Harvest for Arctic Register of Marine Species Created 25 Nov 10:00

Harvesting Log

# Logfile created on 2019-11-25 10:00:19 -0500 by logger.rb/56815
[START] [2019-11-25 10:00:19] logged process
[START] [2019-11-25 10:00:19] create_harvest_instance
[STOP] [2019-11-25 10:00:20] create_harvest_instance
[START] [2019-11-25 10:00:20] fetch_files
[STOP] [2019-11-25 10:00:20] fetch_files
[START] [2019-11-25 10:00:20] validate_each_file
[STOP] [2019-11-25 10:00:22] validate_each_file
[START] [2019-11-25 10:00:22] convert_to_csv
[CMD] [2019-11-25 10:00:22] /usr/bin/sort /app/public/converted_csv/Arctic_Register__nodes_18753.csv > /app/public/converted_csv/Arctic_Register__nodes_18753.csv_sorted
[CMD] [2019-11-25 10:00:22] /usr/bin/sort /app/public/converted_csv/Arctic_Register__occurrences_18754.csv > /app/public/converted_csv/Arctic_Register__occurrences_18754.csv_sorted
[CMD] [2019-11-25 10:00:23] /usr/bin/sort /app/public/converted_csv/Arctic_Register__measurements_18755.csv > /app/public/converted_csv/Arctic_Register__measurements_18755.csv_sorted
[STOP] [2019-11-25 10:00:23] convert_to_csv
[START] [2019-11-25 10:00:23] calculate_delta
[CMD] [2019-11-25 10:00:23] echo "0a" > /app/public/diff/Arctic_Register__nodes_18753.diff
[CMD] [2019-11-25 10:00:23] tail -n +1 /app/public/converted_csv/Arctic_Register__nodes_18753.csv >> /app/public/diff/Arctic_Register__nodes_18753.diff
[CMD] [2019-11-25 10:00:23] echo "." >> /app/public/diff/Arctic_Register__nodes_18753.diff
[CMD] [2019-11-25 10:00:23] echo "0a" > /app/public/diff/Arctic_Register__occurrences_18754.diff
[CMD] [2019-11-25 10:00:24] tail -n +1 /app/public/converted_csv/Arctic_Register__occurrences_18754.csv >> /app/public/diff/Arctic_Register__occurrences_18754.diff
[CMD] [2019-11-25 10:00:24] echo "." >> /app/public/diff/Arctic_Register__occurrences_18754.diff
[CMD] [2019-11-25 10:00:24] echo "0a" > /app/public/diff/Arctic_Register__measurements_18755.diff
[CMD] [2019-11-25 10:00:24] tail -n +1 /app/public/converted_csv/Arctic_Register__measurements_18755.csv >> /app/public/diff/Arctic_Register__measurements_18755.diff
[CMD] [2019-11-25 10:00:25] echo "." >> /app/public/diff/Arctic_Register__measurements_18755.diff
[STOP] [2019-11-25 10:00:25] calculate_delta
[START] [2019-11-25 10:00:25] parse_diff_and_store
[INFO] [2019-11-25 10:00:25] Loading nodes diff file into memory (true lines)...
[WARN] [2019-11-25 10:00:29] Filtered Scientific Name `Triconia minuta (Giesbrecht, 1893 ["1892"])` to `Triconia minuta (Giesbrecht, 1893 [1892])`
[INFO] [2019-11-25 10:00:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-25 10:00:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-25 10:00:49] Storing 6026 ScientificNames
[INFO] [2019-11-25 10:00:49] Processing group of 6026 in 7 groups of 1000
[INFO] [2019-11-25 10:00:51] Average Time: 0.32
[INFO] [2019-11-25 10:00:51] Total Time: 3s
[INFO] [2019-11-25 10:00:51] last 3 / first 3: 0.6
[INFO] [2019-11-25 10:00:51] Std.Dev: 0.1414213562373095; Max: 0.45
[INFO] [2019-11-25 10:00:51] Storing 6026 Nodes
[INFO] [2019-11-25 10:00:51] Processing group of 6026 in 7 groups of 1000
[INFO] [2019-11-25 10:00:53] Average Time: 0.253
[INFO] [2019-11-25 10:00:53] Total Time: 2s
[INFO] [2019-11-25 10:00:53] last 3 / first 3: 0.69
[INFO] [2019-11-25 10:00:53] Std.Dev: 0.10954451150103323; Max: 0.35
[INFO] [2019-11-25 10:00:53] Storing 4142 Occurrences
[INFO] [2019-11-25 10:00:53] Processing group of 4142 in 5 groups of 1000
[INFO] [2019-11-25 10:00:53] Average Time: 0.086
[INFO] [2019-11-25 10:00:53] Total Time: 1s
[INFO] [2019-11-25 10:00:53] Storing 4242 Traits
[INFO] [2019-11-25 10:00:53] Processing group of 4242 in 5 groups of 1000
[INFO] [2019-11-25 10:00:54] Average Time: 0.256
[INFO] [2019-11-25 10:00:54] Total Time: 2s
[INFO] [2019-11-25 10:00:54] Storing 8484 MetaTraits
[INFO] [2019-11-25 10:00:54] Processing group of 8484 in 9 groups of 1000
[INFO] [2019-11-25 10:00:56] Average Time: 0.119
[INFO] [2019-11-25 10:00:56] Total Time: 2s
[INFO] [2019-11-25 10:00:56] last 3 / first 3: 0.65
[INFO] [2019-11-25 10:00:56] Std.Dev: 0.03162277660168379; Max: 0.17
[STOP] [2019-11-25 10:00:56] parse_diff_and_store
[START] [2019-11-25 10:00:56] resolve_keys
[INFO] [2019-11-25 10:01:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-25 10:01:01] traits to occurrences...
[INFO] [2019-11-25 10:01:01] traits to nodes (through occurrences)...
[INFO] [2019-11-25 10:01:02] Traits to sex term...
[INFO] [2019-11-25 10:01:02] Traits to lifestage term...
[INFO] [2019-11-25 10:01:02] MetaTraits to traits...
[INFO] [2019-11-25 10:01:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-25 10:01:02] Assocs to occurrences...
[INFO] [2019-11-25 10:01:02] Assocs to nodes...
[INFO] [2019-11-25 10:01:02] Assoc to sex term...
[INFO] [2019-11-25 10:01:02] Assoc to lifestage term...
[STOP] [2019-11-25 10:01:02] resolve_keys
[START] [2019-11-25 10:01:02] hold_for_later_1
[STOP] [2019-11-25 10:01:02] hold_for_later_1
[START] [2019-11-25 10:01:02] hold_for_later_2
[STOP] [2019-11-25 10:01:02] hold_for_later_2
[START] [2019-11-25 10:01:02] resolve_missing_parents
[STOP] [2019-11-25 10:01:03] resolve_missing_parents
[START] [2019-11-25 10:01:03] rebuild_nodes
[START] [2019-11-25 10:01:03] Flattener#flatten
[START] [2019-11-25 10:01:03] Flattener#study_resource
[START] [2019-11-25 10:01:03] Flattener#build_ancestry
[STOP] [2019-11-25 10:01:03] Flattener#build_ancestry
[INFO] [2019-11-25 10:01:03] 6026 ancestry keys
[START] [2019-11-25 10:01:03] build_node_ancestors
[INFO] [2019-11-25 10:01:03] old ancestors deleted.
[STOP] [2019-11-25 10:01:04] build_node_ancestors
[START] [2019-11-25 10:01:05] Flattener#propagate_ancestor_ids
[STOP] [2019-11-25 10:01:05] Flattener#propagate_ancestor_ids
[STOP] [2019-11-25 10:01:05] Flattener#flatten
[STOP] [2019-11-25 10:01:05] rebuild_nodes
[START] [2019-11-25 10:01:05] resolve_missing_media_owners
[STOP] [2019-11-25 10:01:05] resolve_missing_media_owners
[START] [2019-11-25 10:01:05] sanitize_media_verbatims
[STOP] [2019-11-25 10:01:05] sanitize_media_verbatims
[START] [2019-11-25 10:01:05] queue_downloads
[STOP] [2019-11-25 10:01:05] queue_downloads
[START] [2019-11-25 10:01:05] parse_names
[WARN] [2019-11-25 10:01:05] I see 6026 names which still need to be parsed.
[STOP] [2019-11-25 10:01:11] parse_names
[START] [2019-11-25 10:01:11] denormalize_canonical_names_to_nodes
[STOP] [2019-11-25 10:01:11] denormalize_canonical_names_to_nodes
[START] [2019-11-25 10:01:11] match_nodes
[START] [2019-11-25 10:01:11] map_all_nodes_to_pages
[STOP] [2019-11-25 10:04:25] map_all_nodes_to_pages
[INFO] [2019-11-25 10:04:25] 305 Unmatched nodes (of 6026)! That's too many to output. First 10: Anatoma crispata (#55571474); Beringius behringi (#55571835); Curtitoma trevelliana (#55572511); Cylichnoides densistriata (#55572557); Limacina retroversa (#55574132); Limapontia senestra (#55574136); Tochuina tetraquetra (#55576685); Turrisipho fenestratus (#55576809); Xylophaga dorsalis (#55576929); Zirfaea pilsbryi (#55576956)
[START] [2019-11-25 10:04:25] update_nodes
[STOP] [2019-11-25 10:04:27] update_nodes
[STOP] [2019-11-25 10:04:27] match_nodes
[START] [2019-11-25 10:04:27] reindex_search
[STOP] [2019-11-25 10:04:37] reindex_search
[START] [2019-11-25 10:04:37] normalize_units
[STOP] [2019-11-25 10:04:37] normalize_units
[START] [2019-11-25 10:04:37] calculate_statistics
[STOP] [2019-11-25 10:04:37] calculate_statistics
[START] [2019-11-25 10:04:37] complete_harvest_instance
[START] [2019-11-25 10:04:37] overall_tsv_creation
[INFO] [2019-11-25 10:04:37] Processing group of 6026 in 1 batches of 10000
[INFO] [2019-11-25 10:06:06] 4242 Traits (unfiltered)...
[INFO] [2019-11-25 10:06:19] 4242 Traits (filtered)...
[INFO] [2019-11-25 10:06:19] 0 Associations (filtered)...
[INFO] [2019-11-25 10:07:03] 8484 metadata added.
[INFO] [2019-11-25 10:07:03] 0 metadata added.
[INFO] [2019-11-25 10:07:03] Average Time: 103.89
[INFO] [2019-11-25 10:07:03] Total Time: 2m27s
[STOP] [2019-11-25 10:07:03] overall_tsv_creation
[INFO] [2019-11-25 10:07:03] Done. Check your files:
[INFO] [2019-11-25 10:07:04] (6026 lines) /app/public/data/Arctic_Register_/publish_nodes.tsv
[INFO] [2019-11-25 10:07:04] (10145 lines) /app/public/data/Arctic_Register_/publish_node_ancestors.tsv
[INFO] [2019-11-25 10:07:04] (6026 lines) /app/public/data/Arctic_Register_/publish_scientific_names.tsv
[INFO] [2019-11-25 10:07:04] (4243 lines) /app/public/data/Arctic_Register_/publish_traits.tsv
[INFO] [2019-11-25 10:07:04] (8485 lines) /app/public/data/Arctic_Register_/publish_metadata.tsv
[STOP] [2019-11-25 10:07:05] complete_harvest_instance
[START] [2019-11-25 10:07:05] completed
[STOP] [2019-11-25 10:07:05] completed
[STOP] [2019-11-25 10:07:05] logged process, took 405.89

Latest Process

25 Nov 10:00 EXITED currently processing 0