Harvest for Alboran Sea Species List Created 22 Dec 17:32

Stage: completed
Fetched: 22 Dec 17:32
Validated: 22 Dec 17:32
Deltas Created 22 Dec 17:32
Units Normalized: 22 Dec 17:38
Ancestry Built: 22 Dec 17:32
Nodes Matched: 22 Dec 17:38
Names Parsed: 22 Dec 17:32
New Models Stored: 22 Dec 17:32
Indexed: 22 Dec 17:38
Completed: 22 Dec 17:40
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 17:32:05 -0500 by logger.rb/56815
[START] [2019-12-22 17:32:05] logged process
[START] [2019-12-22 17:32:05] create_harvest_instance
[STOP] [2019-12-22 17:32:06] create_harvest_instance
[START] [2019-12-22 17:32:06] fetch_files
[STOP] [2019-12-22 17:32:06] fetch_files
[START] [2019-12-22 17:32:06] validate_each_file
[STOP] [2019-12-22 17:32:06] validate_each_file
[START] [2019-12-22 17:32:06] convert_to_csv
[CMD] [2019-12-22 17:32:06] /usr/bin/sort /app/public/converted_csv/alboran_sea_sp_l_refs_18994.csv > /app/public/converted_csv/alboran_sea_sp_l_refs_18994.csv_sorted
[CMD] [2019-12-22 17:32:06] /usr/bin/sort /app/public/converted_csv/alboran_sea_sp_l_nodes_18995.csv > /app/public/converted_csv/alboran_sea_sp_l_nodes_18995.csv_sorted
[CMD] [2019-12-22 17:32:06] /usr/bin/sort /app/public/converted_csv/alboran_sea_sp_l_occurrences_18996.csv > /app/public/converted_csv/alboran_sea_sp_l_occurrences_18996.csv_sorted
[CMD] [2019-12-22 17:32:06] /usr/bin/sort /app/public/converted_csv/alboran_sea_sp_l_measurements_18997.csv > /app/public/converted_csv/alboran_sea_sp_l_measurements_18997.csv_sorted
[STOP] [2019-12-22 17:32:06] convert_to_csv
[START] [2019-12-22 17:32:06] calculate_delta
[CMD] [2019-12-22 17:32:06] echo "0a" > /app/public/diff/alboran_sea_sp_l_refs_18994.diff
[CMD] [2019-12-22 17:32:06] tail -n +1 /app/public/converted_csv/alboran_sea_sp_l_refs_18994.csv >> /app/public/diff/alboran_sea_sp_l_refs_18994.diff
[CMD] [2019-12-22 17:32:06] echo "." >> /app/public/diff/alboran_sea_sp_l_refs_18994.diff
[CMD] [2019-12-22 17:32:06] echo "0a" > /app/public/diff/alboran_sea_sp_l_nodes_18995.diff
[CMD] [2019-12-22 17:32:06] tail -n +1 /app/public/converted_csv/alboran_sea_sp_l_nodes_18995.csv >> /app/public/diff/alboran_sea_sp_l_nodes_18995.diff
[CMD] [2019-12-22 17:32:06] echo "." >> /app/public/diff/alboran_sea_sp_l_nodes_18995.diff
[CMD] [2019-12-22 17:32:06] echo "0a" > /app/public/diff/alboran_sea_sp_l_occurrences_18996.diff
[CMD] [2019-12-22 17:32:06] tail -n +1 /app/public/converted_csv/alboran_sea_sp_l_occurrences_18996.csv >> /app/public/diff/alboran_sea_sp_l_occurrences_18996.diff
[CMD] [2019-12-22 17:32:06] echo "." >> /app/public/diff/alboran_sea_sp_l_occurrences_18996.diff
[CMD] [2019-12-22 17:32:06] echo "0a" > /app/public/diff/alboran_sea_sp_l_measurements_18997.diff
[CMD] [2019-12-22 17:32:06] tail -n +1 /app/public/converted_csv/alboran_sea_sp_l_measurements_18997.csv >> /app/public/diff/alboran_sea_sp_l_measurements_18997.diff
[CMD] [2019-12-22 17:32:06] echo "." >> /app/public/diff/alboran_sea_sp_l_measurements_18997.diff
[STOP] [2019-12-22 17:32:07] calculate_delta
[START] [2019-12-22 17:32:07] parse_diff_and_store
[INFO] [2019-12-22 17:32:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 17:32:07] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 17:32:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 17:32:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 17:32:15] Storing 2 References
[INFO] [2019-12-22 17:32:15] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 17:32:15] Average Time: 0.0
[INFO] [2019-12-22 17:32:15] Total Time: 1s
[INFO] [2019-12-22 17:32:15] Storing 2565 ScientificNames
[INFO] [2019-12-22 17:32:15] Processing group of 2565 in 3 groups of 1000
[INFO] [2019-12-22 17:32:16] Average Time: 0.34
[INFO] [2019-12-22 17:32:16] Total Time: 2s
[INFO] [2019-12-22 17:32:16] Storing 2565 Nodes
[INFO] [2019-12-22 17:32:16] Processing group of 2565 in 3 groups of 1000
[INFO] [2019-12-22 17:32:17] Average Time: 0.29
[INFO] [2019-12-22 17:32:17] Total Time: 1s
[INFO] [2019-12-22 17:32:17] Storing 1103 Occurrences
[INFO] [2019-12-22 17:32:17] Processing group of 1103 in 2 groups of 1000
[INFO] [2019-12-22 17:32:17] Average Time: 0.075
[INFO] [2019-12-22 17:32:17] Total Time: 1s
[INFO] [2019-12-22 17:32:17] Storing 2206 TraitsReferences
[INFO] [2019-12-22 17:32:17] Processing group of 2206 in 3 groups of 1000
[INFO] [2019-12-22 17:32:17] Average Time: 0.087
[INFO] [2019-12-22 17:32:17] Total Time: 1s
[INFO] [2019-12-22 17:32:17] Storing 2206 Traits
[INFO] [2019-12-22 17:32:17] Processing group of 2206 in 3 groups of 1000
[INFO] [2019-12-22 17:32:18] Average Time: 0.297
[INFO] [2019-12-22 17:32:18] Total Time: 1s
[INFO] [2019-12-22 17:32:18] Storing 2206 MetaTraits
[INFO] [2019-12-22 17:32:18] Processing group of 2206 in 3 groups of 1000
[INFO] [2019-12-22 17:32:19] Average Time: 0.107
[INFO] [2019-12-22 17:32:19] Total Time: 1s
[STOP] [2019-12-22 17:32:19] parse_diff_and_store
[START] [2019-12-22 17:32:19] resolve_keys
[INFO] [2019-12-22 17:32:31] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 17:32:32] traits to occurrences...
[INFO] [2019-12-22 17:32:32] traits to nodes (through occurrences)...
[INFO] [2019-12-22 17:32:32] Traits to sex term...
[INFO] [2019-12-22 17:32:33] Traits to lifestage term...
[INFO] [2019-12-22 17:32:33] MetaTraits to traits...
[INFO] [2019-12-22 17:32:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 17:32:34] Assocs to occurrences...
[INFO] [2019-12-22 17:32:34] Assocs to nodes...
[INFO] [2019-12-22 17:32:34] Assoc to sex term...
[INFO] [2019-12-22 17:32:34] Assoc to lifestage term...
[STOP] [2019-12-22 17:32:34] resolve_keys
[START] [2019-12-22 17:32:34] hold_for_later_1
[STOP] [2019-12-22 17:32:34] hold_for_later_1
[START] [2019-12-22 17:32:34] hold_for_later_2
[STOP] [2019-12-22 17:32:34] hold_for_later_2
[START] [2019-12-22 17:32:34] resolve_missing_parents
[STOP] [2019-12-22 17:32:38] resolve_missing_parents
[START] [2019-12-22 17:32:38] rebuild_nodes
[START] [2019-12-22 17:32:38] Flattener#flatten
[START] [2019-12-22 17:32:38] Flattener#study_resource
[START] [2019-12-22 17:32:38] Flattener#build_ancestry
[STOP] [2019-12-22 17:32:38] Flattener#build_ancestry
[INFO] [2019-12-22 17:32:38] 2565 ancestry keys
[START] [2019-12-22 17:32:38] build_node_ancestors
[INFO] [2019-12-22 17:32:38] old ancestors deleted.
[STOP] [2019-12-22 17:32:39] build_node_ancestors
[START] [2019-12-22 17:32:40] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:32:40] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 17:32:40] Flattener#flatten
[STOP] [2019-12-22 17:32:40] rebuild_nodes
[START] [2019-12-22 17:32:40] resolve_missing_media_owners
[STOP] [2019-12-22 17:32:40] resolve_missing_media_owners
[START] [2019-12-22 17:32:40] sanitize_media_verbatims
[STOP] [2019-12-22 17:32:40] sanitize_media_verbatims
[START] [2019-12-22 17:32:41] queue_downloads
[STOP] [2019-12-22 17:32:41] queue_downloads
[START] [2019-12-22 17:32:41] parse_names
[WARN] [2019-12-22 17:32:41] I see 2565 names which still need to be parsed.
[STOP] [2019-12-22 17:32:44] parse_names
[START] [2019-12-22 17:32:44] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 17:32:44] denormalize_canonical_names_to_nodes
[START] [2019-12-22 17:32:44] match_nodes
[START] [2019-12-22 17:32:44] map_all_nodes_to_pages
[STOP] [2019-12-22 17:38:20] map_all_nodes_to_pages
[INFO] [2019-12-22 17:38:20] 175 Unmatched nodes (of 2565)! That's too many to output. First 10: Lagenida (#61658211); Vaginulinidae (#61658469); Hemirobulina (#61659080); Hemirobulina angistoma (#61659079); Astacolus (#61659824); Astacolus insolitus (#61659823); Marginulina (#61659914); Marginulina striatula (#61659913); Marginulina striata (#61659931); Stilostomellidae (#61658903)
[START] [2019-12-22 17:38:20] update_nodes
[STOP] [2019-12-22 17:38:21] update_nodes
[STOP] [2019-12-22 17:38:21] match_nodes
[START] [2019-12-22 17:38:21] reindex_search
[STOP] [2019-12-22 17:38:26] reindex_search
[START] [2019-12-22 17:38:26] normalize_units
[STOP] [2019-12-22 17:38:26] normalize_units
[START] [2019-12-22 17:38:26] calculate_statistics
[STOP] [2019-12-22 17:38:26] calculate_statistics
[START] [2019-12-22 17:38:26] complete_harvest_instance
[START] [2019-12-22 17:38:26] overall_tsv_creation
[INFO] [2019-12-22 17:38:26] Processing group of 2565 in 1 batches of 10000
[INFO] [2019-12-22 17:39:25] 1103 Traits (unfiltered)...
[INFO] [2019-12-22 17:39:39] 1103 Traits (filtered)...
[INFO] [2019-12-22 17:39:39] 0 Associations (filtered)...
[INFO] [2019-12-22 17:40:17] 5515 metadata added.
[INFO] [2019-12-22 17:40:17] 0 metadata added.
[INFO] [2019-12-22 17:40:17] Average Time: 85.41
[INFO] [2019-12-22 17:40:17] Total Time: 1m52s
[STOP] [2019-12-22 17:40:17] overall_tsv_creation
[INFO] [2019-12-22 17:40:17] Done. Check your files:
[INFO] [2019-12-22 17:40:17] (2565 lines) /app/public/data/alboran_sea_sp_l/publish_nodes.tsv
[INFO] [2019-12-22 17:40:17] (12048 lines) /app/public/data/alboran_sea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-22 17:40:18] (2565 lines) /app/public/data/alboran_sea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-22 17:40:18] (1104 lines) /app/public/data/alboran_sea_sp_l/publish_traits.tsv
[INFO] [2019-12-22 17:40:18] (5516 lines) /app/public/data/alboran_sea_sp_l/publish_metadata.tsv
[STOP] [2019-12-22 17:40:18] complete_harvest_instance
[START] [2019-12-22 17:40:18] completed
[STOP] [2019-12-22 17:40:18] completed
[STOP] [2019-12-22 17:40:18] logged process, took 492.4
Latest Process

22 Dec 17:32 EXITED currently processing 0