def get_display_options():
"""Get the list of possible formats to display the result.
This function returns the possible formats to display the result of a query on ENA. Each format is described.
"""
options = enasearch.get_display_options(verbose=False)
print_simple_dict(options)
def write_display_options():
"""
Write the display options
"""
s = '%s<xml name="display_options">\n' % (spaces)
when_s = '%s<xml name="when_display_options">\n' % (spaces)
options = enasearch.get_display_options(verbose=False)
for opt in options:
s += '%s<option value="%s">%s</option>\n' % (2 * spaces, opt, options[opt]['description'])
when_s += '%s<when value="%s">\n' % (2 * spaces, opt)
if opt == 'fasta' or opt == 'fastq':
when_s += '%s<param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/>\n' % (3 * spaces)
when_s += '%s<param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/>\n' % (3 * spaces)
else:
when_s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (3 * spaces)
when_s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (3 * spaces)
when_s += '%s</when>\n' % (2 * spaces)
s += '%s</xml>\n' % (spaces)
when_s += '%s</xml>\n' % (spaces)
s += when_s
return s
def test_get_display_options():
"""Test get_display_options function"""
display_options = enasearch.get_display_options(verbose=False)
assert "html" in display_options
assert "fasta" in display_options
def write_result_parameters(fts=False):
"""
Write the parameters that are dependant of results
"""
res = enasearch.get_results(verbose=False)
options = enasearch.get_display_options(verbose=False)
ft = enasearch.get_filter_types(verbose=False)
# Format the filter type related parameters
ft_parameters = {}
for t in ft:
s = ''
if 'operators' in ft[t]:
s = '%s<param name="operation" type="select" label="Operator">\n' % (7 * spaces)
for o in ft[t]['operators']:
on = o
if o in operator_names:
on = operator_names[o]
s += '%s<option value="%s">%s</option>\n' % (8 * spaces, on, on)
s += '%s</param>\n' % (7 * spaces)
if 'value' in ft[t]:
value_format = 'float' if t == 'Number' else 'text'
s += '%s<param name="value" type="%s" value="" label="%s"/>\n' % (7 * spaces, value_format, ft[t]['value'])
elif 'values' in ft[t]:
s += '%s<param name="value" type="select" label="Value">\n' % (7 * spaces)
for v in ft[t]['values']:
s += '%s<option value="%s">%s</option>\n' % (8 * spaces, v, v)
s += '%s</param>\n' % (7 * spaces)
else:
s += '%s<conditional name="op">\n' % (7 * spaces)
s += '%s<param name="operation" type="select" label="Operation">\n' % (8 * spaces)
for op in ft[t]:
s += '%s<option value="%s">%s</option>\n' % (9 * spaces, op, ft[t][op]['description'])
s += '%s</param>\n' % (8 * spaces)
for op in ft[t]:
s += '%s<when value="%s">\n' % (8 * spaces, op)
s += '%s<param name="values" type="text" value="" label="%s" help="Values separated by simple comma"/>\n' % (9 * spaces, ",".join(ft[t][op]['parameters']))
s += '%s</when>\n' % (8 * spaces)
s += '%s</conditional>\n' % (7 * spaces)
ft_parameters[t] = s
# Start adding the conditional
s = '%s<conditional name="res">\n' % (2 * spaces)
# Add result parameter
s += '%s<param argument="--result" type="select" label="Result to return">\n' % (3 * spaces)
for r in res:
s += '%s<option value="%s">%s</option>\n' % (4 * spaces, r, res[r]['description'])
s += '%s</param>\n' % (3 * spaces)
for r in res:
sf = enasearch.get_sortable_fields(r)
ff = res[r]['filter_fields']
s += '%s<when value="%s">\n' % (3 * spaces, r)
if not fts:
s += '%s<repeat name="queries" title="Add a query">\n' % (4 * spaces)
# Add combination operator
s += '%s<param name="combination_operation" type="select" label="Combination operation">\n' % (5 * spaces)
s += '%s<option value="AND">AND</option>\n' % (6 * spaces)
s += '%s<option value="OR">OR</option>\n' % (6 * spaces)
s += '%s<option value="NOT">NOT</option>\n' % (6 * spaces)
s += '%s</param>\n' % (5 * spaces)
s += '%s<conditional name="filter_field">\n' % (5 * spaces)
s += '%s<param name="field" type="select" label="Field to query">\n' % (6 * spaces)
for f in ff:
s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, ff[f]['description'])
s += '%s</param>\n' % (6 * spaces)
for f in ff:
# Add the correct parameter given the type of field
typ = ff[f]['type'].capitalize()
if typ not in ft_parameters:
if f == 'location':
typ = 'Geospatial'
else:
continue
s += '%s<when value="%s">\n' % (6 * spaces, f)
s += ft_parameters[typ]
s += '%s</when>\n' % (6 * spaces)
s += '%s</conditional>\n' % (5 * spaces)
s += '%s</repeat>\n' % (4 * spaces)
# Add display opt
s += '%s<conditional name="display_opt">\n' % (4 * spaces)
s += '%s<param argument="--display" type="select" label="Display option to specify the display format">\n' % (5 * spaces)
s += '%s<expand macro="display_options"/>\n' % (6 * spaces)
s += '%s</param>\n' % (5 * spaces)
for opt in options:
s += '%s<when value="%s"' % (5 * spaces, opt)
if opt != 'fasta' and opt != 'fastq':
s += '>\n'
s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (6 * spaces)
s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (6 * spaces)
if opt == 'report':
s += '%s<param argument="--fields" type="select" multiple="true" label="Fields to return">\n' % (6 * spaces)
for f in res[r]['returnable_fields']:
s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, f)
s += '%s</param>\n' % (6 * spaces)
s += '%s<param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">\n' % (6 * spaces)
for f in sf:
s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, sf[f]['description'])
s += '%s</param>\n' % (6 * spaces)
s += '%s</when>\n' % (5 * spaces)
else:
s += '/>\n'
s += '%s</conditional>\n' % (4 * spaces)
s += '%s</when>\n' % (3 * spaces)
s += '%s</conditional>\n' % (2 * spaces)
return s
def get_display_options():
""" Get the display options to specify the display format """
options = enasearch.get_display_options(verbose=False)
print_simple_dict(options)