Harvest for Bolivia Species List Created 11 Oct 15:50

Stage: completed
Fetched: 11 Oct 15:50
Validated: 11 Oct 15:50
Deltas Created 11 Oct 15:50
Units Normalized: 11 Oct 16:16
Ancestry Built: 11 Oct 15:59
Nodes Matched: 11 Oct 16:15
Names Parsed: 11 Oct 16:00
New Models Stored: 11 Oct 15:55
Indexed: 11 Oct 16:16
Completed: 11 Oct 16:27
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-11 15:50:53 -0400 by logger.rb/56815
[START] [2019-10-11 15:50:53] logged process
[START] [2019-10-11 15:50:53] create_harvest_instance
[STOP] [2019-10-11 15:50:54] create_harvest_instance
[START] [2019-10-11 15:50:54] fetch_files
[STOP] [2019-10-11 15:50:54] fetch_files
[START] [2019-10-11 15:50:54] validate_each_file
[STOP] [2019-10-11 15:50:59] validate_each_file
[START] [2019-10-11 15:50:59] convert_to_csv
[CMD] [2019-10-11 15:50:59] /usr/bin/sort /app/public/converted_csv/bolivia_sp_list_refs_15212.csv > /app/public/converted_csv/bolivia_sp_list_refs_15212.csv_sorted
[CMD] [2019-10-11 15:50:59] /usr/bin/sort /app/public/converted_csv/bolivia_sp_list_nodes_15213.csv > /app/public/converted_csv/bolivia_sp_list_nodes_15213.csv_sorted
[CMD] [2019-10-11 15:50:59] /usr/bin/sort /app/public/converted_csv/bolivia_sp_list_occurrences_15214.csv > /app/public/converted_csv/bolivia_sp_list_occurrences_15214.csv_sorted
[CMD] [2019-10-11 15:50:59] /usr/bin/sort /app/public/converted_csv/bolivia_sp_list_measurements_15215.csv > /app/public/converted_csv/bolivia_sp_list_measurements_15215.csv_sorted
[STOP] [2019-10-11 15:50:59] convert_to_csv
[START] [2019-10-11 15:50:59] calculate_delta
[CMD] [2019-10-11 15:50:59] echo "0a" > /app/public/diff/bolivia_sp_list_refs_15212.diff
[CMD] [2019-10-11 15:50:59] tail -n +1 /app/public/converted_csv/bolivia_sp_list_refs_15212.csv >> /app/public/diff/bolivia_sp_list_refs_15212.diff
[CMD] [2019-10-11 15:50:59] echo "." >> /app/public/diff/bolivia_sp_list_refs_15212.diff
[CMD] [2019-10-11 15:50:59] echo "0a" > /app/public/diff/bolivia_sp_list_nodes_15213.diff
[CMD] [2019-10-11 15:50:59] tail -n +1 /app/public/converted_csv/bolivia_sp_list_nodes_15213.csv >> /app/public/diff/bolivia_sp_list_nodes_15213.diff
[CMD] [2019-10-11 15:50:59] echo "." >> /app/public/diff/bolivia_sp_list_nodes_15213.diff
[CMD] [2019-10-11 15:50:59] echo "0a" > /app/public/diff/bolivia_sp_list_occurrences_15214.diff
[CMD] [2019-10-11 15:50:59] tail -n +1 /app/public/converted_csv/bolivia_sp_list_occurrences_15214.csv >> /app/public/diff/bolivia_sp_list_occurrences_15214.diff
[CMD] [2019-10-11 15:50:59] echo "." >> /app/public/diff/bolivia_sp_list_occurrences_15214.diff
[CMD] [2019-10-11 15:50:59] echo "0a" > /app/public/diff/bolivia_sp_list_measurements_15215.diff
[CMD] [2019-10-11 15:50:59] tail -n +1 /app/public/converted_csv/bolivia_sp_list_measurements_15215.csv >> /app/public/diff/bolivia_sp_list_measurements_15215.diff
[CMD] [2019-10-11 15:50:59] echo "." >> /app/public/diff/bolivia_sp_list_measurements_15215.diff
[STOP] [2019-10-11 15:50:59] calculate_delta
[START] [2019-10-11 15:50:59] parse_diff_and_store
[INFO] [2019-10-11 15:50:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 15:50:59] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 15:51:13] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 15:51:18] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 15:54:10] Storing 2 References
[INFO] [2019-10-11 15:54:10] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 15:54:10] Average Time: 0.0
[INFO] [2019-10-11 15:54:10] Total Time: 1s
[INFO] [2019-10-11 15:54:10] Storing 36368 ScientificNames
[INFO] [2019-10-11 15:54:10] Processing group of 36368 in 37 groups of 1000
[INFO] [2019-10-11 15:54:25] Average Time: 0.399
[INFO] [2019-10-11 15:54:25] Total Time: 15s
[INFO] [2019-10-11 15:54:25] last 3 / first 3: 0.73
[INFO] [2019-10-11 15:54:25] Std.Dev: 0.1224744871391589; Max: 0.84
[INFO] [2019-10-11 15:54:25] Storing 36368 Nodes
[INFO] [2019-10-11 15:54:25] Processing group of 36368 in 37 groups of 1000
[INFO] [2019-10-11 15:54:37] Average Time: 0.305
[INFO] [2019-10-11 15:54:37] Total Time: 12s
[INFO] [2019-10-11 15:54:37] last 3 / first 3: 0.75
[INFO] [2019-10-11 15:54:37] Std.Dev: 0.044721359549995794; Max: 0.42
[INFO] [2019-10-11 15:54:37] Storing 28920 Occurrences
[INFO] [2019-10-11 15:54:37] Processing group of 28920 in 29 groups of 1000
[INFO] [2019-10-11 15:54:40] Average Time: 0.109
[INFO] [2019-10-11 15:54:40] Total Time: 4s
[INFO] [2019-10-11 15:54:40] last 3 / first 3: 1.07
[INFO] [2019-10-11 15:54:40] Std.Dev: 0.0; Max: 0.19
[INFO] [2019-10-11 15:54:40] Storing 58430 TraitsReferences
[INFO] [2019-10-11 15:54:40] Processing group of 58430 in 59 groups of 1000
[INFO] [2019-10-11 15:54:46] Average Time: 0.103
[INFO] [2019-10-11 15:54:46] Total Time: 7s
[INFO] [2019-10-11 15:54:46] last 3 / first 3: 0.57
[INFO] [2019-10-11 15:54:46] Std.Dev: 0.12649110640673517; Max: 1.05
[INFO] [2019-10-11 15:54:46] Storing 58429 Traits
[INFO] [2019-10-11 15:54:46] Processing group of 58429 in 59 groups of 1000
[INFO] [2019-10-11 15:55:10] Average Time: 0.392
[INFO] [2019-10-11 15:55:10] Total Time: 24s
[INFO] [2019-10-11 15:55:10] last 3 / first 3: 0.79
[INFO] [2019-10-11 15:55:10] Std.Dev: 0.3065941943351178; Max: 2.15
[INFO] [2019-10-11 15:55:10] Storing 58381 MetaTraits
[INFO] [2019-10-11 15:55:10] Processing group of 58381 in 59 groups of 1000
[INFO] [2019-10-11 15:55:22] Average Time: 0.207
[INFO] [2019-10-11 15:55:22] Total Time: 13s
[INFO] [2019-10-11 15:55:22] last 3 / first 3: 0.73
[INFO] [2019-10-11 15:55:22] Std.Dev: 0.3301514803843836; Max: 2.0
[STOP] [2019-10-11 15:55:22] parse_diff_and_store
[START] [2019-10-11 15:55:22] resolve_keys
[INFO] [2019-10-11 15:57:24] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 15:57:32] traits to occurrences...
[INFO] [2019-10-11 15:57:43] traits to nodes (through occurrences)...
[INFO] [2019-10-11 15:57:44] Traits to sex term...
[INFO] [2019-10-11 15:57:52] Traits to lifestage term...
[INFO] [2019-10-11 15:58:00] MetaTraits to traits...
[INFO] [2019-10-11 15:58:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 15:58:12] Assocs to occurrences...
[INFO] [2019-10-11 15:58:12] Assocs to nodes...
[INFO] [2019-10-11 15:58:12] Assoc to sex term...
[INFO] [2019-10-11 15:58:12] Assoc to lifestage term...
[STOP] [2019-10-11 15:58:12] resolve_keys
[START] [2019-10-11 15:58:12] hold_for_later_1
[STOP] [2019-10-11 15:58:12] hold_for_later_1
[START] [2019-10-11 15:58:12] hold_for_later_2
[STOP] [2019-10-11 15:58:12] hold_for_later_2
[START] [2019-10-11 15:58:12] resolve_missing_parents
[STOP] [2019-10-11 15:59:16] resolve_missing_parents
[START] [2019-10-11 15:59:16] rebuild_nodes
[START] [2019-10-11 15:59:16] Flattener#flatten
[START] [2019-10-11 15:59:16] Flattener#study_resource
[START] [2019-10-11 15:59:17] Flattener#build_ancestry
[STOP] [2019-10-11 15:59:23] Flattener#build_ancestry
[INFO] [2019-10-11 15:59:23] 36368 ancestry keys
[START] [2019-10-11 15:59:23] build_node_ancestors
[INFO] [2019-10-11 15:59:23] old ancestors deleted.
[STOP] [2019-10-11 15:59:40] build_node_ancestors
[START] [2019-10-11 15:59:40] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 15:59:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 15:59:42] Flattener#flatten
[STOP] [2019-10-11 15:59:42] rebuild_nodes
[START] [2019-10-11 15:59:42] resolve_missing_media_owners
[STOP] [2019-10-11 15:59:42] resolve_missing_media_owners
[START] [2019-10-11 15:59:42] sanitize_media_verbatims
[STOP] [2019-10-11 15:59:42] sanitize_media_verbatims
[START] [2019-10-11 15:59:42] queue_downloads
[STOP] [2019-10-11 15:59:42] queue_downloads
[START] [2019-10-11 15:59:42] parse_names
[WARN] [2019-10-11 15:59:42] I see 36368 names which still need to be parsed.
[STOP] [2019-10-11 16:00:10] parse_names
[START] [2019-10-11 16:00:10] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 16:00:10] denormalize_canonical_names_to_nodes
[START] [2019-10-11 16:00:10] match_nodes
[START] [2019-10-11 16:00:10] map_all_nodes_to_pages
[STOP] [2019-10-11 16:15:27] map_all_nodes_to_pages
[INFO] [2019-10-11 16:15:27] 2708 Unmatched nodes (of 36368)! That's too many to output. First 10: Geonoma acaulis (#48816875); Geonoma orbigniana (#48825528); Desmoncus longifolius (#48825946); Desmoncus macroacantha (#48830049); Calomys fecundus (#48814925); Neotoma lepidus (#48796448); Hylaeamys capito (#48803839); Agouti (#48808392); Myocastoridae (#48807481); Hydrochaeridae (#48816798)
[START] [2019-10-11 16:15:27] update_nodes
[STOP] [2019-10-11 16:15:40] update_nodes
[STOP] [2019-10-11 16:15:40] match_nodes
[START] [2019-10-11 16:15:40] reindex_search
[STOP] [2019-10-11 16:16:39] reindex_search
[START] [2019-10-11 16:16:39] normalize_units
[STOP] [2019-10-11 16:16:39] normalize_units
[START] [2019-10-11 16:16:39] calculate_statistics
[STOP] [2019-10-11 16:16:39] calculate_statistics
[START] [2019-10-11 16:16:39] complete_harvest_instance
[START] [2019-10-11 16:16:39] overall_tsv_creation
[INFO] [2019-10-11 16:16:39] Processing group of 36368 in 4 batches of 10000
[INFO] [2019-10-11 16:18:11] 6716 Traits (unfiltered)...
[INFO] [2019-10-11 16:18:25] 6716 Traits (filtered)...
[INFO] [2019-10-11 16:18:25] 0 Associations (filtered)...
[INFO] [2019-10-11 16:19:16] 33577 metadata added.
[INFO] [2019-10-11 16:19:16] 0 metadata added.
[INFO] [2019-10-11 16:20:49] 8280 Traits (unfiltered)...
[INFO] [2019-10-11 16:21:03] 8280 Traits (filtered)...
[INFO] [2019-10-11 16:21:03] 0 Associations (filtered)...
[INFO] [2019-10-11 16:22:02] 41396 metadata added.
[INFO] [2019-10-11 16:22:02] 0 metadata added.
[INFO] [2019-10-11 16:23:35] 8491 Traits (unfiltered)...
[INFO] [2019-10-11 16:23:49] 8491 Traits (filtered)...
[INFO] [2019-10-11 16:23:49] 0 Associations (filtered)...
[INFO] [2019-10-11 16:24:46] 42435 metadata added.
[INFO] [2019-10-11 16:24:46] 0 metadata added.
[INFO] [2019-10-11 16:26:02] 5433 Traits (unfiltered)...
[INFO] [2019-10-11 16:26:16] 5433 Traits (filtered)...
[INFO] [2019-10-11 16:26:16] 0 Associations (filtered)...
[INFO] [2019-10-11 16:27:06] 27145 metadata added.
[INFO] [2019-10-11 16:27:06] 0 metadata added.
[INFO] [2019-10-11 16:27:07] Average Time: 130.323
[INFO] [2019-10-11 16:27:07] Total Time: 10m28s
[STOP] [2019-10-11 16:27:07] overall_tsv_creation
[INFO] [2019-10-11 16:27:07] Done. Check your files:
[INFO] [2019-10-11 16:27:07] (36368 lines) /app/public/data/bolivia_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 16:27:07] (100055 lines) /app/public/data/bolivia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 16:27:07] (36368 lines) /app/public/data/bolivia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 16:27:07] (28921 lines) /app/public/data/bolivia_sp_list/publish_traits.tsv
[INFO] [2019-10-11 16:27:07] (144554 lines) /app/public/data/bolivia_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 16:27:07] complete_harvest_instance
[START] [2019-10-11 16:27:07] completed
[STOP] [2019-10-11 16:27:07] completed
[STOP] [2019-10-11 16:27:07] logged process, took 2173.8

Latest Process