Stage:
completed
Fetched:
23 Dec 17:31
Validated:
23 Dec 17:31
Deltas Created
23 Dec 17:32
Units Normalized:
23 Dec 18:05
Ancestry Built:
23 Dec 17:33
Nodes Matched:
23 Dec 18:05
Names Parsed:
23 Dec 17:33
New Models Stored:
23 Dec 17:32
Indexed:
23 Dec 18:05
Completed:
23 Dec 18:07
Time to Harvest:
1 minute
Harvesting Log
(143 lines)
# Logfile created on 2019-12-23 17:31:54 -0500 by logger.rb/56815
[START] [2019-12-23 17:31:54] logged process
[START] [2019-12-23 17:31:54] create_harvest_instance
[STOP] [2019-12-23 17:31:54] create_harvest_instance
[START] [2019-12-23 17:31:54] fetch_files
[STOP] [2019-12-23 17:31:54] fetch_files
[START] [2019-12-23 17:31:54] validate_each_file
[STOP] [2019-12-23 17:31:55] validate_each_file
[START] [2019-12-23 17:31:55] convert_to_csv
[CMD] [2019-12-23 17:31:55] /usr/bin/sort /app/public/converted_csv/kattegat_sp_list_refs_19450.csv > /app/public/converted_csv/kattegat_sp_list_refs_19450.csv_sorted
[CMD] [2019-12-23 17:31:56] /usr/bin/sort /app/public/converted_csv/kattegat_sp_list_nodes_19451.csv > /app/public/converted_csv/kattegat_sp_list_nodes_19451.csv_sorted
[CMD] [2019-12-23 17:31:56] /usr/bin/sort /app/public/converted_csv/kattegat_sp_list_occurrences_19452.csv > /app/public/converted_csv/kattegat_sp_list_occurrences_19452.csv_sorted
[CMD] [2019-12-23 17:31:57] /usr/bin/sort /app/public/converted_csv/kattegat_sp_list_measurements_19453.csv > /app/public/converted_csv/kattegat_sp_list_measurements_19453.csv_sorted
[STOP] [2019-12-23 17:31:58] convert_to_csv
[START] [2019-12-23 17:31:58] calculate_delta
[CMD] [2019-12-23 17:31:58] echo "0a" > /app/public/diff/kattegat_sp_list_refs_19450.diff
[CMD] [2019-12-23 17:31:58] tail -n +1 /app/public/converted_csv/kattegat_sp_list_refs_19450.csv >> /app/public/diff/kattegat_sp_list_refs_19450.diff
[CMD] [2019-12-23 17:31:59] echo "." >> /app/public/diff/kattegat_sp_list_refs_19450.diff
[CMD] [2019-12-23 17:32:00] echo "0a" > /app/public/diff/kattegat_sp_list_nodes_19451.diff
[CMD] [2019-12-23 17:32:00] tail -n +1 /app/public/converted_csv/kattegat_sp_list_nodes_19451.csv >> /app/public/diff/kattegat_sp_list_nodes_19451.diff
[CMD] [2019-12-23 17:32:01] echo "." >> /app/public/diff/kattegat_sp_list_nodes_19451.diff
[CMD] [2019-12-23 17:32:02] echo "0a" > /app/public/diff/kattegat_sp_list_occurrences_19452.diff
[CMD] [2019-12-23 17:32:02] tail -n +1 /app/public/converted_csv/kattegat_sp_list_occurrences_19452.csv >> /app/public/diff/kattegat_sp_list_occurrences_19452.diff
[CMD] [2019-12-23 17:32:03] echo "." >> /app/public/diff/kattegat_sp_list_occurrences_19452.diff
[CMD] [2019-12-23 17:32:04] echo "0a" > /app/public/diff/kattegat_sp_list_measurements_19453.diff
[CMD] [2019-12-23 17:32:04] tail -n +1 /app/public/converted_csv/kattegat_sp_list_measurements_19453.csv >> /app/public/diff/kattegat_sp_list_measurements_19453.diff
[CMD] [2019-12-23 17:32:05] echo "." >> /app/public/diff/kattegat_sp_list_measurements_19453.diff
[STOP] [2019-12-23 17:32:06] calculate_delta
[START] [2019-12-23 17:32:06] parse_diff_and_store
[INFO] [2019-12-23 17:32:06] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 17:32:07] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 17:32:10] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 17:32:11] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 17:32:28] Storing 2 References
[INFO] [2019-12-23 17:32:28] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 17:32:29] Average Time: 0.0
[INFO] [2019-12-23 17:32:29] Total Time: 1s
[INFO] [2019-12-23 17:32:29] Storing 6117 ScientificNames
[INFO] [2019-12-23 17:32:29] Processing group of 6117 in 7 groups of 1000
[INFO] [2019-12-23 17:32:31] Average Time: 0.363
[INFO] [2019-12-23 17:32:31] Total Time: 3s
[INFO] [2019-12-23 17:32:31] last 3 / first 3: 0.62
[INFO] [2019-12-23 17:32:31] Std.Dev: 0.14491376746189438; Max: 0.5
[INFO] [2019-12-23 17:32:31] Storing 6117 Nodes
[INFO] [2019-12-23 17:32:31] Processing group of 6117 in 7 groups of 1000
[INFO] [2019-12-23 17:32:33] Average Time: 0.281
[INFO] [2019-12-23 17:32:33] Total Time: 3s
[INFO] [2019-12-23 17:32:33] last 3 / first 3: 0.72
[INFO] [2019-12-23 17:32:33] Std.Dev: 0.10954451150103323; Max: 0.34
[INFO] [2019-12-23 17:32:33] Storing 2938 Occurrences
[INFO] [2019-12-23 17:32:33] Processing group of 2938 in 3 groups of 1000
[INFO] [2019-12-23 17:32:33] Average Time: 0.123
[INFO] [2019-12-23 17:32:33] Total Time: 1s
[INFO] [2019-12-23 17:32:33] Storing 5876 TraitsReferences
[INFO] [2019-12-23 17:32:33] Processing group of 5876 in 6 groups of 1000
[INFO] [2019-12-23 17:32:34] Average Time: 0.092
[INFO] [2019-12-23 17:32:34] Total Time: 1s
[INFO] [2019-12-23 17:32:34] Storing 5876 Traits
[INFO] [2019-12-23 17:32:34] Processing group of 5876 in 6 groups of 1000
[INFO] [2019-12-23 17:32:36] Average Time: 0.362
[INFO] [2019-12-23 17:32:36] Total Time: 3s
[INFO] [2019-12-23 17:32:36] Storing 5871 MetaTraits
[INFO] [2019-12-23 17:32:36] Processing group of 5871 in 6 groups of 1000
[INFO] [2019-12-23 17:32:38] Average Time: 0.207
[INFO] [2019-12-23 17:32:38] Total Time: 2s
[STOP] [2019-12-23 17:32:38] parse_diff_and_store
[START] [2019-12-23 17:32:38] resolve_keys
[INFO] [2019-12-23 17:33:04] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 17:33:06] traits to occurrences...
[INFO] [2019-12-23 17:33:08] traits to nodes (through occurrences)...
[INFO] [2019-12-23 17:33:08] Traits to sex term...
[INFO] [2019-12-23 17:33:09] Traits to lifestage term...
[INFO] [2019-12-23 17:33:10] MetaTraits to traits...
[INFO] [2019-12-23 17:33:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 17:33:12] Assocs to occurrences...
[INFO] [2019-12-23 17:33:12] Assocs to nodes...
[INFO] [2019-12-23 17:33:12] Assoc to sex term...
[INFO] [2019-12-23 17:33:12] Assoc to lifestage term...
[STOP] [2019-12-23 17:33:12] resolve_keys
[START] [2019-12-23 17:33:12] hold_for_later_1
[STOP] [2019-12-23 17:33:12] hold_for_later_1
[START] [2019-12-23 17:33:12] hold_for_later_2
[STOP] [2019-12-23 17:33:12] hold_for_later_2
[START] [2019-12-23 17:33:12] resolve_missing_parents
[STOP] [2019-12-23 17:33:25] resolve_missing_parents
[START] [2019-12-23 17:33:25] rebuild_nodes
[START] [2019-12-23 17:33:25] Flattener#flatten
[START] [2019-12-23 17:33:25] Flattener#study_resource
[START] [2019-12-23 17:33:25] Flattener#build_ancestry
[STOP] [2019-12-23 17:33:25] Flattener#build_ancestry
[INFO] [2019-12-23 17:33:25] 6117 ancestry keys
[START] [2019-12-23 17:33:25] build_node_ancestors
[INFO] [2019-12-23 17:33:25] old ancestors deleted.
[STOP] [2019-12-23 17:33:27] build_node_ancestors
[START] [2019-12-23 17:33:30] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 17:33:31] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 17:33:31] Flattener#flatten
[STOP] [2019-12-23 17:33:31] rebuild_nodes
[START] [2019-12-23 17:33:31] resolve_missing_media_owners
[STOP] [2019-12-23 17:33:31] resolve_missing_media_owners
[START] [2019-12-23 17:33:31] sanitize_media_verbatims
[STOP] [2019-12-23 17:33:31] sanitize_media_verbatims
[START] [2019-12-23 17:33:31] queue_downloads
[STOP] [2019-12-23 17:33:31] queue_downloads
[START] [2019-12-23 17:33:31] parse_names
[WARN] [2019-12-23 17:33:31] I see 6117 names which still need to be parsed.
[STOP] [2019-12-23 17:33:37] parse_names
[START] [2019-12-23 17:33:37] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 17:33:37] denormalize_canonical_names_to_nodes
[START] [2019-12-23 17:33:37] match_nodes
[START] [2019-12-23 17:33:37] map_all_nodes_to_pages
[STOP] [2019-12-23 18:05:07] map_all_nodes_to_pages
[INFO] [2019-12-23 18:05:07] 395 Unmatched nodes (of 6117)! That's too many to output. First 10: Larus melanocephalus (#62095974); Philomachus (#62095770); Philomachus pugnax (#62095769); Limicola (#62095938); Limicola falcinellus (#62095937); Limnodromus (#62099035); Anas penelope (#62095711); Anas clypeata (#62095744); Anas strepera (#62095760); Anas querquedula (#62095831)
[START] [2019-12-23 18:05:07] update_nodes
[STOP] [2019-12-23 18:05:09] update_nodes
[STOP] [2019-12-23 18:05:09] match_nodes
[START] [2019-12-23 18:05:09] reindex_search
[STOP] [2019-12-23 18:05:22] reindex_search
[START] [2019-12-23 18:05:22] normalize_units
[STOP] [2019-12-23 18:05:22] normalize_units
[START] [2019-12-23 18:05:22] calculate_statistics
[STOP] [2019-12-23 18:05:22] calculate_statistics
[START] [2019-12-23 18:05:22] complete_harvest_instance
[START] [2019-12-23 18:05:22] overall_tsv_creation
[INFO] [2019-12-23 18:05:22] Processing group of 6117 in 1 batches of 10000
[INFO] [2019-12-23 18:06:37] 2938 Traits (unfiltered)...
[INFO] [2019-12-23 18:06:50] 2938 Traits (filtered)...
[INFO] [2019-12-23 18:06:50] 0 Associations (filtered)...
[INFO] [2019-12-23 18:07:35] 14685 metadata added.
[INFO] [2019-12-23 18:07:35] 0 metadata added.
[INFO] [2019-12-23 18:07:35] Average Time: 103.83
[INFO] [2019-12-23 18:07:35] Total Time: 2m13s
[STOP] [2019-12-23 18:07:35] overall_tsv_creation
[INFO] [2019-12-23 18:07:35] Done. Check your files:
[INFO] [2019-12-23 18:07:35] (6117 lines) /app/public/data/kattegat_sp_list/publish_nodes.tsv
[INFO] [2019-12-23 18:07:36] (29873 lines) /app/public/data/kattegat_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-23 18:07:36] (6117 lines) /app/public/data/kattegat_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-23 18:07:37] (2939 lines) /app/public/data/kattegat_sp_list/publish_traits.tsv
[INFO] [2019-12-23 18:07:38] (14686 lines) /app/public/data/kattegat_sp_list/publish_metadata.tsv
[STOP] [2019-12-23 18:07:38] complete_harvest_instance
[START] [2019-12-23 18:07:38] completed
[STOP] [2019-12-23 18:07:38] completed
[STOP] [2019-12-23 18:07:38] logged process, took 2144.34
Latest Process