Harvest for Sea of Azov Species List Created 25 Dec 10:54

Stage: completed
Fetched: 25 Dec 10:54
Validated: 25 Dec 10:54
Deltas Created 25 Dec 10:54
Units Normalized: 25 Dec 10:55
Ancestry Built: 25 Dec 10:54
Nodes Matched: 25 Dec 10:55
Names Parsed: 25 Dec 10:54
New Models Stored: 25 Dec 10:54
Indexed: 25 Dec 10:55
Completed: 25 Dec 10:57
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 10:54:32 -0500 by logger.rb/56815
[START] [2019-12-25 10:54:32] logged process
[START] [2019-12-25 10:54:32] create_harvest_instance
[STOP] [2019-12-25 10:54:33] create_harvest_instance
[START] [2019-12-25 10:54:33] fetch_files
[STOP] [2019-12-25 10:54:33] fetch_files
[START] [2019-12-25 10:54:33] validate_each_file
[STOP] [2019-12-25 10:54:33] validate_each_file
[START] [2019-12-25 10:54:33] convert_to_csv
[CMD] [2019-12-25 10:54:33] /usr/bin/sort /app/public/converted_csv/sea_azov_sp_list_refs_19618.csv > /app/public/converted_csv/sea_azov_sp_list_refs_19618.csv_sorted
[CMD] [2019-12-25 10:54:33] /usr/bin/sort /app/public/converted_csv/sea_azov_sp_list_nodes_19619.csv > /app/public/converted_csv/sea_azov_sp_list_nodes_19619.csv_sorted
[CMD] [2019-12-25 10:54:33] /usr/bin/sort /app/public/converted_csv/sea_azov_sp_list_occurrences_19620.csv > /app/public/converted_csv/sea_azov_sp_list_occurrences_19620.csv_sorted
[CMD] [2019-12-25 10:54:34] /usr/bin/sort /app/public/converted_csv/sea_azov_sp_list_measurements_19621.csv > /app/public/converted_csv/sea_azov_sp_list_measurements_19621.csv_sorted
[STOP] [2019-12-25 10:54:34] convert_to_csv
[START] [2019-12-25 10:54:34] calculate_delta
[CMD] [2019-12-25 10:54:34] echo "0a" > /app/public/diff/sea_azov_sp_list_refs_19618.diff
[CMD] [2019-12-25 10:54:34] tail -n +1 /app/public/converted_csv/sea_azov_sp_list_refs_19618.csv >> /app/public/diff/sea_azov_sp_list_refs_19618.diff
[CMD] [2019-12-25 10:54:34] echo "." >> /app/public/diff/sea_azov_sp_list_refs_19618.diff
[CMD] [2019-12-25 10:54:34] echo "0a" > /app/public/diff/sea_azov_sp_list_nodes_19619.diff
[CMD] [2019-12-25 10:54:34] tail -n +1 /app/public/converted_csv/sea_azov_sp_list_nodes_19619.csv >> /app/public/diff/sea_azov_sp_list_nodes_19619.diff
[CMD] [2019-12-25 10:54:35] echo "." >> /app/public/diff/sea_azov_sp_list_nodes_19619.diff
[CMD] [2019-12-25 10:54:35] echo "0a" > /app/public/diff/sea_azov_sp_list_occurrences_19620.diff
[CMD] [2019-12-25 10:54:35] tail -n +1 /app/public/converted_csv/sea_azov_sp_list_occurrences_19620.csv >> /app/public/diff/sea_azov_sp_list_occurrences_19620.diff
[CMD] [2019-12-25 10:54:35] echo "." >> /app/public/diff/sea_azov_sp_list_occurrences_19620.diff
[CMD] [2019-12-25 10:54:35] echo "0a" > /app/public/diff/sea_azov_sp_list_measurements_19621.diff
[CMD] [2019-12-25 10:54:35] tail -n +1 /app/public/converted_csv/sea_azov_sp_list_measurements_19621.csv >> /app/public/diff/sea_azov_sp_list_measurements_19621.diff
[CMD] [2019-12-25 10:54:36] echo "." >> /app/public/diff/sea_azov_sp_list_measurements_19621.diff
[STOP] [2019-12-25 10:54:36] calculate_delta
[START] [2019-12-25 10:54:36] parse_diff_and_store
[INFO] [2019-12-25 10:54:36] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 10:54:36] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 10:54:36] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 10:54:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 10:54:37] Storing 2 References
[INFO] [2019-12-25 10:54:37] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.0
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[INFO] [2019-12-25 10:54:37] Storing 163 ScientificNames
[INFO] [2019-12-25 10:54:37] Processing group of 163 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.08
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[INFO] [2019-12-25 10:54:37] Storing 163 Nodes
[INFO] [2019-12-25 10:54:37] Processing group of 163 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.06
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[INFO] [2019-12-25 10:54:37] Storing 64 Occurrences
[INFO] [2019-12-25 10:54:37] Processing group of 64 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.01
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[INFO] [2019-12-25 10:54:37] Storing 128 TraitsReferences
[INFO] [2019-12-25 10:54:37] Processing group of 128 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.06
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[INFO] [2019-12-25 10:54:37] Storing 128 Traits
[INFO] [2019-12-25 10:54:37] Processing group of 128 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.09
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[INFO] [2019-12-25 10:54:37] Storing 128 MetaTraits
[INFO] [2019-12-25 10:54:37] Processing group of 128 in 1 groups of 1000
[INFO] [2019-12-25 10:54:37] Average Time: 0.04
[INFO] [2019-12-25 10:54:37] Total Time: 1s
[STOP] [2019-12-25 10:54:37] parse_diff_and_store
[START] [2019-12-25 10:54:37] resolve_keys
[INFO] [2019-12-25 10:54:42] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 10:54:42] traits to occurrences...
[INFO] [2019-12-25 10:54:42] traits to nodes (through occurrences)...
[INFO] [2019-12-25 10:54:42] Traits to sex term...
[INFO] [2019-12-25 10:54:42] Traits to lifestage term...
[INFO] [2019-12-25 10:54:42] MetaTraits to traits...
[INFO] [2019-12-25 10:54:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 10:54:42] Assocs to occurrences...
[INFO] [2019-12-25 10:54:42] Assocs to nodes...
[INFO] [2019-12-25 10:54:42] Assoc to sex term...
[INFO] [2019-12-25 10:54:42] Assoc to lifestage term...
[STOP] [2019-12-25 10:54:42] resolve_keys
[START] [2019-12-25 10:54:42] hold_for_later_1
[STOP] [2019-12-25 10:54:42] hold_for_later_1
[START] [2019-12-25 10:54:42] hold_for_later_2
[STOP] [2019-12-25 10:54:42] hold_for_later_2
[START] [2019-12-25 10:54:42] resolve_missing_parents
[STOP] [2019-12-25 10:54:42] resolve_missing_parents
[START] [2019-12-25 10:54:42] rebuild_nodes
[START] [2019-12-25 10:54:42] Flattener#flatten
[START] [2019-12-25 10:54:42] Flattener#study_resource
[START] [2019-12-25 10:54:42] Flattener#build_ancestry
[STOP] [2019-12-25 10:54:42] Flattener#build_ancestry
[INFO] [2019-12-25 10:54:42] 163 ancestry keys
[START] [2019-12-25 10:54:42] build_node_ancestors
[INFO] [2019-12-25 10:54:42] old ancestors deleted.
[STOP] [2019-12-25 10:54:42] build_node_ancestors
[START] [2019-12-25 10:54:42] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:54:42] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 10:54:42] Flattener#flatten
[STOP] [2019-12-25 10:54:42] rebuild_nodes
[START] [2019-12-25 10:54:42] resolve_missing_media_owners
[STOP] [2019-12-25 10:54:42] resolve_missing_media_owners
[START] [2019-12-25 10:54:42] sanitize_media_verbatims
[STOP] [2019-12-25 10:54:42] sanitize_media_verbatims
[START] [2019-12-25 10:54:42] queue_downloads
[STOP] [2019-12-25 10:54:42] queue_downloads
[START] [2019-12-25 10:54:42] parse_names
[WARN] [2019-12-25 10:54:42] I see 163 names which still need to be parsed.
[STOP] [2019-12-25 10:54:44] parse_names
[START] [2019-12-25 10:54:44] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 10:54:44] denormalize_canonical_names_to_nodes
[START] [2019-12-25 10:54:44] match_nodes
[START] [2019-12-25 10:54:44] map_all_nodes_to_pages
[STOP] [2019-12-25 10:55:54] map_all_nodes_to_pages
[INFO] [2019-12-25 10:55:54] Unmatched nodes (8 of 163): Limicola (#62432333); Limicola falcinellus (#62432332); Philomachus (#62432368); Philomachus pugnax (#62432367); Anas querquedula (#62432310); Anas clypeata (#62432334); Magnoliopsida (#62432399); Magnoliophyta (#62432400)
[START] [2019-12-25 10:55:54] update_nodes
[STOP] [2019-12-25 10:55:55] update_nodes
[STOP] [2019-12-25 10:55:55] match_nodes
[START] [2019-12-25 10:55:55] reindex_search
[STOP] [2019-12-25 10:55:55] reindex_search
[START] [2019-12-25 10:55:55] normalize_units
[STOP] [2019-12-25 10:55:55] normalize_units
[START] [2019-12-25 10:55:55] calculate_statistics
[STOP] [2019-12-25 10:55:55] calculate_statistics
[START] [2019-12-25 10:55:55] complete_harvest_instance
[START] [2019-12-25 10:55:55] overall_tsv_creation
[INFO] [2019-12-25 10:55:55] Processing group of 163 in 1 batches of 10000
[INFO] [2019-12-25 10:56:41] 64 Traits (unfiltered)...
[INFO] [2019-12-25 10:56:54] 64 Traits (filtered)...
[INFO] [2019-12-25 10:56:54] 0 Associations (filtered)...
[INFO] [2019-12-25 10:57:31] 320 metadata added.
[INFO] [2019-12-25 10:57:31] 0 metadata added.
[INFO] [2019-12-25 10:57:31] Average Time: 73.85
[INFO] [2019-12-25 10:57:31] Total Time: 1m37s
[STOP] [2019-12-25 10:57:31] overall_tsv_creation
[INFO] [2019-12-25 10:57:31] Done. Check your files:
[INFO] [2019-12-25 10:57:32] (163 lines) /app/public/data/sea_azov_sp_list/publish_nodes.tsv
[INFO] [2019-12-25 10:57:32] (753 lines) /app/public/data/sea_azov_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-25 10:57:32] (163 lines) /app/public/data/sea_azov_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-25 10:57:32] (65 lines) /app/public/data/sea_azov_sp_list/publish_traits.tsv
[INFO] [2019-12-25 10:57:32] (321 lines) /app/public/data/sea_azov_sp_list/publish_metadata.tsv
[STOP] [2019-12-25 10:57:32] complete_harvest_instance
[START] [2019-12-25 10:57:32] completed
[STOP] [2019-12-25 10:57:32] completed
[STOP] [2019-12-25 10:57:32] logged process, took 179.93
Latest Process

25 Dec 10:54 EXITED currently processing 0