Harvest for Bok et al 2016 Created 13 Oct 13:55

Harvesting Log

[INFO] [2023-10-13 13:55:36] Created harvest instance #4462
[STOP] [2023-10-13 13:55:36] create_harvest_instance
[START] [2023-10-13 13:55:36] fetch_files
[STOP] [2023-10-13 13:55:36] fetch_files
[START] [2023-10-13 13:55:36] validate_each_file
[INFO] [2023-10-13 13:55:36] Looping over 4 formats...
[INFO] [2023-10-13 13:55:36] ...refs (/app/public/data/bok_et_al_bok_et/references.tsv)
[INFO] [2023-10-13 13:55:36] Valid: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_refs_30856.csv (17 lines)
[INFO] [2023-10-13 13:55:36] ...nodes (/app/public/data/bok_et_al_bok_et/taxa.txt)
[INFO] [2023-10-13 13:55:36] Valid: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_nodes_30853.csv (16 lines)
[INFO] [2023-10-13 13:55:36] ...occurrences (/app/public/data/bok_et_al_bok_et/occurrences.txt)
[INFO] [2023-10-13 13:55:36] Valid: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_occurrences_30854.csv (16 lines)
[INFO] [2023-10-13 13:55:36] ...measurements (/app/public/data/bok_et_al_bok_et/measurementsorfacts.txt)
[INFO] [2023-10-13 13:55:36] Valid: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_measurements_30855.csv (44 lines)
[STOP] [2023-10-13 13:55:36] validate_each_file
[START] [2023-10-13 13:55:36] convert_to_csv
[INFO] [2023-10-13 13:55:36] Looping over 4 formats...
[INFO] [2023-10-13 13:55:36] ...refs (/app/public/data/bok_et_al_bok_et/references.tsv)
[CMD] [2023-10-13 13:55:36] /usr/bin/sort /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_refs_30856.csv > /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_refs_30856.csv_sorted
[INFO] [2023-10-13 13:55:36] Converted: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_refs_30856.csv (17 lines)
[INFO] [2023-10-13 13:55:36] ...nodes (/app/public/data/bok_et_al_bok_et/taxa.txt)
[CMD] [2023-10-13 13:55:36] /usr/bin/sort /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_nodes_30853.csv > /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_nodes_30853.csv_sorted
[INFO] [2023-10-13 13:55:36] Converted: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_nodes_30853.csv (16 lines)
[INFO] [2023-10-13 13:55:36] ...occurrences (/app/public/data/bok_et_al_bok_et/occurrences.txt)
[CMD] [2023-10-13 13:55:36] /usr/bin/sort /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_occurrences_30854.csv > /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_occurrences_30854.csv_sorted
[INFO] [2023-10-13 13:55:36] Converted: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_occurrences_30854.csv (16 lines)
[INFO] [2023-10-13 13:55:36] ...measurements (/app/public/data/bok_et_al_bok_et/measurementsorfacts.txt)
[CMD] [2023-10-13 13:55:36] /usr/bin/sort /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_measurements_30855.csv > /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_measurements_30855.csv_sorted
[INFO] [2023-10-13 13:55:37] Converted: /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_measurements_30855.csv (44 lines)
[STOP] [2023-10-13 13:55:37] convert_to_csv
[START] [2023-10-13 13:55:37] calculate_delta
[INFO] [2023-10-13 13:55:37] Looping over 4 formats...
[INFO] [2023-10-13 13:55:37] ...refs (/app/public/data/bok_et_al_bok_et/references.tsv)
[CMD] [2023-10-13 13:55:37] echo "0a" > /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_refs_30856.diff
[CMD] [2023-10-13 13:55:37] tail -n +1 /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_refs_30856.csv >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_refs_30856.diff
[CMD] [2023-10-13 13:55:37] echo "." >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_refs_30856.diff
[INFO] [2023-10-13 13:55:37] Created diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_refs_30856.diff (19 lines)
[INFO] [2023-10-13 13:55:37] ...nodes (/app/public/data/bok_et_al_bok_et/taxa.txt)
[CMD] [2023-10-13 13:55:37] echo "0a" > /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_nodes_30853.diff
[CMD] [2023-10-13 13:55:37] tail -n +1 /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_nodes_30853.csv >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_nodes_30853.diff
[CMD] [2023-10-13 13:55:37] echo "." >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_nodes_30853.diff
[INFO] [2023-10-13 13:55:37] Created diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_nodes_30853.diff (18 lines)
[INFO] [2023-10-13 13:55:37] ...occurrences (/app/public/data/bok_et_al_bok_et/occurrences.txt)
[CMD] [2023-10-13 13:55:37] echo "0a" > /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_occurrences_30854.diff
[CMD] [2023-10-13 13:55:37] tail -n +1 /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_occurrences_30854.csv >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_occurrences_30854.diff
[CMD] [2023-10-13 13:55:37] echo "." >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_occurrences_30854.diff
[INFO] [2023-10-13 13:55:37] Created diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_occurrences_30854.diff (18 lines)
[INFO] [2023-10-13 13:55:37] ...measurements (/app/public/data/bok_et_al_bok_et/measurementsorfacts.txt)
[CMD] [2023-10-13 13:55:37] echo "0a" > /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_measurements_30855.diff
[CMD] [2023-10-13 13:55:38] tail -n +1 /app/public/data/bok_et_al_bok_et/converted_csv/bok_et_al_bok_et_measurements_30855.csv >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_measurements_30855.diff
[CMD] [2023-10-13 13:55:38] echo "." >> /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_measurements_30855.diff
[INFO] [2023-10-13 13:55:39] Created diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_measurements_30855.diff (46 lines)
[STOP] [2023-10-13 13:55:39] calculate_delta
[START] [2023-10-13 13:55:39] parse_diff_and_store
[INFO] [2023-10-13 13:55:39] Handling diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_refs_30856.diff (19 lines)
[INFO] [2023-10-13 13:55:39] Loading refs diff file into memory (19 lines)...
[INFO] [2023-10-13 13:55:39] Storing 17 References (17/17/19)
[INFO] [2023-10-13 13:55:39] Handling diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_nodes_30853.diff (18 lines)
[INFO] [2023-10-13 13:55:39] Loading nodes diff file into memory (18 lines)...
[WARN] [2023-10-13 13:55:39] Filtered Scientific Name `Parasabella  aulaconota` to `Parasabella aulaconota`
[WARN] [2023-10-13 13:55:39] Filtered Scientific Name `Parasabella  bioculata` to `Parasabella bioculata`
[INFO] [2023-10-13 13:55:39] Storing 16 ScientificNames (32/16/18)
[INFO] [2023-10-13 13:55:39] Storing 16 Nodes (32/16/18)
[INFO] [2023-10-13 13:55:39] Handling diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_occurrences_30854.diff (18 lines)
[INFO] [2023-10-13 13:55:39] Loading occurrences diff file into memory (18 lines)...
[INFO] [2023-10-13 13:55:39] Storing 16 Occurrences (16/16/18)
[INFO] [2023-10-13 13:55:39] Handling diff: /app/public/data/bok_et_al_bok_et/diff/bok_et_al_bok_et_measurements_30855.diff (46 lines)
[INFO] [2023-10-13 13:55:39] Loading measurements diff file into memory (46 lines)...
[INFO] [2023-10-13 13:55:39] Storing 44 Traits (104/44/46)
[INFO] [2023-10-13 13:55:39] Storing 27 MetaTraits (104/44/46)
[INFO] [2023-10-13 13:55:39] Storing 33 TraitsReferences (104/44/46)
[STOP] [2023-10-13 13:55:39] parse_diff_and_store
[START] [2023-10-13 13:55:39] resolve_keys
[2023-10-13 13:55:39] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:55:47] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:55:47] traits to occurrences...
[INFO] [2023-10-13 13:55:47] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:55:47] Traits to sex term...
[INFO] [2023-10-13 13:55:47] Traits to lifestage term...
[INFO] [2023-10-13 13:55:47] MetaTraits to traits...
[INFO] [2023-10-13 13:55:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:55:47] Assocs to occurrences...
[INFO] [2023-10-13 13:55:47] Assocs to nodes...
[INFO] [2023-10-13 13:55:47] Assoc to sex term...
[INFO] [2023-10-13 13:55:47] Assoc to lifestage term...
[INFO] [2023-10-13 13:55:47] MetaAssoc to assocs...
[STOP] [2023-10-13 13:55:47] resolve_keys
[START] [2023-10-13 13:55:47] hold_for_later_1
[STOP] [2023-10-13 13:55:47] hold_for_later_1
[START] [2023-10-13 13:55:47] hold_for_later_2
[STOP] [2023-10-13 13:55:47] hold_for_later_2
[START] [2023-10-13 13:55:47] resolve_missing_parents
[STOP] [2023-10-13 13:55:47] resolve_missing_parents
[START] [2023-10-13 13:55:47] rebuild_nodes
[START] [2023-10-13 13:55:47] Flattener#flatten
[START] [2023-10-13 13:55:47] Flattener#study_resource
[START] [2023-10-13 13:55:47] Flattener#build_ancestry
[STOP] [2023-10-13 13:55:47] Flattener#build_ancestry
[INFO] [2023-10-13 13:55:47] 16 ancestry keys
[START] [2023-10-13 13:55:47] build_node_ancestors
[INFO] [2023-10-13 13:55:47] old ancestors deleted.
[STOP] [2023-10-13 13:55:47] build_node_ancestors
[WARN] [2023-10-13 13:55:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:55:47] Flattener#flatten
[STOP] [2023-10-13 13:55:47] rebuild_nodes
[START] [2023-10-13 13:55:47] resolve_missing_media_owners
[STOP] [2023-10-13 13:55:47] resolve_missing_media_owners
[START] [2023-10-13 13:55:47] sanitize_media_verbatims
[STOP] [2023-10-13 13:55:47] sanitize_media_verbatims
[START] [2023-10-13 13:55:47] queue_downloads
[STOP] [2023-10-13 13:55:47] queue_downloads
[START] [2023-10-13 13:55:47] parse_names
[WARN] [2023-10-13 13:55:47] I see 16 names which still need to be parsed.
[WARN] [2023-10-13 13:55:47] Names to parse: 16 formatted: 16 learned: 16 parsed: 16
[STOP] [2023-10-13 13:55:48] parse_names
[START] [2023-10-13 13:55:48] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:55:48] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:55:48] match_nodes
[START] [2023-10-13 13:55:48] map_all_nodes_to_pages
[STOP] [2023-10-13 13:55:48] map_all_nodes_to_pages
[INFO] [2023-10-13 13:55:48] ZERO unmatched nodes (of 16)! Nicely done.
[START] [2023-10-13 13:55:48] update_nodes
[STOP] [2023-10-13 13:55:48] update_nodes
[STOP] [2023-10-13 13:55:48] match_nodes
[START] [2023-10-13 13:55:48] reindex_search
[STOP] [2023-10-13 13:55:48] reindex_search
[START] [2023-10-13 13:55:48] normalize_units
[STOP] [2023-10-13 13:55:48] normalize_units
[START] [2023-10-13 13:55:48] calculate_statistics
[2023-10-13 13:55:48] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:55:48] Duplicate page_id count: 0
[STOP] [2023-10-13 13:55:48] calculate_statistics
[START] [2023-10-13 13:55:48] complete_harvest_instance
[START] [2023-10-13 13:55:48] overall_tsv_creation
[INFO] [2023-10-13 13:55:48] Exporting 16 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:55:48] Processing group of 16 in 1 batches of 10000
[INFO] [2023-10-13 13:55:48] 16 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:55:48] Building Traits map for 16 nodes (this can take a while)...
[INFO] [2023-10-13 13:55:48] Mapped 16 traits (27 meta) for 16 nodes.
[INFO] [2023-10-13 13:55:48] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:55:48] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:55:48] Adding 16 traits...
[INFO] [2023-10-13 13:55:48] 56 metadata added.
[INFO] [2023-10-13 13:55:48] Adding 0 assocs...
[INFO] [2023-10-13 13:55:48] 0 metadata added.
[INFO] [2023-10-13 13:56:32] Processed 16/16 nodes
[INFO] [2023-10-13 13:56:32] Average Time: 44.01
[INFO] [2023-10-13 13:56:32] Total Time: 45s
[STOP] [2023-10-13 13:56:32] overall_tsv_creation
[INFO] [2023-10-13 13:56:32] Done. Check your files:
[INFO] [2023-10-13 13:56:32] (16 lines) /app/public/data/bok_et_al_bok_et/publish_nodes.tsv
[INFO] [2023-10-13 13:56:32] (16 lines) /app/public/data/bok_et_al_bok_et/publish_scientific_names.tsv
[INFO] [2023-10-13 13:56:32] (17 lines) /app/public/data/bok_et_al_bok_et/publish_traits.tsv
[INFO] [2023-10-13 13:56:33] (57 lines) /app/public/data/bok_et_al_bok_et/publish_metadata.tsv
[STOP] [2023-10-13 13:56:33] complete_harvest_instance
[START] [2023-10-13 13:56:33] completed
[STOP] [2023-10-13 13:56:33] completed
[STOP] [2023-10-13 13:56:33] logged process, took 56.57

Latest Process

13 Oct 13:55 EXITED currently processing 0