Harvest for Paul, 1988 Created 17 May 13:58

Stage: completed
Fetched: 17 May 13:58
Validated: 17 May 13:58
Deltas Created 17 May 13:58
Units Normalized: 17 May 13:59
Ancestry Built: 17 May 13:58
Nodes Matched: 17 May 13:59
Names Parsed: 17 May 13:58
New Models Stored: 17 May 13:58
Indexed: 17 May 13:59
Completed: 17 May 14:00
Time to Harvest: less than a minute
Harvesting Log

(146 lines)
[INFO] [2021-05-17 13:58:44] Created harvest instance #3863
[STOP] [2021-05-17 13:58:44] create_harvest_instance
[START] [2021-05-17 13:58:44] fetch_files
[STOP] [2021-05-17 13:58:44] fetch_files
[START] [2021-05-17 13:58:44] validate_each_file
[INFO] [2021-05-17 13:58:44] Looping over 3 formats...
[INFO] [2021-05-17 13:58:44] ...nodes (/app/public/data/paul_paul_1988/taxa.txt)
[INFO] [2021-05-17 13:58:44] Valid: /app/public/converted_csv/paul_paul_1988_nodes_3863.csv (101 lines)
[INFO] [2021-05-17 13:58:44] ...occurrences (/app/public/data/paul_paul_1988/occurrences.txt)
[INFO] [2021-05-17 13:58:44] Valid: /app/public/converted_csv/paul_paul_1988_occurrences_3863.csv (101 lines)
[INFO] [2021-05-17 13:58:44] ...measurements (/app/public/data/paul_paul_1988/measurements-or-facts.tsv)
[INFO] [2021-05-17 13:58:44] Valid: /app/public/converted_csv/paul_paul_1988_measurements_3863.csv (101 lines)
[STOP] [2021-05-17 13:58:44] validate_each_file
[START] [2021-05-17 13:58:44] convert_to_csv
[INFO] [2021-05-17 13:58:44] Looping over 3 formats...
[INFO] [2021-05-17 13:58:44] ...nodes (/app/public/data/paul_paul_1988/taxa.txt)
[CMD] [2021-05-17 13:58:44] /usr/bin/sort /app/public/converted_csv/paul_paul_1988_nodes_3863.csv > /app/public/converted_csv/paul_paul_1988_nodes_3863.csv_sorted
[INFO] [2021-05-17 13:58:44] Converted: /app/public/converted_csv/paul_paul_1988_nodes_3863.csv (101 lines)
[INFO] [2021-05-17 13:58:44] ...occurrences (/app/public/data/paul_paul_1988/occurrences.txt)
[CMD] [2021-05-17 13:58:44] /usr/bin/sort /app/public/converted_csv/paul_paul_1988_occurrences_3863.csv > /app/public/converted_csv/paul_paul_1988_occurrences_3863.csv_sorted
[INFO] [2021-05-17 13:58:44] Converted: /app/public/converted_csv/paul_paul_1988_occurrences_3863.csv (101 lines)
[INFO] [2021-05-17 13:58:44] ...measurements (/app/public/data/paul_paul_1988/measurements-or-facts.tsv)
[CMD] [2021-05-17 13:58:44] /usr/bin/sort /app/public/converted_csv/paul_paul_1988_measurements_3863.csv > /app/public/converted_csv/paul_paul_1988_measurements_3863.csv_sorted
[INFO] [2021-05-17 13:58:44] Converted: /app/public/converted_csv/paul_paul_1988_measurements_3863.csv (101 lines)
[STOP] [2021-05-17 13:58:44] convert_to_csv
[START] [2021-05-17 13:58:44] calculate_delta
[INFO] [2021-05-17 13:58:44] Looping over 3 formats...
[INFO] [2021-05-17 13:58:44] ...nodes (/app/public/data/paul_paul_1988/taxa.txt)
[CMD] [2021-05-17 13:58:44] echo "0a" > /app/public/diff/paul_paul_1988_nodes_3863.diff
[CMD] [2021-05-17 13:58:44] tail -n +1 /app/public/converted_csv/paul_paul_1988_nodes_3863.csv >> /app/public/diff/paul_paul_1988_nodes_3863.diff
[CMD] [2021-05-17 13:58:44] echo "." >> /app/public/diff/paul_paul_1988_nodes_3863.diff
[INFO] [2021-05-17 13:58:44] Created diff: /app/public/diff/paul_paul_1988_nodes_3863.diff (103 lines)
[INFO] [2021-05-17 13:58:44] ...occurrences (/app/public/data/paul_paul_1988/occurrences.txt)
[CMD] [2021-05-17 13:58:44] echo "0a" > /app/public/diff/paul_paul_1988_occurrences_3863.diff
[CMD] [2021-05-17 13:58:44] tail -n +1 /app/public/converted_csv/paul_paul_1988_occurrences_3863.csv >> /app/public/diff/paul_paul_1988_occurrences_3863.diff
[CMD] [2021-05-17 13:58:44] echo "." >> /app/public/diff/paul_paul_1988_occurrences_3863.diff
[INFO] [2021-05-17 13:58:44] Created diff: /app/public/diff/paul_paul_1988_occurrences_3863.diff (103 lines)
[INFO] [2021-05-17 13:58:44] ...measurements (/app/public/data/paul_paul_1988/measurements-or-facts.tsv)
[CMD] [2021-05-17 13:58:44] echo "0a" > /app/public/diff/paul_paul_1988_measurements_3863.diff
[CMD] [2021-05-17 13:58:44] tail -n +1 /app/public/converted_csv/paul_paul_1988_measurements_3863.csv >> /app/public/diff/paul_paul_1988_measurements_3863.diff
[CMD] [2021-05-17 13:58:44] echo "." >> /app/public/diff/paul_paul_1988_measurements_3863.diff
[INFO] [2021-05-17 13:58:44] Created diff: /app/public/diff/paul_paul_1988_measurements_3863.diff (103 lines)
[STOP] [2021-05-17 13:58:44] calculate_delta
[START] [2021-05-17 13:58:44] parse_diff_and_store
[INFO] [2021-05-17 13:58:44] Handling diff: /app/public/diff/paul_paul_1988_nodes_3863.diff (103 lines)
[INFO] [2021-05-17 13:58:44] Loading nodes diff file into memory (103 /app/public/diff/paul_paul_1988_nodes_3863.diff lines)...
[INFO] [2021-05-17 13:58:44] Handling diff: /app/public/diff/paul_paul_1988_occurrences_3863.diff (103 lines)
[INFO] [2021-05-17 13:58:44] Loading occurrences diff file into memory (103 /app/public/diff/paul_paul_1988_occurrences_3863.diff lines)...
[INFO] [2021-05-17 13:58:44] Handling diff: /app/public/diff/paul_paul_1988_measurements_3863.diff (103 lines)
[INFO] [2021-05-17 13:58:44] Loading measurements diff file into memory (103 /app/public/diff/paul_paul_1988_measurements_3863.diff lines)...
[INFO] [2021-05-17 13:58:44] Storing 202 ScientificNames
[INFO] [2021-05-17 13:58:44] Processing group of 202 in 1 groups of 1000
[INFO] [2021-05-17 13:58:44] Average Time: 0.06
[INFO] [2021-05-17 13:58:44] Total Time: 1s
[INFO] [2021-05-17 13:58:44] Storing 202 Nodes
[INFO] [2021-05-17 13:58:44] Processing group of 202 in 1 groups of 1000
[INFO] [2021-05-17 13:58:44] Average Time: 0.06
[INFO] [2021-05-17 13:58:44] Total Time: 1s
[INFO] [2021-05-17 13:58:44] Storing 101 Occurrences
[INFO] [2021-05-17 13:58:44] Processing group of 101 in 1 groups of 1000
[INFO] [2021-05-17 13:58:44] Average Time: 0.01
[INFO] [2021-05-17 13:58:44] Total Time: 1s
[INFO] [2021-05-17 13:58:44] Storing 101 Traits
[INFO] [2021-05-17 13:58:44] Processing group of 101 in 1 groups of 1000
[INFO] [2021-05-17 13:58:44] Average Time: 0.03
[INFO] [2021-05-17 13:58:44] Total Time: 1s
[STOP] [2021-05-17 13:58:44] parse_diff_and_store
[START] [2021-05-17 13:58:44] resolve_keys
[INFO] [2021-05-17 13:58:50] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-17 13:58:50] traits to occurrences...
[INFO] [2021-05-17 13:58:50] traits to nodes (through occurrences)...
[INFO] [2021-05-17 13:58:50] Traits to sex term...
[INFO] [2021-05-17 13:58:50] Traits to lifestage term...
[INFO] [2021-05-17 13:58:50] MetaTraits to traits...
[INFO] [2021-05-17 13:58:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-17 13:58:50] Assocs to occurrences...
[INFO] [2021-05-17 13:58:50] Assocs to nodes...
[INFO] [2021-05-17 13:58:50] Assoc to sex term...
[INFO] [2021-05-17 13:58:50] Assoc to lifestage term...
[INFO] [2021-05-17 13:58:50] MetaAssoc to assocs...
[STOP] [2021-05-17 13:58:50] resolve_keys
[START] [2021-05-17 13:58:50] hold_for_later_1
[STOP] [2021-05-17 13:58:50] hold_for_later_1
[START] [2021-05-17 13:58:50] hold_for_later_2
[STOP] [2021-05-17 13:58:50] hold_for_later_2
[START] [2021-05-17 13:58:50] resolve_missing_parents
[STOP] [2021-05-17 13:58:50] resolve_missing_parents
[START] [2021-05-17 13:58:50] rebuild_nodes
[START] [2021-05-17 13:58:50] Flattener#flatten
[START] [2021-05-17 13:58:50] Flattener#study_resource
[START] [2021-05-17 13:58:50] Flattener#build_ancestry
[STOP] [2021-05-17 13:58:50] Flattener#build_ancestry
[INFO] [2021-05-17 13:58:50] 202 ancestry keys
[START] [2021-05-17 13:58:50] build_node_ancestors
[INFO] [2021-05-17 13:58:50] old ancestors deleted.
[STOP] [2021-05-17 13:58:50] build_node_ancestors
[START] [2021-05-17 13:58:50] Flattener#propagate_ancestor_ids
[STOP] [2021-05-17 13:58:50] Flattener#propagate_ancestor_ids
[STOP] [2021-05-17 13:58:50] Flattener#flatten
[STOP] [2021-05-17 13:58:50] rebuild_nodes
[START] [2021-05-17 13:58:50] resolve_missing_media_owners
[STOP] [2021-05-17 13:58:50] resolve_missing_media_owners
[START] [2021-05-17 13:58:50] sanitize_media_verbatims
[STOP] [2021-05-17 13:58:50] sanitize_media_verbatims
[START] [2021-05-17 13:58:50] queue_downloads
[STOP] [2021-05-17 13:58:50] queue_downloads
[START] [2021-05-17 13:58:51] parse_names
[WARN] [2021-05-17 13:58:51] I see 202 names which still need to be parsed.
[WARN] [2021-05-17 13:58:52] I see 2 names which still need to be parsed.
[STOP] [2021-05-17 13:58:53] parse_names
[START] [2021-05-17 13:58:53] denormalize_canonical_names_to_nodes
[STOP] [2021-05-17 13:58:53] denormalize_canonical_names_to_nodes
[START] [2021-05-17 13:58:53] match_nodes
[START] [2021-05-17 13:58:53] map_all_nodes_to_pages
[STOP] [2021-05-17 13:59:03] map_all_nodes_to_pages
[INFO] [2021-05-17 13:59:03] 27 Unmatched nodes (of 202)! That's too many to output. Full list in /app/public/data/paul_paul_1988/unmatched_nodes.txt ; First 10: Canonical: Carnotaurus sasterei; Node#94021519; ResourceID: Carnotaurus_sasterei; Canonical: Albertosaurus lancensis; Node#94021479; ResourceID: Albertosaurus_lancensis; Canonical: Albertosaurus liberatus; Node#94021480; ResourceID: Albertosaurus_liberatus; Canonical: Aublysodon huoyanshaensis; Node#94021501; ResourceID: Aublysodon_huoyanshaensis; Canonical: Aliwalia; Node#94021487; ResourceID: Aliwalia; Canonical: Frenguellisaurus; Node#94021557; ResourceID: Frenguellisaurus; Canonical: Ischisaurus; Node#94021575; ResourceID: Ischisaurus; Canonical: Aristosuchus oweni; Node#94021499; ResourceID: Aristosuchus_oweni; Canonical: Bahariasauridae; Node#94021507; ResourceID: Bahariasauridae; Canonical: Bradycneme; Node#94021514; ResourceID: Bradycneme
[START] [2021-05-17 13:59:03] update_nodes
[STOP] [2021-05-17 13:59:03] update_nodes
[STOP] [2021-05-17 13:59:03] match_nodes
[START] [2021-05-17 13:59:03] reindex_search
[STOP] [2021-05-17 13:59:03] reindex_search
[START] [2021-05-17 13:59:03] normalize_units
[STOP] [2021-05-17 13:59:03] normalize_units
[START] [2021-05-17 13:59:03] calculate_statistics
[STOP] [2021-05-17 13:59:03] calculate_statistics
[START] [2021-05-17 13:59:03] complete_harvest_instance
[START] [2021-05-17 13:59:03] overall_tsv_creation
[INFO] [2021-05-17 13:59:03] Processing group of 202 in 1 batches of 10000
[INFO] [2021-05-17 13:59:41] 101 Traits (unfiltered)...
[INFO] [2021-05-17 14:00:17] 101 Traits (filtered)...
[INFO] [2021-05-17 14:00:17] 0 Associations (filtered)...
[INFO] [2021-05-17 14:00:17] 0 metadata added.
[INFO] [2021-05-17 14:00:17] 0 metadata added.
[INFO] [2021-05-17 14:00:44] Average Time: 74.45
[INFO] [2021-05-17 14:00:44] Total Time: 1m41s
[STOP] [2021-05-17 14:00:44] overall_tsv_creation
[INFO] [2021-05-17 14:00:44] Done. Check your files:
[INFO] [2021-05-17 14:00:44] (200 lines) /app/public/data/paul_paul_1988/publish_nodes.tsv
[INFO] [2021-05-17 14:00:44] (442 lines) /app/public/data/paul_paul_1988/publish_node_ancestors.tsv
[INFO] [2021-05-17 14:00:44] (202 lines) /app/public/data/paul_paul_1988/publish_scientific_names.tsv
[INFO] [2021-05-17 14:00:44] (102 lines) /app/public/data/paul_paul_1988/publish_traits.tsv
[INFO] [2021-05-17 14:00:44] (1 lines) /app/public/data/paul_paul_1988/publish_metadata.tsv
[STOP] [2021-05-17 14:00:44] complete_harvest_instance
[START] [2021-05-17 14:00:44] completed
[STOP] [2021-05-17 14:00:44] completed
[STOP] [2021-05-17 14:00:44] logged process, took 120.91
Latest Process

17 May 13:55 EXITED currently processing 0