Harvest for EOL Dynamic Hierarchy 1.1 Created 17 Jun 13:36

Stage: completed
Fetched: 17 Jun 13:36
Validated: 17 Jun 13:42
Deltas Created 17 Jun 13:42
Units Normalized: 21 Jun 21:31
Ancestry Built: 19 Jun 08:30
Nodes Matched: 21 Jun 19:26
Names Parsed: 19 Jun 10:54
New Models Stored: 19 Jun 00:42
Indexed: 21 Jun 21:31
Completed: 22 Jun 08:49
Time to Harvest: 23 minutes

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-06-17 13:36:53 -0400 by logger.rb/56815
[START] [2019-06-17 13:36:53] logged process
[START] [2019-06-17 13:36:53] create_harvest_instance
[STOP] [2019-06-17 13:36:53] create_harvest_instance
[START] [2019-06-17 13:36:53] fetch_files
[STOP] [2019-06-17 13:36:53] fetch_files
[START] [2019-06-17 13:36:53] validate_each_file
[STOP] [2019-06-17 13:42:27] validate_each_file
[START] [2019-06-17 13:42:27] convert_to_csv
[CMD] [2019-06-17 13:42:27] /usr/bin/sort /app/public/converted_csv/dvdtg_nodes_13586.csv > /app/public/converted_csv/dvdtg_nodes_13586.csv_sorted
[STOP] [2019-06-17 13:42:30] convert_to_csv
[START] [2019-06-17 13:42:30] calculate_delta
[CMD] [2019-06-17 13:42:30] echo "0a" > /app/public/diff/dvdtg_nodes_13586.diff
[CMD] [2019-06-17 13:42:30] tail -n +1 /app/public/converted_csv/dvdtg_nodes_13586.csv >> /app/public/diff/dvdtg_nodes_13586.diff
[CMD] [2019-06-17 13:42:31] echo "." >> /app/public/diff/dvdtg_nodes_13586.diff
[STOP] [2019-06-17 13:42:31] calculate_delta
[START] [2019-06-17 13:42:31] parse_diff_and_store
[INFO] [2019-06-17 13:42:37] Loading nodes diff file into memory (true lines)...
[INFO] [2019-06-17 16:20:39] Storing 4011066 ScientificNames
[INFO] [2019-06-17 16:20:39] Processing group of 4011066 in 4012 groups of 1000
[INFO] [2019-06-17 19:32:09] Average Time: 0.0
[INFO] [2019-06-17 19:32:09] Total Time: 3h11m30s
[INFO] [2019-06-17 19:32:09] last 3 / first 3: 0.65
[STOP] [2019-06-17 19:32:10] parse_diff_and_store
[INFO] [2019-06-18 16:11:45] Loading nodes diff file into memory (4011068 lines)...
[INFO] [2019-06-18 18:45:38] Storing 4011066 ScientificNames
[INFO] [2019-06-18 18:45:38] Processing group of 4011066 in 4012 groups of 1000
[INFO] [2019-06-18 21:51:59] Average Time: 2.748
[INFO] [2019-06-18 21:51:59] Total Time: 3h6m21s
[INFO] [2019-06-18 21:51:59] last 3 / first 3: 0.35
[INFO] [2019-06-18 21:51:59] Std.Dev: 11.522239365678878; Max: 72.77
[INFO] [2019-06-18 21:51:59] Storing 4028487 Identifiers
[INFO] [2019-06-18 21:51:59] Processing group of 4028487 in 4029 groups of 1000
[INFO] [2019-06-18 22:31:37] Average Time: 0.529
[INFO] [2019-06-18 22:31:37] Total Time: 39m39s
[INFO] [2019-06-18 22:31:37] last 3 / first 3: 0.83
[INFO] [2019-06-18 22:31:37] Std.Dev: 5.432218699573868; Max: 74.42
[INFO] [2019-06-18 22:31:37] Storing 2328980 Nodes
[INFO] [2019-06-18 22:31:37] Processing group of 2328980 in 2329 groups of 1000
[INFO] [2019-06-19 00:42:31] Average Time: 3.366
[INFO] [2019-06-19 00:42:31] Total Time: 2h10m55s
[INFO] [2019-06-19 00:42:31] last 3 / first 3: 2.24
[INFO] [2019-06-19 00:42:31] Std.Dev: 14.832902615469434; Max: 84.5
[STOP] [2019-06-19 00:42:31] parse_diff_and_store
[START] [2019-06-19 00:42:31] resolve_keys
[INFO] [2019-06-19 01:03:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-06-19 01:03:35] traits to occurrences...
[INFO] [2019-06-19 01:03:35] traits to nodes (through occurrences)...
[INFO] [2019-06-19 01:03:35] Traits to sex term...
[INFO] [2019-06-19 01:03:35] Traits to lifestage term...
[INFO] [2019-06-19 01:03:35] MetaTraits to traits...
[INFO] [2019-06-19 01:03:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-06-19 01:03:35] Assocs to occurrences...
[INFO] [2019-06-19 01:03:35] Assocs to nodes...
[INFO] [2019-06-19 01:03:35] Assoc to sex term...
[INFO] [2019-06-19 01:03:35] Assoc to lifestage term...
[STOP] [2019-06-19 01:03:35] resolve_keys
[START] [2019-06-19 01:03:35] hold_for_later_1
[STOP] [2019-06-19 01:03:35] hold_for_later_1
[START] [2019-06-19 01:03:35] hold_for_later_2
[STOP] [2019-06-19 01:03:35] hold_for_later_2
[START] [2019-06-19 01:03:35] resolve_missing_parents
[STOP] [2019-06-19 01:04:02] resolve_missing_parents
[START] [2019-06-19 01:04:02] rebuild_nodes
[START] [2019-06-19 01:04:02] Flattener#flatten
[START] [2019-06-19 01:04:02] Flattener#study_resource
[START] [2019-06-19 01:05:59] Flattener#build_ancestry
[STOP] [2019-06-19 05:40:50] Flattener#build_ancestry
[INFO] [2019-06-19 05:40:50] 2328980 ancestry keys
[START] [2019-06-19 05:40:50] build_node_ancestors
[INFO] [2019-06-19 05:40:50] old ancestors deleted.
[STOP] [2019-06-19 07:37:08] build_node_ancestors
[START] [2019-06-19 07:37:16] Flattener#propagate_ancestor_ids
[STOP] [2019-06-19 08:30:30] Flattener#propagate_ancestor_ids
[STOP] [2019-06-19 08:30:30] Flattener#flatten
[STOP] [2019-06-19 08:30:30] rebuild_nodes
[START] [2019-06-19 08:30:30] resolve_missing_media_owners
[STOP] [2019-06-19 08:30:30] resolve_missing_media_owners
[START] [2019-06-19 08:30:30] sanitize_media_verbatims
[STOP] [2019-06-19 08:30:30] sanitize_media_verbatims
[START] [2019-06-19 08:30:30] queue_downloads
[STOP] [2019-06-19 08:30:30] queue_downloads
[START] [2019-06-19 08:30:30] parse_names
[WARN] [2019-06-19 08:30:41] I see 8022132 names which still need to be parsed.
[WARN] [2019-06-19 10:48:32] I see 7136 names which still need to be parsed.
[WARN] [2019-06-19 10:49:12] I see 4162 names which still need to be parsed.
[WARN] [2019-06-19 10:49:49] I see 1326 names which still need to be parsed.
[WARN] [2019-06-19 10:50:22] I see 1003 names which still need to be parsed.
[WARN] [2019-06-19 10:50:55] I see 689 names which still need to be parsed.
[WARN] [2019-06-19 10:51:29] I see 584 names which still need to be parsed.
[WARN] [2019-06-19 10:52:01] I see 481 names which still need to be parsed.
[WARN] [2019-06-19 10:52:34] I see 418 names which still need to be parsed.
[WARN] [2019-06-19 10:53:06] I see 355 names which still need to be parsed.
[WARN] [2019-06-19 10:53:38] I see 311 names which still need to be parsed.
[STOP] [2019-06-19 10:54:10] parse_names
[START] [2019-06-19 10:54:10] denormalize_canonical_names_to_nodes
[STOP] [2019-06-19 10:55:17] denormalize_canonical_names_to_nodes
[START] [2019-06-19 10:55:17] match_nodes
[START] [2019-06-19 10:55:17] map_all_nodes_to_pages
[STOP] [2019-06-19 20:31:32] map_all_nodes_to_pages
[INFO] [2019-06-19 20:31:33] 285331 Unmatched nodes (of 2328980)! That's too many to output. First 10: Terrabacteria (#41089453); Candidatus (#41089455); Candidatus (#41089484); Candidatus (#41089485); Candidatus (#41089486); Candidatus (#41089487); Candidatus (#41089488); Candidatus (#41089489); Candidatus (#41089490); Candidatus (#41089491)
[START] [2019-06-19 20:31:33] update_nodes
[STOP] [2019-06-19 20:42:10] update_nodes
[STOP] [2019-06-19 20:42:10] match_nodes
[START] [2019-06-21 10:18:11] map_all_nodes_to_pages
[START] [2019-07-19 13:02:33] logged process
[START] [2019-07-19 13:02:33] overall_tsv_creation
[INFO] [2019-07-19 13:02:38] Processing group of 2328980 in 233 batches of 10000
[START] [2019-07-19 13:03:43] logged process
[START] [2019-07-19 13:03:43] overall_tsv_creation
[INFO] [2019-07-19 13:03:47] Processing group of 2328980 in 233 batches of 10000
[INFO] [2019-07-20 00:25:54] Average Time: 122.746
[INFO] [2019-07-20 00:25:54] Total Time: 11h22m7s
[INFO] [2019-07-20 00:25:54] last 3 / first 3: 1.57
[INFO] [2019-07-20 00:25:54] Std.Dev: 26.516881415430436; Max: 238.6
[STOP] [2019-07-20 00:25:54] overall_tsv_creation
[INFO] [2019-07-20 00:25:54] Done. Check your files:
[INFO] [2019-07-20 00:25:57] (2328980 lines) /app/public/data/dvdtg/publish_nodes.tsv
[INFO] [2019-07-20 00:25:59] (2347642 lines) /app/public/data/dvdtg/publish_identifiers.tsv
[INFO] [2019-07-20 00:26:20] (44297750 lines) /app/public/data/dvdtg/publish_node_ancestors.tsv
[INFO] [2019-07-20 00:26:42] (8022132 lines) /app/public/data/dvdtg/publish_scientific_names.tsv
[START] [2020-02-10 16:15:02] logged process
[START] [2020-02-10 16:15:02] overall_tsv_creation
[INFO] [2020-02-10 16:15:07] Processing group of 2328980 in 233 batches of 10000
[2020-02-10 16:32:25] Encountered new taxonomic status, please assign set its alternative/preferred/problematic/mergeable: not accepted
[INFO] [2020-02-11 02:47:37] Average Time: 111.158
[INFO] [2020-02-11 02:47:37] Total Time: 10h32m30s
[INFO] [2020-02-11 02:47:37] last 3 / first 3: 1.28
[INFO] [2020-02-11 02:47:37] Std.Dev: 25.453349484890982; Max: 232.06
[STOP] [2020-02-11 02:47:37] overall_tsv_creation
[INFO] [2020-02-11 02:47:37] Done. Check your files:
[INFO] [2020-02-11 02:47:37] (2328980 lines) /app/public/data/dvdtg/publish_nodes.tsv
[INFO] [2020-02-11 02:47:37] (2347642 lines) /app/public/data/dvdtg/publish_identifiers.tsv
[INFO] [2020-02-11 02:47:38] (44297750 lines) /app/public/data/dvdtg/publish_node_ancestors.tsv
[INFO] [2020-02-11 02:47:38] (8022132 lines) /app/public/data/dvdtg/publish_scientific_names.tsv

Latest Process