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many improvements
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- show warning messages (not errors)
- upload test datasets with a correct type according to the tool's .xml file (no 'auto' detection)
- add more checks to improve the overall stability
- fix tour messages
- other bugfixes
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@anatskiy
anatskiy committed Apr 26, 2017
1 parent ed4fa04 commit 47a5f17
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Showing 2 changed files with 139 additions and 106 deletions.
236 changes: 134 additions & 102 deletions config/plugins/webhooks/demo/tour_generator/helper/__init__.py
View file
Expand Up @@ -29,21 +29,28 @@ def _upload_test_data(self):
raise ValueError('Tests are not defined.')

self._test = self._tool.tests[0]
input_keys = [k for k, v in self._tool.inputs.data.items() if
v.type == 'data']
input_datasets = [
self._test.inputs[input_key]
for input_key in input_keys
]

if not input_datasets:

# All inputs with the type 'data'
data_inputs = {k: v for k, v in self._tool.inputs.items() if
v.type == 'data'}

# Datasets from the <test></test> section
test_datasets = {
input_name: self._test.inputs[input_name][0]
for input_name in data_inputs.keys()
if input_name in self._test.inputs.keys()
}

if not test_datasets.keys():
not_supported_input_types = [
k for k, v in self._tool.inputs.data.items() if
k for k, v in self._tool.inputs.items() if
v.type == 'repeat' or v.type == 'data_collection'
]
if not_supported_input_types:
raise ValueError('Cannot generate a tour.')
raise ValueError('Not supported input types.')
else:
# Some tests don't have data inputs at all,
# so we can generate a tour without them
self._use_datasets = False
return

Expand All @@ -52,61 +59,65 @@ def _upload_test_data(self):
os.environ.get('GALAXY_TEST_DATA_REPO_CACHE', 'test-data-cache'))
test_data_paths.extend([
x[0] for x in os.walk(test_data_cache_dir) if '.git' not in x[0]])
if self._tool.tool_shed:
test_data_paths.append(os.path.abspath(os.path.join(
self._tool.tool_dir, 'test-data')))

# Upload all test datasets
for i, input in enumerate(input_datasets):
input_name = input[0]

for j, data_path in enumerate(test_data_paths):
input_path = os.path.join(data_path, input_name)
if os.path.exists(input_path):
break
elif j + 1 == len(test_data_paths): # the last path
raise ValueError('Test dataset "%s" doesn\'t exist.' %
input_name)

upload_tool = self._trans.app.toolbox.get_tool('upload1')
filename = os.path.basename(input_path)

with open(input_path, 'r') as f:
content = f.read()
headers = {
'content-disposition':
'form-data; name="{}"; filename="{}"'.format(
'files_0|file_data', filename
),
}

input_file = FieldStorage(headers=headers)
input_file.file = input_file.make_file()
input_file.file.write(content)

inputs = {
'dbkey': '?', # is it always a question mark?
'file_type': 'auto',
'files_0|type': 'upload_dataset',
'files_0|space_to_tab': None,
'files_0|to_posix_lines': 'Yes',
'files_0|file_data': input_file,
}

params = Params(inputs, sanitize=False)
incoming = params.__dict__
output = upload_tool.handle_input(self._trans, incoming,
history=None)

job_errors = output.get('job_errors', [])
if job_errors:
# self._errors.extend(job_errors)
raise ValueError('Cannot upload a dataset.')
else:
self._hids.update({
input_keys[i]: output['out_data'][0][1].hid
})
for input_name, input in data_inputs.items():
if input_name in test_datasets.keys():
for i, data_path in enumerate(test_data_paths):
input_path = os.path.join(data_path,
test_datasets[input_name])
if os.path.exists(input_path):
break
elif i + 1 == len(test_data_paths): # the last path
raise ValueError('Test dataset "%s" doesn\'t exist.' %
input_name)

upload_tool = self._trans.app.toolbox.get_tool('upload1')
filename = os.path.basename(input_path)

with open(input_path, 'r') as f:
content = f.read()
headers = {
'content-disposition':
'form-data; name="{}"; filename="{}"'.format(
'files_0|file_data', filename
),
}

input_file = FieldStorage(headers=headers)
input_file.file = input_file.make_file()
input_file.file.write(content)

inputs = {
'dbkey': '?', # is it always a question mark?
'file_type': input.extensions[0],
'files_0|type': 'upload_dataset',
'files_0|space_to_tab': None,
'files_0|to_posix_lines': 'Yes',
'files_0|file_data': input_file,
}

params = Params(inputs, sanitize=False)
incoming = params.__dict__
output = upload_tool.handle_input(self._trans, incoming,
history=None)

job_errors = output.get('job_errors', [])
if job_errors:
# self._errors.extend(job_errors)
raise ValueError('Cannot upload a dataset.')
else:
self._hids.update({
input_name: output['out_data'][0][1].hid
})

def _generate_tour(self):
""" Generate a tour. """
tour_name = self._tool.name + ' Tour'
test_inputs = self._test.inputs.keys()

steps = [{
'title': tour_name,
Expand All @@ -129,78 +140,99 @@ def _generate_tour(self):
}

if input.type == 'text':
text_param = self._test.inputs[name]
step['content'] = 'Enter parameter(s): <b>%s</b>' % text_param
if name in test_inputs:
param = self._test.inputs[name]
step['content'] = 'Enter value(s): <b>%s</b>' % param
else:
step['content'] = 'Enter a value.'

elif input.type == 'integer' or input.type == 'float':
num_param = self._test.inputs[name][0]
step['content'] = 'Enter parameter: <b>%s</b>' % num_param
if name in test_inputs:
num_param = self._test.inputs[name][0]
step['content'] = 'Enter number: <b>%s</b>' % num_param
else:
step['content'] = 'Enter a number.'

elif input.type == 'boolean':
choice = 'Yes' if self._test.inputs[name][0] is True else 'No'
step['content'] = 'Choose <b>%s</b>' % choice
if name in test_inputs:
choice = 'Yes' if self._test.inputs[name][0] is True \
else 'No'
step['content'] = 'Choose <b>%s</b>' % choice
else:
step['content'] = 'Choose Yes/No.'

elif input.type == 'select':
select_param = input.label
params = []
for option in self._tool.inputs[name].static_options:
if name in self._test.inputs.keys():
if name in test_inputs:
for option in self._tool.inputs[name].static_options:
for test_option in self._test.inputs[name]:
if test_option == option[1]:
params.append(option[0])
if params:
select_param = ', '.join(params)
step['content'] = 'Select parameter(s): <b>%s</b>' % \
select_param
step['content'] = 'Select parameter(s): <b>%s</b>' % \
select_param
else:
step['content'] = 'Select a parameter.'

elif input.type == 'data':
hid = self._hids[name]
dataset = self._test.inputs[name][0]
step['content'] = 'Select dataset <b>%s: %s</b>' % (
hid, dataset
)
if name in test_inputs:
hid = self._hids[name]
dataset = self._test.inputs[name][0]
step['content'] = 'Select dataset <b>%s: %s</b>' % (
hid, dataset
)
else:
step['content'] = 'Select a dataset.'

elif input.type == 'conditional':
param_id = '%s|%s' % (input.name, input.test_param.name)
step['title'] = input.test_param.label
step['element'] = '[tour_id="%s"]' % param_id
cond_param = input.label
params = []
for option in input.test_param.static_options:
if param_id in self._test.inputs.keys():

if param_id in self._test.inputs.keys():
for option in input.test_param.static_options:
for test_option in self._test.inputs[param_id]:
if test_option == option[1]:
params.append(option[0])

# Conditional param cases
cases = {}
for case in input.cases:
for key, value in case.inputs.items():
if key not in cases.keys():
cases[key] = value.label

for case_id, case_title in cases.items():
tour_id = '%s|%s' % (input.name, case_id)
if tour_id in self._test.inputs.keys():
case_params = ', '.join(
self._test.inputs[tour_id])
cond_case_steps.append({
'title': case_title,
'element': '[tour_id="%s"]' % tour_id,
'placement': 'right',
'content': 'Select parameter(s): <b>%s</b>' %
case_params
})

if params:
cond_param = ', '.join(params)
step['content'] = 'Select parameter(s): <b>%s</b>' % \
cond_param

# Conditional param cases
cases = {}
for case in input.cases:
for key, value in case.inputs.items():
if key not in cases.keys():
cases[key] = value.label

for case_id, case_title in cases.items():
tour_id = '%s|%s' % (input.name, case_id)
if tour_id in self._test.inputs.keys():
case_params = ', '.join(self._test.inputs[tour_id])
cond_case_steps.append({
'title': case_title,
'element': '[tour_id="%s"]' % tour_id,
'placement': 'right',
'content': 'Select parameter(s): <b>%s</b>' %
case_params
})
step['content'] = 'Select parameter(s): <b>%s</b>' % \
cond_param
else:
step['content'] = 'Select a parameter.'

elif input.type == 'data_column':
column_param = self._test.inputs[name][0]
step['content'] = 'Select <b>Column: %s</b>' % column_param
if name in test_inputs:
column_param = self._test.inputs[name][0]
step['content'] = 'Select <b>Column: %s</b>' % column_param
else:
step['content'] = 'Select a column.'

else:
step['content'] = 'Select parameter <b>%s</b>' % input.label
step['content'] = 'Select a parameter.'

steps.append(step)
if cond_case_steps:
Expand Down
9 changes: 5 additions & 4 deletions config/plugins/webhooks/demo/tour_generator/static/script.js
View file
Expand Up @@ -36,14 +36,15 @@ $(document).ready(function() {
});
});
} else {
Toastr.error('Some of the test datasets cannot be found in the history.');
Toastr.warning('Cannot generate a tour.');
console.error('Some of the test datasets cannot be found in the history.');
}
}, 1000);
}, 1500);
} else {
me._main(obj.data);
me._generateTour(obj.data.tour);
}
} else {
Toastr.error(obj.error);
Toastr.warning('Cannot generate a tour.');
console.error('Tour Generator: ' + obj.error);
}
});
Expand Down

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