Harvest for Arctic Ocean Species List Created 22 Dec 20:14

Stage: completed
Fetched: 22 Dec 20:14
Validated: 22 Dec 20:14
Deltas Created 22 Dec 20:14
Units Normalized: 22 Dec 20:38
Ancestry Built: 22 Dec 20:15
Nodes Matched: 22 Dec 20:37
Names Parsed: 22 Dec 20:15
New Models Stored: 22 Dec 20:15
Indexed: 22 Dec 20:38
Completed: 22 Dec 20:40
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-12-22 20:14:43 -0500 by logger.rb/56815
[START] [2019-12-22 20:14:43] logged process
[START] [2019-12-22 20:14:43] create_harvest_instance
[STOP] [2019-12-22 20:14:44] create_harvest_instance
[START] [2019-12-22 20:14:44] fetch_files
[STOP] [2019-12-22 20:14:44] fetch_files
[START] [2019-12-22 20:14:44] validate_each_file
[STOP] [2019-12-22 20:14:44] validate_each_file
[START] [2019-12-22 20:14:44] convert_to_csv
[CMD] [2019-12-22 20:14:45] /usr/bin/sort /app/public/converted_csv/Arctic_Ocean_Spe_refs_19066.csv > /app/public/converted_csv/Arctic_Ocean_Spe_refs_19066.csv_sorted
[CMD] [2019-12-22 20:14:45] /usr/bin/sort /app/public/converted_csv/Arctic_Ocean_Spe_nodes_19067.csv > /app/public/converted_csv/Arctic_Ocean_Spe_nodes_19067.csv_sorted
[CMD] [2019-12-22 20:14:46] /usr/bin/sort /app/public/converted_csv/Arctic_Ocean_Spe_occurrences_19068.csv > /app/public/converted_csv/Arctic_Ocean_Spe_occurrences_19068.csv_sorted
[CMD] [2019-12-22 20:14:47] /usr/bin/sort /app/public/converted_csv/Arctic_Ocean_Spe_measurements_19069.csv > /app/public/converted_csv/Arctic_Ocean_Spe_measurements_19069.csv_sorted
[STOP] [2019-12-22 20:14:47] convert_to_csv
[START] [2019-12-22 20:14:47] calculate_delta
[CMD] [2019-12-22 20:14:47] echo "0a" > /app/public/diff/Arctic_Ocean_Spe_refs_19066.diff
[CMD] [2019-12-22 20:14:48] tail -n +1 /app/public/converted_csv/Arctic_Ocean_Spe_refs_19066.csv >> /app/public/diff/Arctic_Ocean_Spe_refs_19066.diff
[CMD] [2019-12-22 20:14:49] echo "." >> /app/public/diff/Arctic_Ocean_Spe_refs_19066.diff
[CMD] [2019-12-22 20:14:49] echo "0a" > /app/public/diff/Arctic_Ocean_Spe_nodes_19067.diff
[CMD] [2019-12-22 20:14:50] tail -n +1 /app/public/converted_csv/Arctic_Ocean_Spe_nodes_19067.csv >> /app/public/diff/Arctic_Ocean_Spe_nodes_19067.diff
[CMD] [2019-12-22 20:14:51] echo "." >> /app/public/diff/Arctic_Ocean_Spe_nodes_19067.diff
[CMD] [2019-12-22 20:14:51] echo "0a" > /app/public/diff/Arctic_Ocean_Spe_occurrences_19068.diff
[CMD] [2019-12-22 20:14:52] tail -n +1 /app/public/converted_csv/Arctic_Ocean_Spe_occurrences_19068.csv >> /app/public/diff/Arctic_Ocean_Spe_occurrences_19068.diff
[CMD] [2019-12-22 20:14:53] echo "." >> /app/public/diff/Arctic_Ocean_Spe_occurrences_19068.diff
[CMD] [2019-12-22 20:14:53] echo "0a" > /app/public/diff/Arctic_Ocean_Spe_measurements_19069.diff
[CMD] [2019-12-22 20:14:54] tail -n +1 /app/public/converted_csv/Arctic_Ocean_Spe_measurements_19069.csv >> /app/public/diff/Arctic_Ocean_Spe_measurements_19069.diff
[CMD] [2019-12-22 20:14:55] echo "." >> /app/public/diff/Arctic_Ocean_Spe_measurements_19069.diff
[STOP] [2019-12-22 20:14:55] calculate_delta
[START] [2019-12-22 20:14:55] parse_diff_and_store
[INFO] [2019-12-22 20:14:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 20:14:57] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 20:14:59] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 20:15:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 20:15:11] Storing 2 References
[INFO] [2019-12-22 20:15:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 20:15:11] Average Time: 0.0
[INFO] [2019-12-22 20:15:11] Total Time: 1s
[INFO] [2019-12-22 20:15:11] Storing 4090 ScientificNames
[INFO] [2019-12-22 20:15:11] Processing group of 4090 in 5 groups of 1000
[INFO] [2019-12-22 20:15:13] Average Time: 0.344
[INFO] [2019-12-22 20:15:13] Total Time: 2s
[INFO] [2019-12-22 20:15:13] Storing 4090 Nodes
[INFO] [2019-12-22 20:15:13] Processing group of 4090 in 5 groups of 1000
[INFO] [2019-12-22 20:15:14] Average Time: 0.262
[INFO] [2019-12-22 20:15:14] Total Time: 2s
[INFO] [2019-12-22 20:15:14] Storing 1952 Occurrences
[INFO] [2019-12-22 20:15:14] Processing group of 1952 in 2 groups of 1000
[INFO] [2019-12-22 20:15:14] Average Time: 0.145
[INFO] [2019-12-22 20:15:14] Total Time: 1s
[INFO] [2019-12-22 20:15:14] Storing 3904 TraitsReferences
[INFO] [2019-12-22 20:15:14] Processing group of 3904 in 4 groups of 1000
[INFO] [2019-12-22 20:15:15] Average Time: 0.095
[INFO] [2019-12-22 20:15:15] Total Time: 1s
[INFO] [2019-12-22 20:15:15] Storing 3904 Traits
[INFO] [2019-12-22 20:15:15] Processing group of 3904 in 4 groups of 1000
[INFO] [2019-12-22 20:15:16] Average Time: 0.36
[INFO] [2019-12-22 20:15:16] Total Time: 2s
[INFO] [2019-12-22 20:15:16] Storing 3904 MetaTraits
[INFO] [2019-12-22 20:15:16] Processing group of 3904 in 4 groups of 1000
[INFO] [2019-12-22 20:15:17] Average Time: 0.133
[INFO] [2019-12-22 20:15:17] Total Time: 1s
[STOP] [2019-12-22 20:15:17] parse_diff_and_store
[START] [2019-12-22 20:15:17] resolve_keys
[INFO] [2019-12-22 20:15:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 20:15:37] traits to occurrences...
[INFO] [2019-12-22 20:15:38] traits to nodes (through occurrences)...
[INFO] [2019-12-22 20:15:38] Traits to sex term...
[INFO] [2019-12-22 20:15:39] Traits to lifestage term...
[INFO] [2019-12-22 20:15:40] MetaTraits to traits...
[INFO] [2019-12-22 20:15:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 20:15:41] Assocs to occurrences...
[INFO] [2019-12-22 20:15:41] Assocs to nodes...
[INFO] [2019-12-22 20:15:41] Assoc to sex term...
[INFO] [2019-12-22 20:15:41] Assoc to lifestage term...
[STOP] [2019-12-22 20:15:41] resolve_keys
[START] [2019-12-22 20:15:41] hold_for_later_1
[STOP] [2019-12-22 20:15:41] hold_for_later_1
[START] [2019-12-22 20:15:41] hold_for_later_2
[STOP] [2019-12-22 20:15:41] hold_for_later_2
[START] [2019-12-22 20:15:41] resolve_missing_parents
[STOP] [2019-12-22 20:15:48] resolve_missing_parents
[START] [2019-12-22 20:15:48] rebuild_nodes
[START] [2019-12-22 20:15:48] Flattener#flatten
[START] [2019-12-22 20:15:48] Flattener#study_resource
[START] [2019-12-22 20:15:48] Flattener#build_ancestry
[STOP] [2019-12-22 20:15:48] Flattener#build_ancestry
[INFO] [2019-12-22 20:15:48] 4090 ancestry keys
[START] [2019-12-22 20:15:48] build_node_ancestors
[INFO] [2019-12-22 20:15:48] old ancestors deleted.
[STOP] [2019-12-22 20:15:49] build_node_ancestors
[START] [2019-12-22 20:15:51] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 20:15:51] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 20:15:51] Flattener#flatten
[STOP] [2019-12-22 20:15:51] rebuild_nodes
[START] [2019-12-22 20:15:51] resolve_missing_media_owners
[STOP] [2019-12-22 20:15:51] resolve_missing_media_owners
[START] [2019-12-22 20:15:51] sanitize_media_verbatims
[STOP] [2019-12-22 20:15:51] sanitize_media_verbatims
[START] [2019-12-22 20:15:51] queue_downloads
[STOP] [2019-12-22 20:15:51] queue_downloads
[START] [2019-12-22 20:15:51] parse_names
[WARN] [2019-12-22 20:15:51] I see 4090 names which still need to be parsed.
[STOP] [2019-12-22 20:15:56] parse_names
[START] [2019-12-22 20:15:56] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 20:15:56] denormalize_canonical_names_to_nodes
[START] [2019-12-22 20:15:56] match_nodes
[START] [2019-12-22 20:15:56] map_all_nodes_to_pages
[STOP] [2019-12-22 20:37:54] map_all_nodes_to_pages
[INFO] [2019-12-22 20:37:54] 397 Unmatched nodes (of 4090)! That's too many to output. First 10: Poecilostomatoida (#61716912); Diosaccidae (#61719255); Paramphiascella hispidus (#61720605); Cerviniidae (#61719268); Cytheropteron vespertilio (#61717180); Cytheropteron arcuatum (#61718667); Cytheropteron biconvexa (#61718879); Cytheropteron paralatissimum (#61718953); Cytheropteron sulense (#61718961); Henryhowella asperrima (#61717165)
[START] [2019-12-22 20:37:54] update_nodes
[STOP] [2019-12-22 20:37:56] update_nodes
[STOP] [2019-12-22 20:37:56] match_nodes
[START] [2019-12-22 20:37:56] reindex_search
[STOP] [2019-12-22 20:38:11] reindex_search
[START] [2019-12-22 20:38:11] normalize_units
[STOP] [2019-12-22 20:38:11] normalize_units
[START] [2019-12-22 20:38:11] calculate_statistics
[STOP] [2019-12-22 20:38:12] calculate_statistics
[START] [2019-12-22 20:38:12] complete_harvest_instance
[START] [2019-12-22 20:38:12] overall_tsv_creation
[INFO] [2019-12-22 20:38:12] Processing group of 4090 in 1 batches of 10000
[INFO] [2019-12-22 20:39:16] 1952 Traits (unfiltered)...
[INFO] [2019-12-22 20:39:29] 1952 Traits (filtered)...
[INFO] [2019-12-22 20:39:29] 0 Associations (filtered)...
[INFO] [2019-12-22 20:40:09] 9760 metadata added.
[INFO] [2019-12-22 20:40:09] 0 metadata added.
[INFO] [2019-12-22 20:40:09] Average Time: 92.98
[INFO] [2019-12-22 20:40:09] Total Time: 1m58s
[STOP] [2019-12-22 20:40:09] overall_tsv_creation
[INFO] [2019-12-22 20:40:09] Done. Check your files:
[INFO] [2019-12-22 20:40:10] (4090 lines) /app/public/data/Arctic_Ocean_Spe/publish_nodes.tsv
[INFO] [2019-12-22 20:40:10] (19704 lines) /app/public/data/Arctic_Ocean_Spe/publish_node_ancestors.tsv
[INFO] [2019-12-22 20:40:11] (4090 lines) /app/public/data/Arctic_Ocean_Spe/publish_scientific_names.tsv
[INFO] [2019-12-22 20:40:12] (1953 lines) /app/public/data/Arctic_Ocean_Spe/publish_traits.tsv
[INFO] [2019-12-22 20:40:12] (9761 lines) /app/public/data/Arctic_Ocean_Spe/publish_metadata.tsv
[STOP] [2019-12-22 20:40:13] complete_harvest_instance
[START] [2019-12-22 20:40:13] completed
[STOP] [2019-12-22 20:40:13] completed
[STOP] [2019-12-22 20:40:13] logged process, took 1529.21

Latest Process