Harvest for Crustacean body sizes Created 13 Oct 11:26

Harvesting Log

[INFO] [2023-10-13 11:26:00] Created harvest instance #4433
[STOP] [2023-10-13 11:26:00] create_harvest_instance
[START] [2023-10-13 11:26:00] fetch_files
[STOP] [2023-10-13 11:26:00] fetch_files
[START] [2023-10-13 11:26:00] validate_each_file
[INFO] [2023-10-13 11:26:00] Looping over 4 formats...
[INFO] [2023-10-13 11:26:00] ...refs (/app/public/data/crustacean_body_/references.txt)
[INFO] [2023-10-13 11:26:00] Valid: /app/public/data/crustacean_body_/converted_csv/crustacean_body__refs_30702.csv (1017 lines)
[INFO] [2023-10-13 11:26:00] ...nodes (/app/public/data/crustacean_body_/taxa.txt)
[INFO] [2023-10-13 11:26:00] Valid: /app/public/data/crustacean_body_/converted_csv/crustacean_body__nodes_30701.csv (3052 lines)
[INFO] [2023-10-13 11:26:00] ...occurrences (/app/public/data/crustacean_body_/occurrences.txt)
[INFO] [2023-10-13 11:26:02] Valid: /app/public/data/crustacean_body_/converted_csv/crustacean_body__occurrences_30703.csv (18744 lines)
[INFO] [2023-10-13 11:26:02] ...measurements (/app/public/data/crustacean_body_/measurements-or-facts.txt)
[INFO] [2023-10-13 11:26:04] Valid: /app/public/data/crustacean_body_/converted_csv/crustacean_body__measurements_30704.csv (16550 lines)
[STOP] [2023-10-13 11:26:04] validate_each_file
[START] [2023-10-13 11:26:04] convert_to_csv
[INFO] [2023-10-13 11:26:04] Looping over 4 formats...
[INFO] [2023-10-13 11:26:04] ...refs (/app/public/data/crustacean_body_/references.txt)
[CMD] [2023-10-13 11:26:04] /usr/bin/sort /app/public/data/crustacean_body_/converted_csv/crustacean_body__refs_30702.csv > /app/public/data/crustacean_body_/converted_csv/crustacean_body__refs_30702.csv_sorted
[INFO] [2023-10-13 11:26:04] Converted: /app/public/data/crustacean_body_/converted_csv/crustacean_body__refs_30702.csv (1017 lines)
[INFO] [2023-10-13 11:26:04] ...nodes (/app/public/data/crustacean_body_/taxa.txt)
[CMD] [2023-10-13 11:26:04] /usr/bin/sort /app/public/data/crustacean_body_/converted_csv/crustacean_body__nodes_30701.csv > /app/public/data/crustacean_body_/converted_csv/crustacean_body__nodes_30701.csv_sorted
[INFO] [2023-10-13 11:26:04] Converted: /app/public/data/crustacean_body_/converted_csv/crustacean_body__nodes_30701.csv (3052 lines)
[INFO] [2023-10-13 11:26:04] ...occurrences (/app/public/data/crustacean_body_/occurrences.txt)
[CMD] [2023-10-13 11:26:04] /usr/bin/sort /app/public/data/crustacean_body_/converted_csv/crustacean_body__occurrences_30703.csv > /app/public/data/crustacean_body_/converted_csv/crustacean_body__occurrences_30703.csv_sorted
[INFO] [2023-10-13 11:26:04] Converted: /app/public/data/crustacean_body_/converted_csv/crustacean_body__occurrences_30703.csv (18744 lines)
[INFO] [2023-10-13 11:26:04] ...measurements (/app/public/data/crustacean_body_/measurements-or-facts.txt)
[CMD] [2023-10-13 11:26:04] /usr/bin/sort /app/public/data/crustacean_body_/converted_csv/crustacean_body__measurements_30704.csv > /app/public/data/crustacean_body_/converted_csv/crustacean_body__measurements_30704.csv_sorted
[INFO] [2023-10-13 11:26:04] Converted: /app/public/data/crustacean_body_/converted_csv/crustacean_body__measurements_30704.csv (16550 lines)
[STOP] [2023-10-13 11:26:04] convert_to_csv
[START] [2023-10-13 11:26:04] calculate_delta
[INFO] [2023-10-13 11:26:04] Looping over 4 formats...
[INFO] [2023-10-13 11:26:04] ...refs (/app/public/data/crustacean_body_/references.txt)
[CMD] [2023-10-13 11:26:04] echo "0a" > /app/public/data/crustacean_body_/diff/crustacean_body__refs_30702.diff
[CMD] [2023-10-13 11:26:04] tail -n +1 /app/public/data/crustacean_body_/converted_csv/crustacean_body__refs_30702.csv >> /app/public/data/crustacean_body_/diff/crustacean_body__refs_30702.diff
[CMD] [2023-10-13 11:26:04] echo "." >> /app/public/data/crustacean_body_/diff/crustacean_body__refs_30702.diff
[INFO] [2023-10-13 11:26:04] Created diff: /app/public/data/crustacean_body_/diff/crustacean_body__refs_30702.diff (1019 lines)
[INFO] [2023-10-13 11:26:04] ...nodes (/app/public/data/crustacean_body_/taxa.txt)
[CMD] [2023-10-13 11:26:04] echo "0a" > /app/public/data/crustacean_body_/diff/crustacean_body__nodes_30701.diff
[CMD] [2023-10-13 11:26:04] tail -n +1 /app/public/data/crustacean_body_/converted_csv/crustacean_body__nodes_30701.csv >> /app/public/data/crustacean_body_/diff/crustacean_body__nodes_30701.diff
[CMD] [2023-10-13 11:26:05] echo "." >> /app/public/data/crustacean_body_/diff/crustacean_body__nodes_30701.diff
[INFO] [2023-10-13 11:26:05] Created diff: /app/public/data/crustacean_body_/diff/crustacean_body__nodes_30701.diff (3054 lines)
[INFO] [2023-10-13 11:26:05] ...occurrences (/app/public/data/crustacean_body_/occurrences.txt)
[CMD] [2023-10-13 11:26:05] echo "0a" > /app/public/data/crustacean_body_/diff/crustacean_body__occurrences_30703.diff
[CMD] [2023-10-13 11:26:05] tail -n +1 /app/public/data/crustacean_body_/converted_csv/crustacean_body__occurrences_30703.csv >> /app/public/data/crustacean_body_/diff/crustacean_body__occurrences_30703.diff
[CMD] [2023-10-13 11:26:05] echo "." >> /app/public/data/crustacean_body_/diff/crustacean_body__occurrences_30703.diff
[INFO] [2023-10-13 11:26:05] Created diff: /app/public/data/crustacean_body_/diff/crustacean_body__occurrences_30703.diff (18746 lines)
[INFO] [2023-10-13 11:26:05] ...measurements (/app/public/data/crustacean_body_/measurements-or-facts.txt)
[CMD] [2023-10-13 11:26:05] echo "0a" > /app/public/data/crustacean_body_/diff/crustacean_body__measurements_30704.diff
[CMD] [2023-10-13 11:26:05] tail -n +1 /app/public/data/crustacean_body_/converted_csv/crustacean_body__measurements_30704.csv >> /app/public/data/crustacean_body_/diff/crustacean_body__measurements_30704.diff
[CMD] [2023-10-13 11:26:05] echo "." >> /app/public/data/crustacean_body_/diff/crustacean_body__measurements_30704.diff
[INFO] [2023-10-13 11:26:05] Created diff: /app/public/data/crustacean_body_/diff/crustacean_body__measurements_30704.diff (16552 lines)
[STOP] [2023-10-13 11:26:05] calculate_delta
[START] [2023-10-13 11:26:05] parse_diff_and_store
[INFO] [2023-10-13 11:26:05] Handling diff: /app/public/data/crustacean_body_/diff/crustacean_body__refs_30702.diff (1019 lines)
[INFO] [2023-10-13 11:26:05] Loading refs diff file into memory (1019 lines)...
[INFO] [2023-10-13 11:26:06] Storing 1017 References (1017/1017/1019)
[INFO] [2023-10-13 11:26:06] Handling diff: /app/public/data/crustacean_body_/diff/crustacean_body__nodes_30701.diff (3054 lines)
[INFO] [2023-10-13 11:26:06] Loading nodes diff file into memory (3054 lines)...
[WARN] [2023-10-13 11:26:06] Filtered Scientific Name `Bosmina liederi/longirostris` to `Bosmina liederilongirostris`
[WARN] [2023-10-13 11:26:06] Filtered Scientific Name `Ryocalanus  brasilianus` to `Ryocalanus brasilianus`
[WARN] [2023-10-13 11:26:07] Filtered Scientific Name `Gippslandia  estuarina` to `Gippslandia estuarina`
[INFO] [2023-10-13 11:26:07] Storing 3476 ScientificNames (6952/3052/3054)
[INFO] [2023-10-13 11:26:08] Storing 3476 Nodes (6952/3052/3054)
[INFO] [2023-10-13 11:26:09] Handling diff: /app/public/data/crustacean_body_/diff/crustacean_body__occurrences_30703.diff (18746 lines)
[INFO] [2023-10-13 11:26:09] Loading occurrences diff file into memory (18746 lines)...
[INFO] [2023-10-13 11:26:10] Storing 9999 Occurrences (12472/10000/18746)
[INFO] [2023-10-13 11:26:12] Storing 2473 OccurrenceMetadata (12472/10000/18746)
[WARN] [2023-10-13 11:26:13] SKIPPED 1772 Occurrence metadata (22989/18744/18746) with resource_pks already be in the database!
[INFO] [2023-10-13 11:26:13] Storing 8745 Occurrences (22989/18744/18746)
[INFO] [2023-10-13 11:26:14] Storing 0 OccurrenceMetadata (22989/18744/18746)
[WARN] [2023-10-13 11:26:14] No models to import, skipping!
[INFO] [2023-10-13 11:26:14] Handling diff: /app/public/data/crustacean_body_/diff/crustacean_body__measurements_30704.diff (16552 lines)
[INFO] [2023-10-13 11:26:14] Loading measurements diff file into memory (16552 lines)...
[INFO] [2023-10-13 11:26:23] Storing 23995 TraitsReferences (68856/10000/16552)
[INFO] [2023-10-13 11:26:24] Storing 9966 Traits (68856/10000/16552)
[INFO] [2023-10-13 11:26:28] Storing 34862 MetaTraits (68856/10000/16552)
[INFO] [2023-10-13 11:26:32] Storing 33 OccurrenceMetadata (68856/10000/16552)
[INFO] [2023-10-13 11:26:38] Storing 23353 TraitsReferences (124759/16550/16552)
[INFO] [2023-10-13 11:26:40] Storing 6551 Traits (124759/16550/16552)
[INFO] [2023-10-13 11:26:42] Storing 25999 MetaTraits (124759/16550/16552)
[STOP] [2023-10-13 11:26:45] parse_diff_and_store
[START] [2023-10-13 11:26:45] resolve_keys
[2023-10-13 11:26:45] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 11:26:53] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 11:26:54] traits to occurrences...
[INFO] [2023-10-13 11:26:54] traits to nodes (through occurrences)...
[INFO] [2023-10-13 11:26:55] Traits to sex term...
[INFO] [2023-10-13 11:26:55] Traits to lifestage term...
[INFO] [2023-10-13 11:26:55] MetaTraits to traits...
[INFO] [2023-10-13 11:26:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 11:26:59] Assocs to occurrences...
[INFO] [2023-10-13 11:26:59] Assocs to nodes...
[INFO] [2023-10-13 11:26:59] Assoc to sex term...
[INFO] [2023-10-13 11:26:59] Assoc to lifestage term...
[INFO] [2023-10-13 11:26:59] MetaAssoc to assocs...
[STOP] [2023-10-13 11:26:59] resolve_keys
[START] [2023-10-13 11:26:59] hold_for_later_1
[STOP] [2023-10-13 11:26:59] hold_for_later_1
[START] [2023-10-13 11:26:59] hold_for_later_2
[STOP] [2023-10-13 11:26:59] hold_for_later_2
[START] [2023-10-13 11:26:59] resolve_missing_parents
[STOP] [2023-10-13 11:26:59] resolve_missing_parents
[START] [2023-10-13 11:26:59] rebuild_nodes
[START] [2023-10-13 11:26:59] Flattener#flatten
[START] [2023-10-13 11:26:59] Flattener#study_resource
[START] [2023-10-13 11:26:59] Flattener#build_ancestry
[STOP] [2023-10-13 11:26:59] Flattener#build_ancestry
[INFO] [2023-10-13 11:26:59] 3476 ancestry keys
[START] [2023-10-13 11:26:59] build_node_ancestors
[INFO] [2023-10-13 11:26:59] old ancestors deleted.
[STOP] [2023-10-13 11:26:59] build_node_ancestors
[START] [2023-10-13 11:27:00] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:27:00] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 11:27:00] Flattener#flatten
[STOP] [2023-10-13 11:27:00] rebuild_nodes
[START] [2023-10-13 11:27:00] resolve_missing_media_owners
[STOP] [2023-10-13 11:27:00] resolve_missing_media_owners
[START] [2023-10-13 11:27:00] sanitize_media_verbatims
[STOP] [2023-10-13 11:27:00] sanitize_media_verbatims
[START] [2023-10-13 11:27:00] queue_downloads
[STOP] [2023-10-13 11:27:00] queue_downloads
[START] [2023-10-13 11:27:00] parse_names
[WARN] [2023-10-13 11:27:00] I see 3476 names which still need to be parsed.
[WARN] [2023-10-13 11:27:01] Names to parse: 3476 formatted: 3476 learned: 3188 parsed: 3476
[STOP] [2023-10-13 11:27:04] parse_names
[START] [2023-10-13 11:27:04] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 11:27:04] denormalize_canonical_names_to_nodes
[START] [2023-10-13 11:27:04] match_nodes
[START] [2023-10-13 11:27:04] map_all_nodes_to_pages
[STOP] [2023-10-13 11:27:51] map_all_nodes_to_pages
[INFO] [2023-10-13 11:27:51] 472 Unmatched nodes (of 3476)! That's too many to output. Full list in /app/public/data/crustacean_body_/unmatched_nodes.txt ; First 10: Canonical: Acanthocyclops robustus; Node#137154475; ResourceID: Acanthocyclops robustus; Canonical: Acanthocyclops vernalis; Node#137154476; ResourceID: Acanthocyclops vernalis; Canonical: Acartia lilljeborgi; Node#137154485; ResourceID: Acartia lilljeborgi; Canonical: Alglaodiaptomus leptopus; Node#137154498; ResourceID: Alglaodiaptomus leptopus; Canonical: Arietellus plumfer; Node#137154509; ResourceID: Arietellus plumfer; Canonical: Beockella delicata; Node#137154512; ResourceID: Beockella delicata; Canonical: Calanus cristanus; Node#137154528; ResourceID: Calanus cristanus; Canonical: Candacia aethiopica; Node#137154553; ResourceID: Candacia aethiopica; Canonical: Centropages abdominaris; Node#137154560; ResourceID: Centropages abdominaris; Canonical: Chirundina streetsi; Node#137154579; ResourceID: Chirundina streetsi
[START] [2023-10-13 11:27:51] update_nodes
[STOP] [2023-10-13 11:27:53] update_nodes
[STOP] [2023-10-13 11:27:53] match_nodes
[START] [2023-10-13 11:27:53] reindex_search
[STOP] [2023-10-13 11:27:55] reindex_search
[START] [2023-10-13 11:27:55] normalize_units
[STOP] [2023-10-13 11:28:51] normalize_units
[START] [2023-10-13 11:28:51] calculate_statistics
[INFO] [2023-10-13 11:28:54] Duplicate page_id count: 0
[STOP] [2023-10-13 11:28:54] calculate_statistics
[START] [2023-10-13 11:28:54] complete_harvest_instance
[START] [2023-10-13 11:28:54] overall_tsv_creation
[INFO] [2023-10-13 11:28:54] Exporting 3476 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 11:28:54] Processing group of 3476 in 1 batches of 10000
[INFO] [2023-10-13 11:29:00] 16322 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 11:29:00] Building Traits map for 3476 nodes (this can take a while)...
[INFO] [2023-10-13 11:29:10] Mapped 16322 traits (60861 meta) for 3476 nodes.
[INFO] [2023-10-13 11:29:10] Building Associations map (this can take a while)...
[INFO] [2023-10-13 11:29:10] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 11:29:10] Adding 16322 traits...
[INFO] [2023-10-13 11:29:17] 62412 metadata added.
[INFO] [2023-10-13 11:29:17] Adding 0 assocs...
[INFO] [2023-10-13 11:29:17] 0 metadata added.
[INFO] [2023-10-13 11:30:04] Processed 3476/3476 nodes
[INFO] [2023-10-13 11:30:04] Average Time: 68.89
[INFO] [2023-10-13 11:30:04] Total Time: 1m11s
[STOP] [2023-10-13 11:30:04] overall_tsv_creation
[INFO] [2023-10-13 11:30:04] Done. Check your files:
[INFO] [2023-10-13 11:30:04] (3476 lines) /app/public/data/crustacean_body_/publish_nodes.tsv
[INFO] [2023-10-13 11:30:04] (10022 lines) /app/public/data/crustacean_body_/publish_node_ancestors.tsv
[INFO] [2023-10-13 11:30:05] (3476 lines) /app/public/data/crustacean_body_/publish_scientific_names.tsv
[INFO] [2023-10-13 11:30:05] (16323 lines) /app/public/data/crustacean_body_/publish_traits.tsv
[INFO] [2023-10-13 11:30:05] (62413 lines) /app/public/data/crustacean_body_/publish_metadata.tsv
[STOP] [2023-10-13 11:30:05] complete_harvest_instance
[START] [2023-10-13 11:30:05] completed
[STOP] [2023-10-13 11:30:05] completed
[STOP] [2023-10-13 11:30:05] logged process, took 245.19

Latest Process

13 Oct 11:25 EXITED currently processing 0