Harvest for Nauru Species List Created 14 Oct 11:30

Stage: completed
Fetched: 14 Oct 11:30
Validated: 14 Oct 11:30
Deltas Created 14 Oct 11:30
Units Normalized: 14 Oct 11:31
Ancestry Built: 14 Oct 11:30
Nodes Matched: 14 Oct 11:31
Names Parsed: 14 Oct 11:30
New Models Stored: 14 Oct 11:30
Indexed: 14 Oct 11:31
Completed: 14 Oct 11:33
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 11:30:41 -0400 by logger.rb/56815
[START] [2019-10-14 11:30:41] logged process
[START] [2019-10-14 11:30:41] create_harvest_instance
[STOP] [2019-10-14 11:30:42] create_harvest_instance
[START] [2019-10-14 11:30:42] fetch_files
[STOP] [2019-10-14 11:30:42] fetch_files
[START] [2019-10-14 11:30:42] validate_each_file
[STOP] [2019-10-14 11:30:42] validate_each_file
[START] [2019-10-14 11:30:42] convert_to_csv
[CMD] [2019-10-14 11:30:42] /usr/bin/sort /app/public/converted_csv/nauru_sp_list_refs_16675.csv > /app/public/converted_csv/nauru_sp_list_refs_16675.csv_sorted
[CMD] [2019-10-14 11:30:42] /usr/bin/sort /app/public/converted_csv/nauru_sp_list_nodes_16676.csv > /app/public/converted_csv/nauru_sp_list_nodes_16676.csv_sorted
[CMD] [2019-10-14 11:30:42] /usr/bin/sort /app/public/converted_csv/nauru_sp_list_occurrences_16677.csv > /app/public/converted_csv/nauru_sp_list_occurrences_16677.csv_sorted
[CMD] [2019-10-14 11:30:42] /usr/bin/sort /app/public/converted_csv/nauru_sp_list_measurements_16678.csv > /app/public/converted_csv/nauru_sp_list_measurements_16678.csv_sorted
[STOP] [2019-10-14 11:30:42] convert_to_csv
[START] [2019-10-14 11:30:42] calculate_delta
[CMD] [2019-10-14 11:30:42] echo "0a" > /app/public/diff/nauru_sp_list_refs_16675.diff
[CMD] [2019-10-14 11:30:42] tail -n +1 /app/public/converted_csv/nauru_sp_list_refs_16675.csv >> /app/public/diff/nauru_sp_list_refs_16675.diff
[CMD] [2019-10-14 11:30:42] echo "." >> /app/public/diff/nauru_sp_list_refs_16675.diff
[CMD] [2019-10-14 11:30:42] echo "0a" > /app/public/diff/nauru_sp_list_nodes_16676.diff
[CMD] [2019-10-14 11:30:42] tail -n +1 /app/public/converted_csv/nauru_sp_list_nodes_16676.csv >> /app/public/diff/nauru_sp_list_nodes_16676.diff
[CMD] [2019-10-14 11:30:43] echo "." >> /app/public/diff/nauru_sp_list_nodes_16676.diff
[CMD] [2019-10-14 11:30:43] echo "0a" > /app/public/diff/nauru_sp_list_occurrences_16677.diff
[CMD] [2019-10-14 11:30:43] tail -n +1 /app/public/converted_csv/nauru_sp_list_occurrences_16677.csv >> /app/public/diff/nauru_sp_list_occurrences_16677.diff
[CMD] [2019-10-14 11:30:43] echo "." >> /app/public/diff/nauru_sp_list_occurrences_16677.diff
[CMD] [2019-10-14 11:30:43] echo "0a" > /app/public/diff/nauru_sp_list_measurements_16678.diff
[CMD] [2019-10-14 11:30:43] tail -n +1 /app/public/converted_csv/nauru_sp_list_measurements_16678.csv >> /app/public/diff/nauru_sp_list_measurements_16678.diff
[CMD] [2019-10-14 11:30:43] echo "." >> /app/public/diff/nauru_sp_list_measurements_16678.diff
[STOP] [2019-10-14 11:30:43] calculate_delta
[START] [2019-10-14 11:30:43] parse_diff_and_store
[INFO] [2019-10-14 11:30:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 11:30:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 11:30:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 11:30:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 11:30:44] Storing 2 References
[INFO] [2019-10-14 11:30:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.0
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[INFO] [2019-10-14 11:30:45] Storing 286 ScientificNames
[INFO] [2019-10-14 11:30:45] Processing group of 286 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.19
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[INFO] [2019-10-14 11:30:45] Storing 286 Nodes
[INFO] [2019-10-14 11:30:45] Processing group of 286 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.33
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[INFO] [2019-10-14 11:30:45] Storing 127 Occurrences
[INFO] [2019-10-14 11:30:45] Processing group of 127 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.03
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[INFO] [2019-10-14 11:30:45] Storing 254 TraitsReferences
[INFO] [2019-10-14 11:30:45] Processing group of 254 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.1
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[INFO] [2019-10-14 11:30:45] Storing 254 Traits
[INFO] [2019-10-14 11:30:45] Processing group of 254 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.16
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[INFO] [2019-10-14 11:30:45] Storing 254 MetaTraits
[INFO] [2019-10-14 11:30:45] Processing group of 254 in 1 groups of 1000
[INFO] [2019-10-14 11:30:45] Average Time: 0.06
[INFO] [2019-10-14 11:30:45] Total Time: 1s
[STOP] [2019-10-14 11:30:45] parse_diff_and_store
[START] [2019-10-14 11:30:45] resolve_keys
[INFO] [2019-10-14 11:30:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 11:30:50] traits to occurrences...
[INFO] [2019-10-14 11:30:50] traits to nodes (through occurrences)...
[INFO] [2019-10-14 11:30:50] Traits to sex term...
[INFO] [2019-10-14 11:30:50] Traits to lifestage term...
[INFO] [2019-10-14 11:30:50] MetaTraits to traits...
[INFO] [2019-10-14 11:30:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 11:30:50] Assocs to occurrences...
[INFO] [2019-10-14 11:30:50] Assocs to nodes...
[INFO] [2019-10-14 11:30:50] Assoc to sex term...
[INFO] [2019-10-14 11:30:50] Assoc to lifestage term...
[STOP] [2019-10-14 11:30:50] resolve_keys
[START] [2019-10-14 11:30:50] hold_for_later_1
[STOP] [2019-10-14 11:30:50] hold_for_later_1
[START] [2019-10-14 11:30:50] hold_for_later_2
[STOP] [2019-10-14 11:30:50] hold_for_later_2
[START] [2019-10-14 11:30:50] resolve_missing_parents
[STOP] [2019-10-14 11:30:50] resolve_missing_parents
[START] [2019-10-14 11:30:50] rebuild_nodes
[START] [2019-10-14 11:30:50] Flattener#flatten
[START] [2019-10-14 11:30:50] Flattener#study_resource
[START] [2019-10-14 11:30:50] Flattener#build_ancestry
[STOP] [2019-10-14 11:30:50] Flattener#build_ancestry
[INFO] [2019-10-14 11:30:50] 286 ancestry keys
[START] [2019-10-14 11:30:50] build_node_ancestors
[INFO] [2019-10-14 11:30:50] old ancestors deleted.
[STOP] [2019-10-14 11:30:50] build_node_ancestors
[START] [2019-10-14 11:30:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:30:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:30:50] Flattener#flatten
[STOP] [2019-10-14 11:30:50] rebuild_nodes
[START] [2019-10-14 11:30:50] resolve_missing_media_owners
[STOP] [2019-10-14 11:30:50] resolve_missing_media_owners
[START] [2019-10-14 11:30:50] sanitize_media_verbatims
[STOP] [2019-10-14 11:30:50] sanitize_media_verbatims
[START] [2019-10-14 11:30:50] queue_downloads
[STOP] [2019-10-14 11:30:50] queue_downloads
[START] [2019-10-14 11:30:50] parse_names
[WARN] [2019-10-14 11:30:50] I see 286 names which still need to be parsed.
[STOP] [2019-10-14 11:30:52] parse_names
[START] [2019-10-14 11:30:52] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 11:30:52] denormalize_canonical_names_to_nodes
[START] [2019-10-14 11:30:52] match_nodes
[START] [2019-10-14 11:30:52] map_all_nodes_to_pages
[STOP] [2019-10-14 11:31:30] map_all_nodes_to_pages
[INFO] [2019-10-14 11:31:30] 27 Unmatched nodes (of 286)! That's too many to output. First 10: Canarium mutabilis (#50861066); Thalessa (#50860847); Drupinia (#50861056); Drupinia grossularia (#50861055); Thais aculeata (#50860966); Thais squamosa (#50861026); Coralliophilidae (#50860997); Oliva annulata (#50861045); Neotaenioglossa (#50860845); Erosaria (#50860905)
[START] [2019-10-14 11:31:30] update_nodes
[STOP] [2019-10-14 11:31:30] update_nodes
[STOP] [2019-10-14 11:31:30] match_nodes
[START] [2019-10-14 11:31:30] reindex_search
[STOP] [2019-10-14 11:31:31] reindex_search
[START] [2019-10-14 11:31:31] normalize_units
[STOP] [2019-10-14 11:31:31] normalize_units
[START] [2019-10-14 11:31:31] calculate_statistics
[STOP] [2019-10-14 11:31:31] calculate_statistics
[START] [2019-10-14 11:31:31] complete_harvest_instance
[START] [2019-10-14 11:31:31] overall_tsv_creation
[INFO] [2019-10-14 11:31:31] Processing group of 286 in 1 batches of 10000
[INFO] [2019-10-14 11:32:16] 127 Traits (unfiltered)...
[INFO] [2019-10-14 11:32:29] 127 Traits (filtered)...
[INFO] [2019-10-14 11:32:29] 0 Associations (filtered)...
[INFO] [2019-10-14 11:33:06] 635 metadata added.
[INFO] [2019-10-14 11:33:06] 0 metadata added.
[INFO] [2019-10-14 11:33:06] Average Time: 74.34
[INFO] [2019-10-14 11:33:06] Total Time: 1m35s
[STOP] [2019-10-14 11:33:06] overall_tsv_creation
[INFO] [2019-10-14 11:33:06] Done. Check your files:
[INFO] [2019-10-14 11:33:06] (286 lines) /app/public/data/nauru_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 11:33:06] (1312 lines) /app/public/data/nauru_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 11:33:06] (286 lines) /app/public/data/nauru_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 11:33:06] (128 lines) /app/public/data/nauru_sp_list/publish_traits.tsv
[INFO] [2019-10-14 11:33:06] (636 lines) /app/public/data/nauru_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 11:33:06] complete_harvest_instance
[START] [2019-10-14 11:33:06] completed
[STOP] [2019-10-14 11:33:06] completed
[STOP] [2019-10-14 11:33:06] logged process, took 145.3
Latest Process

14 Oct 11:30 EXITED currently processing 0