Harvest for Dominican Republic Species List Created 12 Oct 14:33

Stage: completed
Fetched: 12 Oct 14:33
Validated: 12 Oct 14:33
Deltas Created 12 Oct 14:33
Units Normalized: 12 Oct 14:49
Ancestry Built: 12 Oct 14:36
Nodes Matched: 12 Oct 14:49
Names Parsed: 12 Oct 14:36
New Models Stored: 12 Oct 14:34
Indexed: 12 Oct 14:49
Completed: 12 Oct 14:53
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-12 14:33:49 -0400 by logger.rb/56815
[START] [2019-10-12 14:33:49] logged process
[START] [2019-10-12 14:33:49] create_harvest_instance
[STOP] [2019-10-12 14:33:50] create_harvest_instance
[START] [2019-10-12 14:33:50] fetch_files
[STOP] [2019-10-12 14:33:50] fetch_files
[START] [2019-10-12 14:33:50] validate_each_file
[STOP] [2019-10-12 14:33:51] validate_each_file
[START] [2019-10-12 14:33:51] convert_to_csv
[CMD] [2019-10-12 14:33:51] /usr/bin/sort /app/public/converted_csv/dominican_republ_refs_15611.csv > /app/public/converted_csv/dominican_republ_refs_15611.csv_sorted
[CMD] [2019-10-12 14:33:51] /usr/bin/sort /app/public/converted_csv/dominican_republ_nodes_15612.csv > /app/public/converted_csv/dominican_republ_nodes_15612.csv_sorted
[CMD] [2019-10-12 14:33:51] /usr/bin/sort /app/public/converted_csv/dominican_republ_occurrences_15613.csv > /app/public/converted_csv/dominican_republ_occurrences_15613.csv_sorted
[CMD] [2019-10-12 14:33:52] /usr/bin/sort /app/public/converted_csv/dominican_republ_measurements_15614.csv > /app/public/converted_csv/dominican_republ_measurements_15614.csv_sorted
[STOP] [2019-10-12 14:33:52] convert_to_csv
[START] [2019-10-12 14:33:52] calculate_delta
[CMD] [2019-10-12 14:33:52] echo "0a" > /app/public/diff/dominican_republ_refs_15611.diff
[CMD] [2019-10-12 14:33:52] tail -n +1 /app/public/converted_csv/dominican_republ_refs_15611.csv >> /app/public/diff/dominican_republ_refs_15611.diff
[CMD] [2019-10-12 14:33:52] echo "." >> /app/public/diff/dominican_republ_refs_15611.diff
[CMD] [2019-10-12 14:33:52] echo "0a" > /app/public/diff/dominican_republ_nodes_15612.diff
[CMD] [2019-10-12 14:33:52] tail -n +1 /app/public/converted_csv/dominican_republ_nodes_15612.csv >> /app/public/diff/dominican_republ_nodes_15612.diff
[CMD] [2019-10-12 14:33:52] echo "." >> /app/public/diff/dominican_republ_nodes_15612.diff
[CMD] [2019-10-12 14:33:52] echo "0a" > /app/public/diff/dominican_republ_occurrences_15613.diff
[CMD] [2019-10-12 14:33:52] tail -n +1 /app/public/converted_csv/dominican_republ_occurrences_15613.csv >> /app/public/diff/dominican_republ_occurrences_15613.diff
[CMD] [2019-10-12 14:33:52] echo "." >> /app/public/diff/dominican_republ_occurrences_15613.diff
[CMD] [2019-10-12 14:33:52] echo "0a" > /app/public/diff/dominican_republ_measurements_15614.diff
[CMD] [2019-10-12 14:33:53] tail -n +1 /app/public/converted_csv/dominican_republ_measurements_15614.csv >> /app/public/diff/dominican_republ_measurements_15614.diff
[CMD] [2019-10-12 14:33:53] echo "." >> /app/public/diff/dominican_republ_measurements_15614.diff
[STOP] [2019-10-12 14:33:53] calculate_delta
[START] [2019-10-12 14:33:53] parse_diff_and_store
[INFO] [2019-10-12 14:33:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 14:33:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 14:33:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 14:33:58] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 14:34:40] Storing 2 References
[INFO] [2019-10-12 14:34:40] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 14:34:40] Average Time: 0.0
[INFO] [2019-10-12 14:34:40] Total Time: 1s
[INFO] [2019-10-12 14:34:40] Storing 11273 ScientificNames
[INFO] [2019-10-12 14:34:40] Processing group of 11273 in 12 groups of 1000
[INFO] [2019-10-12 14:34:44] Average Time: 0.35
[INFO] [2019-10-12 14:34:44] Total Time: 5s
[INFO] [2019-10-12 14:34:44] last 3 / first 3: 0.74
[INFO] [2019-10-12 14:34:44] Std.Dev: 0.08366600265340755; Max: 0.43
[INFO] [2019-10-12 14:34:44] Storing 11273 Nodes
[INFO] [2019-10-12 14:34:44] Processing group of 11273 in 12 groups of 1000
[INFO] [2019-10-12 14:34:48] Average Time: 0.323
[INFO] [2019-10-12 14:34:48] Total Time: 4s
[INFO] [2019-10-12 14:34:48] last 3 / first 3: 0.9
[INFO] [2019-10-12 14:34:48] Std.Dev: 0.1; Max: 0.46
[INFO] [2019-10-12 14:34:48] Storing 7272 Occurrences
[INFO] [2019-10-12 14:34:48] Processing group of 7272 in 8 groups of 1000
[INFO] [2019-10-12 14:34:49] Average Time: 0.104
[INFO] [2019-10-12 14:34:49] Total Time: 1s
[INFO] [2019-10-12 14:34:49] last 3 / first 3: 0.7
[INFO] [2019-10-12 14:34:49] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-12 14:34:49] Storing 14544 TraitsReferences
[INFO] [2019-10-12 14:34:49] Processing group of 14544 in 15 groups of 1000
[INFO] [2019-10-12 14:34:50] Average Time: 0.071
[INFO] [2019-10-12 14:34:50] Total Time: 2s
[INFO] [2019-10-12 14:34:50] last 3 / first 3: 0.67
[INFO] [2019-10-12 14:34:50] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-12 14:34:50] Storing 14544 Traits
[INFO] [2019-10-12 14:34:50] Processing group of 14544 in 15 groups of 1000
[INFO] [2019-10-12 14:34:55] Average Time: 0.313
[INFO] [2019-10-12 14:34:55] Total Time: 5s
[INFO] [2019-10-12 14:34:55] last 3 / first 3: 0.74
[INFO] [2019-10-12 14:34:55] Std.Dev: 0.06324555320336758; Max: 0.49
[INFO] [2019-10-12 14:34:55] Storing 14531 MetaTraits
[INFO] [2019-10-12 14:34:55] Processing group of 14531 in 15 groups of 1000
[INFO] [2019-10-12 14:34:57] Average Time: 0.133
[INFO] [2019-10-12 14:34:57] Total Time: 3s
[INFO] [2019-10-12 14:34:57] last 3 / first 3: 0.88
[INFO] [2019-10-12 14:34:57] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-10-12 14:34:57] parse_diff_and_store
[START] [2019-10-12 14:34:57] resolve_keys
[INFO] [2019-10-12 14:35:43] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 14:35:47] traits to occurrences...
[INFO] [2019-10-12 14:35:52] traits to nodes (through occurrences)...
[INFO] [2019-10-12 14:35:52] Traits to sex term...
[INFO] [2019-10-12 14:35:57] Traits to lifestage term...
[INFO] [2019-10-12 14:36:01] MetaTraits to traits...
[INFO] [2019-10-12 14:36:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 14:36:04] Assocs to occurrences...
[INFO] [2019-10-12 14:36:04] Assocs to nodes...
[INFO] [2019-10-12 14:36:04] Assoc to sex term...
[INFO] [2019-10-12 14:36:04] Assoc to lifestage term...
[STOP] [2019-10-12 14:36:04] resolve_keys
[START] [2019-10-12 14:36:04] hold_for_later_1
[STOP] [2019-10-12 14:36:04] hold_for_later_1
[START] [2019-10-12 14:36:04] hold_for_later_2
[STOP] [2019-10-12 14:36:04] hold_for_later_2
[START] [2019-10-12 14:36:04] resolve_missing_parents
[STOP] [2019-10-12 14:36:26] resolve_missing_parents
[START] [2019-10-12 14:36:26] rebuild_nodes
[START] [2019-10-12 14:36:26] Flattener#flatten
[START] [2019-10-12 14:36:26] Flattener#study_resource
[START] [2019-10-12 14:36:26] Flattener#build_ancestry
[STOP] [2019-10-12 14:36:27] Flattener#build_ancestry
[INFO] [2019-10-12 14:36:27] 11273 ancestry keys
[START] [2019-10-12 14:36:27] build_node_ancestors
[INFO] [2019-10-12 14:36:27] old ancestors deleted.
[STOP] [2019-10-12 14:36:31] build_node_ancestors
[START] [2019-10-12 14:36:36] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 14:36:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 14:36:37] Flattener#flatten
[STOP] [2019-10-12 14:36:37] rebuild_nodes
[START] [2019-10-12 14:36:37] resolve_missing_media_owners
[STOP] [2019-10-12 14:36:37] resolve_missing_media_owners
[START] [2019-10-12 14:36:37] sanitize_media_verbatims
[STOP] [2019-10-12 14:36:37] sanitize_media_verbatims
[START] [2019-10-12 14:36:37] queue_downloads
[STOP] [2019-10-12 14:36:37] queue_downloads
[START] [2019-10-12 14:36:37] parse_names
[WARN] [2019-10-12 14:36:37] I see 11273 names which still need to be parsed.
[STOP] [2019-10-12 14:36:47] parse_names
[START] [2019-10-12 14:36:47] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 14:36:47] denormalize_canonical_names_to_nodes
[START] [2019-10-12 14:36:47] match_nodes
[START] [2019-10-12 14:36:47] map_all_nodes_to_pages
[STOP] [2019-10-12 14:49:09] map_all_nodes_to_pages
[INFO] [2019-10-12 14:49:09] 787 Unmatched nodes (of 11273)! That's too many to output. First 10: Ameiva chrysolaema (#49455518); Ameiva taeniura (#49455616); Ameiva lineolaia (#49457105); Celestus haetiana (#49455693); Antillophis (#49455631); Ialtris haetiana (#49456519); Coerebidae (#49455484); Seiurus aurocapillus (#49460404); Dendroica (#49456324); Dendroica tigrina (#49456323)
[START] [2019-10-12 14:49:09] update_nodes
[STOP] [2019-10-12 14:49:13] update_nodes
[STOP] [2019-10-12 14:49:13] match_nodes
[START] [2019-10-12 14:49:13] reindex_search
[STOP] [2019-10-12 14:49:40] reindex_search
[START] [2019-10-12 14:49:40] normalize_units
[STOP] [2019-10-12 14:49:40] normalize_units
[START] [2019-10-12 14:49:40] calculate_statistics
[STOP] [2019-10-12 14:49:40] calculate_statistics
[START] [2019-10-12 14:49:40] complete_harvest_instance
[START] [2019-10-12 14:49:40] overall_tsv_creation
[INFO] [2019-10-12 14:49:40] Processing group of 11273 in 2 batches of 10000
[INFO] [2019-10-12 14:51:11] 6304 Traits (unfiltered)...
[INFO] [2019-10-12 14:51:25] 6304 Traits (filtered)...
[INFO] [2019-10-12 14:51:25] 0 Associations (filtered)...
[INFO] [2019-10-12 14:52:16] 31511 metadata added.
[INFO] [2019-10-12 14:52:16] 0 metadata added.
[INFO] [2019-10-12 14:53:05] 968 Traits (unfiltered)...
[INFO] [2019-10-12 14:53:19] 968 Traits (filtered)...
[INFO] [2019-10-12 14:53:19] 0 Associations (filtered)...
[INFO] [2019-10-12 14:53:57] 4836 metadata added.
[INFO] [2019-10-12 14:53:57] 0 metadata added.
[INFO] [2019-10-12 14:53:57] Average Time: 103.845
[INFO] [2019-10-12 14:53:57] Total Time: 4m18s
[STOP] [2019-10-12 14:53:57] overall_tsv_creation
[INFO] [2019-10-12 14:53:57] Done. Check your files:
[INFO] [2019-10-12 14:53:57] (11273 lines) /app/public/data/dominican_republ/publish_nodes.tsv
[INFO] [2019-10-12 14:53:57] (61638 lines) /app/public/data/dominican_republ/publish_node_ancestors.tsv
[INFO] [2019-10-12 14:53:58] (11273 lines) /app/public/data/dominican_republ/publish_scientific_names.tsv
[INFO] [2019-10-12 14:53:58] (7273 lines) /app/public/data/dominican_republ/publish_traits.tsv
[INFO] [2019-10-12 14:53:58] (36348 lines) /app/public/data/dominican_republ/publish_metadata.tsv
[STOP] [2019-10-12 14:53:58] complete_harvest_instance
[START] [2019-10-12 14:53:58] completed
[STOP] [2019-10-12 14:53:58] completed
[STOP] [2019-10-12 14:53:58] logged process, took 1208.69
Latest Process

12 Oct 14:33 EXITED currently processing 0