def test_write_tsv(self):
expected_file = 'test.tsv'
try:
compound_set = pickle.load(open('compound_set.pkl', 'rb'))
file_path = compound_parsing.write_tsv(compound_set, expected_file)
filecmp.cmp(file_path, 'test_out.tsv')
finally:
if os.path.exists(expected_file):
os.remove(expected_file)
def compound_set_to_file(self, ctx, params):
"""
CompoundSetToFile
string compound_set_name
string output_format
:param params: instance of type "compoundset_download_params" ->
structure: parameter "workspace_name" of String, parameter
"compound_set_name" of String, parameter "output_format" of String
:returns: instance of type "compoundset_download_results" ->
structure: parameter "report_name" of String, parameter
"report_ref" of String
"""
# ctx is the context object
# return variables are: output
#BEGIN compound_set_to_file
self._check_required_param(params, ['workspace_name', 'compound_set_name',
'output_format'])
compoundset = self.ws_client.get_objects2({'objects': [
{'workspace': params['workspace_name'],
'name': params['compound_set_name']}]})['data'][0]['data']
ext = params['output_format']
out = "%s/%s.%s" % (self.scratch, compoundset['name'], ext)
if ext == 'sdf':
outfile_path = parse.write_sdf(compoundset, out)
elif ext == 'tsv':
outfile_path = parse.write_tsv(compoundset, out)
else:
raise ValueError('Invalid output file type. Expects tsv or sdf')
report_files = [{'path': outfile_path,
'name': os.path.basename(outfile_path),
'label': os.path.basename(outfile_path),
'description': 'A compound set in %s format' % ext}]
report_params = {
'objects_created': [],
'message': 'Converted %s compound set to %s format.' % (
params['compound_set_name'], params['output_format']),
'file_links': report_files,
'workspace_name': params['workspace_name'],
'report_object_name': 'compound_set_download_report'
}
# Construct the output to send back
report_client = KBaseReport(self.callback_url)
report_info = report_client.create_extended_report(report_params)
output = {'report_name': report_info['name'],
'report_ref': report_info['ref'],
}
#END compound_set_to_file
# At some point might do deeper type checking...
if not isinstance(output, dict):
raise ValueError('Method compound_set_to_file return value ' +
'output is not type dict as required.')
# return the results
return [output]
def _export_compound_set(self, ref, file_type):
logging.info("Exporting {} as {}".format(ref, file_type))
compoundset = self.dfu.get_objects({'object_refs':
[ref]})['data'][0]['data']
temp_dir = "{}/{}".format(self.scratch, uuid.uuid4())
os.mkdir(temp_dir)
out_dir = "{}/{}".format(temp_dir, compoundset['name'])
os.mkdir(out_dir)
target = "{}/{}.{}".format(out_dir, compoundset['name'], file_type)
if file_type == 'tsv':
parse.write_tsv(compoundset, target)
elif file_type == 'sdf':
parse.write_sdf(compoundset, target)
else:
raise ValueError("Bad file_type: {}".format(file_type))
handle = self.dfu.package_for_download({
'file_path': out_dir,
'ws_refs': [ref]
})
output = {'shock_id': handle['shock_id']}
return output
def compound_set_to_file(self, ctx, params):
"""
CompoundSetToFile
string compound_set_name
string output_format
:param params: instance of type "compoundset_download_params" ->
structure: parameter "compound_set_ref" of String, parameter
"output_format" of String
:returns: instance of type "compoundset_download_results" ->
structure: parameter "file_path" of String, parameter
"packed_mol2_files_path" of String, parameter
"comp_id_mol2_file_name_map" of mapping from String to String
"""
# ctx is the context object
# return variables are: output
#BEGIN compound_set_to_file
self._check_param(params, ['compound_set_ref', 'output_format'])
ret = self.dfu.get_objects(
{'object_refs': [params['compound_set_ref']]})['data'][0]
compoundset = ret['data']
ext = params['output_format']
out = f"{self.scratch}/{uuid.uuid4()}"
os.mkdir(out)
out += f"/{compoundset['name']}"
if ext == 'sdf':
outfile_path = parse.write_sdf(compoundset, out)
elif ext == 'tsv':
outfile_path = parse.write_tsv(compoundset, out)
else:
outfile_path = parse.write_mol_dir(compoundset, out, ext)
packed_mol2_files_path, comp_id_mol2_file_name_map = self._fetch_mol2_files(
params['compound_set_ref'])
output = {
'file_path': outfile_path,
'packed_mol2_files_path': packed_mol2_files_path,
'comp_id_mol2_file_name_map': comp_id_mol2_file_name_map
}
#END compound_set_to_file
# At some point might do deeper type checking...
if not isinstance(output, dict):
raise ValueError('Method compound_set_to_file return value ' +
'output is not type dict as required.')
# return the results
return [output]