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remove accidental addition of desc in order by id #43

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merged 11 commits into from
Oct 18, 2023
Merged

remove accidental addition of desc in order by id #43

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a83d0f0
update classifications backfill script to chunk and save in file
yuenmichelle1 Oct 16, 2023
16df964
update to <= remove unused limit in query
yuenmichelle1 Oct 16, 2023
73cfae1
update copy into source
yuenmichelle1 Oct 17, 2023
f8fa8e3
split backfill to file creation then copy from files
yuenmichelle1 Oct 17, 2023
782d043
cast to int
yuenmichelle1 Oct 18, 2023
cf756ca
Merge branch 'main' into update-backfill-scripts-for-classifications
yuenmichelle1 Oct 18, 2023
7ac7786
revert accidental adding commas on limit
yuenmichelle1 Oct 18, 2023
25af5bc
Merge branch 'main' into update-backfill-scripts-for-classifications
yuenmichelle1 Oct 18, 2023
522a0c7
add keepalives to hopefully ensure connection does not get lost
yuenmichelle1 Oct 18, 2023
b31c1cc
remove order by desc
yuenmichelle1 Oct 18, 2023
7828a1c
Merge branch 'main' into update-backfill-scripts-for-classifications
yuenmichelle1 Oct 18, 2023
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6 changes: 3 additions & 3 deletions scripts/save_classifications_chunk_in_files.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
start_time = datetime.now()
print("CLASSIFICATIONS backfill BEFORE Time =", start_time)

classifications_query = "select id::bigint as classification_id, created_at as event_time, updated_at as classification_updated_at, CASE WHEN metadata ->> 'started_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'started_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'started_at', 'YYYY-MM-DD HH24:MI:SS') END started_at, CASE WHEN metadata ->> 'finished_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'finished_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'finished_at', 'YYYY-MM-DD HH24:MI:SS') END finished_at, project_id::bigint, workflow_id::bigint, user_id::bigint, array_remove(string_to_array(replace(replace(replace(metadata ->> 'user_group_ids', '[', ''), ']', ''), ' ', '' ), ','), 'null')::bigint[] as user_group_ids, EXTRACT(EPOCH FROM (CASE WHEN metadata ->> 'finished_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'finished_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'finished_at', 'YYYY-MM-DD HH24:MI:SS') END) - (CASE WHEN metadata ->> 'started_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'started_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'started_at', 'YYYY-MM-DD HH24:MI:SS') END)) as session_time, created_at, updated_at from classifications where id < %s order by id desc"
classifications_query = "select id::bigint as classification_id, created_at as event_time, updated_at as classification_updated_at, CASE WHEN metadata ->> 'started_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'started_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'started_at', 'YYYY-MM-DD HH24:MI:SS') END started_at, CASE WHEN metadata ->> 'finished_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'finished_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'finished_at', 'YYYY-MM-DD HH24:MI:SS') END finished_at, project_id::bigint, workflow_id::bigint, user_id::bigint, array_remove(string_to_array(replace(replace(replace(metadata ->> 'user_group_ids', '[', ''), ']', ''), ' ', '' ), ','), 'null')::bigint[] as user_group_ids, EXTRACT(EPOCH FROM (CASE WHEN metadata ->> 'finished_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'finished_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'finished_at', 'YYYY-MM-DD HH24:MI:SS') END) - (CASE WHEN metadata ->> 'started_at' ~'\d{1,2}\/\d{1,2}\/\d{2,4}' THEN to_timestamp(metadata ->> 'started_at', 'MM/DD/YYYY HH24:MI') ELSE TO_TIMESTAMP(metadata ->> 'started_at', 'YYYY-MM-DD HH24:MI:SS') END)) as session_time, created_at, updated_at from classifications where id < %s order by id"

offset = 0
limit = 10000000
Expand All @@ -30,8 +30,8 @@
with psycopg.connect(f"host={PANOPTES_CONN} port={PANOPTES_PORT} dbname={PANOPTES_DB} user={PANOPTES_USER} password={PANOPTES_PW} sslmode=require keepalives=1 keepalives_idle=30 keepalives_interval=10 keepalives_count=20") as panoptes_db_conn:
with open(f"prod_classifications_{offset}.csv", "wb") as f:
with panoptes_db_conn.cursor(name="panoptes_cursor").copy(f"COPY ({classifications_query}) TO STDOUT WITH CSV HEADER", (FIRST_INGESTED_CLASSIFICATION_ID,)) as panoptes_copy:
for data in panoptes_copy:
f.write(data)
for data in panoptes_copy:
f.write(data)
offset+= 1

finish_copy_time = datetime.now()
Expand Down