Harvest for Paraguay Species List Created 15 Oct 08:16

Stage: completed
Fetched: 15 Oct 08:16
Validated: 15 Oct 08:16
Deltas Created 15 Oct 08:16
Units Normalized: 15 Oct 08:36
Ancestry Built: 15 Oct 08:20
Nodes Matched: 15 Oct 08:35
Names Parsed: 15 Oct 08:20
New Models Stored: 15 Oct 08:18
Indexed: 15 Oct 08:36
Completed: 15 Oct 08:41
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-15 08:16:40 -0400 by logger.rb/56815
[START] [2019-10-15 08:16:40] logged process
[START] [2019-10-15 08:16:40] create_harvest_instance
[STOP] [2019-10-15 08:16:41] create_harvest_instance
[START] [2019-10-15 08:16:41] fetch_files
[STOP] [2019-10-15 08:16:41] fetch_files
[START] [2019-10-15 08:16:41] validate_each_file
[STOP] [2019-10-15 08:16:43] validate_each_file
[START] [2019-10-15 08:16:43] convert_to_csv
[CMD] [2019-10-15 08:16:43] /usr/bin/sort /app/public/converted_csv/paraguay_sp_list_refs_16885.csv > /app/public/converted_csv/paraguay_sp_list_refs_16885.csv_sorted
[CMD] [2019-10-15 08:16:44] /usr/bin/sort /app/public/converted_csv/paraguay_sp_list_nodes_16886.csv > /app/public/converted_csv/paraguay_sp_list_nodes_16886.csv_sorted
[CMD] [2019-10-15 08:16:44] /usr/bin/sort /app/public/converted_csv/paraguay_sp_list_occurrences_16887.csv > /app/public/converted_csv/paraguay_sp_list_occurrences_16887.csv_sorted
[CMD] [2019-10-15 08:16:44] /usr/bin/sort /app/public/converted_csv/paraguay_sp_list_measurements_16888.csv > /app/public/converted_csv/paraguay_sp_list_measurements_16888.csv_sorted
[STOP] [2019-10-15 08:16:45] convert_to_csv
[START] [2019-10-15 08:16:45] calculate_delta
[CMD] [2019-10-15 08:16:45] echo "0a" > /app/public/diff/paraguay_sp_list_refs_16885.diff
[CMD] [2019-10-15 08:16:45] tail -n +1 /app/public/converted_csv/paraguay_sp_list_refs_16885.csv >> /app/public/diff/paraguay_sp_list_refs_16885.diff
[CMD] [2019-10-15 08:16:45] echo "." >> /app/public/diff/paraguay_sp_list_refs_16885.diff
[CMD] [2019-10-15 08:16:45] echo "0a" > /app/public/diff/paraguay_sp_list_nodes_16886.diff
[CMD] [2019-10-15 08:16:46] tail -n +1 /app/public/converted_csv/paraguay_sp_list_nodes_16886.csv >> /app/public/diff/paraguay_sp_list_nodes_16886.diff
[CMD] [2019-10-15 08:16:46] echo "." >> /app/public/diff/paraguay_sp_list_nodes_16886.diff
[CMD] [2019-10-15 08:16:46] echo "0a" > /app/public/diff/paraguay_sp_list_occurrences_16887.diff
[CMD] [2019-10-15 08:16:46] tail -n +1 /app/public/converted_csv/paraguay_sp_list_occurrences_16887.csv >> /app/public/diff/paraguay_sp_list_occurrences_16887.diff
[CMD] [2019-10-15 08:16:47] echo "." >> /app/public/diff/paraguay_sp_list_occurrences_16887.diff
[CMD] [2019-10-15 08:16:47] echo "0a" > /app/public/diff/paraguay_sp_list_measurements_16888.diff
[CMD] [2019-10-15 08:16:47] tail -n +1 /app/public/converted_csv/paraguay_sp_list_measurements_16888.csv >> /app/public/diff/paraguay_sp_list_measurements_16888.diff
[CMD] [2019-10-15 08:16:48] echo "." >> /app/public/diff/paraguay_sp_list_measurements_16888.diff
[STOP] [2019-10-15 08:16:48] calculate_delta
[START] [2019-10-15 08:16:48] parse_diff_and_store
[INFO] [2019-10-15 08:16:48] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 08:16:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 08:16:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 08:16:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 08:18:09] Storing 2 References
[INFO] [2019-10-15 08:18:09] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 08:18:09] Average Time: 0.0
[INFO] [2019-10-15 08:18:09] Total Time: 1s
[INFO] [2019-10-15 08:18:09] Storing 15970 ScientificNames
[INFO] [2019-10-15 08:18:09] Processing group of 15970 in 16 groups of 1000
[INFO] [2019-10-15 08:18:15] Average Time: 0.361
[INFO] [2019-10-15 08:18:15] Total Time: 6s
[INFO] [2019-10-15 08:18:15] last 3 / first 3: 0.88
[INFO] [2019-10-15 08:18:15] Std.Dev: 0.03162277660168379; Max: 0.44
[INFO] [2019-10-15 08:18:15] Storing 15970 Nodes
[INFO] [2019-10-15 08:18:15] Processing group of 15970 in 16 groups of 1000
[INFO] [2019-10-15 08:18:20] Average Time: 0.297
[INFO] [2019-10-15 08:18:20] Total Time: 5s
[INFO] [2019-10-15 08:18:20] last 3 / first 3: 0.97
[INFO] [2019-10-15 08:18:20] Std.Dev: 0.0; Max: 0.35
[INFO] [2019-10-15 08:18:20] Storing 11568 Occurrences
[INFO] [2019-10-15 08:18:20] Processing group of 11568 in 12 groups of 1000
[INFO] [2019-10-15 08:18:21] Average Time: 0.104
[INFO] [2019-10-15 08:18:21] Total Time: 2s
[INFO] [2019-10-15 08:18:21] last 3 / first 3: 1.0
[INFO] [2019-10-15 08:18:21] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-10-15 08:18:21] Storing 23600 TraitsReferences
[INFO] [2019-10-15 08:18:21] Processing group of 23600 in 24 groups of 1000
[INFO] [2019-10-15 08:18:23] Average Time: 0.073
[INFO] [2019-10-15 08:18:23] Total Time: 2s
[INFO] [2019-10-15 08:18:23] last 3 / first 3: 0.52
[INFO] [2019-10-15 08:18:23] Std.Dev: 0.0; Max: 0.16
[INFO] [2019-10-15 08:18:23] Storing 23599 Traits
[INFO] [2019-10-15 08:18:23] Processing group of 23599 in 24 groups of 1000
[INFO] [2019-10-15 08:18:32] Average Time: 0.363
[INFO] [2019-10-15 08:18:32] Total Time: 9s
[INFO] [2019-10-15 08:18:32] last 3 / first 3: 0.73
[INFO] [2019-10-15 08:18:32] Std.Dev: 0.22360679774997896; Max: 1.13
[INFO] [2019-10-15 08:18:32] Storing 23576 MetaTraits
[INFO] [2019-10-15 08:18:32] Processing group of 23576 in 24 groups of 1000
[INFO] [2019-10-15 08:18:34] Average Time: 0.105
[INFO] [2019-10-15 08:18:34] Total Time: 3s
[INFO] [2019-10-15 08:18:34] last 3 / first 3: 0.7
[INFO] [2019-10-15 08:18:34] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-15 08:18:34] parse_diff_and_store
[START] [2019-10-15 08:18:34] resolve_keys
[INFO] [2019-10-15 08:19:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 08:19:43] traits to occurrences...
[INFO] [2019-10-15 08:19:47] traits to nodes (through occurrences)...
[INFO] [2019-10-15 08:19:47] Traits to sex term...
[INFO] [2019-10-15 08:19:50] Traits to lifestage term...
[INFO] [2019-10-15 08:19:54] MetaTraits to traits...
[INFO] [2019-10-15 08:19:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 08:19:59] Assocs to occurrences...
[INFO] [2019-10-15 08:19:59] Assocs to nodes...
[INFO] [2019-10-15 08:19:59] Assoc to sex term...
[INFO] [2019-10-15 08:19:59] Assoc to lifestage term...
[STOP] [2019-10-15 08:19:59] resolve_keys
[START] [2019-10-15 08:19:59] hold_for_later_1
[STOP] [2019-10-15 08:19:59] hold_for_later_1
[START] [2019-10-15 08:19:59] hold_for_later_2
[STOP] [2019-10-15 08:19:59] hold_for_later_2
[START] [2019-10-15 08:19:59] resolve_missing_parents
[STOP] [2019-10-15 08:20:34] resolve_missing_parents
[START] [2019-10-15 08:20:34] rebuild_nodes
[START] [2019-10-15 08:20:34] Flattener#flatten
[START] [2019-10-15 08:20:34] Flattener#study_resource
[START] [2019-10-15 08:20:34] Flattener#build_ancestry
[STOP] [2019-10-15 08:20:36] Flattener#build_ancestry
[INFO] [2019-10-15 08:20:36] 15970 ancestry keys
[START] [2019-10-15 08:20:36] build_node_ancestors
[INFO] [2019-10-15 08:20:36] old ancestors deleted.
[STOP] [2019-10-15 08:20:39] build_node_ancestors
[START] [2019-10-15 08:20:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 08:20:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 08:20:43] Flattener#flatten
[STOP] [2019-10-15 08:20:43] rebuild_nodes
[START] [2019-10-15 08:20:43] resolve_missing_media_owners
[STOP] [2019-10-15 08:20:43] resolve_missing_media_owners
[START] [2019-10-15 08:20:43] sanitize_media_verbatims
[STOP] [2019-10-15 08:20:43] sanitize_media_verbatims
[START] [2019-10-15 08:20:43] queue_downloads
[STOP] [2019-10-15 08:20:43] queue_downloads
[START] [2019-10-15 08:20:43] parse_names
[WARN] [2019-10-15 08:20:43] I see 15970 names which still need to be parsed.
[STOP] [2019-10-15 08:20:56] parse_names
[START] [2019-10-15 08:20:56] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 08:20:56] denormalize_canonical_names_to_nodes
[START] [2019-10-15 08:20:56] match_nodes
[START] [2019-10-15 08:20:56] map_all_nodes_to_pages
[STOP] [2019-10-15 08:35:28] map_all_nodes_to_pages
[INFO] [2019-10-15 08:35:28] 1268 Unmatched nodes (of 15970)! That's too many to output. First 10: Machetornis rixosus (#51499374); Xolmis cinerea (#51501368); Xolmis coronata (#51505458); Xolmis velata (#51506099); Hymenops perspicillata (#51508759); Casiornis rufa (#51499403); Empidonomus aurantioatrocristatus (#51496616); Euscarthmus (#51496625); Euscarthmus meloryphus (#51496624); Conopias trivirgata (#51501708)
[START] [2019-10-15 08:35:28] update_nodes
[STOP] [2019-10-15 08:35:34] update_nodes
[STOP] [2019-10-15 08:35:34] match_nodes
[START] [2019-10-15 08:35:34] reindex_search
[STOP] [2019-10-15 08:36:13] reindex_search
[START] [2019-10-15 08:36:13] normalize_units
[STOP] [2019-10-15 08:36:13] normalize_units
[START] [2019-10-15 08:36:13] calculate_statistics
[STOP] [2019-10-15 08:36:13] calculate_statistics
[START] [2019-10-15 08:36:13] complete_harvest_instance
[START] [2019-10-15 08:36:13] overall_tsv_creation
[INFO] [2019-10-15 08:36:13] Processing group of 15970 in 2 batches of 10000
[INFO] [2019-10-15 08:37:41] 6997 Traits (unfiltered)...
[INFO] [2019-10-15 08:37:55] 6997 Traits (filtered)...
[INFO] [2019-10-15 08:37:55] 0 Associations (filtered)...
[INFO] [2019-10-15 08:38:47] 34979 metadata added.
[INFO] [2019-10-15 08:38:47] 0 metadata added.
[INFO] [2019-10-15 08:39:58] 4571 Traits (unfiltered)...
[INFO] [2019-10-15 08:40:12] 4571 Traits (filtered)...
[INFO] [2019-10-15 08:40:12] 0 Associations (filtered)...
[INFO] [2019-10-15 08:40:59] 22840 metadata added.
[INFO] [2019-10-15 08:40:59] 0 metadata added.
[INFO] [2019-10-15 08:40:59] Average Time: 117.445
[INFO] [2019-10-15 08:40:59] Total Time: 4m47s
[STOP] [2019-10-15 08:40:59] overall_tsv_creation
[INFO] [2019-10-15 08:40:59] Done. Check your files:
[INFO] [2019-10-15 08:40:59] (15970 lines) /app/public/data/paraguay_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 08:40:59] (42381 lines) /app/public/data/paraguay_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 08:41:00] (15970 lines) /app/public/data/paraguay_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 08:41:00] (11569 lines) /app/public/data/paraguay_sp_list/publish_traits.tsv
[INFO] [2019-10-15 08:41:00] (57820 lines) /app/public/data/paraguay_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 08:41:00] complete_harvest_instance
[START] [2019-10-15 08:41:00] completed
[STOP] [2019-10-15 08:41:00] completed
[STOP] [2019-10-15 08:41:00] logged process, took 1460.0
Latest Process

15 Oct 08:16 EXITED currently processing 0