def post(self):
query_strings = [
x.strip() for x in self.get_argument('query', '').split(',')
if x != ''
]
# run the queries
session = Session()
def checkbox_arg(name):
return self.get_argument(name, None) == 'on'
all_models = queries.get_model_list(session)
model_list = [m for m in all_models if checkbox_arg(m)]
include_metabolites = checkbox_arg('include_metabolites')
include_reactions = checkbox_arg('include_reactions')
include_genes = checkbox_arg('include_genes')
metabolite_results = []
reaction_results = []
gene_results = []
# genes
for query_string in query_strings:
if include_genes:
gene_results += queries.search_for_genes(
query_string, session, limit_models=model_list)
if include_reactions:
reaction_results += queries.search_for_reactions(
query_string, session, limit_models=model_list)
if include_metabolites:
metabolite_results += queries.search_for_metabolites(
query_string, session, limit_models=model_list)
result = {
'results': {
'reactions': reaction_results,
'metabolites': metabolite_results,
'genes': gene_results
},
'no_pager': True,
'page_name': 'advanced_search_results',
}
session.close()
self.write(self.template.render(result))
self.finish()
def post(self):
query_strings = [x.strip() for x in
self.get_argument('query', '').split(',')
if x != '']
# run the queries
session = Session()
def checkbox_arg(name):
return self.get_argument(name, None) == 'on'
all_models = queries.get_model_list(session)
model_list = [m for m in all_models if checkbox_arg(m)]
include_metabolites = checkbox_arg('include_metabolites')
include_reactions = checkbox_arg('include_reactions')
include_genes = checkbox_arg('include_genes')
metabolite_results = []
reaction_results = []
gene_results = []
# genes
for query_string in query_strings:
if include_genes:
gene_results += queries.search_for_genes(query_string, session,
limit_models=model_list)
if include_reactions:
reaction_results += queries.search_for_reactions(query_string, session,
limit_models=model_list)
if include_metabolites:
metabolite_results += queries.search_for_metabolites(query_string, session,
limit_models=model_list)
result = {'results': {'reactions': reaction_results,
'metabolites': metabolite_results,
'genes': gene_results},
'no_pager': True}
session.close()
self.write(self.template.render(result))
self.finish()
def get(self):
# get arguments
query_string = self.get_argument('query')
page = self.get_argument('page', None)
size = self.get_argument('size', None)
search_type = self.get_argument('search_type', None)
include_link_urls = 'include_link_urls' in self.request.query_arguments
# defaults
sort_column = None
sort_direction = 'ascending'
# get the sorting column
columns = _parse_col_arg(self.get_argument('columns', None))
sort_column, sort_direction = _get_col_name(self.request.query_arguments, columns,
sort_column, sort_direction)
# run the queries
session = Session()
result = None
if search_type == 'reactions':
# reactions
raw_results = queries.search_for_universal_reactions(query_string, session, page,
size, sort_column, sort_direction)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/universal/reactions/{bigg_id}'.format(**x)})
for x in raw_results]
result = {'results': [dict(x, model_bigg_id='Universal', organism='') for x in raw_results],
'results_count': queries.search_for_universal_reactions_count(query_string,
session)}
elif search_type == 'metabolites':
raw_results = queries.search_for_universal_metabolites(query_string, session,
page, size, sort_column,
sort_direction)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/universal/metabolites/{bigg_id}'.format(**x)})
for x in raw_results]
result = {'results': [dict(x, model_bigg_id='Universal', organism='') for x in raw_results],
'results_count': queries.search_for_universal_metabolites_count(query_string, session)}
elif search_type == 'genes':
raw_results = queries.search_for_genes(query_string, session, page,
size, sort_column,
sort_direction)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/models/{model_bigg_id}/genes/{bigg_id}'.format(**x)})
for x in raw_results]
result = {'results': raw_results,
'results_count': queries.search_for_genes_count(query_string, session)}
elif search_type == 'models':
raw_results = queries.search_for_models(query_string, session, page,
size, sort_column, sort_direction)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/models/{bigg_id}'.format(**x),
'metabolite_count': '/models/{bigg_id}/metabolites'.format(**x),
'reaction_count': '/models/{bigg_id}/reactions'.format(**x),
'gene_count': '/models/{bigg_id}/genes'.format(**x)})
for x in raw_results]
result = {'results': raw_results,
'results_count': queries.search_for_models_count(query_string, session)}
else:
raise HTTPError(400, 'Bad search_type %s' % search_type)
session.close()
self.write(result)
self.finish()
def get(self):
# get arguments
query_string = self.get_argument('query')
page = self.get_argument('page', None)
size = self.get_argument('size', None)
search_type = self.get_argument('search_type', None)
multistrain_off = self.get_argument('multistrain', None) == 'off'
include_link_urls = 'include_link_urls' in self.request.query_arguments
# defaults
sort_column = None
sort_direction = 'ascending'
# get the sorting column
columns = _parse_col_arg(self.get_argument('columns', None))
sort_column, sort_direction = _get_col_name(
self.request.query_arguments,
columns,
sort_column,
sort_direction,
)
# run the queries
session = Session()
result = None
if search_type == 'reactions':
# reactions
raw_results = queries.search_for_universal_reactions(
query_string,
session,
page,
size,
sort_column,
sort_direction,
multistrain_off,
)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/universal/reactions/{bigg_id}'.format(**x)})
for x in raw_results]
result = {
'results': [dict(x, model_bigg_id='Universal', organism='') for x in raw_results],
'results_count': queries.search_for_universal_reactions_count(
query_string,
session,
multistrain_off,
)}
elif search_type == 'metabolites':
raw_results = queries.search_for_universal_metabolites(
query_string,
session,
page,
size,
sort_column,
sort_direction,
multistrain_off,
)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/universal/metabolites/{bigg_id}'.format(**x)})
for x in raw_results]
result = {
'results': [dict(x, model_bigg_id='Universal', organism='') for x in raw_results],
'results_count': queries.search_for_universal_metabolites_count(
query_string,
session,
multistrain_off,
)}
elif search_type == 'genes':
raw_results = queries.search_for_genes(
query_string,
session,
page,
size,
sort_column,
sort_direction,
multistrain_off=multistrain_off,
)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/models/{model_bigg_id}/genes/{bigg_id}'.format(**x)})
for x in raw_results]
result = {
'results': raw_results,
'results_count': queries.search_for_genes_count(
query_string,
session,
multistrain_off=multistrain_off,
)}
elif search_type == 'models':
raw_results = queries.search_for_models(
query_string,
session,
page,
size,
sort_column,
sort_direction,
multistrain_off,
)
if include_link_urls:
raw_results = [dict(x, link_urls={'bigg_id': '/models/{bigg_id}'.format(**x),
'metabolite_count': '/models/{bigg_id}/metabolites'.format(**x),
'reaction_count': '/models/{bigg_id}/reactions'.format(**x),
'gene_count': '/models/{bigg_id}/genes'.format(**x)})
for x in raw_results]
result = {
'results': raw_results,
'results_count': queries.search_for_models_count(
query_string,
session,
multistrain_off,
)
}
else:
raise HTTPError(400, 'Bad search_type %s' % search_type)
session.close()
self.write(result)
self.finish()
