Harvest for Arctic Liverworts Created 24 Jun 17:00

Harvesting Log

# Logfile created on 2019-06-24 17:00:25 -0400 by logger.rb/56815
[START] [2019-06-24 17:00:25] logged process
[START] [2019-06-24 17:00:25] create_harvest_instance
[STOP] [2019-06-24 17:00:29] create_harvest_instance
[START] [2019-06-24 17:00:29] fetch_files
[STOP] [2019-06-24 17:00:29] fetch_files
[START] [2019-06-24 17:00:29] validate_each_file
[STOP] [2019-06-24 17:00:29] validate_each_file
[START] [2019-06-24 17:00:29] convert_to_csv
[CMD] [2019-06-24 17:00:29] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_agents_13735.csv > /app/public/converted_csv/Arctic_Liverwort_agents_13735.csv_sorted
[CMD] [2019-06-24 17:00:29] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_refs_13736.csv > /app/public/converted_csv/Arctic_Liverwort_refs_13736.csv_sorted
[CMD] [2019-06-24 17:00:30] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_nodes_13737.csv > /app/public/converted_csv/Arctic_Liverwort_nodes_13737.csv_sorted
[CMD] [2019-06-24 17:00:30] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_media_13738.csv > /app/public/converted_csv/Arctic_Liverwort_media_13738.csv_sorted
[CMD] [2019-06-24 17:00:30] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_vernaculars_13739.csv > /app/public/converted_csv/Arctic_Liverwort_vernaculars_13739.csv_sorted
[CMD] [2019-06-24 17:00:30] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_occurrences_13740.csv > /app/public/converted_csv/Arctic_Liverwort_occurrences_13740.csv_sorted
[CMD] [2019-06-24 17:00:31] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_assocs_13741.csv > /app/public/converted_csv/Arctic_Liverwort_assocs_13741.csv_sorted
[CMD] [2019-06-24 17:00:31] /usr/bin/sort /app/public/converted_csv/Arctic_Liverwort_measurements_13742.csv > /app/public/converted_csv/Arctic_Liverwort_measurements_13742.csv_sorted
[STOP] [2019-06-24 17:00:31] convert_to_csv
[START] [2019-06-24 17:00:31] calculate_delta
[CMD] [2019-06-24 17:00:31] echo "0a" > /app/public/diff/Arctic_Liverwort_agents_13735.diff
[CMD] [2019-06-24 17:00:32] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_agents_13735.csv >> /app/public/diff/Arctic_Liverwort_agents_13735.diff
[CMD] [2019-06-24 17:00:32] echo "." >> /app/public/diff/Arctic_Liverwort_agents_13735.diff
[CMD] [2019-06-24 17:00:32] echo "0a" > /app/public/diff/Arctic_Liverwort_refs_13736.diff
[CMD] [2019-06-24 17:00:33] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_refs_13736.csv >> /app/public/diff/Arctic_Liverwort_refs_13736.diff
[CMD] [2019-06-24 17:00:33] echo "." >> /app/public/diff/Arctic_Liverwort_refs_13736.diff
[CMD] [2019-06-24 17:00:33] echo "0a" > /app/public/diff/Arctic_Liverwort_nodes_13737.diff
[CMD] [2019-06-24 17:00:33] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_nodes_13737.csv >> /app/public/diff/Arctic_Liverwort_nodes_13737.diff
[CMD] [2019-06-24 17:00:34] echo "." >> /app/public/diff/Arctic_Liverwort_nodes_13737.diff
[CMD] [2019-06-24 17:00:34] echo "0a" > /app/public/diff/Arctic_Liverwort_media_13738.diff
[CMD] [2019-06-24 17:00:34] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_media_13738.csv >> /app/public/diff/Arctic_Liverwort_media_13738.diff
[CMD] [2019-06-24 17:00:35] echo "." >> /app/public/diff/Arctic_Liverwort_media_13738.diff
[CMD] [2019-06-24 17:00:35] echo "0a" > /app/public/diff/Arctic_Liverwort_vernaculars_13739.diff
[CMD] [2019-06-24 17:00:35] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_vernaculars_13739.csv >> /app/public/diff/Arctic_Liverwort_vernaculars_13739.diff
[CMD] [2019-06-24 17:00:35] echo "." >> /app/public/diff/Arctic_Liverwort_vernaculars_13739.diff
[CMD] [2019-06-24 17:00:36] echo "0a" > /app/public/diff/Arctic_Liverwort_occurrences_13740.diff
[CMD] [2019-06-24 17:00:36] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_occurrences_13740.csv >> /app/public/diff/Arctic_Liverwort_occurrences_13740.diff
[CMD] [2019-06-24 17:00:36] echo "." >> /app/public/diff/Arctic_Liverwort_occurrences_13740.diff
[CMD] [2019-06-24 17:00:37] echo "0a" > /app/public/diff/Arctic_Liverwort_assocs_13741.diff
[CMD] [2019-06-24 17:00:37] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_assocs_13741.csv >> /app/public/diff/Arctic_Liverwort_assocs_13741.diff
[CMD] [2019-06-24 17:00:37] echo "." >> /app/public/diff/Arctic_Liverwort_assocs_13741.diff
[CMD] [2019-06-24 17:00:37] echo "0a" > /app/public/diff/Arctic_Liverwort_measurements_13742.diff
[CMD] [2019-06-24 17:00:38] tail -n +1 /app/public/converted_csv/Arctic_Liverwort_measurements_13742.csv >> /app/public/diff/Arctic_Liverwort_measurements_13742.diff
[CMD] [2019-06-24 17:00:38] echo "." >> /app/public/diff/Arctic_Liverwort_measurements_13742.diff
[STOP] [2019-06-24 17:00:38] calculate_delta
[START] [2019-06-24 17:00:38] parse_diff_and_store
[INFO] [2019-06-24 17:00:39] Loading agents diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:39] Loading refs diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:39] Loading nodes diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:40] Loading media diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:40] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:41] Loading assocs diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:41] Loading measurements diff file into memory (true lines)...
[INFO] [2019-06-24 17:00:45] Storing 4 References
[INFO] [2019-06-24 17:00:45] Processing group of 4 in 1 groups of 1000
[INFO] [2019-06-24 17:00:45] Average Time: 0.0
[INFO] [2019-06-24 17:00:45] Total Time: 1s
[INFO] [2019-06-24 17:00:45] Storing 558 ScientificNames
[INFO] [2019-06-24 17:00:45] Processing group of 558 in 1 groups of 1000
[INFO] [2019-06-24 17:00:45] Average Time: 0.33
[INFO] [2019-06-24 17:00:45] Total Time: 1s
[INFO] [2019-06-24 17:00:45] Storing 558 Nodes
[INFO] [2019-06-24 17:00:45] Processing group of 558 in 1 groups of 1000
[INFO] [2019-06-24 17:00:45] Average Time: 0.21
[INFO] [2019-06-24 17:00:45] Total Time: 1s
[INFO] [2019-06-24 17:00:45] Storing 434 Occurrences
[INFO] [2019-06-24 17:00:45] Processing group of 434 in 1 groups of 1000
[INFO] [2019-06-24 17:00:45] Average Time: 0.07
[INFO] [2019-06-24 17:00:45] Total Time: 1s
[INFO] [2019-06-24 17:00:45] Storing 868 TraitsReferences
[INFO] [2019-06-24 17:00:45] Processing group of 868 in 1 groups of 1000
[INFO] [2019-06-24 17:00:46] Average Time: 0.09
[INFO] [2019-06-24 17:00:46] Total Time: 1s
[INFO] [2019-06-24 17:00:46] Storing 868 Traits
[INFO] [2019-06-24 17:00:46] Processing group of 868 in 1 groups of 1000
[INFO] [2019-06-24 17:00:46] Average Time: 0.36
[INFO] [2019-06-24 17:00:46] Total Time: 1s
[INFO] [2019-06-24 17:00:46] Storing 1736 MetaTraits
[INFO] [2019-06-24 17:00:46] Processing group of 1736 in 2 groups of 1000
[INFO] [2019-06-24 17:00:46] Average Time: 0.13
[INFO] [2019-06-24 17:00:46] Total Time: 1s
[STOP] [2019-06-24 17:00:46] parse_diff_and_store
[START] [2019-06-24 17:00:46] resolve_keys
[INFO] [2019-06-24 17:00:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-06-24 17:00:50] traits to occurrences...
[INFO] [2019-06-24 17:00:50] traits to nodes (through occurrences)...
[INFO] [2019-06-24 17:00:50] Traits to sex term...
[INFO] [2019-06-24 17:00:50] Traits to lifestage term...
[INFO] [2019-06-24 17:00:50] MetaTraits to traits...
[INFO] [2019-06-24 17:00:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-06-24 17:00:50] Assocs to occurrences...
[INFO] [2019-06-24 17:00:50] Assocs to nodes...
[INFO] [2019-06-24 17:00:50] Assoc to sex term...
[INFO] [2019-06-24 17:00:50] Assoc to lifestage term...
[STOP] [2019-06-24 17:00:50] resolve_keys
[START] [2019-06-24 17:00:50] hold_for_later_1
[STOP] [2019-06-24 17:00:50] hold_for_later_1
[START] [2019-06-24 17:00:50] hold_for_later_2
[STOP] [2019-06-24 17:00:50] hold_for_later_2
[START] [2019-06-24 17:00:50] resolve_missing_parents
[STOP] [2019-06-24 17:00:50] resolve_missing_parents
[START] [2019-06-24 17:00:50] rebuild_nodes
[START] [2019-06-24 17:00:50] Flattener#flatten
[START] [2019-06-24 17:00:50] Flattener#study_resource
[START] [2019-06-24 17:00:50] Flattener#build_ancestry
[STOP] [2019-06-24 17:00:50] Flattener#build_ancestry
[INFO] [2019-06-24 17:00:50] 558 ancestry keys
[START] [2019-06-24 17:00:50] build_node_ancestors
[INFO] [2019-06-24 17:00:50] old ancestors deleted.
[STOP] [2019-06-24 17:00:50] build_node_ancestors
[START] [2019-06-24 17:00:51] Flattener#propagate_ancestor_ids
[STOP] [2019-06-24 17:00:51] Flattener#propagate_ancestor_ids
[STOP] [2019-06-24 17:00:51] Flattener#flatten
[STOP] [2019-06-24 17:00:51] rebuild_nodes
[START] [2019-06-24 17:00:51] resolve_missing_media_owners
[STOP] [2019-06-24 17:00:51] resolve_missing_media_owners
[START] [2019-06-24 17:00:51] sanitize_media_verbatims
[STOP] [2019-06-24 17:00:51] sanitize_media_verbatims
[START] [2019-06-24 17:00:51] queue_downloads
[STOP] [2019-06-24 17:00:51] queue_downloads
[START] [2019-06-24 17:00:51] parse_names
[WARN] [2019-06-24 17:00:51] I see 558 names which still need to be parsed.
[WARN] [2019-06-24 17:00:52] I see 44 names which still need to be parsed.
[STOP] [2019-06-24 17:00:53] parse_names
[START] [2019-06-24 17:00:53] denormalize_canonical_names_to_nodes
[STOP] [2019-06-24 17:00:53] denormalize_canonical_names_to_nodes
[START] [2019-06-24 17:00:53] match_nodes
[START] [2019-06-24 17:00:53] map_all_nodes_to_pages
[STOP] [2019-06-24 17:01:08] map_all_nodes_to_pages
[INFO] [2019-06-24 17:01:08] 56 Unmatched nodes (of 558)! That's too many to output. First 10: Loeskhypnum (#43421266); Amphidium (#43420993); Anastrophyllum minutum (#43420997); Anastrophyllum saxicola (#43420999); Barbilophozia kunzeana (#43421048); Barbilophozia quadriloba (#43421050); Crypotoclea imbricata (#43421150); Jungermannia obovata (#43421249); Jungermannia sphaerocarpa (#43421253); Lohozia badensis (#43421268)
[START] [2019-06-24 17:01:08] update_nodes
[STOP] [2019-06-24 17:01:08] update_nodes
[STOP] [2019-06-24 17:01:08] match_nodes
[START] [2019-06-24 17:01:08] reindex_search
[STOP] [2019-06-24 17:01:09] reindex_search
[START] [2019-06-24 17:01:09] normalize_units
[STOP] [2019-06-24 17:01:09] normalize_units
[START] [2019-06-24 17:01:09] calculate_statistics
[STOP] [2019-06-24 17:01:09] calculate_statistics
[START] [2019-06-24 17:01:09] complete_harvest_instance
[START] [2019-06-24 17:01:09] overall_tsv_creation
[INFO] [2019-06-24 17:01:09] Processing group of 558 in 1 batches of 10000
[INFO] [2019-06-24 17:01:53] 868 Traits (unfiltered)...
[INFO] [2019-06-24 17:02:04] 868 Traits (filtered)...
[INFO] [2019-06-24 17:02:04] 0 Associations (filtered)...
[INFO] [2019-06-24 17:02:40] 2604 metadata added.
[INFO] [2019-06-24 17:02:40] 0 metadata added.
[INFO] [2019-06-24 17:02:40] Average Time: 69.3
[INFO] [2019-06-24 17:02:40] Total Time: 1m31s
[STOP] [2019-06-24 17:02:40] overall_tsv_creation
[INFO] [2019-06-24 17:02:40] Done. Check your files:
[INFO] [2019-06-24 17:02:40] (517 lines) /app/public/data/Arctic_Liverwort/publish_nodes.tsv
[INFO] [2019-06-24 17:02:40] (1220 lines) /app/public/data/Arctic_Liverwort/publish_node_ancestors.tsv
[INFO] [2019-06-24 17:02:41] (558 lines) /app/public/data/Arctic_Liverwort/publish_scientific_names.tsv
[INFO] [2019-06-24 17:02:41] (869 lines) /app/public/data/Arctic_Liverwort/publish_traits.tsv
[INFO] [2019-06-24 17:02:41] (2605 lines) /app/public/data/Arctic_Liverwort/publish_metadata.tsv
[STOP] [2019-06-24 17:02:41] complete_harvest_instance
[START] [2019-06-24 17:02:41] completed
[STOP] [2019-06-24 17:02:41] completed
[STOP] [2019-06-24 17:02:41] logged process, took 135.83

Latest Process

24 Jun 17:00 EXITED currently processing 0