Harvest for Argentina Species List Created 31 Oct 17:53

Stage: completed
Fetched: 31 Oct 17:53
Validated: 31 Oct 17:53
Deltas Created 31 Oct 17:53
Units Normalized: 31 Oct 18:49
Ancestry Built: 31 Oct 18:00
Nodes Matched: 31 Oct 18:48
Names Parsed: 31 Oct 18:01
New Models Stored: 31 Oct 17:57
Indexed: 31 Oct 18:49
Completed: 31 Oct 18:59
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-31 17:53:18 -0400 by logger.rb/56815
[START] [2019-10-31 17:53:18] logged process
[START] [2019-10-31 17:53:18] create_harvest_instance
[STOP] [2019-10-31 17:53:19] create_harvest_instance
[START] [2019-10-31 17:53:19] fetch_files
[STOP] [2019-10-31 17:53:19] fetch_files
[START] [2019-10-31 17:53:19] validate_each_file
[STOP] [2019-10-31 17:53:24] validate_each_file
[START] [2019-10-31 17:53:24] convert_to_csv
[CMD] [2019-10-31 17:53:24] /usr/bin/sort /app/public/converted_csv/argentina_sp_lis_refs_17960.csv > /app/public/converted_csv/argentina_sp_lis_refs_17960.csv_sorted
[CMD] [2019-10-31 17:53:24] /usr/bin/sort /app/public/converted_csv/argentina_sp_lis_nodes_17961.csv > /app/public/converted_csv/argentina_sp_lis_nodes_17961.csv_sorted
[CMD] [2019-10-31 17:53:25] /usr/bin/sort /app/public/converted_csv/argentina_sp_lis_occurrences_17962.csv > /app/public/converted_csv/argentina_sp_lis_occurrences_17962.csv_sorted
[CMD] [2019-10-31 17:53:25] /usr/bin/sort /app/public/converted_csv/argentina_sp_lis_measurements_17963.csv > /app/public/converted_csv/argentina_sp_lis_measurements_17963.csv_sorted
[STOP] [2019-10-31 17:53:25] convert_to_csv
[START] [2019-10-31 17:53:25] calculate_delta
[CMD] [2019-10-31 17:53:25] echo "0a" > /app/public/diff/argentina_sp_lis_refs_17960.diff
[CMD] [2019-10-31 17:53:25] tail -n +1 /app/public/converted_csv/argentina_sp_lis_refs_17960.csv >> /app/public/diff/argentina_sp_lis_refs_17960.diff
[CMD] [2019-10-31 17:53:26] echo "." >> /app/public/diff/argentina_sp_lis_refs_17960.diff
[CMD] [2019-10-31 17:53:26] echo "0a" > /app/public/diff/argentina_sp_lis_nodes_17961.diff
[CMD] [2019-10-31 17:53:26] tail -n +1 /app/public/converted_csv/argentina_sp_lis_nodes_17961.csv >> /app/public/diff/argentina_sp_lis_nodes_17961.diff
[CMD] [2019-10-31 17:53:26] echo "." >> /app/public/diff/argentina_sp_lis_nodes_17961.diff
[CMD] [2019-10-31 17:53:26] echo "0a" > /app/public/diff/argentina_sp_lis_occurrences_17962.diff
[CMD] [2019-10-31 17:53:27] tail -n +1 /app/public/converted_csv/argentina_sp_lis_occurrences_17962.csv >> /app/public/diff/argentina_sp_lis_occurrences_17962.diff
[CMD] [2019-10-31 17:53:27] echo "." >> /app/public/diff/argentina_sp_lis_occurrences_17962.diff
[CMD] [2019-10-31 17:53:27] echo "0a" > /app/public/diff/argentina_sp_lis_measurements_17963.diff
[CMD] [2019-10-31 17:53:27] tail -n +1 /app/public/converted_csv/argentina_sp_lis_measurements_17963.csv >> /app/public/diff/argentina_sp_lis_measurements_17963.diff
[CMD] [2019-10-31 17:53:27] echo "." >> /app/public/diff/argentina_sp_lis_measurements_17963.diff
[STOP] [2019-10-31 17:53:28] calculate_delta
[START] [2019-10-31 17:53:28] parse_diff_and_store
[INFO] [2019-10-31 17:53:28] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-31 17:53:28] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-31 17:53:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-31 17:53:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-31 17:56:06] Storing 2 References
[INFO] [2019-10-31 17:56:06] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-31 17:56:06] Average Time: 0.0
[INFO] [2019-10-31 17:56:06] Total Time: 1s
[INFO] [2019-10-31 17:56:06] Storing 35948 ScientificNames
[INFO] [2019-10-31 17:56:06] Processing group of 35948 in 36 groups of 1000
[INFO] [2019-10-31 17:56:19] Average Time: 0.377
[INFO] [2019-10-31 17:56:19] Total Time: 14s
[INFO] [2019-10-31 17:56:19] last 3 / first 3: 0.91
[INFO] [2019-10-31 17:56:19] Std.Dev: 0.11401754250991379; Max: 0.84
[INFO] [2019-10-31 17:56:19] Storing 35948 Nodes
[INFO] [2019-10-31 17:56:19] Processing group of 35948 in 36 groups of 1000
[INFO] [2019-10-31 17:56:31] Average Time: 0.328
[INFO] [2019-10-31 17:56:31] Total Time: 12s
[INFO] [2019-10-31 17:56:31] last 3 / first 3: 2.33
[INFO] [2019-10-31 17:56:31] Std.Dev: 0.16431676725154984; Max: 1.21
[INFO] [2019-10-31 17:56:31] Storing 25064 Occurrences
[INFO] [2019-10-31 17:56:31] Processing group of 25064 in 26 groups of 1000
[INFO] [2019-10-31 17:56:34] Average Time: 0.097
[INFO] [2019-10-31 17:56:34] Total Time: 3s
[INFO] [2019-10-31 17:56:34] last 3 / first 3: 1.0
[INFO] [2019-10-31 17:56:34] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-10-31 17:56:34] Storing 50952 TraitsReferences
[INFO] [2019-10-31 17:56:34] Processing group of 50952 in 51 groups of 1000
[INFO] [2019-10-31 17:56:38] Average Time: 0.066
[INFO] [2019-10-31 17:56:38] Total Time: 4s
[INFO] [2019-10-31 17:56:38] last 3 / first 3: 0.67
[INFO] [2019-10-31 17:56:38] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-31 17:56:38] Storing 50951 Traits
[INFO] [2019-10-31 17:56:38] Processing group of 50951 in 51 groups of 1000
[INFO] [2019-10-31 17:56:55] Average Time: 0.343
[INFO] [2019-10-31 17:56:55] Total Time: 18s
[INFO] [2019-10-31 17:56:55] last 3 / first 3: 0.92
[INFO] [2019-10-31 17:56:55] Std.Dev: 0.18973665961010275; Max: 1.61
[INFO] [2019-10-31 17:56:55] Storing 50916 MetaTraits
[INFO] [2019-10-31 17:56:55] Processing group of 50916 in 51 groups of 1000
[INFO] [2019-10-31 17:57:04] Average Time: 0.166
[INFO] [2019-10-31 17:57:04] Total Time: 9s
[INFO] [2019-10-31 17:57:04] last 3 / first 3: 0.74
[INFO] [2019-10-31 17:57:04] Std.Dev: 0.25099800796022265; Max: 1.92
[STOP] [2019-10-31 17:57:04] parse_diff_and_store
[START] [2019-10-31 17:57:04] resolve_keys
[INFO] [2019-10-31 17:58:49] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-31 17:58:58] traits to occurrences...
[INFO] [2019-10-31 17:59:08] traits to nodes (through occurrences)...
[INFO] [2019-10-31 17:59:09] Traits to sex term...
[INFO] [2019-10-31 17:59:18] Traits to lifestage term...
[INFO] [2019-10-31 17:59:27] MetaTraits to traits...
[INFO] [2019-10-31 17:59:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-31 17:59:37] Assocs to occurrences...
[INFO] [2019-10-31 17:59:37] Assocs to nodes...
[INFO] [2019-10-31 17:59:37] Assoc to sex term...
[INFO] [2019-10-31 17:59:37] Assoc to lifestage term...
[STOP] [2019-10-31 17:59:37] resolve_keys
[START] [2019-10-31 17:59:37] hold_for_later_1
[STOP] [2019-10-31 17:59:37] hold_for_later_1
[START] [2019-10-31 17:59:37] hold_for_later_2
[STOP] [2019-10-31 17:59:37] hold_for_later_2
[START] [2019-10-31 17:59:37] resolve_missing_parents
[STOP] [2019-10-31 18:00:35] resolve_missing_parents
[START] [2019-10-31 18:00:35] rebuild_nodes
[START] [2019-10-31 18:00:35] Flattener#flatten
[START] [2019-10-31 18:00:35] Flattener#study_resource
[START] [2019-10-31 18:00:36] Flattener#build_ancestry
[STOP] [2019-10-31 18:00:40] Flattener#build_ancestry
[INFO] [2019-10-31 18:00:40] 35948 ancestry keys
[START] [2019-10-31 18:00:40] build_node_ancestors
[INFO] [2019-10-31 18:00:40] old ancestors deleted.
[STOP] [2019-10-31 18:00:47] build_node_ancestors
[START] [2019-10-31 18:00:53] Flattener#propagate_ancestor_ids
[STOP] [2019-10-31 18:00:55] Flattener#propagate_ancestor_ids
[STOP] [2019-10-31 18:00:55] Flattener#flatten
[STOP] [2019-10-31 18:00:55] rebuild_nodes
[START] [2019-10-31 18:00:55] resolve_missing_media_owners
[STOP] [2019-10-31 18:00:55] resolve_missing_media_owners
[START] [2019-10-31 18:00:55] sanitize_media_verbatims
[STOP] [2019-10-31 18:00:55] sanitize_media_verbatims
[START] [2019-10-31 18:00:55] queue_downloads
[STOP] [2019-10-31 18:00:55] queue_downloads
[START] [2019-10-31 18:00:55] parse_names
[WARN] [2019-10-31 18:00:55] I see 35948 names which still need to be parsed.
[STOP] [2019-10-31 18:01:22] parse_names
[START] [2019-10-31 18:01:22] denormalize_canonical_names_to_nodes
[STOP] [2019-10-31 18:01:23] denormalize_canonical_names_to_nodes
[START] [2019-10-31 18:01:23] match_nodes
[START] [2019-10-31 18:01:23] map_all_nodes_to_pages
[STOP] [2019-10-31 18:48:17] map_all_nodes_to_pages
[INFO] [2019-10-31 18:48:17] 3272 Unmatched nodes (of 35948)! That's too many to output. First 10: Caenohalictus flammeus (#53991119); Bombus tucumana (#53989002); Paratrigona glabella (#53984505); Linepithema micans (#53981105); Linepithema gallardoi (#53981858); Linepithema cerradense (#53992207); Linepithema pulex (#53995059); Pheidole gigaflavens (#53996304); Pogonomyrmex mendozanus (#53992877); Camponotus rosariensis (#53999383)
[START] [2019-10-31 18:48:17] update_nodes
[STOP] [2019-10-31 18:48:29] update_nodes
[STOP] [2019-10-31 18:48:29] match_nodes
[START] [2019-10-31 18:48:29] reindex_search
[STOP] [2019-10-31 18:49:37] reindex_search
[START] [2019-10-31 18:49:37] normalize_units
[STOP] [2019-10-31 18:49:37] normalize_units
[START] [2019-10-31 18:49:37] calculate_statistics
[STOP] [2019-10-31 18:49:38] calculate_statistics
[START] [2019-10-31 18:49:38] complete_harvest_instance
[START] [2019-10-31 18:49:38] overall_tsv_creation
[INFO] [2019-10-31 18:49:38] Processing group of 35948 in 4 batches of 10000
[INFO] [2019-10-31 18:51:06] 6506 Traits (unfiltered)...
[INFO] [2019-10-31 18:51:19] 6506 Traits (filtered)...
[INFO] [2019-10-31 18:51:19] 0 Associations (filtered)...
[INFO] [2019-10-31 18:52:10] 32525 metadata added.
[INFO] [2019-10-31 18:52:10] 0 metadata added.
[INFO] [2019-10-31 18:53:38] 7246 Traits (unfiltered)...
[INFO] [2019-10-31 18:53:52] 7246 Traits (filtered)...
[INFO] [2019-10-31 18:53:52] 0 Associations (filtered)...
[INFO] [2019-10-31 18:54:44] 36222 metadata added.
[INFO] [2019-10-31 18:54:44] 0 metadata added.
[INFO] [2019-10-31 18:56:15] 7157 Traits (unfiltered)...
[INFO] [2019-10-31 18:56:28] 7157 Traits (filtered)...
[INFO] [2019-10-31 18:56:28] 0 Associations (filtered)...
[INFO] [2019-10-31 18:57:23] 35774 metadata added.
[INFO] [2019-10-31 18:57:23] 0 metadata added.
[INFO] [2019-10-31 18:58:35] 4155 Traits (unfiltered)...
[INFO] [2019-10-31 18:58:49] 4155 Traits (filtered)...
[INFO] [2019-10-31 18:58:49] 0 Associations (filtered)...
[INFO] [2019-10-31 18:59:33] 20764 metadata added.
[INFO] [2019-10-31 18:59:33] 0 metadata added.
[INFO] [2019-10-31 18:59:33] Average Time: 121.743
[INFO] [2019-10-31 18:59:33] Total Time: 9m56s
[STOP] [2019-10-31 18:59:33] overall_tsv_creation
[INFO] [2019-10-31 18:59:33] Done. Check your files:
[INFO] [2019-10-31 18:59:33] (35948 lines) /app/public/data/argentina_sp_lis/publish_nodes.tsv
[INFO] [2019-10-31 18:59:34] (92227 lines) /app/public/data/argentina_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-31 18:59:34] (35948 lines) /app/public/data/argentina_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-31 18:59:34] (25065 lines) /app/public/data/argentina_sp_lis/publish_traits.tsv
[INFO] [2019-10-31 18:59:34] (125286 lines) /app/public/data/argentina_sp_lis/publish_metadata.tsv
[STOP] [2019-10-31 18:59:34] complete_harvest_instance
[START] [2019-10-31 18:59:34] completed
[STOP] [2019-10-31 18:59:34] completed
[STOP] [2019-10-31 18:59:34] logged process, took 3976.01

Latest Process