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Apply black formatting.
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Apply isort.
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@dannon
dannon committed Feb 3, 2022
1 parent ff2f360 commit 623a5e1
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37 changes: 18 additions & 19 deletions config/plugins/webhooks/demo/tool_list/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

def main(trans, webhook, params):
data = {}
data['tools'] = []
data["tools"] = []
unique_tools = []

tools = trans.app.toolbox.tools()
Expand All @@ -16,24 +16,23 @@ def main(trans, webhook, params):
except AttributeError:
continue

if (ts_data['name'] + ts_data['installed_changeset_revision'] not in
unique_tools):

unique_tools.append(
ts_data['name'] + ts_data['installed_changeset_revision']
if ts_data["name"] + ts_data["installed_changeset_revision"] not in unique_tools:

unique_tools.append(ts_data["name"] + ts_data["installed_changeset_revision"])

data["tools"].append(
{
"name": ts_data["name"],
"owner": ts_data["owner"],
"tool_panel_section_label": panel[1],
"tool_shed_url": ts_data["tool_shed"],
"install_tool_dependencies": True,
"install_repository_dependencies": True,
"install_resolver_dependencies": True,
"revisions": [ts_data["installed_changeset_revision"]],
}
)

data['tools'].append({
'name': ts_data['name'],
'owner': ts_data['owner'],
'tool_panel_section_label': panel[1],
'tool_shed_url': ts_data['tool_shed'],
'install_tool_dependencies': True,
'install_repository_dependencies': True,
'install_resolver_dependencies': True,
'revisions': [ts_data['installed_changeset_revision']]
})
if panel[0]:
data['tools'][-1]['tool_panel_section_id'] = panel[0]
data["tools"][-1]["tool_panel_section_id"] = panel[0]

return {'yaml': yaml.safe_dump(data, default_flow_style=False)}
return {"yaml": yaml.safe_dump(data, default_flow_style=False)}
210 changes: 95 additions & 115 deletions config/plugins/webhooks/demo/tour_generator/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,13 +28,12 @@ def _upload_test_data(self):
section of the provided tool.
"""
if not self._tool.tests:
raise ValueError('Tests are not defined.')
raise ValueError("Tests are not defined.")

self._test = self._tool.tests[0]

# All inputs with the type 'data'
self._data_inputs = {x.name: x for x in self._tool.input_params if
x.type == 'data'}
self._data_inputs = {x.name: x for x in self._tool.input_params if x.type == "data"}

# Datasets from the <test></test> section
test_datasets = {
Expand All @@ -45,20 +44,17 @@ def _upload_test_data(self):

# Conditional datasets
for name in self._test.inputs.keys():
if '|' in name:
input_name = name.split('|')[1]
if "|" in name:
input_name = name.split("|")[1]
if input_name in self._data_inputs.keys():
test_datasets.update({
input_name: self._test.inputs[name][0]
})
test_datasets.update({input_name: self._test.inputs[name][0]})

if not test_datasets.keys():
not_supported_input_types = [
k for k, v in self._tool.inputs.items() if
v.type == 'repeat' or v.type == 'data_collection'
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('Not supported input types.')
raise ValueError("Not supported input types.")
else:
# Some tests don't have data inputs at all,
# so we can generate a tour without them
Expand All @@ -73,120 +69,108 @@ def _upload_test_data(self):
if not input_path:
raise ValueError('Test dataset "%s" doesn\'t exist.' % input_name)

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

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

input_file = cgi_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,
"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)
output = upload_tool.handle_input(self._trans, incoming, history=None)

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

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

steps = [{
'title': tour_name,
'content': 'This short tour will guide you through the <b>'
+ self._tool.name + '</b> tool.',
'orphan': True
}]
steps = [
{
"title": tour_name,
"content": "This short tour will guide you through the <b>" + self._tool.name + "</b> tool.",
"orphan": True,
}
]

for name, input in self._tool.inputs.items():
cond_case_steps = []

if input.type == 'repeat':
if input.type == "repeat":
continue

step = {
'title': input.label,
'element': '[tour_id=%s]' % name,
'placement': 'right',
'content': ''
}
step = {"title": input.label, "element": "[tour_id=%s]" % name, "placement": "right", "content": ""}

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

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

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

elif input.type == 'select':
elif input.type == "select":
params = []
if name in test_inputs:
for option in input.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
select_param = ", ".join(params)
step["content"] = "Select parameter(s): <b>%s</b>" % select_param
else:
step['content'] = 'Select a parameter'
step["content"] = "Select a parameter"

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

elif input.type == 'conditional':
param_id = f'{input.name}|{input.test_param.name}'
step['title'] = input.test_param.label
step['element'] = '[tour_id="%s"]' % param_id
elif input.type == "conditional":
param_id = f"{input.name}|{input.test_param.name}"
step["title"] = input.test_param.label
step["element"] = '[tour_id="%s"]' % param_id
params = []

if param_id in self._test.inputs.keys():
Expand All @@ -203,92 +187,88 @@ def _generate_tour(self):
cases[key] = value.label

for case_id, case_title in cases.items():
tour_id = f'{input.name}|{case_id}'
tour_id = f"{input.name}|{case_id}"
if tour_id in self._test.inputs.keys():
if case_id in self._data_inputs.keys():
hid = self._hids[case_id]
dataset = self._test.inputs[tour_id][0]
step_msg = 'Select dataset: <b>%s: %s</b>' % \
(hid, dataset)
step_msg = "Select dataset: <b>%s: %s</b>" % (hid, dataset)
else:
case_params = ', '.join(
self._test.inputs[tour_id])
step_msg = 'Select parameter(s): ' + \
'<b>%s</b>' % case_params
cond_case_steps.append({
'title': case_title,
'element': '[tour_id="%s"]' % tour_id,
'placement': 'right',
'content': step_msg
})
case_params = ", ".join(self._test.inputs[tour_id])
step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params
cond_case_steps.append(
{
"title": case_title,
"element": '[tour_id="%s"]' % tour_id,
"placement": "right",
"content": step_msg,
}
)

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

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

else:
step['content'] = 'Select a parameter'
step["content"] = "Select a parameter"

steps.append(step)
if cond_case_steps:
steps.extend(cond_case_steps) # add conditional input steps

# Add the last step
steps.append({
'title': 'Execute tool',
'content': 'Click <b>Execute</b> button to run the tool.',
'element': '#execute',
'placement': 'bottom',
# 'postclick': ['#execute']
})
steps.append(
{
"title": "Execute tool",
"content": "Click <b>Execute</b> button to run the tool.",
"element": "#execute",
"placement": "bottom",
# 'postclick': ['#execute']
}
)

self._tour = {
'title_default': tour_name,
'name': tour_name,
'description': self._tool.name + ' ' + self._tool.description,
'steps': steps
"title_default": tour_name,
"name": tour_name,
"description": self._tool.name + " " + self._tool.description,
"steps": steps,
}

def get_data(self):
"""
Return a dictionary with the uploaded datasets' history ids and
the generated tour.
"""
return {
'useDatasets': self._use_datasets,
'hids': list(self._hids.values()),
'tour': self._tour
}
return {"useDatasets": self._use_datasets, "hids": list(self._hids.values()), "tour": self._tour}


def main(trans, webhook, params):
error = ''
error = ""
data = {}

try:
if not params or 'tool_id' not in params.keys():
raise KeyError('Tool id is missing.')
if not params or "tool_id" not in params.keys():
raise KeyError("Tool id is missing.")

if not params or 'tool_version' not in params.keys():
raise KeyError('Tool version is missing.')
if not params or "tool_version" not in params.keys():
raise KeyError("Tool version is missing.")

tool_id = params['tool_id']
tool_version = params['tool_version']
tool_id = params["tool_id"]
tool_version = params["tool_version"]
tour_generator = TourGenerator(trans, tool_id, tool_version)
data = tour_generator.get_data()

except Exception as e:
error = str(e)
log.exception(e)

return {'success': not error, 'error': error, 'data': data}
return {"success": not error, "error": error, "data": data}
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