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-rw-r--r--extra/stats/2020-02-21-prod-stats.json1
-rw-r--r--extra/stats/2020-02-21-prod-tables-sizes.txt48
-rw-r--r--extra/stats/2020-02-24-prod-dupes.txt5
-rw-r--r--extra/stats/2020-02-24-prod-table-sizes.txt47
-rw-r--r--extra/stats/2020-03-03-prod-stats.json1
-rw-r--r--extra/stats/2020-04-17-prod-stats.json1
-rw-r--r--extra/stats/2020-04-17-prod-table-sizes.txt46
-rw-r--r--python/fatcat_tools/workers/__init__.py2
-rw-r--r--python/fatcat_tools/workers/changelog.py29
-rw-r--r--python/fatcat_tools/workers/elasticsearch.py23
-rwxr-xr-xpython/fatcat_worker.py19
11 files changed, 207 insertions, 15 deletions
diff --git a/extra/stats/2020-02-21-prod-stats.json b/extra/stats/2020-02-21-prod-stats.json
new file mode 100644
index 00000000..3ab6471f
--- /dev/null
+++ b/extra/stats/2020-02-21-prod-stats.json
@@ -0,0 +1 @@
+{"changelog":{"latest":{"index":3528195,"timestamp":"2020-02-22T05:23:18.082262+00:00"}},"container":{"total":148396},"papers":{"in_kbart":60529767,"in_web":20374670,"in_web_not_kbart":9598464,"is_oa":11547112,"total":105732384},"release":{"refs_total":890869519,"total":143867045}}
diff --git a/extra/stats/2020-02-21-prod-tables-sizes.txt b/extra/stats/2020-02-21-prod-tables-sizes.txt
new file mode 100644
index 00000000..bc756ba7
--- /dev/null
+++ b/extra/stats/2020-02-21-prod-tables-sizes.txt
@@ -0,0 +1,48 @@
+
+Size: 478.37G
+
+ table_name | table_size | indexes_size | total_size
+---------------------------------------+------------+--------------+------------
+ "public"."release_contrib" | 53 GB | 43 GB | 96 GB
+ "public"."release_rev" | 58 GB | 33 GB | 91 GB
+ "public"."refs_blob" | 85 GB | 2884 MB | 88 GB
+ "public"."release_edit" | 14 GB | 20 GB | 34 GB
+ "public"."work_edit" | 13 GB | 20 GB | 34 GB
+ "public"."release_ident" | 9515 MB | 15 GB | 24 GB
+ "public"."work_ident" | 9313 MB | 15 GB | 24 GB
+ "public"."abstracts" | 16 GB | 1504 MB | 18 GB
+ "public"."file_rev_url" | 10235 MB | 3587 MB | 13 GB
+ "public"."work_rev" | 6046 MB | 5825 MB | 12 GB
+ "public"."release_ref" | 3997 MB | 5690 MB | 9686 MB
+ "public"."file_rev" | 3635 MB | 5359 MB | 8994 MB
+ "public"."file_edit" | 3111 MB | 4051 MB | 7162 MB
+ "public"."release_rev_abstract" | 2406 MB | 3342 MB | 5749 MB
+ "public"."file_ident" | 1848 MB | 2505 MB | 4354 MB
+ "public"."file_rev_release" | 1698 MB | 2483 MB | 4181 MB
+ "public"."creator_edit" | 702 MB | 942 MB | 1643 MB
+ "public"."creator_rev" | 695 MB | 719 MB | 1413 MB
+ "public"."editgroup" | 767 MB | 405 MB | 1172 MB
+ "public"."creator_ident" | 474 MB | 648 MB | 1121 MB
+ "public"."release_rev_extid" | 200 MB | 312 MB | 512 MB
+ "public"."changelog" | 220 MB | 214 MB | 434 MB
+ "public"."container_rev" | 75 MB | 23 MB | 98 MB
+ "public"."container_edit" | 25 MB | 31 MB | 56 MB
+ "public"."container_ident" | 11 MB | 19 MB | 30 MB
+ "public"."webcapture_rev_cdx" | 64 kB | 32 kB | 96 kB
+ "public"."fileset_rev_file" | 48 kB | 32 kB | 80 kB
+ "public"."auth_oidc" | 16 kB | 48 kB | 64 kB
+ "public"."fileset_edit" | 16 kB | 48 kB | 64 kB
+ "public"."editor" | 16 kB | 48 kB | 64 kB
+ "public"."webcapture_edit" | 16 kB | 48 kB | 64 kB
+ "public"."editgroup_annotation" | 16 kB | 48 kB | 64 kB
+ "public"."fileset_rev_url" | 16 kB | 32 kB | 48 kB
+ "public"."webcapture_rev_url" | 16 kB | 32 kB | 48 kB
+ "public"."fileset_rev_release" | 8192 bytes | 32 kB | 40 kB
+ "public"."fileset_ident" | 8192 bytes | 32 kB | 40 kB
+ "public"."webcapture_rev_release" | 8192 bytes | 32 kB | 40 kB
+ "public"."webcapture_ident" | 8192 bytes | 32 kB | 40 kB
+ "public"."fileset_rev" | 16 kB | 16 kB | 32 kB
+ "public"."webcapture_rev" | 16 kB | 16 kB | 32 kB
+ "public"."__diesel_schema_migrations" | 8192 bytes | 16 kB | 24 kB
+(41 rows)
+
diff --git a/extra/stats/2020-02-24-prod-dupes.txt b/extra/stats/2020-02-24-prod-dupes.txt
new file mode 100644
index 00000000..7d1d09cf
--- /dev/null
+++ b/extra/stats/2020-02-24-prod-dupes.txt
@@ -0,0 +1,5 @@
+ 19409 doi_ident.dupes.tsv
+ 28530 pmcid_ident.dupes.tsv
+ 463523 pmid_ident.dupes.tsv
+ 2025 sha1_ident.dupes.tsv
+ 10 wikidata_ident.dupes.tsv
diff --git a/extra/stats/2020-02-24-prod-table-sizes.txt b/extra/stats/2020-02-24-prod-table-sizes.txt
new file mode 100644
index 00000000..359cb2f3
--- /dev/null
+++ b/extra/stats/2020-02-24-prod-table-sizes.txt
@@ -0,0 +1,47 @@
+
+Size: 560.76G
+
+ table_name | table_size | indexes_size | total_size
+---------------------------------------+------------+--------------+------------
+ "public"."release_contrib" | 53 GB | 43 GB | 96 GB
+ "public"."release_rev" | 58 GB | 33 GB | 91 GB
+ "public"."refs_blob" | 85 GB | 2884 MB | 88 GB
+ "public"."file_rev" | 23 GB | 26 GB | 49 GB
+ "public"."release_edit" | 14 GB | 20 GB | 34 GB
+ "public"."work_edit" | 13 GB | 20 GB | 34 GB
+ "public"."release_ident" | 9517 MB | 15 GB | 24 GB
+ "public"."work_ident" | 9315 MB | 15 GB | 24 GB
+ "public"."file_edit" | 9555 MB | 14 GB | 24 GB
+ "public"."abstracts" | 16 GB | 1505 MB | 18 GB
+ "public"."file_rev_url" | 13 GB | 4730 MB | 17 GB
+ "public"."file_ident" | 5885 MB | 9480 MB | 15 GB
+ "public"."file_rev_release" | 5515 MB | 9536 MB | 15 GB
+ "public"."work_rev" | 6047 MB | 5825 MB | 12 GB
+ "public"."release_ref" | 3997 MB | 5690 MB | 9686 MB
+ "public"."release_rev_abstract" | 2408 MB | 3343 MB | 5751 MB
+ "public"."creator_edit" | 702 MB | 942 MB | 1643 MB
+ "public"."creator_rev" | 695 MB | 719 MB | 1413 MB
+ "public"."editgroup" | 903 MB | 465 MB | 1368 MB
+ "public"."creator_ident" | 474 MB | 648 MB | 1121 MB
+ "public"."release_rev_extid" | 200 MB | 312 MB | 512 MB
+ "public"."changelog" | 261 MB | 229 MB | 490 MB
+ "public"."container_rev" | 75 MB | 23 MB | 98 MB
+ "public"."container_edit" | 25 MB | 31 MB | 56 MB
+ "public"."container_ident" | 11 MB | 19 MB | 30 MB
+ "public"."webcapture_rev_cdx" | 64 kB | 32 kB | 96 kB
+ "public"."fileset_rev_file" | 48 kB | 32 kB | 80 kB
+ "public"."auth_oidc" | 16 kB | 48 kB | 64 kB
+ "public"."editgroup_annotation" | 16 kB | 48 kB | 64 kB
+ "public"."fileset_edit" | 16 kB | 48 kB | 64 kB
+ "public"."webcapture_edit" | 16 kB | 48 kB | 64 kB
+ "public"."editor" | 16 kB | 48 kB | 64 kB
+ "public"."fileset_rev_url" | 16 kB | 32 kB | 48 kB
+ "public"."webcapture_rev_url" | 16 kB | 32 kB | 48 kB
+ "public"."fileset_rev_release" | 8192 bytes | 32 kB | 40 kB
+ "public"."fileset_ident" | 8192 bytes | 32 kB | 40 kB
+ "public"."webcapture_rev_release" | 8192 bytes | 32 kB | 40 kB
+ "public"."webcapture_ident" | 8192 bytes | 32 kB | 40 kB
+ "public"."fileset_rev" | 16 kB | 16 kB | 32 kB
+ "public"."webcapture_rev" | 16 kB | 16 kB | 32 kB
+ "public"."__diesel_schema_migrations" | 8192 bytes | 16 kB | 24 kB
+(41 rows)
diff --git a/extra/stats/2020-03-03-prod-stats.json b/extra/stats/2020-03-03-prod-stats.json
new file mode 100644
index 00000000..0ac977b8
--- /dev/null
+++ b/extra/stats/2020-03-03-prod-stats.json
@@ -0,0 +1 @@
+{"changelog":{"latest":{"index":4242658,"timestamp":"2020-03-03T18:35:06.153130+00:00"}},"container":{"total":148428},"papers":{"in_kbart":60594053,"in_web":22232097,"in_web_not_kbart":10756782,"is_oa":15267353,"total":105933568},"release":{"refs_total":893136234,"total":144138471}}
diff --git a/extra/stats/2020-04-17-prod-stats.json b/extra/stats/2020-04-17-prod-stats.json
new file mode 100644
index 00000000..ddf7fca1
--- /dev/null
+++ b/extra/stats/2020-04-17-prod-stats.json
@@ -0,0 +1 @@
+{"changelog":{"latest":{"index":4460684,"timestamp":"2020-04-17T18:03:34.373631+00:00"}},"container":{"total":149527},"papers":{"in_kbart":60679890,"in_web":24250766,"in_web_not_kbart":11970984,"is_oa":15538739,"total":108761510},"release":{"refs_total":914708032,"total":148081134}}
diff --git a/extra/stats/2020-04-17-prod-table-sizes.txt b/extra/stats/2020-04-17-prod-table-sizes.txt
new file mode 100644
index 00000000..79aa3b98
--- /dev/null
+++ b/extra/stats/2020-04-17-prod-table-sizes.txt
@@ -0,0 +1,46 @@
+Size: 591.60G
+
+ table_name | table_size | indexes_size | total_size
+---------------------------------------+------------+--------------+------------
+ "public"."release_contrib" | 55 GB | 45 GB | 100 GB
+ "public"."release_rev" | 60 GB | 34 GB | 94 GB
+ "public"."refs_blob" | 87 GB | 2885 MB | 89 GB
+ "public"."file_rev" | 26 GB | 29 GB | 55 GB
+ "public"."release_edit" | 14 GB | 21 GB | 35 GB
+ "public"."work_edit" | 14 GB | 21 GB | 34 GB
+ "public"."file_edit" | 11 GB | 16 GB | 27 GB
+ "public"."release_ident" | 9821 MB | 15 GB | 24 GB
+ "public"."work_ident" | 9596 MB | 15 GB | 24 GB
+ "public"."file_rev_url" | 15 GB | 6040 MB | 21 GB
+ "public"."abstracts" | 18 GB | 1688 MB | 19 GB
+ "public"."file_ident" | 6694 MB | 10219 MB | 17 GB
+ "public"."file_rev_release" | 6267 MB | 10109 MB | 16 GB
+ "public"."work_rev" | 6233 MB | 5825 MB | 12 GB
+ "public"."release_ref" | 4441 MB | 6322 MB | 11 GB
+ "public"."release_rev_abstract" | 2637 MB | 3505 MB | 6141 MB
+ "public"."creator_edit" | 702 MB | 942 MB | 1643 MB
+ "public"."editgroup" | 980 MB | 502 MB | 1482 MB
+ "public"."creator_rev" | 695 MB | 719 MB | 1413 MB
+ "public"."creator_ident" | 474 MB | 648 MB | 1121 MB
+ "public"."changelog" | 289 MB | 239 MB | 527 MB
+ "public"."release_rev_extid" | 206 MB | 320 MB | 526 MB
+ "public"."container_rev" | 75 MB | 23 MB | 98 MB
+ "public"."container_edit" | 25 MB | 32 MB | 57 MB
+ "public"."container_ident" | 11 MB | 19 MB | 30 MB
+ "public"."webcapture_rev_cdx" | 64 kB | 32 kB | 96 kB
+ "public"."fileset_rev_file" | 48 kB | 32 kB | 80 kB
+ "public"."auth_oidc" | 16 kB | 48 kB | 64 kB
+ "public"."editgroup_annotation" | 16 kB | 48 kB | 64 kB
+ "public"."fileset_edit" | 16 kB | 48 kB | 64 kB
+ "public"."webcapture_edit" | 16 kB | 48 kB | 64 kB
+ "public"."editor" | 16 kB | 48 kB | 64 kB
+ "public"."fileset_rev_url" | 16 kB | 32 kB | 48 kB
+ "public"."webcapture_rev_url" | 16 kB | 32 kB | 48 kB
+ "public"."fileset_rev_release" | 8192 bytes | 32 kB | 40 kB
+ "public"."fileset_ident" | 8192 bytes | 32 kB | 40 kB
+ "public"."webcapture_rev_release" | 8192 bytes | 32 kB | 40 kB
+ "public"."webcapture_ident" | 8192 bytes | 32 kB | 40 kB
+ "public"."fileset_rev" | 16 kB | 16 kB | 32 kB
+ "public"."webcapture_rev" | 16 kB | 16 kB | 32 kB
+ "public"."__diesel_schema_migrations" | 8192 bytes | 16 kB | 24 kB
+(41 rows)
diff --git a/python/fatcat_tools/workers/__init__.py b/python/fatcat_tools/workers/__init__.py
index 8bea7cdc..32fd330d 100644
--- a/python/fatcat_tools/workers/__init__.py
+++ b/python/fatcat_tools/workers/__init__.py
@@ -1,4 +1,4 @@
from .changelog import ChangelogWorker, EntityUpdatesWorker
-from .elasticsearch import ElasticsearchReleaseWorker, ElasticsearchContainerWorker
+from .elasticsearch import ElasticsearchReleaseWorker, ElasticsearchContainerWorker, ElasticsearchChangelogWorker
from .worker_common import most_recent_message, FatcatWorker
diff --git a/python/fatcat_tools/workers/changelog.py b/python/fatcat_tools/workers/changelog.py
index d1e7c2db..3a49f86e 100644
--- a/python/fatcat_tools/workers/changelog.py
+++ b/python/fatcat_tools/workers/changelog.py
@@ -153,28 +153,33 @@ class EntityUpdatesWorker(FatcatWorker):
doi = ingest_request.get('ext_ids', {}).get('doi')
is_document = release.release_type in (
- 'article-journal',
- 'paper-conference',
'article',
- 'report',
+ 'article-journal',
+ 'article-newspaper',
+ 'book',
'chapter',
- 'manuscript',
- 'review',
- 'thesis',
- 'letter',
'editorial',
- 'abstract',
- 'entry',
+ 'interview',
+ 'legal_case',
+ 'legislation',
+ 'letter',
+ 'manuscript',
+ 'paper-conference',
'patent',
- 'post',
+ 'peer_review',
+ 'report',
+ 'retraction',
+ 'review',
'review-book',
+ 'thesis',
)
is_not_pdf = release.release_type in (
+ 'component',
'dataset',
- 'stub',
- 'software',
'figure',
'graphic',
+ 'software',
+ 'stub',
)
# accept list sets a default "crawl it" despite OA metadata for
diff --git a/python/fatcat_tools/workers/elasticsearch.py b/python/fatcat_tools/workers/elasticsearch.py
index 68d6c304..525f372b 100644
--- a/python/fatcat_tools/workers/elasticsearch.py
+++ b/python/fatcat_tools/workers/elasticsearch.py
@@ -4,7 +4,7 @@ import time
import requests
from confluent_kafka import Consumer, KafkaException
-from fatcat_openapi_client import ReleaseEntity, ContainerEntity, ApiClient
+from fatcat_openapi_client import ReleaseEntity, ContainerEntity, ApiClient, ChangelogEntry
from fatcat_tools import *
from .worker_common import FatcatWorker
@@ -148,3 +148,24 @@ class ElasticsearchContainerWorker(ElasticsearchReleaseWorker):
self.elasticsearch_document_name = "container"
self.transform_func = container_to_elasticsearch
+
+class ElasticsearchChangelogWorker(ElasticsearchReleaseWorker):
+ """
+ Pulls changelog messages from Kafka, runs transformations and indexes them.
+
+ Note: Very early versions of changelog entries did not contain details
+ about the editor or extra fields.
+ """
+ def __init__(self, kafka_hosts, consume_topic, poll_interval=10.0, offset=None,
+ elasticsearch_backend="http://localhost:9200", elasticsearch_index="fatcat_changelog",
+ batch_size=200):
+ super().__init__(kafka_hosts=kafka_hosts,
+ consume_topic=consume_topic)
+ self.consumer_group = "elasticsearch-updates3"
+ self.batch_size = batch_size
+ self.poll_interval = poll_interval
+ self.elasticsearch_backend = elasticsearch_backend
+ self.elasticsearch_index = elasticsearch_index
+ self.entity_type = ChangelogEntry
+ self.elasticsearch_document_name = "changelog"
+ self.transform_func = changelog_to_elasticsearch
diff --git a/python/fatcat_worker.py b/python/fatcat_worker.py
index bfb87a72..03167a3a 100755
--- a/python/fatcat_worker.py
+++ b/python/fatcat_worker.py
@@ -6,7 +6,7 @@ import datetime
import raven
from fatcat_tools import public_api
-from fatcat_tools.workers import ChangelogWorker, EntityUpdatesWorker, ElasticsearchReleaseWorker, ElasticsearchContainerWorker
+from fatcat_tools.workers import ChangelogWorker, EntityUpdatesWorker, ElasticsearchReleaseWorker, ElasticsearchContainerWorker, ElasticsearchChangelogWorker
# Yep, a global. Gets DSN from `SENTRY_DSN` environment variable
sentry_client = raven.Client()
@@ -47,6 +47,13 @@ def run_elasticsearch_container(args):
elasticsearch_index=args.elasticsearch_index)
worker.run()
+def run_elasticsearch_changelog(args):
+ consume_topic = "fatcat-{}.changelog".format(args.env)
+ worker = ElasticsearchChangelogWorker(args.kafka_hosts, consume_topic,
+ elasticsearch_backend=args.elasticsearch_backend,
+ elasticsearch_index=args.elasticsearch_index)
+ worker.run()
+
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -92,6 +99,16 @@ def main():
help="elasticsearch index to push into",
default="fatcat_container")
+ sub_elasticsearch_changelog = subparsers.add_parser('elasticsearch-changelog',
+ help="consume changelog kafka feed, transform and push to search")
+ sub_elasticsearch_changelog.set_defaults(func=run_elasticsearch_changelog)
+ sub_elasticsearch_changelog.add_argument('--elasticsearch-backend',
+ help="elasticsearch backend to connect to",
+ default="http://localhost:9200")
+ sub_elasticsearch_changelog.add_argument('--elasticsearch-index',
+ help="elasticsearch index to push into",
+ default="fatcat_changelog")
+
args = parser.parse_args()
if not args.__dict__.get("func"):
print("tell me what to do!")
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-24 09:23:38 +0000