def _run_query(self, sqa_query):
"""
run SQLAlachemy query,
return SearchResults
"""
search_results = SearchResults()
search_results.items = sqa_query.all()
search_results.total_count = len(search_results.items)
return search_results
def get_clipboard_items(self, _user_key):
"""
Returns all EMAPA clipboard SetMembers for the given user
"""
search_results = SearchResults()
items = SetMember.query.filter_by(_set_key=self.emapa_clipboard_set_key) \
.filter_by(_createdby_key=_user_key) \
.order_by(SetMember.sequencenum) \
.all()
search_results.items = items
search_results.total_count = len(items)
return search_results
def get(self):
"""
Get list of clipboard items
"""
results = SearchResults()
if current_user.is_authenticated:
results = self.clipboard_service.get_clipboard_items(
current_user._user_key)
return results.serialize()
def download_raw_samples(self, experiment_primaryid):
url = 'http://www.ebi.ac.uk/arrayexpress/json/v3/experiments/%s/samples' % experiment_primaryid
urlreader = UrlReader()
logger.debug("Preparing to read: %s" % url)
response = urlreader.get(url)
logger.debug("Read URL, status code (%s), content length(%d bytes)" % (response.statusCode, len(response.content)))
if response.statusCode != 200:
raise Exception("Bad status code (%d) received when retrieving samples" % response.statusCode)
search_result = SearchResults()
search_result.items = JsonHelper().fromJson(response.content)['experiment']['sample']
search_result.items = self.consolidate_samples(search_result.items)
search_result.total_count = len(search_result.items)
return search_result
def _run_paginated_query(self, sqa_query, paginator):
"""
run SQLAlchemy query.paginate(),
return SearchResults
set paginator on SearchResults
"""
search_results = SearchResults()
logger.debug("running paginated query, page_num=%s, page_size=%s" \
% (paginator.page_num, paginator.page_size))
pagination = sqa_query.paginate(
paginator.page_num,
paginator.page_size,
False
)
search_results.items = pagination.items
search_results.total_count = pagination.total
search_results.paginator = paginator
return search_results
