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"""
Helpers for doing elasticsearch queries (used in the web interface; not part of
the formal API)
"""
import datetime
import sys
from dataclasses import dataclass
from typing import Any, Dict, List, Optional, Tuple, Union
import elasticsearch
import elasticsearch_dsl.response
from elasticsearch_dsl import Q, Search
from fatcat_web import app
class FatcatSearchError(Exception):
def __init__(self, status_code: Union[int, str], name: str, description: str = None):
if status_code == "TIMEOUT":
status_code = 504
elif isinstance(status_code, str):
try:
status_code = int(status_code)
except ValueError:
status_code = 503
self.status_code = status_code
self.name = name
self.description = description
@dataclass
class ReleaseQuery:
q: Optional[str] = None
limit: Optional[int] = None
offset: Optional[int] = None
fulltext_only: bool = False
container_id: Optional[str] = None
recent: bool = False
@staticmethod
def from_args(args: Dict[str, Any]) -> "ReleaseQuery":
query_str = args.get("q") or "*"
container_id = args.get("container_id")
# TODO: as filter, not in query string
if container_id:
query_str += ' container_id:"{}"'.format(container_id)
# TODO: where are container_issnl queries actually used?
issnl = args.get("container_issnl")
if issnl and query_str:
query_str += ' container_issnl:"{}"'.format(issnl)
offset = args.get("offset", "0")
offset = max(0, int(offset)) if offset.isnumeric() else 0
return ReleaseQuery(
q=query_str,
offset=offset,
fulltext_only=bool(args.get("fulltext_only")),
container_id=container_id,
recent=bool(args.get("recent")),
)
@dataclass
class GenericQuery:
q: Optional[str] = None
limit: Optional[int] = None
offset: Optional[int] = None
@staticmethod
def from_args(args: Dict[str, Any]) -> "GenericQuery":
query_str = args.get("q")
if not query_str:
query_str = "*"
offset = args.get("offset", "0")
offset = max(0, int(offset)) if offset.isnumeric() else 0
return GenericQuery(
q=query_str,
offset=offset,
)
@dataclass
class SearchHits:
count_returned: int
count_found: int
offset: int
limit: int
deep_page_limit: int
query_time_ms: int
results: List[Any]
def _hits_total_int(val: Any) -> int:
"""
Compatibility hack between ES 6.x and 7.x. In ES 6x, total is returned as
an int in many places, in ES 7 as a dict (JSON object) with 'value' key
"""
if isinstance(val, int):
return val
else:
return int(val["value"])
def results_to_dict(response: elasticsearch_dsl.response.Response) -> List[dict]:
"""
Takes a response returns all the hits as JSON objects.
Also handles surrogate strings that elasticsearch returns sometimes,
probably due to mangled data processing in some pipeline. "Crimes against
Unicode"; production workaround
"""
results = []
for h in response:
r = h._d_
# print(h.meta._d_)
results.append(r)
for h in results:
for key in h:
if type(h[key]) is str:
h[key] = h[key].encode("utf8", "ignore").decode("utf8")
return results
def wrap_es_execution(search: Search) -> Any:
"""
Executes a Search object, and converts various ES error types into
something we can pretty print to the user.
"""
try:
resp = search.execute()
except elasticsearch.exceptions.RequestError as e:
# this is a "user" error
print("elasticsearch 400: " + str(e.info), file=sys.stderr)
description = None
assert isinstance(e.info, dict)
if e.info.get("error", {}).get("root_cause", {}):
description = str(e.info["error"]["root_cause"][0].get("reason"))
raise FatcatSearchError(e.status_code, str(e.error), description)
except elasticsearch.exceptions.ConnectionError as e:
raise FatcatSearchError(e.status_code, "ConnectionError: search engine not available")
except elasticsearch.exceptions.TransportError as e:
# all other errors
print("elasticsearch non-200 status code: {}".format(e.info), file=sys.stderr)
description = None
assert isinstance(e.info, dict)
if e.info and e.info.get("error", {}).get("root_cause", {}):
description = str(e.info["error"]["root_cause"][0].get("reason"))
raise FatcatSearchError(e.status_code, str(e.error), description)
return resp
def agg_to_dict(agg: Any) -> Dict[str, Any]:
"""
Takes a simple term aggregation result (with buckets) and returns a simple
dict with keys as terms and counts as values. Includes an extra value
'_other', and by convention aggregations should be writen to have "missing"
vaules as '_unknown'.
"""
result = dict()
for bucket in agg.buckets:
result[bucket.key] = bucket.doc_count
if agg.sum_other_doc_count:
result["_other"] = agg.sum_other_doc_count
return result
def do_container_search(query: GenericQuery, deep_page_limit: int = 2000) -> SearchHits:
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_CONTAINER_INDEX"])
search = search.query(
"query_string",
query=query.q,
default_operator="AND",
analyze_wildcard=True,
allow_leading_wildcard=False,
lenient=True,
fields=["biblio"],
)
# Sanity checks
limit = min((int(query.limit or 25), 100))
offset = max((int(query.offset or 0), 0))
if offset > deep_page_limit:
# Avoid deep paging problem.
offset = deep_page_limit
search = search[offset : (offset + limit)]
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
results = results_to_dict(resp)
return SearchHits(
count_returned=len(results),
count_found=_hits_total_int(resp.hits.total),
offset=offset,
limit=limit,
deep_page_limit=deep_page_limit,
query_time_ms=int(resp.took),
results=results,
)
def do_release_search(query: ReleaseQuery, deep_page_limit: int = 2000) -> SearchHits:
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
# availability filters
if query.fulltext_only:
search = search.filter("term", in_ia=True)
# Below, we combine several queries to improve scoring.
# this query use the fancy built-in query string parser
basic_biblio = Q(
"query_string",
query=query.q,
default_operator="AND",
analyze_wildcard=True,
allow_leading_wildcard=False,
lenient=True,
fields=[
"title^2",
"biblio",
],
)
has_fulltext = Q("term", in_ia=True)
poor_metadata = Q(
"bool",
should=[
# if these fields aren't set, metadata is poor. The more that do
# not exist, the stronger the signal.
Q("bool", must_not=Q("exists", field="title")),
Q("bool", must_not=Q("exists", field="release_year")),
Q("bool", must_not=Q("exists", field="release_type")),
Q("bool", must_not=Q("exists", field="release_stage")),
Q("bool", must_not=Q("exists", field="container_id")),
],
)
search = search.query(
"boosting",
positive=Q(
"bool",
must=basic_biblio,
should=[has_fulltext],
),
negative=poor_metadata,
negative_boost=0.5,
)
# Sanity checks
limit = min((int(query.limit or 25), 100))
offset = max((int(query.offset or 0), 0))
if offset > deep_page_limit:
# Avoid deep paging problem.
offset = deep_page_limit
search = search[offset : (offset + limit)]
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
results = results_to_dict(resp)
for h in 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"]
]
return SearchHits(
count_returned=len(results),
count_found=_hits_total_int(resp.hits.total),
offset=offset,
limit=limit,
deep_page_limit=deep_page_limit,
query_time_ms=int(resp.took),
results=results,
)
def get_elastic_container_random_releases(ident: str, limit: int = 5) -> List[Dict[str, Any]]:
"""
Returns a list of releases from the container.
"""
assert limit > 0 and limit <= 100
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
search = search.query(
"bool",
must=[
Q("term", container_id=ident),
Q("range", release_year={"lte": datetime.datetime.today().year}),
],
)
search = search.sort("-in_web", "-release_date")
search = search[: int(limit)]
search = search.params(request_cache=True)
# not needed: search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
results = results_to_dict(resp)
return results
def get_elastic_entity_stats() -> dict:
"""
TODO: files, filesets, webcaptures (no schema yet)
Returns dict:
changelog: {latest: {index, datetime}}
release: {total, refs_total}
papers: {total, in_web, in_oa, in_kbart, in_web_not_kbart}
"""
stats = {}
# release totals
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
search.aggs.bucket(
"release_ref_count",
"sum",
field="ref_count",
)
search = search[:0] # pylint: disable=unsubscriptable-object
search = search.params(request_cache=True)
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
stats["release"] = {
"total": _hits_total_int(resp.hits.total),
"refs_total": int(resp.aggregations.release_ref_count.value),
}
# paper counts
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
search = search.query(
"terms",
release_type=[
"article-journal",
"paper-conference",
# "chapter",
# "thesis",
],
)
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]
search = search.params(request_cache=True)
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
buckets = resp.aggregations.paper_like.buckets
stats["papers"] = {
"total": _hits_total_int(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,
}
# container counts
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_CONTAINER_INDEX"])
search.aggs.bucket(
"release_ref_count",
"sum",
field="ref_count",
)
search = search[:0] # pylint: disable=unsubscriptable-object
search = search.params(request_cache=True)
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
stats["container"] = {
"total": _hits_total_int(resp.hits.total),
}
return stats
def get_elastic_search_coverage(query: ReleaseQuery) -> dict:
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
search = search.query(
"query_string",
query=query.q,
default_operator="AND",
analyze_wildcard=True,
allow_leading_wildcard=False,
lenient=True,
fields=["biblio"],
)
search.aggs.bucket(
"preservation",
"terms",
field="preservation",
missing="_unknown",
)
if query.recent:
date_today = datetime.date.today()
start_date = str(date_today - datetime.timedelta(days=60))
end_date = str(date_today + datetime.timedelta(days=1))
search = search.filter("range", release_date=dict(gte=start_date, lte=end_date))
search = search[:0]
search = search.params(request_cache=True)
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
preservation_bucket = agg_to_dict(resp.aggregations.preservation)
preservation_bucket["total"] = _hits_total_int(resp.hits.total)
for k in ("bright", "dark", "shadows_only", "none"):
if k not in preservation_bucket:
preservation_bucket[k] = 0
if app.config["FATCAT_MERGE_SHADOW_PRESERVATION"]:
preservation_bucket["none"] += preservation_bucket["shadows_only"]
preservation_bucket["shadows_only"] = 0
stats = {
"total": _hits_total_int(resp.hits.total),
"preservation": preservation_bucket,
}
return stats
def get_elastic_container_stats(
ident: str,
issnl: Optional[str] = None,
es_client: Optional[elasticsearch.Elasticsearch] = None,
es_index: Optional[str] = None,
merge_shadows: Optional[bool] = None,
) -> Dict[str, Any]:
"""
Returns dict:
ident
issnl (optional)
total
in_web
in_kbart
preserved
"""
if not es_client:
es_client = app.es_client
if not es_index:
es_index = app.config["ELASTICSEARCH_RELEASE_INDEX"]
if merge_shadows is None:
merge_shadows = app.config["FATCAT_MERGE_SHADOW_PRESERVATION"]
search = Search(using=es_client, index=es_index)
search = search.query(
"term",
container_id=ident,
)
search.aggs.bucket(
"container_stats",
"filters",
filters={
"in_web": {
"term": {"in_web": True},
},
"in_kbart": {
"term": {"in_kbart": True},
},
"is_preserved": {
"term": {"is_preserved": True},
},
},
)
search.aggs.bucket(
"preservation",
"terms",
field="preservation",
missing="_unknown",
)
search.aggs.bucket(
"release_type",
"terms",
field="release_type",
missing="_unknown",
)
search = search[:0]
search = search.params(request_cache=True)
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
container_stats = resp.aggregations.container_stats.buckets
preservation_bucket = agg_to_dict(resp.aggregations.preservation)
preservation_bucket["total"] = _hits_total_int(resp.hits.total)
for k in ("bright", "dark", "shadows_only", "none"):
if k not in preservation_bucket:
preservation_bucket[k] = 0
if merge_shadows:
preservation_bucket["none"] += preservation_bucket["shadows_only"]
preservation_bucket["shadows_only"] = 0
release_type_bucket = agg_to_dict(resp.aggregations.release_type)
stats = {
"ident": ident,
"issnl": issnl,
"total": _hits_total_int(resp.hits.total),
"in_web": container_stats["in_web"]["doc_count"],
"in_kbart": container_stats["in_kbart"]["doc_count"],
"is_preserved": container_stats["is_preserved"]["doc_count"],
"preservation": preservation_bucket,
"release_type": release_type_bucket,
}
return stats
def get_elastic_container_histogram_legacy(ident: str) -> List[Tuple[int, bool, int]]:
"""
Fetches a stacked histogram of {year, in_ia}. This is for the older style
of coverage graph (SVG or JSON export). This function should be DEPRECATED
to be removed in the near future.
Filters to the past 500 years (at most), or about 1000 values.
Returns a list of tuples:
(year, in_ia, count)
"""
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
search = search.query(
"bool",
must=[
Q(
"range",
release_year={
"gte": datetime.datetime.today().year - 499,
"lte": datetime.datetime.today().year,
},
),
],
filter=[
Q(
"bool",
minimum_should_match=1,
should=[
Q("match", container_id=ident),
],
),
],
)
search.aggs.bucket(
"year_in_ia",
"composite",
size=1000,
sources=[
{
"year": {
"histogram": {
"field": "release_year",
"interval": 1,
},
}
},
{
"in_ia": {
"terms": {
"field": "in_ia",
},
}
},
],
)
search = search[:0]
search = search.params(request_cache="true")
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
buckets = resp.aggregations.year_in_ia.buckets
vals = [(int(h["key"]["year"]), h["key"]["in_ia"], h["doc_count"]) for h in buckets]
vals = sorted(vals)
return vals
def get_elastic_preservation_by_year(query: ReleaseQuery) -> List[Dict[str, Any]]:
"""
Fetches a stacked histogram of {year, preservation}.
Preservation has 4 potential values; this function filters to the past 250
years (at most), or about 1000 values.
Returns a list of dicts, sorted by year, with keys/values like:
{year (int), bright (int), dark (int), shadows_only (int), none (int)}
"""
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
if query.q not in [None, "*"]:
search = search.query(
"query_string",
query=query.q,
default_operator="AND",
analyze_wildcard=True,
allow_leading_wildcard=False,
lenient=True,
fields=[
"biblio",
],
)
if query.container_id:
search = search.filter(
"term",
container_id=query.container_id,
)
search = search.filter(
"range",
release_year={
"gte": datetime.datetime.today().year - 249,
"lte": datetime.datetime.today().year,
},
)
search.aggs.bucket(
"year_preservation",
"composite",
size=1500,
sources=[
{
"year": {
"histogram": {
"field": "release_year",
"interval": 1,
},
}
},
{
"preservation": {
"terms": {
"field": "preservation",
},
}
},
],
)
search = search[:0]
search = search.params(request_cache="true")
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
buckets = resp.aggregations.year_preservation.buckets
year_nums = set([int(h["key"]["year"]) for h in buckets])
year_dicts = dict()
if year_nums:
for num in range(min(year_nums), max(year_nums) + 1):
year_dicts[num] = dict(year=num, bright=0, dark=0, shadows_only=0, none=0)
for row in buckets:
year_dicts[int(row["key"]["year"])][row["key"]["preservation"]] = int(
row["doc_count"]
)
if app.config["FATCAT_MERGE_SHADOW_PRESERVATION"]:
for k in year_dicts.keys():
year_dicts[k]["none"] += year_dicts[k]["shadows_only"]
year_dicts[k]["shadows_only"] = 0
return sorted(year_dicts.values(), key=lambda x: x["year"])
def get_elastic_preservation_by_date(query: ReleaseQuery) -> List[dict]:
"""
Fetches a stacked histogram of {date, preservation}.
Preservation has 4 potential values; this function filters to the past 250
years (at most), or about 1000 values.
Returns a list of dicts, sorted by date, with keys/values like:
{date (str), bright (int), dark (int), shadows_only (int), none (int)}
"""
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
if query.q not in [None, "*"]:
search = search.query(
"query_string",
query=query.q,
default_operator="AND",
analyze_wildcard=True,
allow_leading_wildcard=False,
lenient=True,
fields=[
"biblio",
],
)
if query.container_id:
search = search.filter(
"term",
container_id=query.container_id,
)
date_today = datetime.date.today()
start_date = date_today - datetime.timedelta(days=60)
end_date = date_today + datetime.timedelta(days=1)
search = search.filter(
"range",
release_date=dict(
gte=str(start_date),
lte=str(end_date),
),
)
search.aggs.bucket(
"date_preservation",
"composite",
size=1500,
sources=[
{
"date": {
"histogram": {
"field": "release_date",
"interval": 1,
},
}
},
{
"preservation": {
"terms": {
"field": "preservation",
},
}
},
],
)
search = search[:0]
search = search.params(request_cache="true")
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
buckets = resp.aggregations.date_preservation.buckets
date_dicts: Dict[str, Dict[str, Any]] = dict()
this_date = start_date
while this_date <= end_date:
date_dicts[str(this_date)] = dict(
date=str(this_date), bright=0, dark=0, shadows_only=0, none=0
)
this_date = this_date + datetime.timedelta(days=1)
for row in buckets:
date_dicts[row["key"]["date"][0:10]][row["key"]["preservation"]] = int(row["doc_count"])
if app.config["FATCAT_MERGE_SHADOW_PRESERVATION"]:
for k in date_dicts.keys():
date_dicts[k]["none"] += date_dicts[k]["shadows_only"]
date_dicts[k]["shadows_only"] = 0
return sorted(date_dicts.values(), key=lambda x: x["date"])
def get_elastic_container_preservation_by_volume(container_id: str) -> List[dict]:
"""
Fetches a stacked histogram of {volume, preservation}.
Currently only includes volume numbers which are simple integers (all chars
are digits).
Returns a list of dicts, sorted by volume, with keys/values like:
{year (int), bright (int), dark (int), shadows_only (int), none (int)}
"""
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
search = search.query(
"bool",
filter=[
Q(
"bool",
must=[
Q("match", container_id=container_id),
Q("exists", field="volume"),
],
),
],
)
search.aggs.bucket(
"volume_preservation",
"composite",
size=1500,
sources=[
{
"volume": {
"terms": {
"field": "volume",
},
}
},
{
"preservation": {
"terms": {
"field": "preservation",
},
}
},
],
)
search = search[:0]
search = search.params(request_cache="true")
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
buckets = resp.aggregations.volume_preservation.buckets
volume_nums = set(
[int(h["key"]["volume"]) for h in buckets if h["key"]["volume"].isdigit()]
)
volume_dicts = dict()
if volume_nums:
for num in range(min(volume_nums), max(volume_nums) + 1):
volume_dicts[num] = dict(volume=num, bright=0, dark=0, shadows_only=0, none=0)
for row in buckets:
if row["key"]["volume"].isdigit():
volume_dicts[int(row["key"]["volume"])][row["key"]["preservation"]] = int(
row["doc_count"]
)
if app.config["FATCAT_MERGE_SHADOW_PRESERVATION"]:
for k in volume_dicts.keys():
volume_dicts[k]["none"] += volume_dicts[k]["shadows_only"]
volume_dicts[k]["shadows_only"] = 0
return sorted(volume_dicts.values(), key=lambda x: x["volume"])
def get_elastic_preservation_by_type(query: ReleaseQuery) -> List[dict]:
"""
Fetches preservation coverage by release type
Returns a list of dicts, sorted by total count, with keys/values like:
{year (int), bright (int), dark (int), shadows_only (int), none (int)}
"""
search = Search(using=app.es_client, index=app.config["ELASTICSEARCH_RELEASE_INDEX"])
if query.q not in [None, "*"]:
search = search.query(
"query_string",
query=query.q,
default_operator="AND",
analyze_wildcard=True,
allow_leading_wildcard=False,
lenient=True,
fields=[
"biblio",
],
)
if query.container_id:
search = search.query(
"bool",
filter=[
Q(
"bool",
must=[
Q("match", container_id=query.container_id),
],
),
],
)
if query.recent:
date_today = datetime.date.today()
start_date = str(date_today - datetime.timedelta(days=60))
end_date = str(date_today + datetime.timedelta(days=1))
search = search.filter("range", release_date=dict(gte=start_date, lte=end_date))
search.aggs.bucket(
"type_preservation",
"composite",
size=1500,
sources=[
{
"release_type": {
"terms": {
"field": "release_type",
},
}
},
{
"preservation": {
"terms": {
"field": "preservation",
},
}
},
],
)
search = search[:0]
search = search.params(request_cache="true")
search = search.params(track_total_hits=True)
resp = wrap_es_execution(search)
buckets = resp.aggregations.type_preservation.buckets
type_set = set([h["key"]["release_type"] for h in buckets])
type_dicts = dict()
for k in type_set:
type_dicts[k] = dict(release_type=k, bright=0, dark=0, shadows_only=0, none=0, total=0)
for row in buckets:
type_dicts[row["key"]["release_type"]][row["key"]["preservation"]] = int(
row["doc_count"]
)
for k in type_set:
for p in ("bright", "dark", "shadows_only", "none"):
type_dicts[k]["total"] += type_dicts[k][p]
if app.config["FATCAT_MERGE_SHADOW_PRESERVATION"]:
for k in type_set:
type_dicts[k]["none"] += type_dicts[k]["shadows_only"]
type_dicts[k]["shadows_only"] = 0
return sorted(type_dicts.values(), key=lambda x: x["total"], reverse=True)
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