Harvest for Northwestern Passages Species List Created 25 Dec 08:41

Stage: completed
Fetched: 25 Dec 08:41
Validated: 25 Dec 08:41
Deltas Created 25 Dec 08:41
Units Normalized: 25 Dec 08:44
Ancestry Built: 25 Dec 08:41
Nodes Matched: 25 Dec 08:44
Names Parsed: 25 Dec 08:41
New Models Stored: 25 Dec 08:41
Indexed: 25 Dec 08:44
Completed: 25 Dec 08:47
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 08:41:28 -0500 by logger.rb/56815
[START] [2019-12-25 08:41:28] logged process
[START] [2019-12-25 08:41:28] create_harvest_instance
[STOP] [2019-12-25 08:41:29] create_harvest_instance
[START] [2019-12-25 08:41:29] fetch_files
[STOP] [2019-12-25 08:41:29] fetch_files
[START] [2019-12-25 08:41:29] validate_each_file
[STOP] [2019-12-25 08:41:29] validate_each_file
[START] [2019-12-25 08:41:29] convert_to_csv
[CMD] [2019-12-25 08:41:29] /usr/bin/sort /app/public/converted_csv/northwestern_pas_refs_19554.csv > /app/public/converted_csv/northwestern_pas_refs_19554.csv_sorted
[CMD] [2019-12-25 08:41:30] /usr/bin/sort /app/public/converted_csv/northwestern_pas_nodes_19555.csv > /app/public/converted_csv/northwestern_pas_nodes_19555.csv_sorted
[CMD] [2019-12-25 08:41:30] /usr/bin/sort /app/public/converted_csv/northwestern_pas_occurrences_19556.csv > /app/public/converted_csv/northwestern_pas_occurrences_19556.csv_sorted
[CMD] [2019-12-25 08:41:31] /usr/bin/sort /app/public/converted_csv/northwestern_pas_measurements_19557.csv > /app/public/converted_csv/northwestern_pas_measurements_19557.csv_sorted
[STOP] [2019-12-25 08:41:32] convert_to_csv
[START] [2019-12-25 08:41:32] calculate_delta
[CMD] [2019-12-25 08:41:32] echo "0a" > /app/public/diff/northwestern_pas_refs_19554.diff
[CMD] [2019-12-25 08:41:32] tail -n +1 /app/public/converted_csv/northwestern_pas_refs_19554.csv >> /app/public/diff/northwestern_pas_refs_19554.diff
[CMD] [2019-12-25 08:41:33] echo "." >> /app/public/diff/northwestern_pas_refs_19554.diff
[CMD] [2019-12-25 08:41:34] echo "0a" > /app/public/diff/northwestern_pas_nodes_19555.diff
[CMD] [2019-12-25 08:41:34] tail -n +1 /app/public/converted_csv/northwestern_pas_nodes_19555.csv >> /app/public/diff/northwestern_pas_nodes_19555.diff
[CMD] [2019-12-25 08:41:35] echo "." >> /app/public/diff/northwestern_pas_nodes_19555.diff
[CMD] [2019-12-25 08:41:35] echo "0a" > /app/public/diff/northwestern_pas_occurrences_19556.diff
[CMD] [2019-12-25 08:41:36] tail -n +1 /app/public/converted_csv/northwestern_pas_occurrences_19556.csv >> /app/public/diff/northwestern_pas_occurrences_19556.diff
[CMD] [2019-12-25 08:41:37] echo "." >> /app/public/diff/northwestern_pas_occurrences_19556.diff
[CMD] [2019-12-25 08:41:37] echo "0a" > /app/public/diff/northwestern_pas_measurements_19557.diff
[CMD] [2019-12-25 08:41:38] tail -n +1 /app/public/converted_csv/northwestern_pas_measurements_19557.csv >> /app/public/diff/northwestern_pas_measurements_19557.diff
[CMD] [2019-12-25 08:41:39] echo "." >> /app/public/diff/northwestern_pas_measurements_19557.diff
[STOP] [2019-12-25 08:41:39] calculate_delta
[START] [2019-12-25 08:41:39] parse_diff_and_store
[INFO] [2019-12-25 08:41:40] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:40] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:42] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 08:41:44] Storing 2 References
[INFO] [2019-12-25 08:41:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 08:41:44] Average Time: 0.0
[INFO] [2019-12-25 08:41:44] Total Time: 1s
[INFO] [2019-12-25 08:41:44] Storing 1144 ScientificNames
[INFO] [2019-12-25 08:41:44] Processing group of 1144 in 2 groups of 1000
[INFO] [2019-12-25 08:41:45] Average Time: 0.24
[INFO] [2019-12-25 08:41:45] Total Time: 1s
[INFO] [2019-12-25 08:41:45] Storing 1144 Nodes
[INFO] [2019-12-25 08:41:45] Processing group of 1144 in 2 groups of 1000
[INFO] [2019-12-25 08:41:45] Average Time: 0.19
[INFO] [2019-12-25 08:41:45] Total Time: 1s
[INFO] [2019-12-25 08:41:45] Storing 446 Occurrences
[INFO] [2019-12-25 08:41:45] Processing group of 446 in 1 groups of 1000
[INFO] [2019-12-25 08:41:45] Average Time: 0.07
[INFO] [2019-12-25 08:41:45] Total Time: 1s
[INFO] [2019-12-25 08:41:45] Storing 892 TraitsReferences
[INFO] [2019-12-25 08:41:45] Processing group of 892 in 1 groups of 1000
[INFO] [2019-12-25 08:41:46] Average Time: 0.16
[INFO] [2019-12-25 08:41:46] Total Time: 1s
[INFO] [2019-12-25 08:41:46] Storing 892 Traits
[INFO] [2019-12-25 08:41:46] Processing group of 892 in 1 groups of 1000
[INFO] [2019-12-25 08:41:46] Average Time: 0.42
[INFO] [2019-12-25 08:41:46] Total Time: 1s
[INFO] [2019-12-25 08:41:46] Storing 890 MetaTraits
[INFO] [2019-12-25 08:41:46] Processing group of 890 in 1 groups of 1000
[INFO] [2019-12-25 08:41:46] Average Time: 0.15
[INFO] [2019-12-25 08:41:46] Total Time: 1s
[STOP] [2019-12-25 08:41:46] parse_diff_and_store
[START] [2019-12-25 08:41:46] resolve_keys
[INFO] [2019-12-25 08:41:53] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 08:41:54] traits to occurrences...
[INFO] [2019-12-25 08:41:54] traits to nodes (through occurrences)...
[INFO] [2019-12-25 08:41:54] Traits to sex term...
[INFO] [2019-12-25 08:41:55] Traits to lifestage term...
[INFO] [2019-12-25 08:41:55] MetaTraits to traits...
[INFO] [2019-12-25 08:41:55] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 08:41:55] Assocs to occurrences...
[INFO] [2019-12-25 08:41:55] Assocs to nodes...
[INFO] [2019-12-25 08:41:55] Assoc to sex term...
[INFO] [2019-12-25 08:41:55] Assoc to lifestage term...
[STOP] [2019-12-25 08:41:55] resolve_keys
[START] [2019-12-25 08:41:55] hold_for_later_1
[STOP] [2019-12-25 08:41:55] hold_for_later_1
[START] [2019-12-25 08:41:55] hold_for_later_2
[STOP] [2019-12-25 08:41:55] hold_for_later_2
[START] [2019-12-25 08:41:55] resolve_missing_parents
[STOP] [2019-12-25 08:41:56] resolve_missing_parents
[START] [2019-12-25 08:41:56] rebuild_nodes
[START] [2019-12-25 08:41:56] Flattener#flatten
[START] [2019-12-25 08:41:56] Flattener#study_resource
[START] [2019-12-25 08:41:56] Flattener#build_ancestry
[STOP] [2019-12-25 08:41:56] Flattener#build_ancestry
[INFO] [2019-12-25 08:41:56] 1144 ancestry keys
[START] [2019-12-25 08:41:56] build_node_ancestors
[INFO] [2019-12-25 08:41:56] old ancestors deleted.
[STOP] [2019-12-25 08:41:57] build_node_ancestors
[START] [2019-12-25 08:41:57] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:41:57] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 08:41:57] Flattener#flatten
[STOP] [2019-12-25 08:41:57] rebuild_nodes
[START] [2019-12-25 08:41:57] resolve_missing_media_owners
[STOP] [2019-12-25 08:41:57] resolve_missing_media_owners
[START] [2019-12-25 08:41:57] sanitize_media_verbatims
[STOP] [2019-12-25 08:41:57] sanitize_media_verbatims
[START] [2019-12-25 08:41:57] queue_downloads
[STOP] [2019-12-25 08:41:57] queue_downloads
[START] [2019-12-25 08:41:57] parse_names
[WARN] [2019-12-25 08:41:57] I see 1144 names which still need to be parsed.
[STOP] [2019-12-25 08:41:59] parse_names
[START] [2019-12-25 08:41:59] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 08:41:59] denormalize_canonical_names_to_nodes
[START] [2019-12-25 08:41:59] match_nodes
[START] [2019-12-25 08:41:59] map_all_nodes_to_pages
[STOP] [2019-12-25 08:44:51] map_all_nodes_to_pages
[INFO] [2019-12-25 08:44:51] 102 Unmatched nodes (of 1144)! That's too many to output. First 10: Limnodromus (#62381475); Larus thayeri (#62380453); Chen (#62380437); Chen caerulescens (#62380436); Chen rossii (#62380691); Anas americana (#62380944); Scorpaeniformes (#62380483); Ulcina (#62380522); Gasterosteiformes (#62380550); Maxillopoda (#62380445)
[START] [2019-12-25 08:44:51] update_nodes
[STOP] [2019-12-25 08:44:51] update_nodes
[STOP] [2019-12-25 08:44:51] match_nodes
[START] [2019-12-25 08:44:51] reindex_search
[STOP] [2019-12-25 08:44:53] reindex_search
[START] [2019-12-25 08:44:53] normalize_units
[STOP] [2019-12-25 08:44:53] normalize_units
[START] [2019-12-25 08:44:53] calculate_statistics
[STOP] [2019-12-25 08:44:53] calculate_statistics
[START] [2019-12-25 08:44:53] complete_harvest_instance
[START] [2019-12-25 08:44:53] overall_tsv_creation
[INFO] [2019-12-25 08:44:53] Processing group of 1144 in 1 batches of 10000
[INFO] [2019-12-25 08:46:05] 446 Traits (unfiltered)...
[INFO] [2019-12-25 08:46:18] 446 Traits (filtered)...
[INFO] [2019-12-25 08:46:18] 0 Associations (filtered)...
[INFO] [2019-12-25 08:46:56] 2228 metadata added.
[INFO] [2019-12-25 08:46:56] 0 metadata added.
[INFO] [2019-12-25 08:46:56] Average Time: 78.69
[INFO] [2019-12-25 08:46:56] Total Time: 2m3s
[STOP] [2019-12-25 08:46:56] overall_tsv_creation
[INFO] [2019-12-25 08:46:56] Done. Check your files:
[INFO] [2019-12-25 08:46:57] (1144 lines) /app/public/data/northwestern_pas/publish_nodes.tsv
[INFO] [2019-12-25 08:46:58] (4972 lines) /app/public/data/northwestern_pas/publish_node_ancestors.tsv
[INFO] [2019-12-25 08:46:58] (1144 lines) /app/public/data/northwestern_pas/publish_scientific_names.tsv
[INFO] [2019-12-25 08:46:59] (447 lines) /app/public/data/northwestern_pas/publish_traits.tsv
[INFO] [2019-12-25 08:47:00] (2229 lines) /app/public/data/northwestern_pas/publish_metadata.tsv
[STOP] [2019-12-25 08:47:00] complete_harvest_instance
[START] [2019-12-25 08:47:00] completed
[STOP] [2019-12-25 08:47:00] completed
[STOP] [2019-12-25 08:47:00] logged process, took 331.55
Latest Process

25 Dec 08:41 EXITED currently processing 0