Harvest for Costa Rica Species List Created 12 Oct 10:59

Stage: completed
Fetched: 12 Oct 10:59
Validated: 12 Oct 10:59
Deltas Created 12 Oct 10:59
Units Normalized: 12 Oct 11:54
Ancestry Built: 12 Oct 11:10
Nodes Matched: 12 Oct 11:52
Names Parsed: 12 Oct 11:10
New Models Stored: 12 Oct 11:05
Indexed: 12 Oct 11:54
Completed: 12 Oct 12:09
Time to Harvest: 1 minute
Harvesting Log

(176 lines)
# Logfile created on 2019-10-12 10:59:01 -0400 by logger.rb/56815
[START] [2019-10-12 10:59:01] logged process
[START] [2019-10-12 10:59:01] create_harvest_instance
[STOP] [2019-10-12 10:59:02] create_harvest_instance
[START] [2019-10-12 10:59:02] fetch_files
[STOP] [2019-10-12 10:59:02] fetch_files
[START] [2019-10-12 10:59:02] validate_each_file
[STOP] [2019-10-12 10:59:09] validate_each_file
[START] [2019-10-12 10:59:09] convert_to_csv
[CMD] [2019-10-12 10:59:09] /usr/bin/sort /app/public/converted_csv/costa_rica_sp_li_refs_15523.csv > /app/public/converted_csv/costa_rica_sp_li_refs_15523.csv_sorted
[CMD] [2019-10-12 10:59:10] /usr/bin/sort /app/public/converted_csv/costa_rica_sp_li_nodes_15524.csv > /app/public/converted_csv/costa_rica_sp_li_nodes_15524.csv_sorted
[CMD] [2019-10-12 10:59:10] /usr/bin/sort /app/public/converted_csv/costa_rica_sp_li_occurrences_15525.csv > /app/public/converted_csv/costa_rica_sp_li_occurrences_15525.csv_sorted
[CMD] [2019-10-12 10:59:10] /usr/bin/sort /app/public/converted_csv/costa_rica_sp_li_measurements_15526.csv > /app/public/converted_csv/costa_rica_sp_li_measurements_15526.csv_sorted
[STOP] [2019-10-12 10:59:10] convert_to_csv
[START] [2019-10-12 10:59:10] calculate_delta
[CMD] [2019-10-12 10:59:10] echo "0a" > /app/public/diff/costa_rica_sp_li_refs_15523.diff
[CMD] [2019-10-12 10:59:10] tail -n +1 /app/public/converted_csv/costa_rica_sp_li_refs_15523.csv >> /app/public/diff/costa_rica_sp_li_refs_15523.diff
[CMD] [2019-10-12 10:59:10] echo "." >> /app/public/diff/costa_rica_sp_li_refs_15523.diff
[CMD] [2019-10-12 10:59:10] echo "0a" > /app/public/diff/costa_rica_sp_li_nodes_15524.diff
[CMD] [2019-10-12 10:59:10] tail -n +1 /app/public/converted_csv/costa_rica_sp_li_nodes_15524.csv >> /app/public/diff/costa_rica_sp_li_nodes_15524.diff
[CMD] [2019-10-12 10:59:10] echo "." >> /app/public/diff/costa_rica_sp_li_nodes_15524.diff
[CMD] [2019-10-12 10:59:11] echo "0a" > /app/public/diff/costa_rica_sp_li_occurrences_15525.diff
[CMD] [2019-10-12 10:59:11] tail -n +1 /app/public/converted_csv/costa_rica_sp_li_occurrences_15525.csv >> /app/public/diff/costa_rica_sp_li_occurrences_15525.diff
[CMD] [2019-10-12 10:59:11] echo "." >> /app/public/diff/costa_rica_sp_li_occurrences_15525.diff
[CMD] [2019-10-12 10:59:11] echo "0a" > /app/public/diff/costa_rica_sp_li_measurements_15526.diff
[CMD] [2019-10-12 10:59:11] tail -n +1 /app/public/converted_csv/costa_rica_sp_li_measurements_15526.csv >> /app/public/diff/costa_rica_sp_li_measurements_15526.diff
[CMD] [2019-10-12 10:59:11] echo "." >> /app/public/diff/costa_rica_sp_li_measurements_15526.diff
[STOP] [2019-10-12 10:59:11] calculate_delta
[START] [2019-10-12 10:59:11] parse_diff_and_store
[INFO] [2019-10-12 10:59:11] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 10:59:11] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 10:59:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 10:59:38] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 11:03:33] Storing 2 References
[INFO] [2019-10-12 11:03:33] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 11:03:33] Average Time: 0.0
[INFO] [2019-10-12 11:03:33] Total Time: 1s
[INFO] [2019-10-12 11:03:33] Storing 52874 ScientificNames
[INFO] [2019-10-12 11:03:33] Processing group of 52874 in 53 groups of 1000
[INFO] [2019-10-12 11:03:55] Average Time: 0.4
[INFO] [2019-10-12 11:03:55] Total Time: 22s
[INFO] [2019-10-12 11:03:55] last 3 / first 3: 0.98
[INFO] [2019-10-12 11:03:55] Std.Dev: 0.17320508075688773; Max: 1.56
[INFO] [2019-10-12 11:03:55] Storing 52874 Nodes
[INFO] [2019-10-12 11:03:55] Processing group of 52874 in 53 groups of 1000
[INFO] [2019-10-12 11:04:16] Average Time: 0.4
[INFO] [2019-10-12 11:04:16] Total Time: 22s
[INFO] [2019-10-12 11:04:16] last 3 / first 3: 1.83
[INFO] [2019-10-12 11:04:16] Std.Dev: 0.30166206257996714; Max: 2.25
[INFO] [2019-10-12 11:04:16] Storing 39524 Occurrences
[INFO] [2019-10-12 11:04:16] Processing group of 39524 in 40 groups of 1000
[INFO] [2019-10-12 11:04:22] Average Time: 0.149
[INFO] [2019-10-12 11:04:22] Total Time: 7s
[INFO] [2019-10-12 11:04:22] last 3 / first 3: 0.37
[INFO] [2019-10-12 11:04:22] Std.Dev: 0.10954451150103323; Max: 0.74
[INFO] [2019-10-12 11:04:22] Storing 79908 TraitsReferences
[INFO] [2019-10-12 11:04:22] Processing group of 79908 in 80 groups of 1000
[INFO] [2019-10-12 11:04:28] Average Time: 0.068
[INFO] [2019-10-12 11:04:28] Total Time: 6s
[INFO] [2019-10-12 11:04:28] last 3 / first 3: 0.71
[INFO] [2019-10-12 11:04:28] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-12 11:04:28] Storing 79907 Traits
[INFO] [2019-10-12 11:04:28] Processing group of 79907 in 80 groups of 1000
[INFO] [2019-10-12 11:05:02] Average Time: 0.421
[INFO] [2019-10-12 11:05:02] Total Time: 34s
[INFO] [2019-10-12 11:05:02] last 3 / first 3: 0.86
[INFO] [2019-10-12 11:05:02] Std.Dev: 0.4505552130427524; Max: 2.76
[INFO] [2019-10-12 11:05:02] Storing 79842 MetaTraits
[INFO] [2019-10-12 11:05:02] Processing group of 79842 in 80 groups of 1000
[INFO] [2019-10-12 11:05:21] Average Time: 0.237
[INFO] [2019-10-12 11:05:21] Total Time: 20s
[INFO] [2019-10-12 11:05:21] last 3 / first 3: 0.87
[INFO] [2019-10-12 11:05:21] Std.Dev: 0.4919349550499537; Max: 2.77
[STOP] [2019-10-12 11:05:21] parse_diff_and_store
[START] [2019-10-12 11:05:21] resolve_keys
[INFO] [2019-10-12 11:07:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 11:07:44] traits to occurrences...
[INFO] [2019-10-12 11:07:51] traits to nodes (through occurrences)...
[INFO] [2019-10-12 11:07:52] Traits to sex term...
[INFO] [2019-10-12 11:07:59] Traits to lifestage term...
[INFO] [2019-10-12 11:08:06] MetaTraits to traits...
[INFO] [2019-10-12 11:08:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 11:08:23] Assocs to occurrences...
[INFO] [2019-10-12 11:08:23] Assocs to nodes...
[INFO] [2019-10-12 11:08:23] Assoc to sex term...
[INFO] [2019-10-12 11:08:23] Assoc to lifestage term...
[STOP] [2019-10-12 11:08:23] resolve_keys
[START] [2019-10-12 11:08:23] hold_for_later_1
[STOP] [2019-10-12 11:08:23] hold_for_later_1
[START] [2019-10-12 11:08:23] hold_for_later_2
[STOP] [2019-10-12 11:08:23] hold_for_later_2
[START] [2019-10-12 11:08:23] resolve_missing_parents
[STOP] [2019-10-12 11:09:39] resolve_missing_parents
[START] [2019-10-12 11:09:39] rebuild_nodes
[START] [2019-10-12 11:09:39] Flattener#flatten
[START] [2019-10-12 11:09:39] Flattener#study_resource
[START] [2019-10-12 11:09:40] Flattener#build_ancestry
[STOP] [2019-10-12 11:09:48] Flattener#build_ancestry
[INFO] [2019-10-12 11:09:48] 52874 ancestry keys
[START] [2019-10-12 11:09:48] build_node_ancestors
[INFO] [2019-10-12 11:09:48] old ancestors deleted.
[STOP] [2019-10-12 11:10:07] build_node_ancestors
[START] [2019-10-12 11:10:12] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 11:10:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 11:10:16] Flattener#flatten
[STOP] [2019-10-12 11:10:16] rebuild_nodes
[START] [2019-10-12 11:10:16] resolve_missing_media_owners
[STOP] [2019-10-12 11:10:16] resolve_missing_media_owners
[START] [2019-10-12 11:10:16] sanitize_media_verbatims
[STOP] [2019-10-12 11:10:16] sanitize_media_verbatims
[START] [2019-10-12 11:10:16] queue_downloads
[STOP] [2019-10-12 11:10:16] queue_downloads
[START] [2019-10-12 11:10:16] parse_names
[WARN] [2019-10-12 11:10:16] I see 52874 names which still need to be parsed.
[STOP] [2019-10-12 11:10:57] parse_names
[START] [2019-10-12 11:10:57] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 11:10:57] denormalize_canonical_names_to_nodes
[START] [2019-10-12 11:10:57] match_nodes
[START] [2019-10-12 11:10:57] map_all_nodes_to_pages
[STOP] [2019-10-12 11:51:45] map_all_nodes_to_pages
[INFO] [2019-10-12 11:51:45] 3496 Unmatched nodes (of 52874)! That's too many to output. First 10: Contopus borealis (#49330851); Conopias parva (#49340555); Ornithion brunneicapillum (#49351136); Pyrocephalus coronatus (#49343821); Ramphocelus costaricensis (#49308243); Molothrus oryzivora (#49335998); Sturnella militaris (#49309649); Cyphorhinus aradus (#49330899); Thryothorus nigricapillus (#49315710); Thryothorus thoracicus (#49316172)
[START] [2019-10-12 11:51:45] update_nodes
[STOP] [2019-10-12 11:52:05] update_nodes
[STOP] [2019-10-12 11:52:05] match_nodes
[START] [2019-10-12 11:52:05] reindex_search
[STOP] [2019-10-12 11:54:15] reindex_search
[START] [2019-10-12 11:54:15] normalize_units
[STOP] [2019-10-12 11:54:15] normalize_units
[START] [2019-10-12 11:54:15] calculate_statistics
[STOP] [2019-10-12 11:54:15] calculate_statistics
[START] [2019-10-12 11:54:15] complete_harvest_instance
[START] [2019-10-12 11:54:15] overall_tsv_creation
[INFO] [2019-10-12 11:54:15] Processing group of 52874 in 6 batches of 10000
[INFO] [2019-10-12 11:55:44] 6395 Traits (unfiltered)...
[INFO] [2019-10-12 11:55:58] 6395 Traits (filtered)...
[INFO] [2019-10-12 11:55:58] 0 Associations (filtered)...
[INFO] [2019-10-12 11:56:48] 31974 metadata added.
[INFO] [2019-10-12 11:56:48] 0 metadata added.
[INFO] [2019-10-12 11:58:20] 7476 Traits (unfiltered)...
[INFO] [2019-10-12 11:58:34] 7476 Traits (filtered)...
[INFO] [2019-10-12 11:58:35] 0 Associations (filtered)...
[INFO] [2019-10-12 11:59:31] 37377 metadata added.
[INFO] [2019-10-12 11:59:31] 0 metadata added.
[INFO] [2019-10-12 12:01:04] 7741 Traits (unfiltered)...
[INFO] [2019-10-12 12:01:18] 7741 Traits (filtered)...
[INFO] [2019-10-12 12:01:18] 0 Associations (filtered)...
[INFO] [2019-10-12 12:02:14] 38692 metadata added.
[INFO] [2019-10-12 12:02:14] 0 metadata added.
[INFO] [2019-10-12 12:03:46] 7859 Traits (unfiltered)...
[INFO] [2019-10-12 12:04:00] 7859 Traits (filtered)...
[INFO] [2019-10-12 12:04:00] 0 Associations (filtered)...
[INFO] [2019-10-12 12:04:55] 39277 metadata added.
[INFO] [2019-10-12 12:04:55] 0 metadata added.
[INFO] [2019-10-12 12:06:29] 8069 Traits (unfiltered)...
[INFO] [2019-10-12 12:06:43] 8069 Traits (filtered)...
[INFO] [2019-10-12 12:06:44] 0 Associations (filtered)...
[INFO] [2019-10-12 12:07:39] 40325 metadata added.
[INFO] [2019-10-12 12:07:39] 0 metadata added.
[INFO] [2019-10-12 12:08:39] 1984 Traits (unfiltered)...
[INFO] [2019-10-12 12:08:53] 1984 Traits (filtered)...
[INFO] [2019-10-12 12:08:53] 0 Associations (filtered)...
[INFO] [2019-10-12 12:09:33] 9911 metadata added.
[INFO] [2019-10-12 12:09:33] 0 metadata added.
[INFO] [2019-10-12 12:09:33] Average Time: 127.652
[INFO] [2019-10-12 12:09:33] Total Time: 15m18s
[STOP] [2019-10-12 12:09:33] overall_tsv_creation
[INFO] [2019-10-12 12:09:33] Done. Check your files:
[INFO] [2019-10-12 12:09:33] (52874 lines) /app/public/data/costa_rica_sp_li/publish_nodes.tsv
[INFO] [2019-10-12 12:09:34] (162387 lines) /app/public/data/costa_rica_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-12 12:09:34] (52874 lines) /app/public/data/costa_rica_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-12 12:09:34] (39525 lines) /app/public/data/costa_rica_sp_li/publish_traits.tsv
[INFO] [2019-10-12 12:09:34] (197557 lines) /app/public/data/costa_rica_sp_li/publish_metadata.tsv
[STOP] [2019-10-12 12:09:34] complete_harvest_instance
[START] [2019-10-12 12:09:34] completed
[STOP] [2019-10-12 12:09:34] completed
[STOP] [2019-10-12 12:09:34] logged process, took 4233.03
Latest Process

12 Oct 10:59 EXITED currently processing 0