Harvest for Arctic Marine Fishes Created 07 Nov 13:01

Stage: completed
Fetched: 07 Nov 13:01
Validated: 07 Nov 13:01
Deltas Created 07 Nov 13:01
Units Normalized: 07 Nov 13:03
Ancestry Built: 07 Nov 13:02
Nodes Matched: 07 Nov 13:03
Names Parsed: 07 Nov 13:02
New Models Stored: 07 Nov 13:01
Indexed: 07 Nov 13:03
Completed: 07 Nov 13:05
Time to Harvest: less than a minute
Harvesting Log

(152 lines)
# Logfile created on 2019-11-07 13:01:44 -0500 by logger.rb/56815
[START] [2019-11-07 13:01:44] logged process
[START] [2019-11-07 13:01:44] create_harvest_instance
[STOP] [2019-11-07 13:01:48] create_harvest_instance
[START] [2019-11-07 13:01:48] fetch_files
[STOP] [2019-11-07 13:01:48] fetch_files
[START] [2019-11-07 13:01:48] validate_each_file
[STOP] [2019-11-07 13:01:49] validate_each_file
[START] [2019-11-07 13:01:49] convert_to_csv
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_agents_18264.csv > /app/public/converted_csv/Arctic_Marine_Fi_agents_18264.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_refs_18265.csv > /app/public/converted_csv/Arctic_Marine_Fi_refs_18265.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_nodes_18266.csv > /app/public/converted_csv/Arctic_Marine_Fi_nodes_18266.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_media_18267.csv > /app/public/converted_csv/Arctic_Marine_Fi_media_18267.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_vernaculars_18268.csv > /app/public/converted_csv/Arctic_Marine_Fi_vernaculars_18268.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_occurrences_18269.csv > /app/public/converted_csv/Arctic_Marine_Fi_occurrences_18269.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_assocs_18270.csv > /app/public/converted_csv/Arctic_Marine_Fi_assocs_18270.csv_sorted
[CMD] [2019-11-07 13:01:49] /usr/bin/sort /app/public/converted_csv/Arctic_Marine_Fi_measurements_18271.csv > /app/public/converted_csv/Arctic_Marine_Fi_measurements_18271.csv_sorted
[STOP] [2019-11-07 13:01:49] convert_to_csv
[START] [2019-11-07 13:01:49] calculate_delta
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_agents_18264.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_agents_18264.csv >> /app/public/diff/Arctic_Marine_Fi_agents_18264.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_agents_18264.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_refs_18265.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_refs_18265.csv >> /app/public/diff/Arctic_Marine_Fi_refs_18265.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_refs_18265.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_nodes_18266.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_nodes_18266.csv >> /app/public/diff/Arctic_Marine_Fi_nodes_18266.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_nodes_18266.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_media_18267.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_media_18267.csv >> /app/public/diff/Arctic_Marine_Fi_media_18267.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_media_18267.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_vernaculars_18268.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_vernaculars_18268.csv >> /app/public/diff/Arctic_Marine_Fi_vernaculars_18268.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_vernaculars_18268.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_occurrences_18269.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_occurrences_18269.csv >> /app/public/diff/Arctic_Marine_Fi_occurrences_18269.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_occurrences_18269.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_assocs_18270.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_assocs_18270.csv >> /app/public/diff/Arctic_Marine_Fi_assocs_18270.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_assocs_18270.diff
[CMD] [2019-11-07 13:01:49] echo "0a" > /app/public/diff/Arctic_Marine_Fi_measurements_18271.diff
[CMD] [2019-11-07 13:01:49] tail -n +1 /app/public/converted_csv/Arctic_Marine_Fi_measurements_18271.csv >> /app/public/diff/Arctic_Marine_Fi_measurements_18271.diff
[CMD] [2019-11-07 13:01:49] echo "." >> /app/public/diff/Arctic_Marine_Fi_measurements_18271.diff
[STOP] [2019-11-07 13:01:49] calculate_delta
[START] [2019-11-07 13:01:49] parse_diff_and_store
[INFO] [2019-11-07 13:01:49] Loading agents diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:49] Loading refs diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:49] Loading nodes diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:50] Loading media diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:50] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:50] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:50] Loading assocs diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:50] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-07 13:01:54] Storing 652 ScientificNames
[INFO] [2019-11-07 13:01:54] Processing group of 652 in 1 groups of 1000
[INFO] [2019-11-07 13:01:55] Average Time: 0.42
[INFO] [2019-11-07 13:01:55] Total Time: 1s
[INFO] [2019-11-07 13:01:55] Storing 652 Nodes
[INFO] [2019-11-07 13:01:55] Processing group of 652 in 1 groups of 1000
[INFO] [2019-11-07 13:01:55] Average Time: 0.35
[INFO] [2019-11-07 13:01:55] Total Time: 1s
[INFO] [2019-11-07 13:01:55] Storing 647 Occurrences
[INFO] [2019-11-07 13:01:55] Processing group of 647 in 1 groups of 1000
[INFO] [2019-11-07 13:01:56] Average Time: 0.27
[INFO] [2019-11-07 13:01:56] Total Time: 1s
[INFO] [2019-11-07 13:01:56] Storing 724 Traits
[INFO] [2019-11-07 13:01:56] Processing group of 724 in 1 groups of 1000
[INFO] [2019-11-07 13:01:56] Average Time: 0.51
[INFO] [2019-11-07 13:01:56] Total Time: 1s
[INFO] [2019-11-07 13:01:56] Storing 1481 MetaTraits
[INFO] [2019-11-07 13:01:56] Processing group of 1481 in 2 groups of 1000
[INFO] [2019-11-07 13:01:56] Average Time: 0.19
[INFO] [2019-11-07 13:01:56] Total Time: 1s
[STOP] [2019-11-07 13:01:56] parse_diff_and_store
[START] [2019-11-07 13:01:56] resolve_keys
[INFO] [2019-11-07 13:02:00] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-07 13:02:00] traits to occurrences...
[INFO] [2019-11-07 13:02:00] traits to nodes (through occurrences)...
[INFO] [2019-11-07 13:02:00] Traits to sex term...
[INFO] [2019-11-07 13:02:00] Traits to lifestage term...
[INFO] [2019-11-07 13:02:00] MetaTraits to traits...
[INFO] [2019-11-07 13:02:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-07 13:02:01] Assocs to occurrences...
[INFO] [2019-11-07 13:02:01] Assocs to nodes...
[INFO] [2019-11-07 13:02:01] Assoc to sex term...
[INFO] [2019-11-07 13:02:01] Assoc to lifestage term...
[STOP] [2019-11-07 13:02:01] resolve_keys
[START] [2019-11-07 13:02:01] hold_for_later_1
[STOP] [2019-11-07 13:02:01] hold_for_later_1
[START] [2019-11-07 13:02:01] hold_for_later_2
[STOP] [2019-11-07 13:02:01] hold_for_later_2
[START] [2019-11-07 13:02:01] resolve_missing_parents
[STOP] [2019-11-07 13:02:01] resolve_missing_parents
[START] [2019-11-07 13:02:01] rebuild_nodes
[START] [2019-11-07 13:02:01] Flattener#flatten
[START] [2019-11-07 13:02:01] Flattener#study_resource
[START] [2019-11-07 13:02:01] Flattener#build_ancestry
[STOP] [2019-11-07 13:02:01] Flattener#build_ancestry
[INFO] [2019-11-07 13:02:01] 652 ancestry keys
[START] [2019-11-07 13:02:01] build_node_ancestors
[INFO] [2019-11-07 13:02:01] old ancestors deleted.
[STOP] [2019-11-07 13:02:01] build_node_ancestors
[START] [2019-11-07 13:02:01] Flattener#propagate_ancestor_ids
[STOP] [2019-11-07 13:02:01] Flattener#propagate_ancestor_ids
[STOP] [2019-11-07 13:02:01] Flattener#flatten
[STOP] [2019-11-07 13:02:01] rebuild_nodes
[START] [2019-11-07 13:02:01] resolve_missing_media_owners
[STOP] [2019-11-07 13:02:01] resolve_missing_media_owners
[START] [2019-11-07 13:02:01] sanitize_media_verbatims
[STOP] [2019-11-07 13:02:01] sanitize_media_verbatims
[START] [2019-11-07 13:02:01] queue_downloads
[STOP] [2019-11-07 13:02:01] queue_downloads
[START] [2019-11-07 13:02:01] parse_names
[WARN] [2019-11-07 13:02:01] I see 652 names which still need to be parsed.
[WARN] [2019-11-07 13:02:03] I see 1 names which still need to be parsed.
[STOP] [2019-11-07 13:02:04] parse_names
[START] [2019-11-07 13:02:04] denormalize_canonical_names_to_nodes
[STOP] [2019-11-07 13:02:04] denormalize_canonical_names_to_nodes
[START] [2019-11-07 13:02:04] match_nodes
[START] [2019-11-07 13:02:04] map_all_nodes_to_pages
[STOP] [2019-11-07 13:03:42] map_all_nodes_to_pages
[INFO] [2019-11-07 13:03:42] Unmatched nodes (8 of 652): ACTINOPTERYGII (#54601238); Bollinia euryptera (#54601341); Gadus morhua marisalbi (#54601483); Macropinna macrostoma (#54601664); Phalocottus obtusus (#54601737); Roueina attrita (#54601793); CHONDRICHTHYES (#54601255); MYXINI (#54601702)
[START] [2019-11-07 13:03:42] update_nodes
[STOP] [2019-11-07 13:03:43] update_nodes
[STOP] [2019-11-07 13:03:43] match_nodes
[START] [2019-11-07 13:03:43] reindex_search
[STOP] [2019-11-07 13:03:45] reindex_search
[START] [2019-11-07 13:03:45] normalize_units
[STOP] [2019-11-07 13:03:45] normalize_units
[START] [2019-11-07 13:03:45] calculate_statistics
[STOP] [2019-11-07 13:03:45] calculate_statistics
[START] [2019-11-07 13:03:45] complete_harvest_instance
[START] [2019-11-07 13:03:45] overall_tsv_creation
[INFO] [2019-11-07 13:03:45] Processing group of 652 in 1 batches of 10000
[INFO] [2019-11-07 13:04:33] 724 Traits (unfiltered)...
[INFO] [2019-11-07 13:04:46] 724 Traits (filtered)...
[INFO] [2019-11-07 13:04:46] 0 Associations (filtered)...
[INFO] [2019-11-07 13:05:24] 1481 metadata added.
[INFO] [2019-11-07 13:05:24] 0 metadata added.
[INFO] [2019-11-07 13:05:24] Average Time: 77.27
[INFO] [2019-11-07 13:05:24] Total Time: 1m39s
[STOP] [2019-11-07 13:05:24] overall_tsv_creation
[INFO] [2019-11-07 13:05:24] Done. Check your files:
[INFO] [2019-11-07 13:05:24] (651 lines) /app/public/data/Arctic_Marine_Fi/publish_nodes.tsv
[INFO] [2019-11-07 13:05:24] (1945 lines) /app/public/data/Arctic_Marine_Fi/publish_node_ancestors.tsv
[INFO] [2019-11-07 13:05:24] (652 lines) /app/public/data/Arctic_Marine_Fi/publish_scientific_names.tsv
[INFO] [2019-11-07 13:05:24] (725 lines) /app/public/data/Arctic_Marine_Fi/publish_traits.tsv
[INFO] [2019-11-07 13:05:24] (1482 lines) /app/public/data/Arctic_Marine_Fi/publish_metadata.tsv
[STOP] [2019-11-07 13:05:24] complete_harvest_instance
[START] [2019-11-07 13:05:24] completed
[STOP] [2019-11-07 13:05:24] completed
[STOP] [2019-11-07 13:05:24] logged process, took 220.02
Latest Process

07 Nov 13:01 EXITED currently processing 0