def test_multiple_sources( self ):
# clean the following contents, write them to tmpfiles, open them,
# and pass as a list to the provider
contents = [
"""
One
Two
Three
Four
Five
""",
"""
Six
Seven
Eight
Nine
Ten
""",
"""
Eleven
Twelve! (<-- http://youtu.be/JZshZp-cxKg)
"""
]
contents = [ utility.clean_multiline_string( c ) for c in contents ]
source_list = [ open( self.tmpfiles.create_tmpfile( c ) ) for c in contents ]
provider = self.provider_class( source_list )
log.debug( 'provider: %s', provider )
data = list( provider )
log.debug( 'data: %s', str( data ) )
self.assertEqual( ''.join( data ), ''.join( contents) )
def test_multiple_sources(self):
# clean the following contents, write them to tmpfiles, open them,
# and pass as a list to the provider
contents = [
"""
One
Two
Three
Four
Five
""", """
Six
Seven
Eight
Nine
Ten
""", """
Eleven
Twelve! (<-- http://youtu.be/JZshZp-cxKg)
"""
]
contents = [utility.clean_multiline_string(c) for c in contents]
source_list = [open(self.tmpfiles.create_tmpfile(c)) for c in contents]
provider = self.provider_class(source_list)
log.debug('provider: %s', provider)
data = list(provider)
log.debug('data: %s', str(data))
self.assertEqual(''.join(data), ''.join(contents))
def test_stringio( self ):
"""should work with StringIO
"""
contents = utility.clean_multiline_string( """
One
Two
Three
""" )
source = StringIO( contents )
provider = self.provider_class( source )
data = list( provider )
log.debug( 'data: %s', str( data ) )
# provider should call close on file
self.assertEqual( data, self.parses_default_content_as() )
self.assertTrue( source.closed )
def test_stringio(self):
"""should work with StringIO
"""
contents = utility.clean_multiline_string("""
One
Two
Three
""")
source = StringIO(contents)
provider = self.provider_class(source)
data = list(provider)
log.debug('data: %s', str(data))
# provider should call close on file
self.assertEqual(data, self.parses_default_content_as())
self.assertTrue(source.closed)
def test_script_entry(self):
""""""
script_entry_config = utility.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_static)
self.assertTrue(script_entry.serves_templates)
self.assertEqual(script_entry.static_path,
os.path.join(script_entry.path, 'static'))
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)
# print response
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_script_entry(self):
""""""
script_entry_config = utility.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_static)
self.assertTrue(script_entry.serves_templates)
self.assertEqual(script_entry.static_path, os.path.join(script_entry.path, 'static'))
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)
# print response
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_multiple_compound_sources(self):
# clean the following contents, write them to tmpfiles, open them,
# and pass as a list to the provider
contents = [
"""
One
Two
Three
Four
Five
""", """
Six
Seven
Eight
Nine
Ten
""", """
Eleven
Twelve! (<-- http://youtu.be/JZshZp-cxKg)
"""
]
contents = [utility.clean_multiline_string(c) for c in contents]
source_list = [open(self.tmpfiles.create_tmpfile(c)) for c in contents]
def no_Fs(string):
return None if string.startswith('F') else string
def no_youtube(string):
return None if ('youtu.be' in string) else string
source_list = [
base.LimitedOffsetDataProvider(source_list[0],
filter_fn=no_Fs,
limit=2,
offset=1),
base.LimitedOffsetDataProvider(source_list[1], limit=1, offset=3),
base.FilteredDataProvider(source_list[2], filter_fn=no_youtube),
]
provider = self.provider_class(source_list)
log.debug('provider: %s', provider)
data = list(provider)
log.debug('data: %s', str(data))
self.assertEqual(''.join(data), 'Two\nThree\nNine\nEleven\n')
def test_multiple_compound_sources( self ):
# clean the following contents, write them to tmpfiles, open them,
# and pass as a list to the provider
contents = [
"""
One
Two
Three
Four
Five
""",
"""
Six
Seven
Eight
Nine
Ten
""",
"""
Eleven
Twelve! (<-- http://youtu.be/JZshZp-cxKg)
"""
]
contents = [ utility.clean_multiline_string( c ) for c in contents ]
source_list = [ open( self.tmpfiles.create_tmpfile( c ) ) for c in contents ]
def no_Fs( string ):
return None if string.startswith( 'F' ) else string
def no_youtube( string ):
return None if ( 'youtu.be' in string ) else string
source_list = [
base.LimitedOffsetDataProvider( source_list[0], filter_fn=no_Fs, limit=2, offset=1 ),
base.LimitedOffsetDataProvider( source_list[1], limit=1, offset=3 ),
base.FilteredDataProvider( source_list[2], filter_fn=no_youtube ),
]
provider = self.provider_class( source_list )
log.debug( 'provider: %s', provider )
data = list( provider )
log.debug( 'data: %s', str( data ) )
self.assertEqual( ''.join( data ), 'Two\nThree\nNine\nEleven\n' )
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 = utility.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, string_types)
self.assertEqual(response.strip(), "True")
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 = utility.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, string_types)
self.assertEqual(response.strip(), "True")
def format_tmpfile_contents( self, contents=None ):
contents = contents or self.default_file_contents
contents = utility.clean_multiline_string( contents )
log.debug( 'file contents:\n%s', contents )
return contents
def contents_and_tmpfile( self, contents=None ):
# TODO: hmmmm...
contents = contents or self.default_file_contents
contents = utility.clean_multiline_string( contents )
return ( contents, self.tmpfiles.create_tmpfile( contents ) )
def test_interactive_environ_plugin_load(self):
"""
"""
ipython_config = utility.clean_multiline_string("""\
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE interactive_environment SYSTEM "../../interactive_environments.dtd">
<interactive_environment name="IPython">
<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>ipython.mako</template>
</interactive_environment>
""")
mock_app_dir = {
'plugins': {
'ipython': {
'config': {
'ipython.xml': ipython_config
},
'templates': {}
},
},
}
# going to use a fake template here to simplify testing
ipython_template = "${ ie_request }-${ get_api_key() }"
mock_app_dir['plugins']['ipython']['templates'][
'ipython.mako'] = ipython_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['caches'] = {}
# and make sure the vis reg uses that
mock_app_dir = galaxy_mock.MockDir(mock_app_dir)
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 = ['ipython']
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)
ipython = plugin_mgr.plugins['ipython']
config = ipython.config
self.assertEqual(ipython.name, 'ipython')
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
ipython.INTENV_REQUEST_FACTORY = lambda t, p: 'mock'
# should return the (new) api key for the above user (see the template above)
response = ipython._render({}, trans=trans)
response.strip()
self.assertIsInstance(response, string_types)
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)
self.assertIsNotNone(match)
self.assertEqual(match.span(), (0, 32))
mock_app_dir.remove()
def test_interactive_environ_plugin_load(self):
"""
"""
jupyter_config = utility.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>
""")
mock_app_dir = {
'plugins': {
'jupyter': {
'config': {
'jupyter.xml': jupyter_config
},
'templates': {}
},
},
}
# going to use a fake template here to simplify testing
jupyter_template = "${ ie_request }-${ get_api_key() }"
mock_app_dir['plugins']['jupyter']['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['caches'] = {}
# and make sure the vis reg uses that
mock_app_dir = galaxy_mock.MockDir(mock_app_dir)
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, string_types)
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)
self.assertIsNotNone(match)
self.assertEqual(match.span(), (0, 32))
mock_app_dir.remove()
def format_tmpfile_contents(self, contents=None):
contents = contents or self.default_file_contents
contents = utility.clean_multiline_string(contents)
log.debug('file contents:\n%s', contents)
return contents
def contents_and_tmpfile(self, contents=None):
# TODO: hmmmm...
contents = contents or self.default_file_contents
contents = utility.clean_multiline_string(contents)
return (contents, self.tmpfiles.create_tmpfile(contents))