Harvest for East Siberian Sea Species List Created 23 Dec 00:44

Stage: completed
Fetched: 23 Dec 00:44
Validated: 23 Dec 00:44
Deltas Created 23 Dec 00:44
Units Normalized: 23 Dec 00:46
Ancestry Built: 23 Dec 00:44
Nodes Matched: 23 Dec 00:46
Names Parsed: 23 Dec 00:44
New Models Stored: 23 Dec 00:44
Indexed: 23 Dec 00:46
Completed: 23 Dec 00:48
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 00:44:29 -0500 by logger.rb/56815
[START] [2019-12-23 00:44:29] logged process
[START] [2019-12-23 00:44:29] create_harvest_instance
[STOP] [2019-12-23 00:44:29] create_harvest_instance
[START] [2019-12-23 00:44:29] fetch_files
[STOP] [2019-12-23 00:44:29] fetch_files
[START] [2019-12-23 00:44:29] validate_each_file
[STOP] [2019-12-23 00:44:30] validate_each_file
[START] [2019-12-23 00:44:30] convert_to_csv
[CMD] [2019-12-23 00:44:30] /usr/bin/sort /app/public/converted_csv/esssl_refs_19210.csv > /app/public/converted_csv/esssl_refs_19210.csv_sorted
[CMD] [2019-12-23 00:44:30] /usr/bin/sort /app/public/converted_csv/esssl_nodes_19211.csv > /app/public/converted_csv/esssl_nodes_19211.csv_sorted
[CMD] [2019-12-23 00:44:30] /usr/bin/sort /app/public/converted_csv/esssl_occurrences_19212.csv > /app/public/converted_csv/esssl_occurrences_19212.csv_sorted
[CMD] [2019-12-23 00:44:30] /usr/bin/sort /app/public/converted_csv/esssl_measurements_19213.csv > /app/public/converted_csv/esssl_measurements_19213.csv_sorted
[STOP] [2019-12-23 00:44:30] convert_to_csv
[START] [2019-12-23 00:44:30] calculate_delta
[CMD] [2019-12-23 00:44:30] echo "0a" > /app/public/diff/esssl_refs_19210.diff
[CMD] [2019-12-23 00:44:30] tail -n +1 /app/public/converted_csv/esssl_refs_19210.csv >> /app/public/diff/esssl_refs_19210.diff
[CMD] [2019-12-23 00:44:30] echo "." >> /app/public/diff/esssl_refs_19210.diff
[CMD] [2019-12-23 00:44:30] echo "0a" > /app/public/diff/esssl_nodes_19211.diff
[CMD] [2019-12-23 00:44:30] tail -n +1 /app/public/converted_csv/esssl_nodes_19211.csv >> /app/public/diff/esssl_nodes_19211.diff
[CMD] [2019-12-23 00:44:30] echo "." >> /app/public/diff/esssl_nodes_19211.diff
[CMD] [2019-12-23 00:44:30] echo "0a" > /app/public/diff/esssl_occurrences_19212.diff
[CMD] [2019-12-23 00:44:30] tail -n +1 /app/public/converted_csv/esssl_occurrences_19212.csv >> /app/public/diff/esssl_occurrences_19212.diff
[CMD] [2019-12-23 00:44:30] echo "." >> /app/public/diff/esssl_occurrences_19212.diff
[CMD] [2019-12-23 00:44:30] echo "0a" > /app/public/diff/esssl_measurements_19213.diff
[CMD] [2019-12-23 00:44:30] tail -n +1 /app/public/converted_csv/esssl_measurements_19213.csv >> /app/public/diff/esssl_measurements_19213.diff
[CMD] [2019-12-23 00:44:30] echo "." >> /app/public/diff/esssl_measurements_19213.diff
[STOP] [2019-12-23 00:44:30] calculate_delta
[START] [2019-12-23 00:44:30] parse_diff_and_store
[INFO] [2019-12-23 00:44:30] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 00:44:30] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 00:44:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 00:44:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 00:44:32] Storing 2 References
[INFO] [2019-12-23 00:44:32] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 00:44:32] Average Time: 0.0
[INFO] [2019-12-23 00:44:32] Total Time: 1s
[INFO] [2019-12-23 00:44:32] Storing 435 ScientificNames
[INFO] [2019-12-23 00:44:32] Processing group of 435 in 1 groups of 1000
[INFO] [2019-12-23 00:44:32] Average Time: 0.28
[INFO] [2019-12-23 00:44:32] Total Time: 1s
[INFO] [2019-12-23 00:44:32] Storing 435 Nodes
[INFO] [2019-12-23 00:44:32] Processing group of 435 in 1 groups of 1000
[INFO] [2019-12-23 00:44:32] Average Time: 0.18
[INFO] [2019-12-23 00:44:32] Total Time: 1s
[INFO] [2019-12-23 00:44:32] Storing 150 Occurrences
[INFO] [2019-12-23 00:44:32] Processing group of 150 in 1 groups of 1000
[INFO] [2019-12-23 00:44:32] Average Time: 0.04
[INFO] [2019-12-23 00:44:32] Total Time: 1s
[INFO] [2019-12-23 00:44:32] Storing 300 TraitsReferences
[INFO] [2019-12-23 00:44:32] Processing group of 300 in 1 groups of 1000
[INFO] [2019-12-23 00:44:32] Average Time: 0.09
[INFO] [2019-12-23 00:44:32] Total Time: 1s
[INFO] [2019-12-23 00:44:32] Storing 300 Traits
[INFO] [2019-12-23 00:44:32] Processing group of 300 in 1 groups of 1000
[INFO] [2019-12-23 00:44:33] Average Time: 0.29
[INFO] [2019-12-23 00:44:33] Total Time: 1s
[INFO] [2019-12-23 00:44:33] Storing 300 MetaTraits
[INFO] [2019-12-23 00:44:33] Processing group of 300 in 1 groups of 1000
[INFO] [2019-12-23 00:44:33] Average Time: 0.07
[INFO] [2019-12-23 00:44:33] Total Time: 1s
[STOP] [2019-12-23 00:44:33] parse_diff_and_store
[START] [2019-12-23 00:44:33] resolve_keys
[INFO] [2019-12-23 00:44:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 00:44:38] traits to occurrences...
[INFO] [2019-12-23 00:44:38] traits to nodes (through occurrences)...
[INFO] [2019-12-23 00:44:38] Traits to sex term...
[INFO] [2019-12-23 00:44:38] Traits to lifestage term...
[INFO] [2019-12-23 00:44:38] MetaTraits to traits...
[INFO] [2019-12-23 00:44:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 00:44:38] Assocs to occurrences...
[INFO] [2019-12-23 00:44:38] Assocs to nodes...
[INFO] [2019-12-23 00:44:38] Assoc to sex term...
[INFO] [2019-12-23 00:44:38] Assoc to lifestage term...
[STOP] [2019-12-23 00:44:38] resolve_keys
[START] [2019-12-23 00:44:38] hold_for_later_1
[STOP] [2019-12-23 00:44:38] hold_for_later_1
[START] [2019-12-23 00:44:38] hold_for_later_2
[STOP] [2019-12-23 00:44:38] hold_for_later_2
[START] [2019-12-23 00:44:38] resolve_missing_parents
[STOP] [2019-12-23 00:44:38] resolve_missing_parents
[START] [2019-12-23 00:44:38] rebuild_nodes
[START] [2019-12-23 00:44:38] Flattener#flatten
[START] [2019-12-23 00:44:38] Flattener#study_resource
[START] [2019-12-23 00:44:38] Flattener#build_ancestry
[STOP] [2019-12-23 00:44:38] Flattener#build_ancestry
[INFO] [2019-12-23 00:44:38] 435 ancestry keys
[START] [2019-12-23 00:44:38] build_node_ancestors
[INFO] [2019-12-23 00:44:38] old ancestors deleted.
[STOP] [2019-12-23 00:44:38] build_node_ancestors
[START] [2019-12-23 00:44:39] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:44:39] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:44:39] Flattener#flatten
[STOP] [2019-12-23 00:44:39] rebuild_nodes
[START] [2019-12-23 00:44:39] resolve_missing_media_owners
[STOP] [2019-12-23 00:44:39] resolve_missing_media_owners
[START] [2019-12-23 00:44:39] sanitize_media_verbatims
[STOP] [2019-12-23 00:44:39] sanitize_media_verbatims
[START] [2019-12-23 00:44:39] queue_downloads
[STOP] [2019-12-23 00:44:39] queue_downloads
[START] [2019-12-23 00:44:39] parse_names
[WARN] [2019-12-23 00:44:39] I see 435 names which still need to be parsed.
[STOP] [2019-12-23 00:44:40] parse_names
[START] [2019-12-23 00:44:40] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 00:44:40] denormalize_canonical_names_to_nodes
[START] [2019-12-23 00:44:40] match_nodes
[START] [2019-12-23 00:44:40] map_all_nodes_to_pages
[STOP] [2019-12-23 00:46:26] map_all_nodes_to_pages
[INFO] [2019-12-23 00:46:26] 20 Unmatched nodes (of 435)! That's too many to output. First 10: Philomachus (#61859617); Philomachus pugnax (#61859616); Anas penelope (#61859485); Anas formosa (#61859544); Chen (#61859547); Chen caerulescens (#61859546); Scorpaeniformes (#61859442); Ulcina (#61859822); Nuculanoida (#61859499); Carditoida (#61859541)
[START] [2019-12-23 00:46:26] update_nodes
[STOP] [2019-12-23 00:46:27] update_nodes
[STOP] [2019-12-23 00:46:27] match_nodes
[START] [2019-12-23 00:46:27] reindex_search
[STOP] [2019-12-23 00:46:28] reindex_search
[START] [2019-12-23 00:46:28] normalize_units
[STOP] [2019-12-23 00:46:28] normalize_units
[START] [2019-12-23 00:46:28] calculate_statistics
[STOP] [2019-12-23 00:46:28] calculate_statistics
[START] [2019-12-23 00:46:28] complete_harvest_instance
[START] [2019-12-23 00:46:28] overall_tsv_creation
[INFO] [2019-12-23 00:46:28] Processing group of 435 in 1 batches of 10000
[INFO] [2019-12-23 00:47:14] 150 Traits (unfiltered)...
[INFO] [2019-12-23 00:47:27] 150 Traits (filtered)...
[INFO] [2019-12-23 00:47:27] 0 Associations (filtered)...
[INFO] [2019-12-23 00:48:04] 750 metadata added.
[INFO] [2019-12-23 00:48:04] 0 metadata added.
[INFO] [2019-12-23 00:48:04] Average Time: 74.34
[INFO] [2019-12-23 00:48:04] Total Time: 1m37s
[STOP] [2019-12-23 00:48:04] overall_tsv_creation
[INFO] [2019-12-23 00:48:04] Done. Check your files:
[INFO] [2019-12-23 00:48:04] (435 lines) /app/public/data/esssl/publish_nodes.tsv
[INFO] [2019-12-23 00:48:05] (1949 lines) /app/public/data/esssl/publish_node_ancestors.tsv
[INFO] [2019-12-23 00:48:05] (435 lines) /app/public/data/esssl/publish_scientific_names.tsv
[INFO] [2019-12-23 00:48:05] (151 lines) /app/public/data/esssl/publish_traits.tsv
[INFO] [2019-12-23 00:48:05] (751 lines) /app/public/data/esssl/publish_metadata.tsv
[STOP] [2019-12-23 00:48:05] complete_harvest_instance
[START] [2019-12-23 00:48:05] completed
[STOP] [2019-12-23 00:48:05] completed
[STOP] [2019-12-23 00:48:05] logged process, took 215.79
Latest Process

23 Dec 00:44 EXITED currently processing 0