def test_default_init(self):
"""
A plugin with no context passed in should have sane defaults.
"""
vis_dir = galaxy_mock.MockDir({
'config': {
'vis1.xml': ''
},
'static': {},
'templates': {},
})
plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path,
'myvis', {})
self.assertEqual(plugin.name, 'myvis')
self.assertEqual(plugin.path, vis_dir.root_path)
self.assertEqual(plugin.config, {})
self.assertEqual(plugin.base_url, 'myvis')
# template
self.assertTrue(plugin.serves_templates)
self.assertEqual(plugin.template_path,
vis_dir.root_path + '/templates')
self.assertEqual(plugin.template_lookup.__class__.__name__,
'TemplateLookup')
# resource parser
self.assertIsInstance(plugin.resource_parser,
resource_parser.ResourceParser)
def _new_trans(self, allowed_origin_hostnames=None):
app = galaxy_mock.MockApp()
app.config = CORSParsingMockConfig(
allowed_origin_hostnames=allowed_origin_hostnames)
webapp = galaxy_mock.MockWebapp(app.security)
environ = galaxy_mock.buildMockEnviron()
trans = StubGalaxyWebTransaction(environ, app, webapp)
return trans
def test_init_without_static_or_templates(self):
"""
A plugin that has neither template or static directory should serve neither.
"""
vis_dir = galaxy_mock.MockDir({'config': {'vis1.xml': ''}})
plugin = self.plugin_class(galaxy_mock.MockApp(), vis_dir.root_path,
'myvis', dict())
self.assertFalse(plugin.serves_templates)
def test_build_config(self):
"""
"""
plugin_config: dict = dict()
plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis',
plugin_config)
config = plugin._build_config({})
self.assertIsInstance(config, vis_utils.OpenObject)
self.assertEqual(config.__dict__, {})
# existing should flow through
plugin_config = dict()
plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis',
plugin_config)
existing_config = dict(wat=1)
config = plugin._build_config(existing_config)
self.assertEqual(config.wat, 1)
# unlisted/non-param kwargs should NOT overwrite existing
plugin_config = dict()
plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis',
plugin_config)
existing_config = dict(wat=1)
config = plugin._build_config(existing_config, wat=2)
self.assertEqual(config.wat, 1)
# listed/param kwargs *should* overwrite existing
plugin_config = dict(params=dict(wat={
'csv': False,
'required': False,
'type': 'int',
'var_name_in_template': 'wot'
}, ))
plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis',
plugin_config)
existing_config = dict(wat=1)
# send as string like a query would - should be parsed
config = plugin._build_config(existing_config, wat='2')
self.assertEqual(config.wat, 2)
def test_build_render_vars_default(self):
"""
Render vars passed to render should default properly.
"""
# well, that's kind of a lot of typing to say nothing new
config = dict(name='Cat Fancy Magazine\'s Genomic Visualization')
plugin = self.plugin_class(galaxy_mock.MockApp(), '', 'myvis', config)
render_vars = plugin._build_render_vars(config)
self.assertEqual(render_vars['visualization_name'], plugin.name)
self.assertEqual(render_vars['visualization_display_name'],
plugin.config['name'])
self.assertEqual(render_vars['title'], None)
self.assertEqual(render_vars['saved_visualization'], None)
self.assertEqual(render_vars['visualization_id'], None)
self.assertEqual(render_vars['query'], {})
self.assertIsInstance(render_vars['config'], vis_utils.OpenObject)
self.assertEqual(render_vars['config'].__dict__, {})
def test_render(self):
"""
"""
# use the python in a template to test for variables that should be there
# TODO: gotta be a better way
testing_template = clean_multiline_string("""\
<%
found_all = True
should_have = [
title, visualization_name, visualization_display_name,
visualization_id, saved_visualization,
query, config,
embedded,
vars
]
for var in should_have:
try:
var = str( var )
except NameError as name_err:
found_all = False
break
%>
${ found_all }
""")
mock_app_dir = galaxy_mock.MockDir({
'cache': {},
'template.mako': testing_template
})
mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
plugin = self.plugin_class(mock_app, '', 'myvis',
{"name": "Vlad News Bears"})
# somewhat easier to set this up by hand
plugin.config['entry_point'] = {'file': 'template.mako'}
plugin.template_path = mock_app_dir.root_path
plugin.template_lookup = plugin._build_template_lookup(
mock_app_dir.root_path)
response = plugin.render(trans=galaxy_mock.MockTrans(app=mock_app))
self.assertIsInstance(response, str)
self.assertEqual(response.strip(), "True")
def test_script_entry(self):
""""""
script_entry_config = clean_multiline_string("""\
<?xml version="1.0" encoding="UTF-8"?>
<visualization name="js-test">
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
</data_source>
</data_sources>
<entry_point entry_point_type="script" data-main="one" src="bler"></entry_point>
</visualization>
""")
mock_app_dir = galaxy_mock.MockDir({
'plugins': {
'jstest': {
'config': {
'jstest.xml': script_entry_config
},
'static': {}
},
}
})
mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
plugin_mgr = VisualizationsRegistry(mock_app,
directories_setting='plugins',
template_cache_dir=template_cache_dir)
script_entry = plugin_mgr.plugins['jstest']
self.assertIsInstance(script_entry, plugin.ScriptVisualizationPlugin)
self.assertEqual(script_entry.name, 'jstest')
self.assertTrue(script_entry.serves_templates)
trans = galaxy_mock.MockTrans()
script_entry._set_up_template_plugin(mock_app_dir.root_path, [addtional_templates_dir])
response = script_entry._render({}, trans=trans, embedded=True)
self.assertTrue('src="bler"' in response)
self.assertTrue('type="text/javascript"' in response)
self.assertTrue('data-main="one"' in response)
mock_app_dir.remove()
def test_init_with_context(self):
"""
A plugin with context passed in should use those in it's set up.
"""
vis_dir = galaxy_mock.MockDir({
'config': {
'vis1.xml': ''
},
'static': {},
'templates': {},
})
context = dict(base_url='u/wot/m8',
template_cache_dir='template_cache',
additional_template_paths=['one'])
plugin = self.plugin_class(galaxy_mock.MockApp(),
vis_dir.root_path,
'myvis', {},
context=context)
self.assertEqual(plugin.base_url, 'u/wot/m8/myvis')
self.assertEqual(plugin.template_lookup.__class__.__name__,
'TemplateLookup')
def test_plugin_load_from_repo(self):
"""should attempt load if criteria met"""
mock_app = galaxy_mock.MockApp(root=glx_dir)
plugin_mgr = VisualizationsRegistry(mock_app,
directories_setting=vis_reg_path,
template_cache_dir=None)
expected_plugins_path = os.path.join(glx_dir, vis_reg_path)
self.assertEqual(plugin_mgr.base_url, 'visualizations')
self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
scatterplot = plugin_mgr.plugins['scatterplot']
self.assertEqual(scatterplot.name, 'scatterplot')
self.assertEqual(scatterplot.path, os.path.join(expected_plugins_path, 'scatterplot'))
self.assertEqual(scatterplot.base_url, '/'.join((plugin_mgr.base_url, scatterplot.name)))
self.assertTrue(scatterplot.serves_templates)
self.assertEqual(scatterplot.template_path, os.path.join(scatterplot.path, 'templates'))
self.assertEqual(scatterplot.template_lookup.__class__.__name__, 'TemplateLookup')
trackster = plugin_mgr.plugins['trackster']
self.assertEqual(trackster.name, 'trackster')
self.assertEqual(trackster.path, os.path.join(expected_plugins_path, 'trackster'))
self.assertEqual(trackster.base_url, '/'.join((plugin_mgr.base_url, trackster.name)))
self.assertFalse(trackster.serves_templates)
def test_plugin_load(self):
""""""
mock_app_dir = galaxy_mock.MockDir({
'plugins': {
'vis1': {
'config': {
'vis1.xml': config1
},
'static': {},
'templates': {},
},
'vis2': {
'config': {
'vis2.xml': config1
}
},
'not_a_vis1': {
'config': {
'vis1.xml': 'blerbler'
},
},
# empty
'not_a_vis2': {},
'not_a_vis3': 'blerbler',
# bad config
'not_a_vis4': {
'config': {
'not_a_vis4.xml': 'blerbler'
}
},
'not_a_vis5': {
# no config
'static': {},
'templates': {},
},
}
})
mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
plugin_mgr = VisualizationsRegistry(mock_app,
directories_setting='plugins',
template_cache_dir=template_cache_dir)
expected_plugins_path = os.path.join(mock_app_dir.root_path, 'plugins')
expected_plugin_names = ['vis1', 'vis2']
self.assertEqual(plugin_mgr.base_url, 'visualizations')
self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
self.assertEqual(sorted(plugin_mgr.plugins.keys()), expected_plugin_names)
vis1 = plugin_mgr.plugins['vis1']
self.assertEqual(vis1.name, 'vis1')
self.assertEqual(vis1.path, os.path.join(expected_plugins_path, 'vis1'))
self.assertEqual(vis1.base_url, '/'.join((plugin_mgr.base_url, vis1.name)))
self.assertTrue(vis1.serves_templates)
self.assertEqual(vis1.template_path, os.path.join(vis1.path, 'templates'))
self.assertEqual(vis1.template_lookup.__class__.__name__, 'TemplateLookup')
vis1_as_dict = vis1.to_dict()
assert vis1_as_dict["specs"]
specs = vis1_as_dict["specs"]
assert "exports" in specs
exports = specs["exports"]
assert len(exports) == 3
assert "png" in exports
assert "svg" in exports
assert "pdf" in exports
vis2 = plugin_mgr.plugins['vis2']
self.assertEqual(vis2.name, 'vis2')
self.assertEqual(vis2.path, os.path.join(expected_plugins_path, 'vis2'))
self.assertEqual(vis2.base_url, '/'.join((plugin_mgr.base_url, vis2.name)))
self.assertFalse(vis2.serves_templates)
mock_app_dir.remove()
template_cache_dir
def test_interactive_environ_plugin_load(self):
"""
"""
jupyter_config = clean_multiline_string("""\
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
<interactive_environment name="Jupyter">
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Text</test>
<to_param param_attr="id">dataset_id</to_param>
</data_source>
</data_sources>
<params>
<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
</params>
<template>jupyter.mako</template>
</interactive_environment>
""")
templates: Dict[str, str] = {}
mock_app_dir_config = {
'plugins': {
'jupyter': {
'config': {
'jupyter.xml': jupyter_config
},
'templates': templates,
},
},
}
# going to use a fake template here to simplify testing
jupyter_template = "${ ie_request }-${ get_api_key() }"
templates['jupyter.mako'] = jupyter_template
# so that we don't create a cached version of that fake template in the real mako caches
# we'll set up a cache in the temp dir
mock_app_dir_config['caches'] = {}
# and make sure the vis reg uses that
mock_app_dir = galaxy_mock.MockDir(mock_app_dir_config)
mock_app = galaxy_mock.MockApp(root=mock_app_dir.root_path)
plugin_mgr = VisualizationsRegistry(mock_app,
directories_setting='plugins',
template_cache_dir=os.path.join(mock_app_dir.root_path, 'caches'))
# ...then start testing
expected_plugins_path = os.path.join(mock_app_dir.root_path, 'plugins')
expected_plugin_names = ['jupyter']
self.assertEqual(plugin_mgr.base_url, 'visualizations')
self.assertEqual(plugin_mgr.directories, [expected_plugins_path])
self.assertEqual(sorted(plugin_mgr.plugins.keys()), expected_plugin_names)
jupyter = plugin_mgr.plugins['jupyter']
config = jupyter.config
self.assertEqual(jupyter.name, 'jupyter')
self.assertEqual(config.get('plugin_type'), 'interactive_environment')
# get_api_key needs a user, fill_template a trans
user = model.User(email="*****@*****.**", password="******")
trans = galaxy_mock.MockTrans(user=user)
# use a mock request factory - this will be written into the filled template to show it was used
jupyter.INTENV_REQUEST_FACTORY = lambda t, p: 'mock'
# should return the (new) api key for the above user (see the template above)
response = jupyter._render({}, trans=trans)
response.strip()
self.assertIsInstance(response, str)
self.assertTrue('-' in response)
ie_request, api_key = response.split('-')
self.assertEqual(ie_request, 'mock')
match = re.match(r'[a-f0-9]{32}', api_key)
assert match
self.assertEqual(match.span(), (0, 32))
mock_app_dir.remove()
def create_base_test(connection, amqp_type, amqp_connection=None):
app = galaxy_mock.MockApp(database_connection=connection)
app.config.database_connection = connection
app.config.amqp_internal_connection = amqp_connection or "sqlalchemy+%s" % app.config.database_connection
app.amqp_type = amqp_type
return app
