Harvest for Tyrrhenian Sea Species List Created 25 Dec 17:37

Stage: completed
Fetched: 25 Dec 17:37
Validated: 25 Dec 17:37
Deltas Created 25 Dec 17:37
Units Normalized: 25 Dec 18:01
Ancestry Built: 25 Dec 17:38
Nodes Matched: 25 Dec 18:01
Names Parsed: 25 Dec 17:39
New Models Stored: 25 Dec 17:38
Indexed: 25 Dec 18:01
Completed: 25 Dec 18:04
Time to Harvest: less than a minute

Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 17:37:16 -0500 by logger.rb/56815
[START] [2019-12-25 17:37:16] logged process
[START] [2019-12-25 17:37:16] create_harvest_instance
[STOP] [2019-12-25 17:37:16] create_harvest_instance
[START] [2019-12-25 17:37:16] fetch_files
[STOP] [2019-12-25 17:37:16] fetch_files
[START] [2019-12-25 17:37:16] validate_each_file
[STOP] [2019-12-25 17:37:17] validate_each_file
[START] [2019-12-25 17:37:17] convert_to_csv
[CMD] [2019-12-25 17:37:17] /usr/bin/sort /app/public/converted_csv/tyrrhenian_sea_s_refs_19730.csv > /app/public/converted_csv/tyrrhenian_sea_s_refs_19730.csv_sorted
[CMD] [2019-12-25 17:37:18] /usr/bin/sort /app/public/converted_csv/tyrrhenian_sea_s_nodes_19731.csv > /app/public/converted_csv/tyrrhenian_sea_s_nodes_19731.csv_sorted
[CMD] [2019-12-25 17:37:19] /usr/bin/sort /app/public/converted_csv/tyrrhenian_sea_s_occurrences_19732.csv > /app/public/converted_csv/tyrrhenian_sea_s_occurrences_19732.csv_sorted
[CMD] [2019-12-25 17:37:19] /usr/bin/sort /app/public/converted_csv/tyrrhenian_sea_s_measurements_19733.csv > /app/public/converted_csv/tyrrhenian_sea_s_measurements_19733.csv_sorted
[STOP] [2019-12-25 17:37:20] convert_to_csv
[START] [2019-12-25 17:37:20] calculate_delta
[CMD] [2019-12-25 17:37:20] echo "0a" > /app/public/diff/tyrrhenian_sea_s_refs_19730.diff
[CMD] [2019-12-25 17:37:21] tail -n +1 /app/public/converted_csv/tyrrhenian_sea_s_refs_19730.csv >> /app/public/diff/tyrrhenian_sea_s_refs_19730.diff
[CMD] [2019-12-25 17:37:21] echo "." >> /app/public/diff/tyrrhenian_sea_s_refs_19730.diff
[CMD] [2019-12-25 17:37:22] echo "0a" > /app/public/diff/tyrrhenian_sea_s_nodes_19731.diff
[CMD] [2019-12-25 17:37:23] tail -n +1 /app/public/converted_csv/tyrrhenian_sea_s_nodes_19731.csv >> /app/public/diff/tyrrhenian_sea_s_nodes_19731.diff
[CMD] [2019-12-25 17:37:23] echo "." >> /app/public/diff/tyrrhenian_sea_s_nodes_19731.diff
[CMD] [2019-12-25 17:37:24] echo "0a" > /app/public/diff/tyrrhenian_sea_s_occurrences_19732.diff
[CMD] [2019-12-25 17:37:25] tail -n +1 /app/public/converted_csv/tyrrhenian_sea_s_occurrences_19732.csv >> /app/public/diff/tyrrhenian_sea_s_occurrences_19732.diff
[CMD] [2019-12-25 17:37:25] echo "." >> /app/public/diff/tyrrhenian_sea_s_occurrences_19732.diff
[CMD] [2019-12-25 17:37:26] echo "0a" > /app/public/diff/tyrrhenian_sea_s_measurements_19733.diff
[CMD] [2019-12-25 17:37:27] tail -n +1 /app/public/converted_csv/tyrrhenian_sea_s_measurements_19733.csv >> /app/public/diff/tyrrhenian_sea_s_measurements_19733.diff
[CMD] [2019-12-25 17:37:27] echo "." >> /app/public/diff/tyrrhenian_sea_s_measurements_19733.diff
[STOP] [2019-12-25 17:37:28] calculate_delta
[START] [2019-12-25 17:37:28] parse_diff_and_store
[INFO] [2019-12-25 17:37:29] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 17:37:29] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 17:37:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 17:37:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 17:37:52] Storing 2 References
[INFO] [2019-12-25 17:37:52] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 17:37:52] Average Time: 0.0
[INFO] [2019-12-25 17:37:52] Total Time: 1s
[INFO] [2019-12-25 17:37:52] Storing 5916 ScientificNames
[INFO] [2019-12-25 17:37:52] Processing group of 5916 in 6 groups of 1000
[INFO] [2019-12-25 17:37:55] Average Time: 0.385
[INFO] [2019-12-25 17:37:55] Total Time: 3s
[INFO] [2019-12-25 17:37:55] Storing 5916 Nodes
[INFO] [2019-12-25 17:37:55] Processing group of 5916 in 6 groups of 1000
[INFO] [2019-12-25 17:37:57] Average Time: 0.32
[INFO] [2019-12-25 17:37:57] Total Time: 2s
[INFO] [2019-12-25 17:37:57] Storing 2906 Occurrences
[INFO] [2019-12-25 17:37:57] Processing group of 2906 in 3 groups of 1000
[INFO] [2019-12-25 17:37:57] Average Time: 0.107
[INFO] [2019-12-25 17:37:57] Total Time: 1s
[INFO] [2019-12-25 17:37:57] Storing 5812 TraitsReferences
[INFO] [2019-12-25 17:37:57] Processing group of 5812 in 6 groups of 1000
[INFO] [2019-12-25 17:37:58] Average Time: 0.085
[INFO] [2019-12-25 17:37:58] Total Time: 1s
[INFO] [2019-12-25 17:37:58] Storing 5812 Traits
[INFO] [2019-12-25 17:37:58] Processing group of 5812 in 6 groups of 1000
[INFO] [2019-12-25 17:38:00] Average Time: 0.382
[INFO] [2019-12-25 17:38:00] Total Time: 3s
[INFO] [2019-12-25 17:38:00] Storing 5808 MetaTraits
[INFO] [2019-12-25 17:38:00] Processing group of 5808 in 6 groups of 1000
[INFO] [2019-12-25 17:38:01] Average Time: 0.15
[INFO] [2019-12-25 17:38:01] Total Time: 1s
[STOP] [2019-12-25 17:38:01] parse_diff_and_store
[START] [2019-12-25 17:38:01] resolve_keys
[INFO] [2019-12-25 17:38:26] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 17:38:28] traits to occurrences...
[INFO] [2019-12-25 17:38:31] traits to nodes (through occurrences)...
[INFO] [2019-12-25 17:38:31] Traits to sex term...
[INFO] [2019-12-25 17:38:34] Traits to lifestage term...
[INFO] [2019-12-25 17:38:37] MetaTraits to traits...
[INFO] [2019-12-25 17:38:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 17:38:38] Assocs to occurrences...
[INFO] [2019-12-25 17:38:38] Assocs to nodes...
[INFO] [2019-12-25 17:38:38] Assoc to sex term...
[INFO] [2019-12-25 17:38:38] Assoc to lifestage term...
[STOP] [2019-12-25 17:38:38] resolve_keys
[START] [2019-12-25 17:38:38] hold_for_later_1
[STOP] [2019-12-25 17:38:38] hold_for_later_1
[START] [2019-12-25 17:38:38] hold_for_later_2
[STOP] [2019-12-25 17:38:38] hold_for_later_2
[START] [2019-12-25 17:38:38] resolve_missing_parents
[STOP] [2019-12-25 17:38:49] resolve_missing_parents
[START] [2019-12-25 17:38:49] rebuild_nodes
[START] [2019-12-25 17:38:49] Flattener#flatten
[START] [2019-12-25 17:38:49] Flattener#study_resource
[START] [2019-12-25 17:38:49] Flattener#build_ancestry
[STOP] [2019-12-25 17:38:49] Flattener#build_ancestry
[INFO] [2019-12-25 17:38:49] 5916 ancestry keys
[START] [2019-12-25 17:38:49] build_node_ancestors
[INFO] [2019-12-25 17:38:49] old ancestors deleted.
[STOP] [2019-12-25 17:38:52] build_node_ancestors
[START] [2019-12-25 17:38:54] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 17:38:55] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 17:38:55] Flattener#flatten
[STOP] [2019-12-25 17:38:55] rebuild_nodes
[START] [2019-12-25 17:38:55] resolve_missing_media_owners
[STOP] [2019-12-25 17:38:55] resolve_missing_media_owners
[START] [2019-12-25 17:38:55] sanitize_media_verbatims
[STOP] [2019-12-25 17:38:55] sanitize_media_verbatims
[START] [2019-12-25 17:38:55] queue_downloads
[STOP] [2019-12-25 17:38:55] queue_downloads
[START] [2019-12-25 17:38:55] parse_names
[WARN] [2019-12-25 17:38:55] I see 5916 names which still need to be parsed.
[STOP] [2019-12-25 17:39:01] parse_names
[START] [2019-12-25 17:39:01] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 17:39:01] denormalize_canonical_names_to_nodes
[START] [2019-12-25 17:39:01] match_nodes
[START] [2019-12-25 17:39:01] map_all_nodes_to_pages
[STOP] [2019-12-25 18:01:32] map_all_nodes_to_pages
[INFO] [2019-12-25 18:01:32] 397 Unmatched nodes (of 5916)! That's too many to output. First 10: Gyroidinoides soldanii (#62546164); Gyroidinoides umbonatus (#62547093); Cibicidoides bradyi (#62546191); Pleurostomella (#62546209); Pleurostomella alternans (#62546208); Pleurostomella acuminata (#62547521); Globocassidulina oblonga (#62546831); Bolivina subspinescens (#62547127); Bolivina seminuda (#62551711); Uvigerina proboscidea (#62547348)
[START] [2019-12-25 18:01:32] update_nodes
[STOP] [2019-12-25 18:01:34] update_nodes
[STOP] [2019-12-25 18:01:34] match_nodes
[START] [2019-12-25 18:01:34] reindex_search
[STOP] [2019-12-25 18:01:47] reindex_search
[START] [2019-12-25 18:01:47] normalize_units
[STOP] [2019-12-25 18:01:47] normalize_units
[START] [2019-12-25 18:01:47] calculate_statistics
[STOP] [2019-12-25 18:01:47] calculate_statistics
[START] [2019-12-25 18:01:47] complete_harvest_instance
[START] [2019-12-25 18:01:47] overall_tsv_creation
[INFO] [2019-12-25 18:01:47] Processing group of 5916 in 1 batches of 10000
[INFO] [2019-12-25 18:03:05] 2906 Traits (unfiltered)...
[INFO] [2019-12-25 18:03:19] 2906 Traits (filtered)...
[INFO] [2019-12-25 18:03:19] 0 Associations (filtered)...
[INFO] [2019-12-25 18:04:03] 14526 metadata added.
[INFO] [2019-12-25 18:04:03] 0 metadata added.
[INFO] [2019-12-25 18:04:03] Average Time: 105.24
[INFO] [2019-12-25 18:04:03] Total Time: 2m16s
[STOP] [2019-12-25 18:04:03] overall_tsv_creation
[INFO] [2019-12-25 18:04:03] Done. Check your files:
[INFO] [2019-12-25 18:04:03] (5916 lines) /app/public/data/tyrrhenian_sea_s/publish_nodes.tsv
[INFO] [2019-12-25 18:04:04] (28888 lines) /app/public/data/tyrrhenian_sea_s/publish_node_ancestors.tsv
[INFO] [2019-12-25 18:04:05] (5916 lines) /app/public/data/tyrrhenian_sea_s/publish_scientific_names.tsv
[INFO] [2019-12-25 18:04:05] (2907 lines) /app/public/data/tyrrhenian_sea_s/publish_traits.tsv
[INFO] [2019-12-25 18:04:06] (14527 lines) /app/public/data/tyrrhenian_sea_s/publish_metadata.tsv
[STOP] [2019-12-25 18:04:06] complete_harvest_instance
[START] [2019-12-25 18:04:06] completed
[STOP] [2019-12-25 18:04:06] completed
[STOP] [2019-12-25 18:04:06] logged process, took 1610.51

Latest Process