Harvest for Slovenia Species List Created 15 Oct 19:39

Stage: completed
Fetched: 15 Oct 19:39
Validated: 15 Oct 19:39
Deltas Created 15 Oct 19:39
Units Normalized: 15 Oct 19:59
Ancestry Built: 15 Oct 19:42
Nodes Matched: 15 Oct 19:59
Names Parsed: 15 Oct 19:42
New Models Stored: 15 Oct 19:40
Indexed: 15 Oct 19:59
Completed: 15 Oct 20:04
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-15 19:39:36 -0400 by logger.rb/56815
[START] [2019-10-15 19:39:36] logged process
[START] [2019-10-15 19:39:36] create_harvest_instance
[STOP] [2019-10-15 19:39:37] create_harvest_instance
[START] [2019-10-15 19:39:37] fetch_files
[STOP] [2019-10-15 19:39:37] fetch_files
[START] [2019-10-15 19:39:37] validate_each_file
[STOP] [2019-10-15 19:39:39] validate_each_file
[START] [2019-10-15 19:39:39] convert_to_csv
[CMD] [2019-10-15 19:39:39] /usr/bin/sort /app/public/converted_csv/slovenia_sp_list_refs_17229.csv > /app/public/converted_csv/slovenia_sp_list_refs_17229.csv_sorted
[CMD] [2019-10-15 19:39:39] /usr/bin/sort /app/public/converted_csv/slovenia_sp_list_nodes_17230.csv > /app/public/converted_csv/slovenia_sp_list_nodes_17230.csv_sorted
[CMD] [2019-10-15 19:39:39] /usr/bin/sort /app/public/converted_csv/slovenia_sp_list_occurrences_17231.csv > /app/public/converted_csv/slovenia_sp_list_occurrences_17231.csv_sorted
[CMD] [2019-10-15 19:39:39] /usr/bin/sort /app/public/converted_csv/slovenia_sp_list_measurements_17232.csv > /app/public/converted_csv/slovenia_sp_list_measurements_17232.csv_sorted
[STOP] [2019-10-15 19:39:40] convert_to_csv
[START] [2019-10-15 19:39:40] calculate_delta
[CMD] [2019-10-15 19:39:40] echo "0a" > /app/public/diff/slovenia_sp_list_refs_17229.diff
[CMD] [2019-10-15 19:39:40] tail -n +1 /app/public/converted_csv/slovenia_sp_list_refs_17229.csv >> /app/public/diff/slovenia_sp_list_refs_17229.diff
[CMD] [2019-10-15 19:39:40] echo "." >> /app/public/diff/slovenia_sp_list_refs_17229.diff
[CMD] [2019-10-15 19:39:41] echo "0a" > /app/public/diff/slovenia_sp_list_nodes_17230.diff
[CMD] [2019-10-15 19:39:41] tail -n +1 /app/public/converted_csv/slovenia_sp_list_nodes_17230.csv >> /app/public/diff/slovenia_sp_list_nodes_17230.diff
[CMD] [2019-10-15 19:39:41] echo "." >> /app/public/diff/slovenia_sp_list_nodes_17230.diff
[CMD] [2019-10-15 19:39:42] echo "0a" > /app/public/diff/slovenia_sp_list_occurrences_17231.diff
[CMD] [2019-10-15 19:39:42] tail -n +1 /app/public/converted_csv/slovenia_sp_list_occurrences_17231.csv >> /app/public/diff/slovenia_sp_list_occurrences_17231.diff
[CMD] [2019-10-15 19:39:42] echo "." >> /app/public/diff/slovenia_sp_list_occurrences_17231.diff
[CMD] [2019-10-15 19:39:42] echo "0a" > /app/public/diff/slovenia_sp_list_measurements_17232.diff
[CMD] [2019-10-15 19:39:43] tail -n +1 /app/public/converted_csv/slovenia_sp_list_measurements_17232.csv >> /app/public/diff/slovenia_sp_list_measurements_17232.diff
[CMD] [2019-10-15 19:39:43] echo "." >> /app/public/diff/slovenia_sp_list_measurements_17232.diff
[STOP] [2019-10-15 19:39:43] calculate_delta
[START] [2019-10-15 19:39:43] parse_diff_and_store
[INFO] [2019-10-15 19:39:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 19:39:44] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 19:39:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 19:39:50] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 19:40:39] Storing 2 References
[INFO] [2019-10-15 19:40:39] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 19:40:39] Average Time: 0.0
[INFO] [2019-10-15 19:40:39] Total Time: 1s
[INFO] [2019-10-15 19:40:39] Storing 12650 ScientificNames
[INFO] [2019-10-15 19:40:39] Processing group of 12650 in 13 groups of 1000
[INFO] [2019-10-15 19:40:44] Average Time: 0.403
[INFO] [2019-10-15 19:40:44] Total Time: 6s
[INFO] [2019-10-15 19:40:44] last 3 / first 3: 1.37
[INFO] [2019-10-15 19:40:44] Std.Dev: 0.21213203435596426; Max: 1.09
[INFO] [2019-10-15 19:40:44] Storing 12650 Nodes
[INFO] [2019-10-15 19:40:44] Processing group of 12650 in 13 groups of 1000
[INFO] [2019-10-15 19:40:48] Average Time: 0.296
[INFO] [2019-10-15 19:40:48] Total Time: 4s
[INFO] [2019-10-15 19:40:48] last 3 / first 3: 0.85
[INFO] [2019-10-15 19:40:48] Std.Dev: 0.044721359549995794; Max: 0.38
[INFO] [2019-10-15 19:40:48] Storing 8194 Occurrences
[INFO] [2019-10-15 19:40:48] Processing group of 8194 in 9 groups of 1000
[INFO] [2019-10-15 19:40:49] Average Time: 0.093
[INFO] [2019-10-15 19:40:49] Total Time: 1s
[INFO] [2019-10-15 19:40:49] last 3 / first 3: 0.69
[INFO] [2019-10-15 19:40:49] Std.Dev: 0.03162277660168379; Max: 0.12
[INFO] [2019-10-15 19:40:49] Storing 16610 TraitsReferences
[INFO] [2019-10-15 19:40:49] Processing group of 16610 in 17 groups of 1000
[INFO] [2019-10-15 19:40:50] Average Time: 0.076
[INFO] [2019-10-15 19:40:50] Total Time: 2s
[INFO] [2019-10-15 19:40:50] last 3 / first 3: 0.64
[INFO] [2019-10-15 19:40:50] Std.Dev: 0.03162277660168379; Max: 0.18
[INFO] [2019-10-15 19:40:50] Storing 16609 Traits
[INFO] [2019-10-15 19:40:50] Processing group of 16609 in 17 groups of 1000
[INFO] [2019-10-15 19:40:55] Average Time: 0.298
[INFO] [2019-10-15 19:40:55] Total Time: 6s
[INFO] [2019-10-15 19:40:55] last 3 / first 3: 0.81
[INFO] [2019-10-15 19:40:55] Std.Dev: 0.05477225575051661; Max: 0.45
[INFO] [2019-10-15 19:40:55] Storing 16599 MetaTraits
[INFO] [2019-10-15 19:40:55] Processing group of 16599 in 17 groups of 1000
[INFO] [2019-10-15 19:40:57] Average Time: 0.11
[INFO] [2019-10-15 19:40:57] Total Time: 2s
[INFO] [2019-10-15 19:40:57] last 3 / first 3: 0.76
[INFO] [2019-10-15 19:40:57] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-15 19:40:57] parse_diff_and_store
[START] [2019-10-15 19:40:57] resolve_keys
[INFO] [2019-10-15 19:41:46] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 19:41:50] traits to occurrences...
[INFO] [2019-10-15 19:41:56] traits to nodes (through occurrences)...
[INFO] [2019-10-15 19:41:56] Traits to sex term...
[INFO] [2019-10-15 19:42:01] Traits to lifestage term...
[INFO] [2019-10-15 19:42:06] MetaTraits to traits...
[INFO] [2019-10-15 19:42:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 19:42:09] Assocs to occurrences...
[INFO] [2019-10-15 19:42:09] Assocs to nodes...
[INFO] [2019-10-15 19:42:09] Assoc to sex term...
[INFO] [2019-10-15 19:42:09] Assoc to lifestage term...
[STOP] [2019-10-15 19:42:09] resolve_keys
[START] [2019-10-15 19:42:09] hold_for_later_1
[STOP] [2019-10-15 19:42:09] hold_for_later_1
[START] [2019-10-15 19:42:09] hold_for_later_2
[STOP] [2019-10-15 19:42:09] hold_for_later_2
[START] [2019-10-15 19:42:09] resolve_missing_parents
[STOP] [2019-10-15 19:42:34] resolve_missing_parents
[START] [2019-10-15 19:42:34] rebuild_nodes
[START] [2019-10-15 19:42:34] Flattener#flatten
[START] [2019-10-15 19:42:34] Flattener#study_resource
[START] [2019-10-15 19:42:34] Flattener#build_ancestry
[STOP] [2019-10-15 19:42:37] Flattener#build_ancestry
[INFO] [2019-10-15 19:42:37] 12650 ancestry keys
[START] [2019-10-15 19:42:37] build_node_ancestors
[INFO] [2019-10-15 19:42:37] old ancestors deleted.
[STOP] [2019-10-15 19:42:39] build_node_ancestors
[START] [2019-10-15 19:42:41] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 19:42:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 19:42:42] Flattener#flatten
[STOP] [2019-10-15 19:42:42] rebuild_nodes
[START] [2019-10-15 19:42:42] resolve_missing_media_owners
[STOP] [2019-10-15 19:42:42] resolve_missing_media_owners
[START] [2019-10-15 19:42:42] sanitize_media_verbatims
[STOP] [2019-10-15 19:42:42] sanitize_media_verbatims
[START] [2019-10-15 19:42:42] queue_downloads
[STOP] [2019-10-15 19:42:42] queue_downloads
[START] [2019-10-15 19:42:42] parse_names
[WARN] [2019-10-15 19:42:42] I see 12650 names which still need to be parsed.
[STOP] [2019-10-15 19:42:52] parse_names
[START] [2019-10-15 19:42:52] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 19:42:52] denormalize_canonical_names_to_nodes
[START] [2019-10-15 19:42:52] match_nodes
[START] [2019-10-15 19:42:52] map_all_nodes_to_pages
[STOP] [2019-10-15 19:58:58] map_all_nodes_to_pages
[INFO] [2019-10-15 19:58:58] 1576 Unmatched nodes (of 12650)! That's too many to output. First 10: Russula olivaceoviolascens (#51841858); Russula acetolens (#51841994); Russula erythropoda (#51842575); Artomyces pyxidata (#51846101); Gloiothele citrinus (#51848154); Stephanospora caroticola (#51849256); Clitopilus caelata (#51848603); Entoloma chalybaeum (#51843793); Entocybe nitidum (#51840594); Rhodocybe piperata (#51842572)
[START] [2019-10-15 19:58:58] update_nodes
[STOP] [2019-10-15 19:59:02] update_nodes
[STOP] [2019-10-15 19:59:02] match_nodes
[START] [2019-10-15 19:59:02] reindex_search
[STOP] [2019-10-15 19:59:49] reindex_search
[START] [2019-10-15 19:59:49] normalize_units
[STOP] [2019-10-15 19:59:49] normalize_units
[START] [2019-10-15 19:59:49] calculate_statistics
[STOP] [2019-10-15 19:59:49] calculate_statistics
[START] [2019-10-15 19:59:49] complete_harvest_instance
[START] [2019-10-15 19:59:49] overall_tsv_creation
[INFO] [2019-10-15 19:59:49] Processing group of 12650 in 2 batches of 10000
[INFO] [2019-10-15 20:01:17] 6463 Traits (unfiltered)...
[INFO] [2019-10-15 20:01:31] 6463 Traits (filtered)...
[INFO] [2019-10-15 20:01:31] 0 Associations (filtered)...
[INFO] [2019-10-15 20:02:24] 32308 metadata added.
[INFO] [2019-10-15 20:02:24] 0 metadata added.
[INFO] [2019-10-15 20:03:22] 1731 Traits (unfiltered)...
[INFO] [2019-10-15 20:03:36] 1731 Traits (filtered)...
[INFO] [2019-10-15 20:03:36] 0 Associations (filtered)...
[INFO] [2019-10-15 20:04:18] 8651 metadata added.
[INFO] [2019-10-15 20:04:18] 0 metadata added.
[INFO] [2019-10-15 20:04:18] Average Time: 109.94
[INFO] [2019-10-15 20:04:18] Total Time: 4m29s
[STOP] [2019-10-15 20:04:18] overall_tsv_creation
[INFO] [2019-10-15 20:04:18] Done. Check your files:
[INFO] [2019-10-15 20:04:18] (12650 lines) /app/public/data/slovenia_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 20:04:18] (30145 lines) /app/public/data/slovenia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 20:04:19] (12650 lines) /app/public/data/slovenia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 20:04:19] (8195 lines) /app/public/data/slovenia_sp_list/publish_traits.tsv
[INFO] [2019-10-15 20:04:19] (40960 lines) /app/public/data/slovenia_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 20:04:20] complete_harvest_instance
[START] [2019-10-15 20:04:20] completed
[STOP] [2019-10-15 20:04:20] completed
[STOP] [2019-10-15 20:04:20] logged process, took 1483.31
Latest Process

15 Oct 19:39 EXITED currently processing 0