Harvest for Bali Sea Species List Created 22 Dec 19:44

Stage: completed
Fetched: 22 Dec 19:44
Validated: 22 Dec 19:44
Deltas Created 22 Dec 19:44
Units Normalized: 22 Dec 20:03
Ancestry Built: 22 Dec 19:45
Nodes Matched: 22 Dec 20:03
Names Parsed: 22 Dec 19:45
New Models Stored: 22 Dec 19:44
Indexed: 22 Dec 20:03
Completed: 22 Dec 20:05
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 19:44:36 -0500 by logger.rb/56815
[START] [2019-12-22 19:44:36] logged process
[START] [2019-12-22 19:44:36] create_harvest_instance
[STOP] [2019-12-22 19:44:36] create_harvest_instance
[START] [2019-12-22 19:44:36] fetch_files
[STOP] [2019-12-22 19:44:36] fetch_files
[START] [2019-12-22 19:44:37] validate_each_file
[STOP] [2019-12-22 19:44:37] validate_each_file
[START] [2019-12-22 19:44:37] convert_to_csv
[CMD] [2019-12-22 19:44:37] /usr/bin/sort /app/public/converted_csv/bali_sea_sp_list_refs_19050.csv > /app/public/converted_csv/bali_sea_sp_list_refs_19050.csv_sorted
[CMD] [2019-12-22 19:44:37] /usr/bin/sort /app/public/converted_csv/bali_sea_sp_list_nodes_19051.csv > /app/public/converted_csv/bali_sea_sp_list_nodes_19051.csv_sorted
[CMD] [2019-12-22 19:44:37] /usr/bin/sort /app/public/converted_csv/bali_sea_sp_list_occurrences_19052.csv > /app/public/converted_csv/bali_sea_sp_list_occurrences_19052.csv_sorted
[CMD] [2019-12-22 19:44:37] /usr/bin/sort /app/public/converted_csv/bali_sea_sp_list_measurements_19053.csv > /app/public/converted_csv/bali_sea_sp_list_measurements_19053.csv_sorted
[STOP] [2019-12-22 19:44:37] convert_to_csv
[START] [2019-12-22 19:44:37] calculate_delta
[CMD] [2019-12-22 19:44:37] echo "0a" > /app/public/diff/bali_sea_sp_list_refs_19050.diff
[CMD] [2019-12-22 19:44:37] tail -n +1 /app/public/converted_csv/bali_sea_sp_list_refs_19050.csv >> /app/public/diff/bali_sea_sp_list_refs_19050.diff
[CMD] [2019-12-22 19:44:37] echo "." >> /app/public/diff/bali_sea_sp_list_refs_19050.diff
[CMD] [2019-12-22 19:44:37] echo "0a" > /app/public/diff/bali_sea_sp_list_nodes_19051.diff
[CMD] [2019-12-22 19:44:37] tail -n +1 /app/public/converted_csv/bali_sea_sp_list_nodes_19051.csv >> /app/public/diff/bali_sea_sp_list_nodes_19051.diff
[CMD] [2019-12-22 19:44:37] echo "." >> /app/public/diff/bali_sea_sp_list_nodes_19051.diff
[CMD] [2019-12-22 19:44:37] echo "0a" > /app/public/diff/bali_sea_sp_list_occurrences_19052.diff
[CMD] [2019-12-22 19:44:37] tail -n +1 /app/public/converted_csv/bali_sea_sp_list_occurrences_19052.csv >> /app/public/diff/bali_sea_sp_list_occurrences_19052.diff
[CMD] [2019-12-22 19:44:38] echo "." >> /app/public/diff/bali_sea_sp_list_occurrences_19052.diff
[CMD] [2019-12-22 19:44:38] echo "0a" > /app/public/diff/bali_sea_sp_list_measurements_19053.diff
[CMD] [2019-12-22 19:44:38] tail -n +1 /app/public/converted_csv/bali_sea_sp_list_measurements_19053.csv >> /app/public/diff/bali_sea_sp_list_measurements_19053.diff
[CMD] [2019-12-22 19:44:38] echo "." >> /app/public/diff/bali_sea_sp_list_measurements_19053.diff
[STOP] [2019-12-22 19:44:38] calculate_delta
[START] [2019-12-22 19:44:38] parse_diff_and_store
[INFO] [2019-12-22 19:44:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 19:44:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 19:44:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 19:44:39] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 19:44:49] Storing 2 References
[INFO] [2019-12-22 19:44:49] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 19:44:49] Average Time: 0.0
[INFO] [2019-12-22 19:44:49] Total Time: 1s
[INFO] [2019-12-22 19:44:49] Storing 2871 ScientificNames
[INFO] [2019-12-22 19:44:49] Processing group of 2871 in 3 groups of 1000
[INFO] [2019-12-22 19:44:50] Average Time: 0.427
[INFO] [2019-12-22 19:44:50] Total Time: 2s
[INFO] [2019-12-22 19:44:50] Storing 2871 Nodes
[INFO] [2019-12-22 19:44:50] Processing group of 2871 in 3 groups of 1000
[INFO] [2019-12-22 19:44:51] Average Time: 0.33
[INFO] [2019-12-22 19:44:51] Total Time: 2s
[INFO] [2019-12-22 19:44:51] Storing 1596 Occurrences
[INFO] [2019-12-22 19:44:51] Processing group of 1596 in 2 groups of 1000
[INFO] [2019-12-22 19:44:51] Average Time: 0.095
[INFO] [2019-12-22 19:44:51] Total Time: 1s
[INFO] [2019-12-22 19:44:51] Storing 3192 TraitsReferences
[INFO] [2019-12-22 19:44:51] Processing group of 3192 in 4 groups of 1000
[INFO] [2019-12-22 19:44:51] Average Time: 0.088
[INFO] [2019-12-22 19:44:51] Total Time: 1s
[INFO] [2019-12-22 19:44:51] Storing 3192 Traits
[INFO] [2019-12-22 19:44:51] Processing group of 3192 in 4 groups of 1000
[INFO] [2019-12-22 19:44:53] Average Time: 0.3
[INFO] [2019-12-22 19:44:53] Total Time: 2s
[INFO] [2019-12-22 19:44:53] Storing 3192 MetaTraits
[INFO] [2019-12-22 19:44:53] Processing group of 3192 in 4 groups of 1000
[INFO] [2019-12-22 19:44:53] Average Time: 0.118
[INFO] [2019-12-22 19:44:53] Total Time: 1s
[STOP] [2019-12-22 19:44:53] parse_diff_and_store
[START] [2019-12-22 19:44:53] resolve_keys
[INFO] [2019-12-22 19:45:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 19:45:09] traits to occurrences...
[INFO] [2019-12-22 19:45:10] traits to nodes (through occurrences)...
[INFO] [2019-12-22 19:45:10] Traits to sex term...
[INFO] [2019-12-22 19:45:10] Traits to lifestage term...
[INFO] [2019-12-22 19:45:11] MetaTraits to traits...
[INFO] [2019-12-22 19:45:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 19:45:12] Assocs to occurrences...
[INFO] [2019-12-22 19:45:12] Assocs to nodes...
[INFO] [2019-12-22 19:45:12] Assoc to sex term...
[INFO] [2019-12-22 19:45:12] Assoc to lifestage term...
[STOP] [2019-12-22 19:45:12] resolve_keys
[START] [2019-12-22 19:45:12] hold_for_later_1
[STOP] [2019-12-22 19:45:12] hold_for_later_1
[START] [2019-12-22 19:45:12] hold_for_later_2
[STOP] [2019-12-22 19:45:12] hold_for_later_2
[START] [2019-12-22 19:45:12] resolve_missing_parents
[STOP] [2019-12-22 19:45:17] resolve_missing_parents
[START] [2019-12-22 19:45:17] rebuild_nodes
[START] [2019-12-22 19:45:17] Flattener#flatten
[START] [2019-12-22 19:45:17] Flattener#study_resource
[START] [2019-12-22 19:45:17] Flattener#build_ancestry
[STOP] [2019-12-22 19:45:17] Flattener#build_ancestry
[INFO] [2019-12-22 19:45:17] 2871 ancestry keys
[START] [2019-12-22 19:45:17] build_node_ancestors
[INFO] [2019-12-22 19:45:17] old ancestors deleted.
[STOP] [2019-12-22 19:45:18] build_node_ancestors
[START] [2019-12-22 19:45:20] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 19:45:20] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 19:45:20] Flattener#flatten
[STOP] [2019-12-22 19:45:20] rebuild_nodes
[START] [2019-12-22 19:45:20] resolve_missing_media_owners
[STOP] [2019-12-22 19:45:20] resolve_missing_media_owners
[START] [2019-12-22 19:45:20] sanitize_media_verbatims
[STOP] [2019-12-22 19:45:20] sanitize_media_verbatims
[START] [2019-12-22 19:45:20] queue_downloads
[STOP] [2019-12-22 19:45:20] queue_downloads
[START] [2019-12-22 19:45:20] parse_names
[WARN] [2019-12-22 19:45:20] I see 2871 names which still need to be parsed.
[STOP] [2019-12-22 19:45:24] parse_names
[START] [2019-12-22 19:45:24] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 19:45:24] denormalize_canonical_names_to_nodes
[START] [2019-12-22 19:45:24] match_nodes
[START] [2019-12-22 19:45:24] map_all_nodes_to_pages
[STOP] [2019-12-22 20:03:20] map_all_nodes_to_pages
[INFO] [2019-12-22 20:03:20] 62 Unmatched nodes (of 2871)! That's too many to output. First 10: Scorpaeniformes (#61705120); Sunagocia malayanus (#61707398); Caracanthidae (#61707588); Gasterosteiformes (#61706445); Limnodromus (#61706380); Egretta intermedia (#61705496); Megalaima (#61705288); Megalaima haemacephala (#61705287); Hydrophiidae (#61705957); Acalyptophis (#61707861)
[START] [2019-12-22 20:03:20] update_nodes
[STOP] [2019-12-22 20:03:21] update_nodes
[STOP] [2019-12-22 20:03:21] match_nodes
[START] [2019-12-22 20:03:21] reindex_search
[STOP] [2019-12-22 20:03:35] reindex_search
[START] [2019-12-22 20:03:35] normalize_units
[STOP] [2019-12-22 20:03:35] normalize_units
[START] [2019-12-22 20:03:35] calculate_statistics
[STOP] [2019-12-22 20:03:35] calculate_statistics
[START] [2019-12-22 20:03:35] complete_harvest_instance
[START] [2019-12-22 20:03:35] overall_tsv_creation
[INFO] [2019-12-22 20:03:35] Processing group of 2871 in 1 batches of 10000
[INFO] [2019-12-22 20:04:35] 1596 Traits (unfiltered)...
[INFO] [2019-12-22 20:04:50] 1596 Traits (filtered)...
[INFO] [2019-12-22 20:04:50] 0 Associations (filtered)...
[INFO] [2019-12-22 20:05:33] 7980 metadata added.
[INFO] [2019-12-22 20:05:33] 0 metadata added.
[INFO] [2019-12-22 20:05:33] Average Time: 91.05
[INFO] [2019-12-22 20:05:33] Total Time: 1m58s
[STOP] [2019-12-22 20:05:33] overall_tsv_creation
[INFO] [2019-12-22 20:05:33] Done. Check your files:
[INFO] [2019-12-22 20:05:33] (2871 lines) /app/public/data/bali_sea_sp_list/publish_nodes.tsv
[INFO] [2019-12-22 20:05:33] (15033 lines) /app/public/data/bali_sea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-22 20:05:33] (2871 lines) /app/public/data/bali_sea_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-22 20:05:33] (1597 lines) /app/public/data/bali_sea_sp_list/publish_traits.tsv
[INFO] [2019-12-22 20:05:33] (7981 lines) /app/public/data/bali_sea_sp_list/publish_metadata.tsv
[STOP] [2019-12-22 20:05:34] complete_harvest_instance
[START] [2019-12-22 20:05:34] completed
[STOP] [2019-12-22 20:05:34] completed
[STOP] [2019-12-22 20:05:34] logged process, took 1257.69
Latest Process

22 Dec 19:44 EXITED currently processing 0