ingest backfill notes

3 files changed, 150 insertions, 0 deletions

diff --git a/notes/tasks/2020-02-04_ingest_backfills.md b/notes/tasks/2020-02-04_ingest_backfills.md
index 07f265c..73a42ef 100644
--- a/notes/tasks/2020-02-04_ingest_backfills.md
+++ b/notes/tasks/2020-02-04_ingest_backfills.md
@@ -135,10 +135,14 @@ end of weekend?
 As follow-ups:
 
     elife: https://fatcat.wiki/container/en4qj5ijrbf5djxx7p5zzpjyoq/coverage
+        => 2020-02-24: 7187 / 8101 = 88% preserved
     archivist: https://fatcat.wiki/container/zpobyv4vbranllc7oob56tgci4/coverage
         => 85 preserved
+        => 2020-02-24: 85 / 3005 preserved (TODO)
     jcancer: https://fatcat.wiki/container/nkkzpwht7jd3zdftc6gq4eoeey/coverage
         => 2020 preserved
         => 2520 preserved
+        => 2020-02-24: 2700 / 2766 preserved
     plos: https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm/coverage
+        => 2020-02-24: 7580 / 7730 = 98% preserved
 
diff --git a/notes/tasks/2020-02-18_ingest_backfills.md b/notes/tasks/2020-02-18_ingest_backfills.md
new file mode 100644
index 0000000..1ab18f4
--- /dev/null
+++ b/notes/tasks/2020-02-18_ingest_backfills.md
@@ -0,0 +1,42 @@
+
+Select:
+
+    COPY (
+        SELECT row_to_json(ingest_request.*) FROM ingest_request
+        LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+        WHERE ingest_request.ingest_type = 'pdf'
+            AND ingest_file_result.ingest_type = 'pdf'
+            AND ingest_file_result.updated < NOW() - '2 day'::INTERVAL
+            AND ingest_file_result.hit = false
+            AND ingest_file_result.status like 'spn2-error%'
+    ) TO '/grande/snapshots/reingest_spn2err_20200218.rows.json';
+    => COPY 6537
+
+    COPY (
+        SELECT row_to_json(ingest_request.*) FROM ingest_request
+        LEFT JOIN ingest_file_result ON ingest_file_result.base_url = ingest_request.base_url
+        WHERE ingest_request.ingest_type = 'pdf'
+            AND ingest_file_result.ingest_type = 'pdf'
+            AND ingest_file_result.hit = false
+            AND ingest_file_result.status like 'wayback-error'
+    ) TO '/grande/snapshots/reingest_waybackerr_20200218.rows.json';
+    => COPY 33022
+
+Transform:
+
+    ./scripts/ingestrequest_row2json.py reingest_spn2err_20200218.rows.json > reingest_spn2err_20200218.json
+    ./scripts/ingestrequest_row2json.py reingest_waybackerr_20200218.rows.json > reingest_waybackerr_20200218.json
+
+Push to kafka:
+
+    cat reingest_spn2err_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1
+    cat reingest_waybackerr_20200218.json | jq . -c | kafkacat -P -b wbgrp-svc263.us.archive.org -t sandcrawler-prod.ingest-file-requests -p -1
+
+Many had null `ingest_request_source`, so won't actually import into fatcat:
+
+    bnewbold@ia601101$ cat reingest_waybackerr_20200218.json | jq .ingest_request_source | sort | uniq -c | sort -n
+          1 "savepapernow-web"
+        112 "fatcat-ingest-container"
+      11750 "fatcat-changelog"
+      21159 null
+
diff --git a/notes/tasks/2020-02-21_ingest_backfills.md b/notes/tasks/2020-02-21_ingest_backfills.md
new file mode 100644
index 0000000..48df910
--- /dev/null
+++ b/notes/tasks/2020-02-21_ingest_backfills.md
@@ -0,0 +1,104 @@
+
+Follow-ups to last ingest backfill. Only run these when ingest request topic is
+empty, and full persist chain has run successfully.
+
+## Corona virus stuff
+
+    ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query coronavirus
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query 2019-nCoV
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa query MERS-CoV
+
+## Large OA Publishers
+
+Should probably check domain stats/success for all of these first.
+
+Would also be good to have a "randomize" option. Could fake that by dumping to
+disk first.
+
+    ./fatcat_ingest.py --limit 2000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher elsevier
+
+    ./fatcat_ingest.py --dry-run --limit 500 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --after-year 2020 container --publisher springer
+
+    # ???
+    ./fatcat_ingest.py --limit 1000 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4
+
+## Fixed OA Publishers (small tests)
+
+    # american archivist
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4
+    => Expecting 2920 release objects in search queries
+    => Counter({'estimate': 2920, 'elasticsearch_release': 26, 'ingest_request': 25, 'kafka': 25})
+    => good
+
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter
+    => Expecting 42897 release objects in search queries
+    => Counter({'estimate': 42897, 'ingest_request': 25, 'kafka': 25, 'elasticsearch_release': 25})
+
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher frontiers
+    => Expecting 35427 release objects in search queries
+    => Counter({'estimate': 35427, 'kafka': 25, 'elasticsearch_release': 25, 'ingest_request': 25})
+    => mixed results?
+
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi
+    => Expecting 43111 release objects in search queries
+    => Counter({'estimate': 43111, 'elasticsearch_release': 25, 'ingest_request': 25, 'kafka': 25})
+    => success, fast
+
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher "American Heart Association"
+    => Expecting 185240 release objects in search queries
+    => Counter({'estimate': 185240, 'kafka': 25, 'ingest_request': 25, 'elasticsearch_release': 25})
+    => no success? or mixed? skip for now
+
+    # Environmental Health Perspectives (NIH)
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --container-id 3w6amv3ecja7fa3ext35ndpiky
+    => ["no-pdf-link",null,"https://ehp.niehs.nih.gov/doi/10.1289/ehp.113-a51"]
+    => ["no-pdf-link",null,"https://ehp.niehs.nih.gov/doi/10.1289/ehp.113-a51"]
+    => FIXED
+    => good (but slow?)
+
+    ./fatcat_ingest.py --limit 50 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher "Tomsk State University"
+    => Expecting 578057 release objects in search queries
+    => Counter({'estimate': 578057, 'elasticsearch_release': 50, 'kafka': 50, 'ingest_request': 50})
+    => nothing from tsu.ru? skip for now
+
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name "cogent"
+    => Expecting 4602 release objects in search queries
+    => Counter({'estimate': 4602, 'kafka': 25, 'elasticsearch_release': 25, 'ingest_request': 25})
+    => good
+
+    ./fatcat_ingest.py --limit 25 --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*"
+    => Expecting 5690 release objects in search queries
+    => Counter({'estimate': 5690, 'ingest_request': 25, 'kafka': 25, 'elasticsearch_release': 25})
+    => good
+
+
+## Fixed OA Publishers (full runs)
+
+    # american archivist
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org --allow-non-oa container --container-id zpobyv4vbranllc7oob56tgci4
+    Expecting 2920 release objects in search queries
+    Counter({'estimate': 2920, 'elasticsearch_release': 2920, 'kafka': 2911, 'ingest_request': 2911})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher Gruyter
+    Expecting 42986 release objects in search queries
+    Counter({'estimate': 42986, 'elasticsearch_release': 42986, 'kafka': 42935, 'ingest_request': 42935})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --publisher mdpi
+    Expecting 43108 release objects in search queries
+    Counter({'estimate': 43108, 'elasticsearch_release': 43108, 'ingest_request': 41262, 'kafka': 41262})
+
+    # Environmental Health Perspectives (NIH)
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --container-id 3w6amv3ecja7fa3ext35ndpiky
+    Expecting 12699 release objects in search queries
+    Counter({'elasticsearch_release': 12699, 'estimate': 12699, 'kafka': 12615, 'ingest_request': 12615})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org container --name "cogent"
+    Expecting 4602 release objects in search queries
+    Counter({'estimate': 4602, 'ingest_request': 4602, 'kafka': 4602, 'elasticsearch_release': 4602})
+
+    ./fatcat_ingest.py --env prod --enqueue-kafka --kafka-hosts wbgrp-svc263.us.archive.org query "doi:10.26434\/chemrxiv*"
+    Expecting 5690 release objects in search queries
+    Counter({'ingest_request': 5690, 'kafka': 5690, 'estimate': 5690, 'elasticsearch_release': 5690})
+