Harvest for Suriname Species List Created 16 Oct 07:35

Stage: completed
Fetched: 16 Oct 07:35
Validated: 16 Oct 07:35
Deltas Created 16 Oct 07:35
Units Normalized: 16 Oct 07:46
Ancestry Built: 16 Oct 07:37
Nodes Matched: 16 Oct 07:46
Names Parsed: 16 Oct 07:37
New Models Stored: 16 Oct 07:36
Indexed: 16 Oct 07:46
Completed: 16 Oct 07:49
Time to Harvest: less than a minute

Harvesting Log

(151 lines)
# Logfile created on 2019-10-16 07:35:04 -0400 by logger.rb/56815
[START] [2019-10-16 07:35:04] logged process
[START] [2019-10-16 07:35:04] create_harvest_instance
[STOP] [2019-10-16 07:35:05] create_harvest_instance
[START] [2019-10-16 07:35:05] fetch_files
[STOP] [2019-10-16 07:35:05] fetch_files
[START] [2019-10-16 07:35:05] validate_each_file
[STOP] [2019-10-16 07:35:06] validate_each_file
[START] [2019-10-16 07:35:06] convert_to_csv
[CMD] [2019-10-16 07:35:06] /usr/bin/sort /app/public/converted_csv/suriname_sp_list_refs_17349.csv > /app/public/converted_csv/suriname_sp_list_refs_17349.csv_sorted
[CMD] [2019-10-16 07:35:07] /usr/bin/sort /app/public/converted_csv/suriname_sp_list_nodes_17350.csv > /app/public/converted_csv/suriname_sp_list_nodes_17350.csv_sorted
[CMD] [2019-10-16 07:35:07] /usr/bin/sort /app/public/converted_csv/suriname_sp_list_occurrences_17351.csv > /app/public/converted_csv/suriname_sp_list_occurrences_17351.csv_sorted
[CMD] [2019-10-16 07:35:07] /usr/bin/sort /app/public/converted_csv/suriname_sp_list_measurements_17352.csv > /app/public/converted_csv/suriname_sp_list_measurements_17352.csv_sorted
[STOP] [2019-10-16 07:35:08] convert_to_csv
[START] [2019-10-16 07:35:08] calculate_delta
[CMD] [2019-10-16 07:35:08] echo "0a" > /app/public/diff/suriname_sp_list_refs_17349.diff
[CMD] [2019-10-16 07:35:08] tail -n +1 /app/public/converted_csv/suriname_sp_list_refs_17349.csv >> /app/public/diff/suriname_sp_list_refs_17349.diff
[CMD] [2019-10-16 07:35:08] echo "." >> /app/public/diff/suriname_sp_list_refs_17349.diff
[CMD] [2019-10-16 07:35:08] echo "0a" > /app/public/diff/suriname_sp_list_nodes_17350.diff
[CMD] [2019-10-16 07:35:09] tail -n +1 /app/public/converted_csv/suriname_sp_list_nodes_17350.csv >> /app/public/diff/suriname_sp_list_nodes_17350.diff
[CMD] [2019-10-16 07:35:09] echo "." >> /app/public/diff/suriname_sp_list_nodes_17350.diff
[CMD] [2019-10-16 07:35:09] echo "0a" > /app/public/diff/suriname_sp_list_occurrences_17351.diff
[CMD] [2019-10-16 07:35:10] tail -n +1 /app/public/converted_csv/suriname_sp_list_occurrences_17351.csv >> /app/public/diff/suriname_sp_list_occurrences_17351.diff
[CMD] [2019-10-16 07:35:10] echo "." >> /app/public/diff/suriname_sp_list_occurrences_17351.diff
[CMD] [2019-10-16 07:35:10] echo "0a" > /app/public/diff/suriname_sp_list_measurements_17352.diff
[CMD] [2019-10-16 07:35:10] tail -n +1 /app/public/converted_csv/suriname_sp_list_measurements_17352.csv >> /app/public/diff/suriname_sp_list_measurements_17352.diff
[CMD] [2019-10-16 07:35:11] echo "." >> /app/public/diff/suriname_sp_list_measurements_17352.diff
[STOP] [2019-10-16 07:35:11] calculate_delta
[START] [2019-10-16 07:35:11] parse_diff_and_store
[INFO] [2019-10-16 07:35:11] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 07:35:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 07:35:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 07:35:17] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 07:35:54] Storing 2 References
[INFO] [2019-10-16 07:35:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 07:35:54] Average Time: 0.0
[INFO] [2019-10-16 07:35:54] Total Time: 1s
[INFO] [2019-10-16 07:35:54] Storing 9624 ScientificNames
[INFO] [2019-10-16 07:35:54] Processing group of 9624 in 10 groups of 1000
[INFO] [2019-10-16 07:35:58] Average Time: 0.36
[INFO] [2019-10-16 07:35:58] Total Time: 4s
[INFO] [2019-10-16 07:35:58] last 3 / first 3: 0.79
[INFO] [2019-10-16 07:35:58] Std.Dev: 0.06324555320336758; Max: 0.47
[INFO] [2019-10-16 07:35:58] Storing 9624 Nodes
[INFO] [2019-10-16 07:35:58] Processing group of 9624 in 10 groups of 1000
[INFO] [2019-10-16 07:36:01] Average Time: 0.34
[INFO] [2019-10-16 07:36:01] Total Time: 4s
[INFO] [2019-10-16 07:36:01] last 3 / first 3: 0.58
[INFO] [2019-10-16 07:36:01] Std.Dev: 0.1341640786499874; Max: 0.71
[INFO] [2019-10-16 07:36:01] Storing 6266 Occurrences
[INFO] [2019-10-16 07:36:01] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-16 07:36:02] Average Time: 0.093
[INFO] [2019-10-16 07:36:02] Total Time: 1s
[INFO] [2019-10-16 07:36:02] last 3 / first 3: 0.7
[INFO] [2019-10-16 07:36:02] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-16 07:36:02] Storing 12850 TraitsReferences
[INFO] [2019-10-16 07:36:02] Processing group of 12850 in 13 groups of 1000
[INFO] [2019-10-16 07:36:03] Average Time: 0.073
[INFO] [2019-10-16 07:36:03] Total Time: 2s
[INFO] [2019-10-16 07:36:03] last 3 / first 3: 0.68
[INFO] [2019-10-16 07:36:03] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-16 07:36:03] Storing 12849 Traits
[INFO] [2019-10-16 07:36:03] Processing group of 12849 in 13 groups of 1000
[INFO] [2019-10-16 07:36:07] Average Time: 0.3
[INFO] [2019-10-16 07:36:07] Total Time: 4s
[INFO] [2019-10-16 07:36:07] last 3 / first 3: 0.77
[INFO] [2019-10-16 07:36:07] Std.Dev: 0.05477225575051661; Max: 0.48
[INFO] [2019-10-16 07:36:07] Storing 12845 MetaTraits
[INFO] [2019-10-16 07:36:07] Processing group of 12845 in 13 groups of 1000
[INFO] [2019-10-16 07:36:09] Average Time: 0.115
[INFO] [2019-10-16 07:36:09] Total Time: 2s
[INFO] [2019-10-16 07:36:09] last 3 / first 3: 0.87
[INFO] [2019-10-16 07:36:09] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-10-16 07:36:09] parse_diff_and_store
[START] [2019-10-16 07:36:09] resolve_keys
[INFO] [2019-10-16 07:36:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 07:36:49] traits to occurrences...
[INFO] [2019-10-16 07:36:53] traits to nodes (through occurrences)...
[INFO] [2019-10-16 07:36:54] Traits to sex term...
[INFO] [2019-10-16 07:36:58] Traits to lifestage term...
[INFO] [2019-10-16 07:37:02] MetaTraits to traits...
[INFO] [2019-10-16 07:37:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 07:37:04] Assocs to occurrences...
[INFO] [2019-10-16 07:37:04] Assocs to nodes...
[INFO] [2019-10-16 07:37:04] Assoc to sex term...
[INFO] [2019-10-16 07:37:04] Assoc to lifestage term...
[STOP] [2019-10-16 07:37:04] resolve_keys
[START] [2019-10-16 07:37:04] hold_for_later_1
[STOP] [2019-10-16 07:37:04] hold_for_later_1
[START] [2019-10-16 07:37:04] hold_for_later_2
[STOP] [2019-10-16 07:37:04] hold_for_later_2
[START] [2019-10-16 07:37:04] resolve_missing_parents
[STOP] [2019-10-16 07:37:24] resolve_missing_parents
[START] [2019-10-16 07:37:24] rebuild_nodes
[START] [2019-10-16 07:37:24] Flattener#flatten
[START] [2019-10-16 07:37:24] Flattener#study_resource
[START] [2019-10-16 07:37:24] Flattener#build_ancestry
[STOP] [2019-10-16 07:37:25] Flattener#build_ancestry
[INFO] [2019-10-16 07:37:25] 9624 ancestry keys
[START] [2019-10-16 07:37:25] build_node_ancestors
[INFO] [2019-10-16 07:37:25] old ancestors deleted.
[STOP] [2019-10-16 07:37:27] build_node_ancestors
[START] [2019-10-16 07:37:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 07:37:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 07:37:29] Flattener#flatten
[STOP] [2019-10-16 07:37:29] rebuild_nodes
[START] [2019-10-16 07:37:29] resolve_missing_media_owners
[STOP] [2019-10-16 07:37:29] resolve_missing_media_owners
[START] [2019-10-16 07:37:29] sanitize_media_verbatims
[STOP] [2019-10-16 07:37:29] sanitize_media_verbatims
[START] [2019-10-16 07:37:29] queue_downloads
[STOP] [2019-10-16 07:37:29] queue_downloads
[START] [2019-10-16 07:37:29] parse_names
[WARN] [2019-10-16 07:37:29] I see 9624 names which still need to be parsed.
[STOP] [2019-10-16 07:37:37] parse_names
[START] [2019-10-16 07:37:37] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 07:37:37] denormalize_canonical_names_to_nodes
[START] [2019-10-16 07:37:37] match_nodes
[START] [2019-10-16 07:37:37] map_all_nodes_to_pages
[STOP] [2019-10-16 07:46:19] map_all_nodes_to_pages
[INFO] [2019-10-16 07:46:19] 530 Unmatched nodes (of 9624)! That's too many to output. First 10: Artibeus gnoma (#52219750); Lophostoma silvicola (#52211859); Dermanura cinereus (#52211009); Dermanura glaucus (#52211183); Dermanura gnomus (#52212155); Spanglerodessus (#52211004); Spanglerodessus shorti (#52211003); Canthydrus buqueti (#52210793); Canthydrus clayae (#52214414); Siolius (#52210661)
[START] [2019-10-16 07:46:19] update_nodes
[STOP] [2019-10-16 07:46:23] update_nodes
[STOP] [2019-10-16 07:46:23] match_nodes
[START] [2019-10-16 07:46:23] reindex_search
[STOP] [2019-10-16 07:46:46] reindex_search
[START] [2019-10-16 07:46:46] normalize_units
[STOP] [2019-10-16 07:46:46] normalize_units
[START] [2019-10-16 07:46:46] calculate_statistics
[STOP] [2019-10-16 07:46:46] calculate_statistics
[START] [2019-10-16 07:46:46] complete_harvest_instance
[START] [2019-10-16 07:46:46] overall_tsv_creation
[INFO] [2019-10-16 07:46:46] Processing group of 9624 in 1 batches of 10000
[INFO] [2019-10-16 07:48:12] 6266 Traits (unfiltered)...
[INFO] [2019-10-16 07:48:28] 6266 Traits (filtered)...
[INFO] [2019-10-16 07:48:28] 0 Associations (filtered)...
[INFO] [2019-10-16 07:49:20] 31325 metadata added.
[INFO] [2019-10-16 07:49:20] 0 metadata added.
[INFO] [2019-10-16 07:49:20] Average Time: 127.21
[INFO] [2019-10-16 07:49:20] Total Time: 2m35s
[STOP] [2019-10-16 07:49:20] overall_tsv_creation
[INFO] [2019-10-16 07:49:20] Done. Check your files:
[INFO] [2019-10-16 07:49:21] (9624 lines) /app/public/data/suriname_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 07:49:21] (24568 lines) /app/public/data/suriname_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 07:49:21] (9624 lines) /app/public/data/suriname_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 07:49:21] (6267 lines) /app/public/data/suriname_sp_list/publish_traits.tsv
[INFO] [2019-10-16 07:49:22] (31326 lines) /app/public/data/suriname_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 07:49:22] complete_harvest_instance
[START] [2019-10-16 07:49:22] completed
[STOP] [2019-10-16 07:49:22] completed
[STOP] [2019-10-16 07:49:22] logged process, took 857.8

Latest Process