Harvest for Sweden Species List Created 16 Oct 07:51

Harvesting Log

# Logfile created on 2019-10-16 07:51:00 -0400 by logger.rb/56815
[START] [2019-10-16 07:51:00] logged process
[START] [2019-10-16 07:51:00] create_harvest_instance
[STOP] [2019-10-16 07:51:00] create_harvest_instance
[START] [2019-10-16 07:51:00] fetch_files
[STOP] [2019-10-16 07:51:00] fetch_files
[START] [2019-10-16 07:51:00] validate_each_file
[STOP] [2019-10-16 07:51:08] validate_each_file
[START] [2019-10-16 07:51:08] convert_to_csv
[CMD] [2019-10-16 07:51:08] /usr/bin/sort /app/public/converted_csv/sweden_sp_list_refs_17357.csv > /app/public/converted_csv/sweden_sp_list_refs_17357.csv_sorted
[CMD] [2019-10-16 07:51:09] /usr/bin/sort /app/public/converted_csv/sweden_sp_list_nodes_17358.csv > /app/public/converted_csv/sweden_sp_list_nodes_17358.csv_sorted
[CMD] [2019-10-16 07:51:09] /usr/bin/sort /app/public/converted_csv/sweden_sp_list_occurrences_17359.csv > /app/public/converted_csv/sweden_sp_list_occurrences_17359.csv_sorted
[CMD] [2019-10-16 07:51:09] /usr/bin/sort /app/public/converted_csv/sweden_sp_list_measurements_17360.csv > /app/public/converted_csv/sweden_sp_list_measurements_17360.csv_sorted
[STOP] [2019-10-16 07:51:10] convert_to_csv
[START] [2019-10-16 07:51:10] calculate_delta
[CMD] [2019-10-16 07:51:10] echo "0a" > /app/public/diff/sweden_sp_list_refs_17357.diff
[CMD] [2019-10-16 07:51:10] tail -n +1 /app/public/converted_csv/sweden_sp_list_refs_17357.csv >> /app/public/diff/sweden_sp_list_refs_17357.diff
[CMD] [2019-10-16 07:51:10] echo "." >> /app/public/diff/sweden_sp_list_refs_17357.diff
[CMD] [2019-10-16 07:51:11] echo "0a" > /app/public/diff/sweden_sp_list_nodes_17358.diff
[CMD] [2019-10-16 07:51:11] tail -n +1 /app/public/converted_csv/sweden_sp_list_nodes_17358.csv >> /app/public/diff/sweden_sp_list_nodes_17358.diff
[CMD] [2019-10-16 07:51:11] echo "." >> /app/public/diff/sweden_sp_list_nodes_17358.diff
[CMD] [2019-10-16 07:51:11] echo "0a" > /app/public/diff/sweden_sp_list_occurrences_17359.diff
[CMD] [2019-10-16 07:51:12] tail -n +1 /app/public/converted_csv/sweden_sp_list_occurrences_17359.csv >> /app/public/diff/sweden_sp_list_occurrences_17359.diff
[CMD] [2019-10-16 07:51:12] echo "." >> /app/public/diff/sweden_sp_list_occurrences_17359.diff
[CMD] [2019-10-16 07:51:12] echo "0a" > /app/public/diff/sweden_sp_list_measurements_17360.diff
[CMD] [2019-10-16 07:51:13] tail -n +1 /app/public/converted_csv/sweden_sp_list_measurements_17360.csv >> /app/public/diff/sweden_sp_list_measurements_17360.diff
[CMD] [2019-10-16 07:51:13] echo "." >> /app/public/diff/sweden_sp_list_measurements_17360.diff
[STOP] [2019-10-16 07:51:13] calculate_delta
[START] [2019-10-16 07:51:13] parse_diff_and_store
[INFO] [2019-10-16 07:51:13] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 07:51:14] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 07:51:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 07:51:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 07:56:39] Storing 2 References
[INFO] [2019-10-16 07:56:39] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 07:56:39] Average Time: 0.0
[INFO] [2019-10-16 07:56:39] Total Time: 1s
[INFO] [2019-10-16 07:56:39] Storing 66354 ScientificNames
[INFO] [2019-10-16 07:56:39] Processing group of 66354 in 67 groups of 1000
[INFO] [2019-10-16 07:57:11] Average Time: 0.472
[INFO] [2019-10-16 07:57:11] Total Time: 32s
[INFO] [2019-10-16 07:57:11] last 3 / first 3: 0.87
[INFO] [2019-10-16 07:57:11] Std.Dev: 0.33763886032268264; Max: 2.62
[INFO] [2019-10-16 07:57:11] Storing 66354 Nodes
[INFO] [2019-10-16 07:57:11] Processing group of 66354 in 67 groups of 1000
[INFO] [2019-10-16 07:57:37] Average Time: 0.394
[INFO] [2019-10-16 07:57:37] Total Time: 27s
[INFO] [2019-10-16 07:57:37] last 3 / first 3: 0.86
[INFO] [2019-10-16 07:57:37] Std.Dev: 0.38858718455450897; Max: 2.9
[INFO] [2019-10-16 07:57:37] Storing 48682 Occurrences
[INFO] [2019-10-16 07:57:37] Processing group of 48682 in 49 groups of 1000
[INFO] [2019-10-16 07:57:43] Average Time: 0.113
[INFO] [2019-10-16 07:57:43] Total Time: 6s
[INFO] [2019-10-16 07:57:43] last 3 / first 3: 1.06
[INFO] [2019-10-16 07:57:43] Std.Dev: 0.03162277660168379; Max: 0.25
[INFO] [2019-10-16 07:57:43] Storing 97690 TraitsReferences
[INFO] [2019-10-16 07:57:43] Processing group of 97690 in 98 groups of 1000
[INFO] [2019-10-16 07:57:56] Average Time: 0.13
[INFO] [2019-10-16 07:57:56] Total Time: 14s
[INFO] [2019-10-16 07:57:56] last 3 / first 3: 0.63
[INFO] [2019-10-16 07:57:56] Std.Dev: 0.3449637662132068; Max: 2.94
[INFO] [2019-10-16 07:57:56] Storing 97689 Traits
[INFO] [2019-10-16 07:57:56] Processing group of 97689 in 98 groups of 1000
[INFO] [2019-10-16 07:58:34] Average Time: 0.383
[INFO] [2019-10-16 07:58:34] Total Time: 38s
[INFO] [2019-10-16 07:58:34] last 3 / first 3: 1.89
[INFO] [2019-10-16 07:58:34] Std.Dev: 0.3781534080237807; Max: 3.42
[INFO] [2019-10-16 07:58:34] Storing 97614 MetaTraits
[INFO] [2019-10-16 07:58:34] Processing group of 97614 in 98 groups of 1000
[INFO] [2019-10-16 07:58:47] Average Time: 0.128
[INFO] [2019-10-16 07:58:47] Total Time: 14s
[INFO] [2019-10-16 07:58:47] last 3 / first 3: 0.13
[INFO] [2019-10-16 07:58:47] Std.Dev: 0.161245154965971; Max: 1.66
[STOP] [2019-10-16 07:58:47] parse_diff_and_store
[START] [2019-10-16 07:58:47] resolve_keys
[INFO] [2019-10-16 08:01:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 08:01:21] traits to occurrences...
[INFO] [2019-10-16 08:01:29] traits to nodes (through occurrences)...
[INFO] [2019-10-16 08:01:30] Traits to sex term...
[INFO] [2019-10-16 08:01:37] Traits to lifestage term...
[INFO] [2019-10-16 08:01:45] MetaTraits to traits...
[INFO] [2019-10-16 08:01:51] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 08:02:04] Assocs to occurrences...
[INFO] [2019-10-16 08:02:04] Assocs to nodes...
[INFO] [2019-10-16 08:02:04] Assoc to sex term...
[INFO] [2019-10-16 08:02:04] Assoc to lifestage term...
[STOP] [2019-10-16 08:02:04] resolve_keys
[START] [2019-10-16 08:02:04] hold_for_later_1
[STOP] [2019-10-16 08:02:04] hold_for_later_1
[START] [2019-10-16 08:02:04] hold_for_later_2
[STOP] [2019-10-16 08:02:04] hold_for_later_2
[START] [2019-10-16 08:02:04] resolve_missing_parents
[STOP] [2019-10-16 08:03:30] resolve_missing_parents
[START] [2019-10-16 08:03:30] rebuild_nodes
[START] [2019-10-16 08:03:30] Flattener#flatten
[START] [2019-10-16 08:03:30] Flattener#study_resource
[START] [2019-10-16 08:03:30] Flattener#build_ancestry
[STOP] [2019-10-16 08:03:45] Flattener#build_ancestry
[INFO] [2019-10-16 08:03:45] 66354 ancestry keys
[START] [2019-10-16 08:03:45] build_node_ancestors
[INFO] [2019-10-16 08:03:45] old ancestors deleted.
[STOP] [2019-10-16 08:04:30] build_node_ancestors
[START] [2019-10-16 08:04:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 08:04:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 08:04:39] Flattener#flatten
[STOP] [2019-10-16 08:04:39] rebuild_nodes
[START] [2019-10-16 08:04:39] resolve_missing_media_owners
[STOP] [2019-10-16 08:04:39] resolve_missing_media_owners
[START] [2019-10-16 08:04:39] sanitize_media_verbatims
[STOP] [2019-10-16 08:04:39] sanitize_media_verbatims
[START] [2019-10-16 08:04:39] queue_downloads
[STOP] [2019-10-16 08:04:39] queue_downloads
[START] [2019-10-16 08:04:39] parse_names
[WARN] [2019-10-16 08:04:39] I see 66354 names which still need to be parsed.
[STOP] [2019-10-16 08:05:32] parse_names
[START] [2019-10-16 08:05:32] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 08:05:33] denormalize_canonical_names_to_nodes
[START] [2019-10-16 08:05:33] match_nodes
[START] [2019-10-16 08:05:33] map_all_nodes_to_pages
[STOP] [2019-10-16 09:16:00] map_all_nodes_to_pages
[INFO] [2019-10-16 09:16:00] 7367 Unmatched nodes (of 66354)! That's too many to output. First 10: Parus caeruleus (#52220101); Parus ater (#52220643); Parus palustris (#52220719); Parus montanus (#52221147); Parus cristatus (#52227075); Poecile montana (#52269790); Poecile cincta (#52276594); Regulus ignicapillus (#52241209); Carduelis chloris (#52220000); Carduelis spinus (#52220048)
[START] [2019-10-16 09:16:00] update_nodes
[STOP] [2019-10-16 09:16:24] update_nodes
[STOP] [2019-10-16 09:16:24] match_nodes
[START] [2019-10-16 09:16:24] reindex_search
[STOP] [2019-10-16 09:19:30] reindex_search
[START] [2019-10-16 09:19:30] normalize_units
[STOP] [2019-10-16 09:19:30] normalize_units
[START] [2019-10-16 09:19:30] calculate_statistics
[STOP] [2019-10-16 09:19:30] calculate_statistics
[START] [2019-10-16 09:19:30] complete_harvest_instance
[START] [2019-10-16 09:19:30] overall_tsv_creation
[INFO] [2019-10-16 09:19:30] Processing group of 66354 in 7 batches of 10000
[INFO] [2019-10-16 09:20:59] 6027 Traits (unfiltered)...
[INFO] [2019-10-16 09:21:13] 6027 Traits (filtered)...
[INFO] [2019-10-16 09:21:13] 0 Associations (filtered)...
[INFO] [2019-10-16 09:22:02] 30132 metadata added.
[INFO] [2019-10-16 09:22:02] 0 metadata added.
[INFO] [2019-10-16 09:23:35] 7124 Traits (unfiltered)...
[INFO] [2019-10-16 09:23:48] 7124 Traits (filtered)...
[INFO] [2019-10-16 09:23:48] 0 Associations (filtered)...
[INFO] [2019-10-16 09:24:42] 35611 metadata added.
[INFO] [2019-10-16 09:24:42] 0 metadata added.
[INFO] [2019-10-16 09:26:17] 7458 Traits (unfiltered)...
[INFO] [2019-10-16 09:26:30] 7458 Traits (filtered)...
[INFO] [2019-10-16 09:26:30] 0 Associations (filtered)...
[INFO] [2019-10-16 09:27:28] 37279 metadata added.
[INFO] [2019-10-16 09:27:28] 0 metadata added.
[INFO] [2019-10-16 09:29:04] 7619 Traits (unfiltered)...
[INFO] [2019-10-16 09:29:17] 7619 Traits (filtered)...
[INFO] [2019-10-16 09:29:17] 0 Associations (filtered)...
[INFO] [2019-10-16 09:30:13] 38085 metadata added.
[INFO] [2019-10-16 09:30:13] 0 metadata added.
[INFO] [2019-10-16 09:31:47] 7610 Traits (unfiltered)...
[INFO] [2019-10-16 09:32:01] 7610 Traits (filtered)...
[INFO] [2019-10-16 09:32:01] 0 Associations (filtered)...
[INFO] [2019-10-16 09:32:56] 38036 metadata added.
[INFO] [2019-10-16 09:32:56] 0 metadata added.
[INFO] [2019-10-16 09:34:31] 7815 Traits (unfiltered)...
[INFO] [2019-10-16 09:34:44] 7815 Traits (filtered)...
[INFO] [2019-10-16 09:34:44] 0 Associations (filtered)...
[INFO] [2019-10-16 09:35:40] 39061 metadata added.
[INFO] [2019-10-16 09:35:40] 0 metadata added.
[INFO] [2019-10-16 09:36:56] 5029 Traits (unfiltered)...
[INFO] [2019-10-16 09:37:09] 5029 Traits (filtered)...
[INFO] [2019-10-16 09:37:09] 0 Associations (filtered)...
[INFO] [2019-10-16 09:37:55] 25130 metadata added.
[INFO] [2019-10-16 09:37:55] 0 metadata added.
[INFO] [2019-10-16 09:37:55] Average Time: 130.941
[INFO] [2019-10-16 09:37:55] Total Time: 18m26s
[INFO] [2019-10-16 09:37:55] last 3 / first 3: 0.97
[INFO] [2019-10-16 09:37:55] Std.Dev: 9.868687856042465; Max: 139.34
[STOP] [2019-10-16 09:37:55] overall_tsv_creation
[INFO] [2019-10-16 09:37:55] Done. Check your files:
[INFO] [2019-10-16 09:37:56] (66354 lines) /app/public/data/sweden_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 09:37:56] (303783 lines) /app/public/data/sweden_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 09:37:56] (66354 lines) /app/public/data/sweden_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 09:37:56] (48683 lines) /app/public/data/sweden_sp_list/publish_traits.tsv
[INFO] [2019-10-16 09:37:57] (243335 lines) /app/public/data/sweden_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 09:37:57] complete_harvest_instance
[START] [2019-10-16 09:37:57] completed
[STOP] [2019-10-16 09:37:57] completed
[STOP] [2019-10-16 09:37:57] logged process, took 6417.3

Latest Process

16 Oct 07:51 EXITED currently processing 0