Harvest for Ionian Sea Species List Created 23 Dec 13:59

Stage: completed
Fetched: 23 Dec 14:00
Validated: 23 Dec 14:00
Deltas Created 23 Dec 14:00
Units Normalized: 23 Dec 14:24
Ancestry Built: 23 Dec 14:00
Nodes Matched: 23 Dec 14:24
Names Parsed: 23 Dec 14:01
New Models Stored: 23 Dec 14:00
Indexed: 23 Dec 14:24
Completed: 23 Dec 14:26
Time to Harvest: less than a minute

Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 13:59:59 -0500 by logger.rb/56815
[START] [2019-12-23 13:59:59] logged process
[START] [2019-12-23 13:59:59] create_harvest_instance
[STOP] [2019-12-23 14:00:00] create_harvest_instance
[START] [2019-12-23 14:00:00] fetch_files
[STOP] [2019-12-23 14:00:00] fetch_files
[START] [2019-12-23 14:00:00] validate_each_file
[STOP] [2019-12-23 14:00:00] validate_each_file
[START] [2019-12-23 14:00:00] convert_to_csv
[CMD] [2019-12-23 14:00:00] /usr/bin/sort /app/public/converted_csv/ionian_sea_sp_li_refs_19394.csv > /app/public/converted_csv/ionian_sea_sp_li_refs_19394.csv_sorted
[CMD] [2019-12-23 14:00:01] /usr/bin/sort /app/public/converted_csv/ionian_sea_sp_li_nodes_19395.csv > /app/public/converted_csv/ionian_sea_sp_li_nodes_19395.csv_sorted
[CMD] [2019-12-23 14:00:02] /usr/bin/sort /app/public/converted_csv/ionian_sea_sp_li_occurrences_19396.csv > /app/public/converted_csv/ionian_sea_sp_li_occurrences_19396.csv_sorted
[CMD] [2019-12-23 14:00:02] /usr/bin/sort /app/public/converted_csv/ionian_sea_sp_li_measurements_19397.csv > /app/public/converted_csv/ionian_sea_sp_li_measurements_19397.csv_sorted
[STOP] [2019-12-23 14:00:03] convert_to_csv
[START] [2019-12-23 14:00:03] calculate_delta
[CMD] [2019-12-23 14:00:03] echo "0a" > /app/public/diff/ionian_sea_sp_li_refs_19394.diff
[CMD] [2019-12-23 14:00:04] tail -n +1 /app/public/converted_csv/ionian_sea_sp_li_refs_19394.csv >> /app/public/diff/ionian_sea_sp_li_refs_19394.diff
[CMD] [2019-12-23 14:00:04] echo "." >> /app/public/diff/ionian_sea_sp_li_refs_19394.diff
[CMD] [2019-12-23 14:00:05] echo "0a" > /app/public/diff/ionian_sea_sp_li_nodes_19395.diff
[CMD] [2019-12-23 14:00:06] tail -n +1 /app/public/converted_csv/ionian_sea_sp_li_nodes_19395.csv >> /app/public/diff/ionian_sea_sp_li_nodes_19395.diff
[CMD] [2019-12-23 14:00:06] echo "." >> /app/public/diff/ionian_sea_sp_li_nodes_19395.diff
[CMD] [2019-12-23 14:00:07] echo "0a" > /app/public/diff/ionian_sea_sp_li_occurrences_19396.diff
[CMD] [2019-12-23 14:00:08] tail -n +1 /app/public/converted_csv/ionian_sea_sp_li_occurrences_19396.csv >> /app/public/diff/ionian_sea_sp_li_occurrences_19396.diff
[CMD] [2019-12-23 14:00:08] echo "." >> /app/public/diff/ionian_sea_sp_li_occurrences_19396.diff
[CMD] [2019-12-23 14:00:09] echo "0a" > /app/public/diff/ionian_sea_sp_li_measurements_19397.diff
[CMD] [2019-12-23 14:00:10] tail -n +1 /app/public/converted_csv/ionian_sea_sp_li_measurements_19397.csv >> /app/public/diff/ionian_sea_sp_li_measurements_19397.diff
[CMD] [2019-12-23 14:00:10] echo "." >> /app/public/diff/ionian_sea_sp_li_measurements_19397.diff
[STOP] [2019-12-23 14:00:11] calculate_delta
[START] [2019-12-23 14:00:11] parse_diff_and_store
[INFO] [2019-12-23 14:00:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 14:00:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 14:00:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 14:00:15] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 14:00:25] Storing 2 References
[INFO] [2019-12-23 14:00:25] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 14:00:25] Average Time: 0.0
[INFO] [2019-12-23 14:00:25] Total Time: 1s
[INFO] [2019-12-23 14:00:25] Storing 3394 ScientificNames
[INFO] [2019-12-23 14:00:25] Processing group of 3394 in 4 groups of 1000
[INFO] [2019-12-23 14:00:26] Average Time: 0.37
[INFO] [2019-12-23 14:00:26] Total Time: 2s
[INFO] [2019-12-23 14:00:26] Storing 3394 Nodes
[INFO] [2019-12-23 14:00:26] Processing group of 3394 in 4 groups of 1000
[INFO] [2019-12-23 14:00:27] Average Time: 0.275
[INFO] [2019-12-23 14:00:27] Total Time: 2s
[INFO] [2019-12-23 14:00:27] Storing 1627 Occurrences
[INFO] [2019-12-23 14:00:27] Processing group of 1627 in 2 groups of 1000
[INFO] [2019-12-23 14:00:27] Average Time: 0.1
[INFO] [2019-12-23 14:00:27] Total Time: 1s
[INFO] [2019-12-23 14:00:27] Storing 3254 TraitsReferences
[INFO] [2019-12-23 14:00:27] Processing group of 3254 in 4 groups of 1000
[INFO] [2019-12-23 14:00:28] Average Time: 0.103
[INFO] [2019-12-23 14:00:28] Total Time: 1s
[INFO] [2019-12-23 14:00:28] Storing 3254 Traits
[INFO] [2019-12-23 14:00:28] Processing group of 3254 in 4 groups of 1000
[INFO] [2019-12-23 14:00:29] Average Time: 0.303
[INFO] [2019-12-23 14:00:29] Total Time: 2s
[INFO] [2019-12-23 14:00:29] Storing 3253 MetaTraits
[INFO] [2019-12-23 14:00:29] Processing group of 3253 in 4 groups of 1000
[INFO] [2019-12-23 14:00:30] Average Time: 0.148
[INFO] [2019-12-23 14:00:30] Total Time: 1s
[STOP] [2019-12-23 14:00:30] parse_diff_and_store
[START] [2019-12-23 14:00:30] resolve_keys
[INFO] [2019-12-23 14:00:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 14:00:47] traits to occurrences...
[INFO] [2019-12-23 14:00:48] traits to nodes (through occurrences)...
[INFO] [2019-12-23 14:00:48] Traits to sex term...
[INFO] [2019-12-23 14:00:48] Traits to lifestage term...
[INFO] [2019-12-23 14:00:49] MetaTraits to traits...
[INFO] [2019-12-23 14:00:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 14:00:50] Assocs to occurrences...
[INFO] [2019-12-23 14:00:50] Assocs to nodes...
[INFO] [2019-12-23 14:00:50] Assoc to sex term...
[INFO] [2019-12-23 14:00:50] Assoc to lifestage term...
[STOP] [2019-12-23 14:00:50] resolve_keys
[START] [2019-12-23 14:00:50] hold_for_later_1
[STOP] [2019-12-23 14:00:50] hold_for_later_1
[START] [2019-12-23 14:00:50] hold_for_later_2
[STOP] [2019-12-23 14:00:50] hold_for_later_2
[START] [2019-12-23 14:00:50] resolve_missing_parents
[STOP] [2019-12-23 14:00:55] resolve_missing_parents
[START] [2019-12-23 14:00:55] rebuild_nodes
[START] [2019-12-23 14:00:55] Flattener#flatten
[START] [2019-12-23 14:00:55] Flattener#study_resource
[START] [2019-12-23 14:00:55] Flattener#build_ancestry
[STOP] [2019-12-23 14:00:55] Flattener#build_ancestry
[INFO] [2019-12-23 14:00:55] 3394 ancestry keys
[START] [2019-12-23 14:00:55] build_node_ancestors
[INFO] [2019-12-23 14:00:55] old ancestors deleted.
[STOP] [2019-12-23 14:00:57] build_node_ancestors
[START] [2019-12-23 14:00:58] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 14:00:59] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 14:00:59] Flattener#flatten
[STOP] [2019-12-23 14:00:59] rebuild_nodes
[START] [2019-12-23 14:00:59] resolve_missing_media_owners
[STOP] [2019-12-23 14:00:59] resolve_missing_media_owners
[START] [2019-12-23 14:00:59] sanitize_media_verbatims
[STOP] [2019-12-23 14:00:59] sanitize_media_verbatims
[START] [2019-12-23 14:00:59] queue_downloads
[STOP] [2019-12-23 14:00:59] queue_downloads
[START] [2019-12-23 14:00:59] parse_names
[WARN] [2019-12-23 14:00:59] I see 3394 names which still need to be parsed.
[STOP] [2019-12-23 14:01:02] parse_names
[START] [2019-12-23 14:01:02] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 14:01:02] denormalize_canonical_names_to_nodes
[START] [2019-12-23 14:01:02] match_nodes
[START] [2019-12-23 14:01:02] map_all_nodes_to_pages
[STOP] [2019-12-23 14:24:26] map_all_nodes_to_pages
[INFO] [2019-12-23 14:24:26] 182 Unmatched nodes (of 3394)! That's too many to output. First 10: Lingulodinium machaerophorum (#62069534); Spiniferites pachydermus (#62070397); Spiniferites membranaceus (#62072603); Bitectatodinium tepikiense (#62069549); Impagidinium aculeatum (#62069551); Impagidinium sphaericum (#62069555); Impagidinium patulum (#62069596); Impagidinium paradoxum (#62069630); Impagidinium strialatum (#62070033); Impagidinium velorum (#62072854)
[START] [2019-12-23 14:24:26] update_nodes
[STOP] [2019-12-23 14:24:28] update_nodes
[STOP] [2019-12-23 14:24:28] match_nodes
[START] [2019-12-23 14:24:28] reindex_search
[STOP] [2019-12-23 14:24:41] reindex_search
[START] [2019-12-23 14:24:41] normalize_units
[STOP] [2019-12-23 14:24:41] normalize_units
[START] [2019-12-23 14:24:41] calculate_statistics
[STOP] [2019-12-23 14:24:41] calculate_statistics
[START] [2019-12-23 14:24:41] complete_harvest_instance
[START] [2019-12-23 14:24:41] overall_tsv_creation
[INFO] [2019-12-23 14:24:41] Processing group of 3394 in 1 batches of 10000
[INFO] [2019-12-23 14:25:41] 1627 Traits (unfiltered)...
[INFO] [2019-12-23 14:25:54] 1627 Traits (filtered)...
[INFO] [2019-12-23 14:25:54] 0 Associations (filtered)...
[INFO] [2019-12-23 14:26:34] 8134 metadata added.
[INFO] [2019-12-23 14:26:34] 0 metadata added.
[INFO] [2019-12-23 14:26:34] Average Time: 89.52
[INFO] [2019-12-23 14:26:34] Total Time: 1m54s
[STOP] [2019-12-23 14:26:34] overall_tsv_creation
[INFO] [2019-12-23 14:26:34] Done. Check your files:
[INFO] [2019-12-23 14:26:35] (3394 lines) /app/public/data/ionian_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-23 14:26:36] (16494 lines) /app/public/data/ionian_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-23 14:26:36] (3394 lines) /app/public/data/ionian_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-23 14:26:37] (1628 lines) /app/public/data/ionian_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-23 14:26:37] (8135 lines) /app/public/data/ionian_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-23 14:26:38] complete_harvest_instance
[START] [2019-12-23 14:26:38] completed
[STOP] [2019-12-23 14:26:38] completed
[STOP] [2019-12-23 14:26:38] logged process, took 1598.57

Latest Process