ]) )
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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_static )
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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_static )
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self.assertEqual( vis1.static_path, os.path.join( vis1.path, 'static' ) )
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self.assertEqual( vis1.static_url, '/'.join([ vis1.base_url, 'static' ]) )
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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_static )
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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 = utility.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, string_types )
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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 = utility.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_static )
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self.assertTrue( script_entry.serves_templates )
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self.assertEqual( script_entry.static_path, os.path.join( script_entry.path, 'static' ) )
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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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# print response
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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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