Harvest for France Species List Created 12 Oct 22:28

Harvesting Log

# Logfile created on 2019-10-12 22:28:37 -0400 by logger.rb/56815
[START] [2019-10-12 22:28:37] logged process
[START] [2019-10-12 22:28:37] create_harvest_instance
[STOP] [2019-10-12 22:28:38] create_harvest_instance
[START] [2019-10-12 22:28:38] fetch_files
[STOP] [2019-10-12 22:28:38] fetch_files
[START] [2019-10-12 22:28:38] validate_each_file
[STOP] [2019-10-12 22:28:46] validate_each_file
[START] [2019-10-12 22:28:46] convert_to_csv
[CMD] [2019-10-12 22:28:46] /usr/bin/sort /app/public/converted_csv/france_sp_list_refs_15779.csv > /app/public/converted_csv/france_sp_list_refs_15779.csv_sorted
[CMD] [2019-10-12 22:28:46] /usr/bin/sort /app/public/converted_csv/france_sp_list_nodes_15780.csv > /app/public/converted_csv/france_sp_list_nodes_15780.csv_sorted
[CMD] [2019-10-12 22:28:46] /usr/bin/sort /app/public/converted_csv/france_sp_list_occurrences_15781.csv > /app/public/converted_csv/france_sp_list_occurrences_15781.csv_sorted
[CMD] [2019-10-12 22:28:46] /usr/bin/sort /app/public/converted_csv/france_sp_list_measurements_15782.csv > /app/public/converted_csv/france_sp_list_measurements_15782.csv_sorted
[STOP] [2019-10-12 22:28:47] convert_to_csv
[START] [2019-10-12 22:28:47] calculate_delta
[CMD] [2019-10-12 22:28:47] echo "0a" > /app/public/diff/france_sp_list_refs_15779.diff
[CMD] [2019-10-12 22:28:47] tail -n +1 /app/public/converted_csv/france_sp_list_refs_15779.csv >> /app/public/diff/france_sp_list_refs_15779.diff
[CMD] [2019-10-12 22:28:47] echo "." >> /app/public/diff/france_sp_list_refs_15779.diff
[CMD] [2019-10-12 22:28:47] echo "0a" > /app/public/diff/france_sp_list_nodes_15780.diff
[CMD] [2019-10-12 22:28:47] tail -n +1 /app/public/converted_csv/france_sp_list_nodes_15780.csv >> /app/public/diff/france_sp_list_nodes_15780.diff
[CMD] [2019-10-12 22:28:47] echo "." >> /app/public/diff/france_sp_list_nodes_15780.diff
[CMD] [2019-10-12 22:28:47] echo "0a" > /app/public/diff/france_sp_list_occurrences_15781.diff
[CMD] [2019-10-12 22:28:47] tail -n +1 /app/public/converted_csv/france_sp_list_occurrences_15781.csv >> /app/public/diff/france_sp_list_occurrences_15781.diff
[CMD] [2019-10-12 22:28:47] echo "." >> /app/public/diff/france_sp_list_occurrences_15781.diff
[CMD] [2019-10-12 22:28:47] echo "0a" > /app/public/diff/france_sp_list_measurements_15782.diff
[CMD] [2019-10-12 22:28:47] tail -n +1 /app/public/converted_csv/france_sp_list_measurements_15782.csv >> /app/public/diff/france_sp_list_measurements_15782.diff
[CMD] [2019-10-12 22:28:48] echo "." >> /app/public/diff/france_sp_list_measurements_15782.diff
[STOP] [2019-10-12 22:28:48] calculate_delta
[START] [2019-10-12 22:28:48] parse_diff_and_store
[INFO] [2019-10-12 22:28:48] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 22:28:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 22:29:13] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 22:29:19] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 22:33:50] Storing 2 References
[INFO] [2019-10-12 22:33:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 22:33:50] Average Time: 0.0
[INFO] [2019-10-12 22:33:50] Total Time: 1s
[INFO] [2019-10-12 22:33:50] Storing 65237 ScientificNames
[INFO] [2019-10-12 22:33:50] Processing group of 65237 in 66 groups of 1000
[INFO] [2019-10-12 22:34:17] Average Time: 0.411
[INFO] [2019-10-12 22:34:17] Total Time: 28s
[INFO] [2019-10-12 22:34:17] last 3 / first 3: 1.3
[INFO] [2019-10-12 22:34:17] Std.Dev: 0.2; Max: 1.83
[INFO] [2019-10-12 22:34:17] Storing 65237 Nodes
[INFO] [2019-10-12 22:34:17] Processing group of 65237 in 66 groups of 1000
[INFO] [2019-10-12 22:34:45] Average Time: 0.406
[INFO] [2019-10-12 22:34:45] Total Time: 28s
[INFO] [2019-10-12 22:34:45] last 3 / first 3: 0.39
[INFO] [2019-10-12 22:34:45] Std.Dev: 0.3492849839314596; Max: 2.53
[INFO] [2019-10-12 22:34:45] Storing 45308 Occurrences
[INFO] [2019-10-12 22:34:45] Processing group of 45308 in 46 groups of 1000
[INFO] [2019-10-12 22:34:50] Average Time: 0.11
[INFO] [2019-10-12 22:34:50] Total Time: 6s
[INFO] [2019-10-12 22:34:50] last 3 / first 3: 0.86
[INFO] [2019-10-12 22:34:50] Std.Dev: 0.03162277660168379; Max: 0.24
[INFO] [2019-10-12 22:34:50] Storing 91270 TraitsReferences
[INFO] [2019-10-12 22:34:50] Processing group of 91270 in 92 groups of 1000
[INFO] [2019-10-12 22:34:57] Average Time: 0.071
[INFO] [2019-10-12 22:34:57] Total Time: 7s
[INFO] [2019-10-12 22:34:57] last 3 / first 3: 0.54
[INFO] [2019-10-12 22:34:57] Std.Dev: 0.03162277660168379; Max: 0.21
[INFO] [2019-10-12 22:34:57] Storing 91270 Traits
[INFO] [2019-10-12 22:34:57] Processing group of 91270 in 92 groups of 1000
[INFO] [2019-10-12 22:35:39] Average Time: 0.449
[INFO] [2019-10-12 22:35:39] Total Time: 42s
[INFO] [2019-10-12 22:35:39] last 3 / first 3: 0.64
[INFO] [2019-10-12 22:35:39] Std.Dev: 0.5744562646538028; Max: 3.27
[INFO] [2019-10-12 22:35:39] Storing 91121 MetaTraits
[INFO] [2019-10-12 22:35:39] Processing group of 91121 in 92 groups of 1000
[INFO] [2019-10-12 22:35:58] Average Time: 0.208
[INFO] [2019-10-12 22:35:58] Total Time: 20s
[INFO] [2019-10-12 22:35:58] last 3 / first 3: 0.71
[INFO] [2019-10-12 22:35:58] Std.Dev: 0.4505552130427524; Max: 3.26
[STOP] [2019-10-12 22:35:58] parse_diff_and_store
[START] [2019-10-12 22:35:58] resolve_keys
[INFO] [2019-10-12 22:38:03] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 22:38:12] traits to occurrences...
[INFO] [2019-10-12 22:38:21] traits to nodes (through occurrences)...
[INFO] [2019-10-12 22:38:22] Traits to sex term...
[INFO] [2019-10-12 22:38:29] Traits to lifestage term...
[INFO] [2019-10-12 22:38:38] MetaTraits to traits...
[INFO] [2019-10-12 22:38:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 22:38:56] Assocs to occurrences...
[INFO] [2019-10-12 22:38:56] Assocs to nodes...
[INFO] [2019-10-12 22:38:56] Assoc to sex term...
[INFO] [2019-10-12 22:38:56] Assoc to lifestage term...
[STOP] [2019-10-12 22:38:56] resolve_keys
[START] [2019-10-12 22:38:56] hold_for_later_1
[STOP] [2019-10-12 22:38:56] hold_for_later_1
[START] [2019-10-12 22:38:56] hold_for_later_2
[STOP] [2019-10-12 22:38:56] hold_for_later_2
[START] [2019-10-12 22:38:56] resolve_missing_parents
[STOP] [2019-10-12 22:40:09] resolve_missing_parents
[START] [2019-10-12 22:40:09] rebuild_nodes
[START] [2019-10-12 22:40:09] Flattener#flatten
[START] [2019-10-12 22:40:09] Flattener#study_resource
[START] [2019-10-12 22:40:09] Flattener#build_ancestry
[STOP] [2019-10-12 22:40:22] Flattener#build_ancestry
[INFO] [2019-10-12 22:40:22] 65237 ancestry keys
[START] [2019-10-12 22:40:22] build_node_ancestors
[INFO] [2019-10-12 22:40:22] old ancestors deleted.
[STOP] [2019-10-12 22:40:57] build_node_ancestors
[START] [2019-10-12 22:41:03] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 22:41:10] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 22:41:10] Flattener#flatten
[STOP] [2019-10-12 22:41:10] rebuild_nodes
[START] [2019-10-12 22:41:10] resolve_missing_media_owners
[STOP] [2019-10-12 22:41:10] resolve_missing_media_owners
[START] [2019-10-12 22:41:10] sanitize_media_verbatims
[STOP] [2019-10-12 22:41:10] sanitize_media_verbatims
[START] [2019-10-12 22:41:10] queue_downloads
[STOP] [2019-10-12 22:41:10] queue_downloads
[START] [2019-10-12 22:41:10] parse_names
[WARN] [2019-10-12 22:41:10] I see 65237 names which still need to be parsed.
[STOP] [2019-10-12 22:42:00] parse_names
[START] [2019-10-12 22:42:00] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 22:42:01] denormalize_canonical_names_to_nodes
[START] [2019-10-12 22:42:01] match_nodes
[START] [2019-10-12 22:42:01] map_all_nodes_to_pages
[STOP] [2019-10-12 23:54:34] map_all_nodes_to_pages
[INFO] [2019-10-12 23:54:34] 9574 Unmatched nodes (of 65237)! That's too many to output. First 10: Larus melanocephalus (#49692080); Larus audouinii (#49705732); Thalaseus (#49691432); Thalaseus sandvicensis (#49691431); Thalaseus bengalensis (#49724820); Tringa hypoleucos (#49728578); Limosa laponica (#49750602); Philomachus (#49692257); Philomachus pugnax (#49692256); Xenus cinerea (#49733709)
[START] [2019-10-12 23:54:34] update_nodes
[STOP] [2019-10-12 23:54:58] update_nodes
[STOP] [2019-10-12 23:54:58] match_nodes
[START] [2019-10-12 23:54:58] reindex_search
[STOP] [2019-10-12 23:57:38] reindex_search
[START] [2019-10-12 23:57:38] normalize_units
[STOP] [2019-10-12 23:57:38] normalize_units
[START] [2019-10-12 23:57:38] calculate_statistics
[STOP] [2019-10-12 23:57:38] calculate_statistics
[START] [2019-10-12 23:57:38] complete_harvest_instance
[START] [2019-10-12 23:57:38] overall_tsv_creation
[INFO] [2019-10-12 23:57:38] Processing group of 65237 in 7 batches of 10000
[INFO] [2019-10-12 23:59:06] 6632 Traits (unfiltered)...
[INFO] [2019-10-12 23:59:20] 6632 Traits (filtered)...
[INFO] [2019-10-12 23:59:20] 0 Associations (filtered)...
[INFO] [2019-10-13 00:00:11] 33152 metadata added.
[INFO] [2019-10-13 00:00:11] 0 metadata added.
[INFO] [2019-10-13 00:01:45] 6552 Traits (unfiltered)...
[INFO] [2019-10-13 00:01:59] 6552 Traits (filtered)...
[INFO] [2019-10-13 00:01:59] 0 Associations (filtered)...
[INFO] [2019-10-13 00:02:52] 32749 metadata added.
[INFO] [2019-10-13 00:02:52] 0 metadata added.
[INFO] [2019-10-13 00:04:28] 6754 Traits (unfiltered)...
[INFO] [2019-10-13 00:04:42] 6754 Traits (filtered)...
[INFO] [2019-10-13 00:04:42] 0 Associations (filtered)...
[INFO] [2019-10-13 00:05:36] 33740 metadata added.
[INFO] [2019-10-13 00:05:36] 0 metadata added.
[INFO] [2019-10-13 00:07:11] 7055 Traits (unfiltered)...
[INFO] [2019-10-13 00:07:25] 7055 Traits (filtered)...
[INFO] [2019-10-13 00:07:25] 0 Associations (filtered)...
[INFO] [2019-10-13 00:08:20] 35247 metadata added.
[INFO] [2019-10-13 00:08:20] 0 metadata added.
[INFO] [2019-10-13 00:09:54] 7131 Traits (unfiltered)...
[INFO] [2019-10-13 00:10:08] 7131 Traits (filtered)...
[INFO] [2019-10-13 00:10:08] 0 Associations (filtered)...
[INFO] [2019-10-13 00:11:01] 35636 metadata added.
[INFO] [2019-10-13 00:11:01] 0 metadata added.
[INFO] [2019-10-13 00:12:35] 7462 Traits (unfiltered)...
[INFO] [2019-10-13 00:12:49] 7462 Traits (filtered)...
[INFO] [2019-10-13 00:12:49] 0 Associations (filtered)...
[INFO] [2019-10-13 00:13:44] 37284 metadata added.
[INFO] [2019-10-13 00:13:44] 0 metadata added.
[INFO] [2019-10-13 00:14:55] 3722 Traits (unfiltered)...
[INFO] [2019-10-13 00:15:09] 3722 Traits (filtered)...
[INFO] [2019-10-13 00:15:09] 0 Associations (filtered)...
[INFO] [2019-10-13 00:15:53] 18585 metadata added.
[INFO] [2019-10-13 00:15:53] 0 metadata added.
[INFO] [2019-10-13 00:15:53] Average Time: 130.374
[INFO] [2019-10-13 00:15:53] Total Time: 18m15s
[INFO] [2019-10-13 00:15:53] last 3 / first 3: 0.95
[INFO] [2019-10-13 00:15:53] Std.Dev: 11.506910966892896; Max: 138.35
[STOP] [2019-10-13 00:15:53] overall_tsv_creation
[INFO] [2019-10-13 00:15:53] Done. Check your files:
[INFO] [2019-10-13 00:15:53] (65237 lines) /app/public/data/france_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 00:15:53] (274703 lines) /app/public/data/france_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 00:15:53] (65237 lines) /app/public/data/france_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 00:15:53] (45309 lines) /app/public/data/france_sp_list/publish_traits.tsv
[INFO] [2019-10-13 00:15:53] (226394 lines) /app/public/data/france_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 00:15:54] complete_harvest_instance
[START] [2019-10-13 00:15:54] completed
[STOP] [2019-10-13 00:15:54] completed
[STOP] [2019-10-13 00:15:54] logged process, took 6436.57

Latest Process

12 Oct 22:28 EXITED currently processing 0