Harvest for Christmas Island Species List Created 12 Oct 05:36

Stage: completed
Fetched: 12 Oct 05:36
Validated: 12 Oct 05:36
Deltas Created 12 Oct 05:36
Units Normalized: 12 Oct 05:39
Ancestry Built: 12 Oct 05:36
Nodes Matched: 12 Oct 05:38
Names Parsed: 12 Oct 05:36
New Models Stored: 12 Oct 05:36
Indexed: 12 Oct 05:39
Completed: 12 Oct 05:40
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 05:36:00 -0400 by logger.rb/56815
[START] [2019-10-12 05:36:00] logged process
[START] [2019-10-12 05:36:00] create_harvest_instance
[STOP] [2019-10-12 05:36:00] create_harvest_instance
[START] [2019-10-12 05:36:00] fetch_files
[STOP] [2019-10-12 05:36:00] fetch_files
[START] [2019-10-12 05:36:00] validate_each_file
[STOP] [2019-10-12 05:36:01] validate_each_file
[START] [2019-10-12 05:36:01] convert_to_csv
[CMD] [2019-10-12 05:36:01] /usr/bin/sort /app/public/converted_csv/christmas_island_refs_15435.csv > /app/public/converted_csv/christmas_island_refs_15435.csv_sorted
[CMD] [2019-10-12 05:36:01] /usr/bin/sort /app/public/converted_csv/christmas_island_nodes_15436.csv > /app/public/converted_csv/christmas_island_nodes_15436.csv_sorted
[CMD] [2019-10-12 05:36:01] /usr/bin/sort /app/public/converted_csv/christmas_island_occurrences_15437.csv > /app/public/converted_csv/christmas_island_occurrences_15437.csv_sorted
[CMD] [2019-10-12 05:36:01] /usr/bin/sort /app/public/converted_csv/christmas_island_measurements_15438.csv > /app/public/converted_csv/christmas_island_measurements_15438.csv_sorted
[STOP] [2019-10-12 05:36:01] convert_to_csv
[START] [2019-10-12 05:36:01] calculate_delta
[CMD] [2019-10-12 05:36:01] echo "0a" > /app/public/diff/christmas_island_refs_15435.diff
[CMD] [2019-10-12 05:36:01] tail -n +1 /app/public/converted_csv/christmas_island_refs_15435.csv >> /app/public/diff/christmas_island_refs_15435.diff
[CMD] [2019-10-12 05:36:01] echo "." >> /app/public/diff/christmas_island_refs_15435.diff
[CMD] [2019-10-12 05:36:01] echo "0a" > /app/public/diff/christmas_island_nodes_15436.diff
[CMD] [2019-10-12 05:36:01] tail -n +1 /app/public/converted_csv/christmas_island_nodes_15436.csv >> /app/public/diff/christmas_island_nodes_15436.diff
[CMD] [2019-10-12 05:36:01] echo "." >> /app/public/diff/christmas_island_nodes_15436.diff
[CMD] [2019-10-12 05:36:01] echo "0a" > /app/public/diff/christmas_island_occurrences_15437.diff
[CMD] [2019-10-12 05:36:02] tail -n +1 /app/public/converted_csv/christmas_island_occurrences_15437.csv >> /app/public/diff/christmas_island_occurrences_15437.diff
[CMD] [2019-10-12 05:36:02] echo "." >> /app/public/diff/christmas_island_occurrences_15437.diff
[CMD] [2019-10-12 05:36:02] echo "0a" > /app/public/diff/christmas_island_measurements_15438.diff
[CMD] [2019-10-12 05:36:02] tail -n +1 /app/public/converted_csv/christmas_island_measurements_15438.csv >> /app/public/diff/christmas_island_measurements_15438.diff
[CMD] [2019-10-12 05:36:02] echo "." >> /app/public/diff/christmas_island_measurements_15438.diff
[STOP] [2019-10-12 05:36:02] calculate_delta
[START] [2019-10-12 05:36:02] parse_diff_and_store
[INFO] [2019-10-12 05:36:02] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 05:36:02] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 05:36:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 05:36:04] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 05:36:14] Storing 2 References
[INFO] [2019-10-12 05:36:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 05:36:14] Average Time: 0.0
[INFO] [2019-10-12 05:36:14] Total Time: 1s
[INFO] [2019-10-12 05:36:14] Storing 3226 ScientificNames
[INFO] [2019-10-12 05:36:14] Processing group of 3226 in 4 groups of 1000
[INFO] [2019-10-12 05:36:15] Average Time: 0.325
[INFO] [2019-10-12 05:36:15] Total Time: 2s
[INFO] [2019-10-12 05:36:15] Storing 3226 Nodes
[INFO] [2019-10-12 05:36:15] Processing group of 3226 in 4 groups of 1000
[INFO] [2019-10-12 05:36:16] Average Time: 0.263
[INFO] [2019-10-12 05:36:16] Total Time: 2s
[INFO] [2019-10-12 05:36:16] Storing 1446 Occurrences
[INFO] [2019-10-12 05:36:16] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-12 05:36:16] Average Time: 0.08
[INFO] [2019-10-12 05:36:16] Total Time: 1s
[INFO] [2019-10-12 05:36:16] Storing 3490 TraitsReferences
[INFO] [2019-10-12 05:36:16] Processing group of 3490 in 4 groups of 1000
[INFO] [2019-10-12 05:36:17] Average Time: 0.083
[INFO] [2019-10-12 05:36:17] Total Time: 1s
[INFO] [2019-10-12 05:36:17] Storing 3489 Traits
[INFO] [2019-10-12 05:36:17] Processing group of 3489 in 4 groups of 1000
[INFO] [2019-10-12 05:36:18] Average Time: 0.272
[INFO] [2019-10-12 05:36:18] Total Time: 2s
[INFO] [2019-10-12 05:36:18] Storing 3489 MetaTraits
[INFO] [2019-10-12 05:36:18] Processing group of 3489 in 4 groups of 1000
[INFO] [2019-10-12 05:36:18] Average Time: 0.105
[INFO] [2019-10-12 05:36:18] Total Time: 1s
[STOP] [2019-10-12 05:36:18] parse_diff_and_store
[START] [2019-10-12 05:36:18] resolve_keys
[INFO] [2019-10-12 05:36:34] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 05:36:35] traits to occurrences...
[INFO] [2019-10-12 05:36:36] traits to nodes (through occurrences)...
[INFO] [2019-10-12 05:36:36] Traits to sex term...
[INFO] [2019-10-12 05:36:37] Traits to lifestage term...
[INFO] [2019-10-12 05:36:37] MetaTraits to traits...
[INFO] [2019-10-12 05:36:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 05:36:38] Assocs to occurrences...
[INFO] [2019-10-12 05:36:38] Assocs to nodes...
[INFO] [2019-10-12 05:36:38] Assoc to sex term...
[INFO] [2019-10-12 05:36:38] Assoc to lifestage term...
[STOP] [2019-10-12 05:36:38] resolve_keys
[START] [2019-10-12 05:36:38] hold_for_later_1
[STOP] [2019-10-12 05:36:38] hold_for_later_1
[START] [2019-10-12 05:36:38] hold_for_later_2
[STOP] [2019-10-12 05:36:38] hold_for_later_2
[START] [2019-10-12 05:36:38] resolve_missing_parents
[STOP] [2019-10-12 05:36:45] resolve_missing_parents
[START] [2019-10-12 05:36:45] rebuild_nodes
[START] [2019-10-12 05:36:45] Flattener#flatten
[START] [2019-10-12 05:36:45] Flattener#study_resource
[START] [2019-10-12 05:36:45] Flattener#build_ancestry
[STOP] [2019-10-12 05:36:46] Flattener#build_ancestry
[INFO] [2019-10-12 05:36:46] 3226 ancestry keys
[START] [2019-10-12 05:36:46] build_node_ancestors
[INFO] [2019-10-12 05:36:46] old ancestors deleted.
[STOP] [2019-10-12 05:36:46] build_node_ancestors
[START] [2019-10-12 05:36:47] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 05:36:47] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 05:36:47] Flattener#flatten
[STOP] [2019-10-12 05:36:47] rebuild_nodes
[START] [2019-10-12 05:36:47] resolve_missing_media_owners
[STOP] [2019-10-12 05:36:47] resolve_missing_media_owners
[START] [2019-10-12 05:36:47] sanitize_media_verbatims
[STOP] [2019-10-12 05:36:47] sanitize_media_verbatims
[START] [2019-10-12 05:36:47] queue_downloads
[STOP] [2019-10-12 05:36:47] queue_downloads
[START] [2019-10-12 05:36:47] parse_names
[WARN] [2019-10-12 05:36:47] I see 3226 names which still need to be parsed.
[STOP] [2019-10-12 05:36:51] parse_names
[START] [2019-10-12 05:36:51] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 05:36:51] denormalize_canonical_names_to_nodes
[START] [2019-10-12 05:36:51] match_nodes
[START] [2019-10-12 05:36:51] map_all_nodes_to_pages
[STOP] [2019-10-12 05:38:54] map_all_nodes_to_pages
[INFO] [2019-10-12 05:38:54] 96 Unmatched nodes (of 3226)! That's too many to output. First 10: Locustella certhiola (#49206371); Pelamis (#49206057); Onychoprion fuscata (#49205256); Procelsterna (#49206410); Procelsterna cerulea (#49206409); Thalaseus (#49207308); Thalaseus bergii (#49207307); Porites belli (#49205908); Pectiniidae (#49204474); Mussidae (#49205056)
[START] [2019-10-12 05:38:54] update_nodes
[STOP] [2019-10-12 05:38:55] update_nodes
[STOP] [2019-10-12 05:38:55] match_nodes
[START] [2019-10-12 05:38:55] reindex_search
[STOP] [2019-10-12 05:39:01] reindex_search
[START] [2019-10-12 05:39:01] normalize_units
[STOP] [2019-10-12 05:39:01] normalize_units
[START] [2019-10-12 05:39:01] calculate_statistics
[STOP] [2019-10-12 05:39:01] calculate_statistics
[START] [2019-10-12 05:39:01] complete_harvest_instance
[START] [2019-10-12 05:39:01] overall_tsv_creation
[INFO] [2019-10-12 05:39:01] Processing group of 3226 in 1 batches of 10000
[INFO] [2019-10-12 05:40:00] 1446 Traits (unfiltered)...
[INFO] [2019-10-12 05:40:14] 1446 Traits (filtered)...
[INFO] [2019-10-12 05:40:14] 0 Associations (filtered)...
[INFO] [2019-10-12 05:40:54] 7230 metadata added.
[INFO] [2019-10-12 05:40:54] 0 metadata added.
[INFO] [2019-10-12 05:40:54] Average Time: 89.8
[INFO] [2019-10-12 05:40:54] Total Time: 1m53s
[STOP] [2019-10-12 05:40:54] overall_tsv_creation
[INFO] [2019-10-12 05:40:54] Done. Check your files:
[INFO] [2019-10-12 05:40:54] (3226 lines) /app/public/data/christmas_island/publish_nodes.tsv
[INFO] [2019-10-12 05:40:54] (6705 lines) /app/public/data/christmas_island/publish_node_ancestors.tsv
[INFO] [2019-10-12 05:40:55] (3226 lines) /app/public/data/christmas_island/publish_scientific_names.tsv
[INFO] [2019-10-12 05:40:55] (1447 lines) /app/public/data/christmas_island/publish_traits.tsv
[INFO] [2019-10-12 05:40:55] (7231 lines) /app/public/data/christmas_island/publish_metadata.tsv
[STOP] [2019-10-12 05:40:55] complete_harvest_instance
[START] [2019-10-12 05:40:55] completed
[STOP] [2019-10-12 05:40:55] completed
[STOP] [2019-10-12 05:40:55] logged process, took 295.47
Latest Process

12 Oct 05:36 EXITED currently processing 0