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Api example #1463

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merged 4 commits into from
Jan 29, 2025
Merged

Api example #1463

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3bd8138
Made some variables to int_args
haohangyan Jan 27, 2025
d9580f4
Fixed the args value in Flask-RESTx model
haohangyan Jan 27, 2025
f1e7502
TODO's for reach api
haohangyan Jan 27, 2025
92eb04d
Fixed test_get_urll with new link
haohangyan Jan 28, 2025
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2 changes: 1 addition & 1 deletion indra/tests/test_crossref_client.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def test_get_license_links():
@pytest.mark.webservice
def test_get_url():
url = crossref_client.get_url(test_doi)
assert url == 'http://dx.doi.org/10.1016/j.ccell.2016.02.010'
assert url == 'https://doi.org/10.1016/j.ccell.2016.02.010'
assert unicode_strs(url)
url = crossref_client.get_url('xyz')
assert url is None
8 changes: 7 additions & 1 deletion rest_api/api.py
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Expand Up @@ -74,7 +74,7 @@
'genes': fields.List(fields.String, example=['BRAF', 'MAP2K1'])})

# Store the arguments by type
int_args = ['poolsize', 'size_cutoff']
int_args = ['members_allowed', 'protocol', 'poolsize', 'size_cutoff']
float_args = ['score_threshold', 'belief_cutoff']
boolean_args = [
'do_rename', 'use_adeft', 'do_methionine_offset', 'do_orthology_mapping',
Expand All @@ -89,6 +89,8 @@
dict_args = [
'grounding_map', 'misgrounding_map', 'whitelist', 'mutations']

str_args = {'stmt_type': "Modification", 'policy': 'all'}


def _return_stmts(stmts):
if stmts:
Expand Down Expand Up @@ -225,6 +227,8 @@ def make_preassembly_model(func):
fields.String, example=default)
elif arg in dict_args:
model_fields[arg] = fields.Nested(dict_model)
elif arg in str_args.keys():
model_fields[arg] = fields.String(example=str_args[arg])
else:
model_fields[arg] = fields.String(example=default)
new_model = api.inherit(
Expand Down Expand Up @@ -316,6 +320,7 @@ def post(self):
@sources_ns.expect(reach_text_model)
@sources_ns.route('/reach/process_text')
class ReachProcessText(Resource):
# TODO: REACH web service is down. Need to use a local Reach
@api.doc(False)
def options(self):
return {}
Expand Down Expand Up @@ -397,6 +402,7 @@ def post(self):
@sources_ns.expect(reach_pmc_model)
@sources_ns.route('/reach/process_pmc')
class ReachProcessPmc(Resource):
#TODO: REACH web service is down. Need to use a local Reach
@api.doc(False)
def options(self):
return {}
Expand Down
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