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import json
import datetime
import requests
from flask import abort, flash
from fatcat_covid19.webface import app
def do_search(index, request, limit=30, offset=0, deep_page_limit=2000):
# Sanity checks
if limit > 100:
limit = 100
if offset < 0:
offset = 0
if offset > deep_page_limit:
# Avoid deep paging problem.
offset = deep_page_limit
request["size"] = int(limit)
request["from"] = int(offset)
# print(request)
resp = requests.get("%s/%s/_search" %
(app.config['ELASTICSEARCH_BACKEND'], index),
json=request)
if resp.status_code == 400:
print("elasticsearch 400: " + str(resp.content))
#flash("Search query failed to parse; you might need to use quotes.<p><code>{}</code>".format(resp.content))
abort(resp.status_code)
elif resp.status_code != 200:
print("elasticsearch non-200 status code: " + str(resp.status_code))
print(resp.content)
abort(resp.status_code)
content = resp.json()
#print(json.dumps(content, indent=2))
results = []
for h in content['hits']['hits']:
r = h['_source']
r['_highlights'] = []
highlights = h.get('highlight', {})
for k in highlights:
r['_highlights'] += highlights[k]
results.append(r)
#print(json.dumps(results, indent=2))
for h in results:
# Handle surrogate strings that elasticsearch returns sometimes,
# probably due to mangled data processing in some pipeline.
# "Crimes against Unicode"; production workaround
for key in h:
if type(h[key]) is str:
h[key] = h[key].encode('utf8', 'ignore').decode('utf8')
return {"count_returned": len(results),
"count_found": content['hits']['total'],
"results": results,
"offset": offset,
"deep_page_limit": deep_page_limit}
def do_fulltext_search(q, limit=30, offset=0):
#print("Search hit: " + q)
if limit > 100:
# Sanity check
limit = 100
# Convert raw DOIs to DOI queries
if len(q.split()) == 1 and q.startswith("10.") and q.count("/") >= 1:
q = 'doi:"{}"'.format(q)
search_request = {
"query": {
"query_string": {
"query": q,
"default_operator": "AND",
"analyze_wildcard": True,
"lenient": True,
"fields": [
"everything",
"abstract",
"fulltext.body",
"fulltext.annex",
],
},
},
"highlight" : {
"number_of_fragments" : 3,
"fragment_size" : 150,
"fields" : {
"abstract": { },
"fulltext.body": { },
"fulltext.annex": { },
#"everything": { "number_of_fragments" : 3 },
#"fulltext.abstract": { "number_of_fragments" : 3 },
#"fulltext.body": { "number_of_fragments" : 3 },
#"fulltext.annex": { "number_of_fragments" : 3 },
},
},
}
resp = do_search(app.config['ELASTICSEARCH_FULLTEXT_INDEX'], search_request, offset=offset)
for h in resp['results']:
# Ensure 'contrib_names' is a list, not a single string
if type(h['contrib_names']) is not list:
h['contrib_names'] = [h['contrib_names'], ]
h['contrib_names'] = [name.encode('utf8', 'ignore').decode('utf8') for name in h['contrib_names']]
resp["query"] = { "q": q }
resp["limit"] = limit
return resp
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