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Adding backfill scripts #33

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merged 9 commits into from
Sep 21, 2023
Merged

Adding backfill scripts #33

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3af1d86
Create backfill_talk_comments.py
yuenmichelle1 Sep 15, 2023
3f4b759
backfill classifications
yuenmichelle1 Sep 15, 2023
2df9139
Update backfill_classifications.py
yuenmichelle1 Sep 15, 2023
0a5824f
add user_group_membership_backfill and update select query of backfil…
yuenmichelle1 Sep 20, 2023
64be6a4
add update classification events
yuenmichelle1 Sep 20, 2023
4d49c33
Merge branch 'main' into adding-backfill-scripts
yuenmichelle1 Sep 21, 2023
f186f60
add sslmode require to connection strings
yuenmichelle1 Sep 21, 2023
8c147b8
casting ids to big ints and taking care of case when date comes in fo…
yuenmichelle1 Sep 21, 2023
87a32ff
Merge branch 'main' into adding-backfill-scripts
yuenmichelle1 Sep 21, 2023
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2 changes: 1 addition & 1 deletion scripts/backfill_classifications.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
print("CLASSIFICATIONS backfill BEFORE Time =", current_time)

with psycopg.connect(f"host={PANOPTES_CONN} port={PANOPTES_PORT} dbname={PANOPTES_DB} user={PANOPTES_USER} password={PANOPTES_PW} sslmode=require") as panoptes_db_conn, psycopg.connect(f"host={TIMESCALE_CONNECTION} port={TIMESCALE_PORT} dbname={ERAS_DB} user={ERAS_USER} password={ERAS_PW} sslmode=require") as timescale_db_conn:
with panoptes_db_conn.cursor(name="panoptes_cursor").copy("COPY (select id as classification_id, created_at as event_time, updated_at as classification_updated_at, TO_TIMESTAMP(metadata ->> 'started_at', 'YYYY-MM-DD HH24:MI:SS') as started_at, TO_TIMESTAMP(metadata ->> 'finished_at', 'YYYY-MM-DD HH24:MI:SS') as finished_at, project_id, workflow_id, user_id, string_to_array(replace(replace(replace(metadata ->> 'user_group_ids', '[', ''), ']', ''), ' ', '' ), ',')::int[] as user_group_ids, EXTRACT(EPOCH FROM TO_TIMESTAMP(metadata ->> 'finished_at', 'YYYY-MM-DD HH24:MI:SS') - TO_TIMESTAMP(metadata ->> 'started_at', 'YYYY-MM-DD HH24:MI:SS')) as session_time, created_at, updated_at from classifications where id < %s) TO STDOUT (FORMAT BINARY)", (FIRST_INGESTED_CLASSIFICATION_ID,)) as panoptes_copy:
with panoptes_db_conn.cursor(name="panoptes_cursor").copy("COPY (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, string_to_array(replace(replace(replace(metadata ->> 'user_group_ids', '[', ''), ']', ''), ' ', '' ), ',')::int[] 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) TO STDOUT (FORMAT BINARY)", (FIRST_INGESTED_CLASSIFICATION_ID,)) as panoptes_copy:
with timescale_db_conn.cursor().copy("COPY classification_events FROM STDIN (FORMAT BINARY)") as timescale_copy:
for data in panoptes_copy:
timescale_copy.write(data)
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