Harvest for Falkland Islands Species List Created 12 Oct 20:38

Stage: completed
Fetched: 12 Oct 20:38
Validated: 12 Oct 20:38
Deltas Created 12 Oct 20:38
Units Normalized: 12 Oct 20:42
Ancestry Built: 12 Oct 20:39
Nodes Matched: 12 Oct 20:42
Names Parsed: 12 Oct 20:39
New Models Stored: 12 Oct 20:38
Indexed: 12 Oct 20:42
Completed: 12 Oct 20:44
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 20:38:36 -0400 by logger.rb/56815
[START] [2019-10-12 20:38:36] logged process
[START] [2019-10-12 20:38:36] create_harvest_instance
[STOP] [2019-10-12 20:38:37] create_harvest_instance
[START] [2019-10-12 20:38:37] fetch_files
[STOP] [2019-10-12 20:38:37] fetch_files
[START] [2019-10-12 20:38:37] validate_each_file
[STOP] [2019-10-12 20:38:37] validate_each_file
[START] [2019-10-12 20:38:37] convert_to_csv
[CMD] [2019-10-12 20:38:37] /usr/bin/sort /app/public/converted_csv/falkland_islands_refs_15731.csv > /app/public/converted_csv/falkland_islands_refs_15731.csv_sorted
[CMD] [2019-10-12 20:38:37] /usr/bin/sort /app/public/converted_csv/falkland_islands_nodes_15732.csv > /app/public/converted_csv/falkland_islands_nodes_15732.csv_sorted
[CMD] [2019-10-12 20:38:37] /usr/bin/sort /app/public/converted_csv/falkland_islands_occurrences_15733.csv > /app/public/converted_csv/falkland_islands_occurrences_15733.csv_sorted
[CMD] [2019-10-12 20:38:37] /usr/bin/sort /app/public/converted_csv/falkland_islands_measurements_15734.csv > /app/public/converted_csv/falkland_islands_measurements_15734.csv_sorted
[STOP] [2019-10-12 20:38:37] convert_to_csv
[START] [2019-10-12 20:38:37] calculate_delta
[CMD] [2019-10-12 20:38:37] echo "0a" > /app/public/diff/falkland_islands_refs_15731.diff
[CMD] [2019-10-12 20:38:38] tail -n +1 /app/public/converted_csv/falkland_islands_refs_15731.csv >> /app/public/diff/falkland_islands_refs_15731.diff
[CMD] [2019-10-12 20:38:38] echo "." >> /app/public/diff/falkland_islands_refs_15731.diff
[CMD] [2019-10-12 20:38:38] echo "0a" > /app/public/diff/falkland_islands_nodes_15732.diff
[CMD] [2019-10-12 20:38:38] tail -n +1 /app/public/converted_csv/falkland_islands_nodes_15732.csv >> /app/public/diff/falkland_islands_nodes_15732.diff
[CMD] [2019-10-12 20:38:38] echo "." >> /app/public/diff/falkland_islands_nodes_15732.diff
[CMD] [2019-10-12 20:38:38] echo "0a" > /app/public/diff/falkland_islands_occurrences_15733.diff
[CMD] [2019-10-12 20:38:38] tail -n +1 /app/public/converted_csv/falkland_islands_occurrences_15733.csv >> /app/public/diff/falkland_islands_occurrences_15733.diff
[CMD] [2019-10-12 20:38:38] echo "." >> /app/public/diff/falkland_islands_occurrences_15733.diff
[CMD] [2019-10-12 20:38:38] echo "0a" > /app/public/diff/falkland_islands_measurements_15734.diff
[CMD] [2019-10-12 20:38:38] tail -n +1 /app/public/converted_csv/falkland_islands_measurements_15734.csv >> /app/public/diff/falkland_islands_measurements_15734.diff
[CMD] [2019-10-12 20:38:38] echo "." >> /app/public/diff/falkland_islands_measurements_15734.diff
[STOP] [2019-10-12 20:38:39] calculate_delta
[START] [2019-10-12 20:38:39] parse_diff_and_store
[INFO] [2019-10-12 20:38:39] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 20:38:39] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 20:38:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 20:38:40] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 20:38:48] Storing 2 References
[INFO] [2019-10-12 20:38:48] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 20:38:48] Average Time: 0.0
[INFO] [2019-10-12 20:38:48] Total Time: 1s
[INFO] [2019-10-12 20:38:48] Storing 2796 ScientificNames
[INFO] [2019-10-12 20:38:48] Processing group of 2796 in 3 groups of 1000
[INFO] [2019-10-12 20:38:49] Average Time: 0.38
[INFO] [2019-10-12 20:38:49] Total Time: 2s
[INFO] [2019-10-12 20:38:49] Storing 2796 Nodes
[INFO] [2019-10-12 20:38:49] Processing group of 2796 in 3 groups of 1000
[INFO] [2019-10-12 20:38:50] Average Time: 0.33
[INFO] [2019-10-12 20:38:50] Total Time: 2s
[INFO] [2019-10-12 20:38:50] Storing 964 Occurrences
[INFO] [2019-10-12 20:38:50] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-12 20:38:51] Average Time: 0.13
[INFO] [2019-10-12 20:38:51] Total Time: 1s
[INFO] [2019-10-12 20:38:51] Storing 2810 TraitsReferences
[INFO] [2019-10-12 20:38:51] Processing group of 2810 in 3 groups of 1000
[INFO] [2019-10-12 20:38:51] Average Time: 0.1
[INFO] [2019-10-12 20:38:51] Total Time: 1s
[INFO] [2019-10-12 20:38:51] Storing 2809 Traits
[INFO] [2019-10-12 20:38:51] Processing group of 2809 in 3 groups of 1000
[INFO] [2019-10-12 20:38:52] Average Time: 0.323
[INFO] [2019-10-12 20:38:52] Total Time: 1s
[INFO] [2019-10-12 20:38:52] Storing 2801 MetaTraits
[INFO] [2019-10-12 20:38:52] Processing group of 2801 in 3 groups of 1000
[INFO] [2019-10-12 20:38:52] Average Time: 0.127
[INFO] [2019-10-12 20:38:52] Total Time: 1s
[STOP] [2019-10-12 20:38:52] parse_diff_and_store
[START] [2019-10-12 20:38:52] resolve_keys
[INFO] [2019-10-12 20:39:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 20:39:07] traits to occurrences...
[INFO] [2019-10-12 20:39:07] traits to nodes (through occurrences)...
[INFO] [2019-10-12 20:39:07] Traits to sex term...
[INFO] [2019-10-12 20:39:08] Traits to lifestage term...
[INFO] [2019-10-12 20:39:08] MetaTraits to traits...
[INFO] [2019-10-12 20:39:08] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 20:39:09] Assocs to occurrences...
[INFO] [2019-10-12 20:39:09] Assocs to nodes...
[INFO] [2019-10-12 20:39:09] Assoc to sex term...
[INFO] [2019-10-12 20:39:09] Assoc to lifestage term...
[STOP] [2019-10-12 20:39:09] resolve_keys
[START] [2019-10-12 20:39:09] hold_for_later_1
[STOP] [2019-10-12 20:39:09] hold_for_later_1
[START] [2019-10-12 20:39:09] hold_for_later_2
[STOP] [2019-10-12 20:39:09] hold_for_later_2
[START] [2019-10-12 20:39:09] resolve_missing_parents
[STOP] [2019-10-12 20:39:14] resolve_missing_parents
[START] [2019-10-12 20:39:14] rebuild_nodes
[START] [2019-10-12 20:39:14] Flattener#flatten
[START] [2019-10-12 20:39:14] Flattener#study_resource
[START] [2019-10-12 20:39:14] Flattener#build_ancestry
[STOP] [2019-10-12 20:39:16] Flattener#build_ancestry
[INFO] [2019-10-12 20:39:16] 2796 ancestry keys
[START] [2019-10-12 20:39:16] build_node_ancestors
[INFO] [2019-10-12 20:39:16] old ancestors deleted.
[STOP] [2019-10-12 20:39:16] build_node_ancestors
[START] [2019-10-12 20:39:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:39:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:39:17] Flattener#flatten
[STOP] [2019-10-12 20:39:17] rebuild_nodes
[START] [2019-10-12 20:39:17] resolve_missing_media_owners
[STOP] [2019-10-12 20:39:17] resolve_missing_media_owners
[START] [2019-10-12 20:39:17] sanitize_media_verbatims
[STOP] [2019-10-12 20:39:17] sanitize_media_verbatims
[START] [2019-10-12 20:39:17] queue_downloads
[STOP] [2019-10-12 20:39:17] queue_downloads
[START] [2019-10-12 20:39:17] parse_names
[WARN] [2019-10-12 20:39:17] I see 2796 names which still need to be parsed.
[STOP] [2019-10-12 20:39:20] parse_names
[START] [2019-10-12 20:39:20] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 20:39:20] denormalize_canonical_names_to_nodes
[START] [2019-10-12 20:39:20] match_nodes
[START] [2019-10-12 20:39:20] map_all_nodes_to_pages
[STOP] [2019-10-12 20:42:00] map_all_nodes_to_pages
[INFO] [2019-10-12 20:42:00] 266 Unmatched nodes (of 2796)! That's too many to output. First 10: Eudyptes crestatus (#49638573); Chloephaga leucoptera (#49638495); Anas sibilatrix (#49635927); Anas versicolor (#49635936); Anas platalea (#49637623); Leucophaeus scoresbyi (#49637546); Stercorarius antarctica (#49636042); Puffinus griseus (#49635914); Puffinus grisea (#49638450); Pelecanoididae (#49635981)
[START] [2019-10-12 20:42:00] update_nodes
[STOP] [2019-10-12 20:42:01] update_nodes
[STOP] [2019-10-12 20:42:01] match_nodes
[START] [2019-10-12 20:42:01] reindex_search
[STOP] [2019-10-12 20:42:08] reindex_search
[START] [2019-10-12 20:42:08] normalize_units
[STOP] [2019-10-12 20:42:08] normalize_units
[START] [2019-10-12 20:42:08] calculate_statistics
[STOP] [2019-10-12 20:42:08] calculate_statistics
[START] [2019-10-12 20:42:08] complete_harvest_instance
[START] [2019-10-12 20:42:08] overall_tsv_creation
[INFO] [2019-10-12 20:42:08] Processing group of 2796 in 1 batches of 10000
[INFO] [2019-10-12 20:43:07] 964 Traits (unfiltered)...
[INFO] [2019-10-12 20:43:21] 964 Traits (filtered)...
[INFO] [2019-10-12 20:43:21] 0 Associations (filtered)...
[INFO] [2019-10-12 20:44:00] 4816 metadata added.
[INFO] [2019-10-12 20:44:00] 0 metadata added.
[INFO] [2019-10-12 20:44:00] Average Time: 89.14
[INFO] [2019-10-12 20:44:00] Total Time: 1m52s
[STOP] [2019-10-12 20:44:00] overall_tsv_creation
[INFO] [2019-10-12 20:44:00] Done. Check your files:
[INFO] [2019-10-12 20:44:00] (2796 lines) /app/public/data/falkland_islands/publish_nodes.tsv
[INFO] [2019-10-12 20:44:00] (5816 lines) /app/public/data/falkland_islands/publish_node_ancestors.tsv
[INFO] [2019-10-12 20:44:00] (2796 lines) /app/public/data/falkland_islands/publish_scientific_names.tsv
[INFO] [2019-10-12 20:44:00] (965 lines) /app/public/data/falkland_islands/publish_traits.tsv
[INFO] [2019-10-12 20:44:00] (4817 lines) /app/public/data/falkland_islands/publish_metadata.tsv
[STOP] [2019-10-12 20:44:00] complete_harvest_instance
[START] [2019-10-12 20:44:00] completed
[STOP] [2019-10-12 20:44:00] completed
[STOP] [2019-10-12 20:44:00] logged process, took 324.26
Latest Process

12 Oct 20:38 EXITED currently processing 0