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authorBryan Newbold <bnewbold@robocracy.org>2020-03-25 13:02:53 -0700
committerBryan Newbold <bnewbold@robocracy.org>2020-07-24 10:07:48 -0700
commit693a6f71b1afef686b6783ba3afb1a67bb14b62b (patch)
tree9be06e4d5c32d7a1ff415788185b51960cf74f2e
parent8b00843af1366cf019c896057706ace4afff27ba (diff)
downloadfatcat-693a6f71b1afef686b6783ba3afb1a67bb14b62b.tar.gz
fatcat-693a6f71b1afef686b6783ba3afb1a67bb14b62b.zip
WIP: refactoring search to use elasticsearch-dsl
-rw-r--r--python/fatcat_web/__init__.py5
-rw-r--r--python/fatcat_web/search.py285
2 files changed, 137 insertions, 153 deletions
diff --git a/python/fatcat_web/__init__.py b/python/fatcat_web/__init__.py
index 562ffeb2..487de58a 100644
--- a/python/fatcat_web/__init__.py
+++ b/python/fatcat_web/__init__.py
@@ -11,6 +11,7 @@ from authlib.flask.client import OAuth
from loginpass import create_flask_blueprint, Gitlab, GitHub, ORCiD
from raven.contrib.flask import Sentry
import fatcat_openapi_client
+import elasticsearch
from fatcat_web.web_config import Config
@@ -71,7 +72,9 @@ mwoauth = MWOAuth(
mwoauth.handshaker.user_agent = "fatcat.wiki;python_web_interface"
app.register_blueprint(mwoauth.bp, url_prefix='/auth/wikipedia')
-from fatcat_web import routes, editing_routes, auth, cors, forms # noqa: E402
+app.es_client = elasticsearch.Elasticsearch(Config.ELASTICSEARCH_BACKEND)
+
+from fatcat_web import routes, editing_routes, auth, cors, forms
# TODO: blocking on ORCID support in loginpass
if Config.ORCID_CLIENT_ID:
diff --git a/python/fatcat_web/search.py b/python/fatcat_web/search.py
index 4a87c735..87d07e55 100644
--- a/python/fatcat_web/search.py
+++ b/python/fatcat_web/search.py
@@ -11,7 +11,10 @@ import requests
from flask import abort, flash
from fatcat_web import app
-def do_search(index, request, limit=30, offset=0, deep_page_limit=2000):
+import elasticsearch
+from elasticsearch_dsl import Search, Q
+
+def generic_search_execute(search, limit=30, offset=0, deep_page_limit=2000):
# Sanity checks
if limit > 100:
@@ -22,25 +25,24 @@ def do_search(index, request, limit=30, offset=0, deep_page_limit=2000):
# 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()
- results = [h['_source'] for h in content['hits']['hits']]
- for h in results:
+ search = search[int(offset):int(offset)+int(limit)]
+
+ try:
+ resp = search.execute()
+ except elasticsearch.exceptions.RequestError as e:
+ # this is a "user" error
+ print("elasticsearch 400: " + str(e.info))
+ flash("Search query failed to parse; you might need to use quotes.<p><code>{}: {}</code>".format(e.error, e.info['error']['root_cause'][0]['reason']))
+ abort(e.status_code)
+ except elasticsearch.exceptions.TransportError as e:
+ # all other errors
+ print("elasticsearch non-200 status code: {}".format(e.info))
+ flash("Elasticsearch error: {}".format(e.error))
+ abort(e.status_code)
+
+ # just the dict()
+ hits = [h._d_ for h in resp]
+ for h in hits:
# Handle surrogate strings that elasticsearch returns sometimes,
# probably due to mangled data processing in some pipeline.
# "Crimes against Unicode"; production workaround
@@ -48,20 +50,16 @@ def do_search(index, request, limit=30, offset=0, deep_page_limit=2000):
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,
+ return {"count_returned": len(hits),
+ "count_found": int(resp.hits.total),
+ "results": hits,
"offset": offset,
+ "limit": limit,
"deep_page_limit": deep_page_limit}
def do_release_search(q, limit=30, fulltext_only=True, 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)
@@ -69,26 +67,25 @@ def do_release_search(q, limit=30, fulltext_only=True, offset=0):
if fulltext_only:
q += " in_web:true"
- search_request = {
- "query": {
- "query_string": {
- "query": q,
- "default_operator": "AND",
- "analyze_wildcard": True,
- "lenient": True,
- "fields": ["biblio"],
- },
- },
- }
+ search = Search(using=app.es_client, index=app.config['ELASTICSEARCH_RELEASE_INDEX']) \
+ .query(
+ 'query_string',
+ query=q,
+ default_operator="AND",
+ analyze_wildcard=True,
+ lenient=True,
+ fields=["biblio"],
+ )
+
+ resp = generic_search_execute(search, offset=offset)
- resp = do_search(app.config['ELASTICSEARCH_RELEASE_INDEX'], search_request, offset=offset)
for h in resp['results']:
+ print(h)
# 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
@@ -98,21 +95,18 @@ def do_container_search(q, limit=30, offset=0):
if len(q.split()) == 1 and len(q) == 9 and q[0:4].isdigit() and q[4] == '-':
q = 'issnl:"{}"'.format(q)
- search_request = {
- "query": {
- "query_string": {
- "query": q,
- "default_operator": "AND",
- "analyze_wildcard": True,
- "lenient": True,
- "fields": ["biblio"],
- },
- },
- }
-
- resp = do_search(app.config['ELASTICSEARCH_CONTAINER_INDEX'], search_request, limit=limit, offset=offset)
+ search = Search(using=app.es_client, index=app.config['ELASTICSEARCH_RELEASE_INDEX']) \
+ .query(
+ 'query_string',
+ query=q,
+ default_operator="AND",
+ analyze_wildcard=True,
+ lenient=True,
+ fields=["biblio"],
+ )
+
+ resp = generic_search_execute(search, offset=offset)
resp["query"] = { "q": q }
- resp["limit"] = limit
return resp
def get_elastic_entity_stats():
@@ -127,85 +121,81 @@ def get_elastic_entity_stats():
stats = {}
- # 2. releases
- # - total count
- # - total citation records
- # - total (paper, chapter, proceeding)
- # - " with fulltext on web
- # - " open access
- # - " not in KBART, in IA
- #
- # Can do the above with two queries:
- # - all releases, aggregate count and sum(ref_count)
- # - in-scope works, aggregate count by (fulltext, OA, kbart/ia)
-
- # 2a. release totals
- query = {
- "size": 0,
- "aggs": {
- "release_ref_count": { "sum": { "field": "ref_count" } }
- }
- }
- resp = requests.get(
- "{}/fatcat_release/_search".format(app.config['ELASTICSEARCH_BACKEND']),
- json=query,
- params=dict(request_cache="true"))
- # TODO: abort()
- resp.raise_for_status()
- resp = resp.json()
+ # release totals
+ search = Search(
+ using=app.es_client,
+ index=app.config['ELASTICSEARCH_RELEASE_INDEX']) \
+ .extra(request_cache=True)
+ search.aggs.bucket(
+ 'release_ref_count',
+ 'sum',
+ field='ref_count',
+ )
+ search = search[:0]
+
+ # NOTE: not catching exceptions
+ resp = search.execute()
stats['release'] = {
- "total": resp['hits']['total'],
- "refs_total": int(resp['aggregations']['release_ref_count']['value']),
+ "total": int(resp.hits.total),
+ "refs_total": int(resp.aggregations.release_ref_count.value),
}
- # 2b. paper counts
- query = {
- "size": 0,
- "query": {
- "terms": { "release_type": [
- # "chapter", "thesis",
- "article-journal", "paper-conference",
- ] } },
- "aggs": { "paper_like": { "filters": { "filters": {
- "in_web": { "term": { "in_web": "true" } },
- "is_oa": { "term": { "is_oa": "true" } },
- "in_kbart": { "term": { "in_kbart": "true" } },
- "in_web_not_kbart": { "bool": { "filter": [
- { "term": { "in_web": "true" } },
- { "term": { "in_kbart": "false" } }
- ]}}
- }}}}
- }
- resp = requests.get(
- "{}/fatcat_release/_search".format(app.config['ELASTICSEARCH_BACKEND']),
- json=query,
- params=dict(request_cache="true"))
- # TODO: abort()
- resp.raise_for_status()
- resp = resp.json()
- buckets = resp['aggregations']['paper_like']['buckets']
+ # paper counts
+ search = Search(
+ using=app.es_client,
+ index=app.config['ELASTICSEARCH_RELEASE_INDEX']) \
+ .query(
+ 'terms',
+ release_type=[
+ "article-journal",
+ "paper-conference",
+ # "chapter",
+ # "thesis",
+ ],
+ ) \
+ .extra(request_cache=True)
+ search.aggs.bucket(
+ 'paper_like',
+ 'filters',
+ filters={
+ "in_web": { "term": { "in_web": "true" } },
+ "is_oa": { "term": { "is_oa": "true" } },
+ "in_kbart": { "term": { "in_kbart": "true" } },
+ "in_web_not_kbart": { "bool": { "filter": [
+ { "term": { "in_web": "true" } },
+ { "term": { "in_kbart": "false" } },
+ ]}},
+ }
+ )
+ search = search[:0]
+
+ # NOTE: not catching exceptions
+ resp = search.execute()
+ buckets = resp.aggregations.paper_like.buckets
stats['papers'] = {
- 'total': resp['hits']['total'],
- 'in_web': buckets['in_web']['doc_count'],
- 'is_oa': buckets['is_oa']['doc_count'],
- 'in_kbart': buckets['in_kbart']['doc_count'],
- 'in_web_not_kbart': buckets['in_web_not_kbart']['doc_count'],
+ 'total': resp.hits.total,
+ 'in_web': buckets.in_web.doc_count,
+ 'is_oa': buckets.is_oa.doc_count,
+ 'in_kbart': buckets.in_kbart.doc_count,
+ 'in_web_not_kbart': buckets.in_web_not_kbart.doc_count,
}
- # 3. containers
- # => total count
- query = {
- "size": 0,
- }
- resp = requests.get(
- "{}/fatcat_container/_search".format(app.config['ELASTICSEARCH_BACKEND']),
- json=query,
- params=dict(request_cache="true"))
- # TODO: abort()
- resp.raise_for_status()
- resp = resp.json()
+ # container counts
+ search = Search(
+ using=app.es_client,
+ index=app.config['ELASTICSEARCH_CONTAINER_INDEX']) \
+ .extra(request_cache=True)
+ search.aggs.bucket(
+ 'release_ref_count',
+ 'sum',
+ field='ref_count',
+ )
+ search = search[:0]
+
+ # NOTE: not catching exceptions
+ resp = search.execute()
stats['container'] = {
- "total": resp['hits']['total'],
+ "total": resp.hits.total,
}
return stats
@@ -259,31 +249,22 @@ def get_elastic_container_random_releases(ident, limit=5):
assert limit > 0 and limit <= 100
- query = {
- "size": int(limit),
- "sort": [
- { "in_web": {"order": "desc"} },
- { "release_date": {"order": "desc"} },
- ],
- "query": {
- "bool": {
- "must": [
- { "term": { "container_id": ident } },
- { "range": { "release_year": { "lte": datetime.datetime.today().year } } },
- ],
- },
- },
- }
- resp = requests.get(
- "{}/fatcat_release/_search".format(app.config['ELASTICSEARCH_BACKEND']),
- json=query,
- params=dict(request_cache="true"))
- # TODO: abort()
- #print(resp.json())
- resp.raise_for_status()
- resp = resp.json()
- #print(resp)
- hits = [h['_source'] for h in resp['hits']['hits']]
+ search = Search(using=app.es_client, index=app.conf.ELASTICSEARCH_RELEASE_INDEX) \
+ .query('bool',
+ must=[
+ Q('term', container_id=ident),
+ Q('range', release_year={ "lte": datetime.datetime.today().year }),
+ ]
+ ) \
+ .sort('-in_web', '-release_date') \
+ .extra(request_cache=True)
+
+ search = search[:int(limit)]
+
+ resp = search.execute()
+
+ hits = [dict(h.source) for h in resp]
+
for h in hits:
# Handle surrogate strings that elasticsearch returns sometimes,
# probably due to mangled data processing in some pipeline.