Harvest for Belarus Species List Created 02 Oct 11:55

Stage: completed
Fetched: 02 Oct 11:55
Validated: 02 Oct 11:55
Deltas Created 02 Oct 11:55
Units Normalized: 02 Oct 12:00
Ancestry Built: 02 Oct 11:56
Nodes Matched: 02 Oct 12:00
Names Parsed: 02 Oct 11:56
New Models Stored: 02 Oct 11:55
Indexed: 02 Oct 12:00
Completed: 02 Oct 12:02
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-02 11:55:08 -0400 by logger.rb/56815
[START] [2019-10-02 11:55:08] logged process
[START] [2019-10-02 11:55:08] create_harvest_instance
[STOP] [2019-10-02 11:55:09] create_harvest_instance
[START] [2019-10-02 11:55:09] fetch_files
[STOP] [2019-10-02 11:55:09] fetch_files
[START] [2019-10-02 11:55:09] validate_each_file
[STOP] [2019-10-02 11:55:09] validate_each_file
[START] [2019-10-02 11:55:09] convert_to_csv
[CMD] [2019-10-02 11:55:09] /usr/bin/sort /app/public/converted_csv/belarus_sp_list_refs_14986.csv > /app/public/converted_csv/belarus_sp_list_refs_14986.csv_sorted
[CMD] [2019-10-02 11:55:10] /usr/bin/sort /app/public/converted_csv/belarus_sp_list_nodes_14987.csv > /app/public/converted_csv/belarus_sp_list_nodes_14987.csv_sorted
[CMD] [2019-10-02 11:55:12] /usr/bin/sort /app/public/converted_csv/belarus_sp_list_occurrences_14988.csv > /app/public/converted_csv/belarus_sp_list_occurrences_14988.csv_sorted
[CMD] [2019-10-02 11:55:13] /usr/bin/sort /app/public/converted_csv/belarus_sp_list_measurements_14989.csv > /app/public/converted_csv/belarus_sp_list_measurements_14989.csv_sorted
[STOP] [2019-10-02 11:55:15] convert_to_csv
[START] [2019-10-02 11:55:15] calculate_delta
[CMD] [2019-10-02 11:55:15] echo "0a" > /app/public/diff/belarus_sp_list_refs_14986.diff
[CMD] [2019-10-02 11:55:16] tail -n +1 /app/public/converted_csv/belarus_sp_list_refs_14986.csv >> /app/public/diff/belarus_sp_list_refs_14986.diff
[CMD] [2019-10-02 11:55:18] echo "." >> /app/public/diff/belarus_sp_list_refs_14986.diff
[CMD] [2019-10-02 11:55:19] echo "0a" > /app/public/diff/belarus_sp_list_nodes_14987.diff
[CMD] [2019-10-02 11:55:21] tail -n +1 /app/public/converted_csv/belarus_sp_list_nodes_14987.csv >> /app/public/diff/belarus_sp_list_nodes_14987.diff
[CMD] [2019-10-02 11:55:22] echo "." >> /app/public/diff/belarus_sp_list_nodes_14987.diff
[CMD] [2019-10-02 11:55:24] echo "0a" > /app/public/diff/belarus_sp_list_occurrences_14988.diff
[CMD] [2019-10-02 11:55:25] tail -n +1 /app/public/converted_csv/belarus_sp_list_occurrences_14988.csv >> /app/public/diff/belarus_sp_list_occurrences_14988.diff
[CMD] [2019-10-02 11:55:27] echo "." >> /app/public/diff/belarus_sp_list_occurrences_14988.diff
[CMD] [2019-10-02 11:55:28] echo "0a" > /app/public/diff/belarus_sp_list_measurements_14989.diff
[CMD] [2019-10-02 11:55:30] tail -n +1 /app/public/converted_csv/belarus_sp_list_measurements_14989.csv >> /app/public/diff/belarus_sp_list_measurements_14989.diff
[CMD] [2019-10-02 11:55:31] echo "." >> /app/public/diff/belarus_sp_list_measurements_14989.diff
[STOP] [2019-10-02 11:55:33] calculate_delta
[START] [2019-10-02 11:55:33] parse_diff_and_store
[INFO] [2019-10-02 11:55:34] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-02 11:55:36] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-02 11:55:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-02 11:55:40] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-02 11:55:49] Storing 2 References
[INFO] [2019-10-02 11:55:49] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-02 11:55:49] Average Time: 0.0
[INFO] [2019-10-02 11:55:49] Total Time: 1s
[INFO] [2019-10-02 11:55:49] Storing 3098 ScientificNames
[INFO] [2019-10-02 11:55:49] Processing group of 3098 in 4 groups of 1000
[INFO] [2019-10-02 11:55:50] Average Time: 0.278
[INFO] [2019-10-02 11:55:50] Total Time: 2s
[INFO] [2019-10-02 11:55:50] Storing 3098 Nodes
[INFO] [2019-10-02 11:55:50] Processing group of 3098 in 4 groups of 1000
[INFO] [2019-10-02 11:55:51] Average Time: 0.225
[INFO] [2019-10-02 11:55:51] Total Time: 1s
[INFO] [2019-10-02 11:55:51] Storing 1446 Occurrences
[INFO] [2019-10-02 11:55:51] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-02 11:55:51] Average Time: 0.075
[INFO] [2019-10-02 11:55:51] Total Time: 1s
[INFO] [2019-10-02 11:55:51] Storing 3210 TraitsReferences
[INFO] [2019-10-02 11:55:51] Processing group of 3210 in 4 groups of 1000
[INFO] [2019-10-02 11:55:52] Average Time: 0.083
[INFO] [2019-10-02 11:55:52] Total Time: 1s
[INFO] [2019-10-02 11:55:52] Storing 3209 Traits
[INFO] [2019-10-02 11:55:52] Processing group of 3209 in 4 groups of 1000
[INFO] [2019-10-02 11:55:53] Average Time: 0.28
[INFO] [2019-10-02 11:55:53] Total Time: 2s
[INFO] [2019-10-02 11:55:53] Storing 3209 MetaTraits
[INFO] [2019-10-02 11:55:53] Processing group of 3209 in 4 groups of 1000
[INFO] [2019-10-02 11:55:53] Average Time: 0.115
[INFO] [2019-10-02 11:55:53] Total Time: 1s
[STOP] [2019-10-02 11:55:53] parse_diff_and_store
[START] [2019-10-02 11:55:53] resolve_keys
[INFO] [2019-10-02 11:56:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-02 11:56:10] traits to occurrences...
[INFO] [2019-10-02 11:56:12] traits to nodes (through occurrences)...
[INFO] [2019-10-02 11:56:12] Traits to sex term...
[INFO] [2019-10-02 11:56:13] Traits to lifestage term...
[INFO] [2019-10-02 11:56:14] MetaTraits to traits...
[INFO] [2019-10-02 11:56:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-02 11:56:15] Assocs to occurrences...
[INFO] [2019-10-02 11:56:15] Assocs to nodes...
[INFO] [2019-10-02 11:56:15] Assoc to sex term...
[INFO] [2019-10-02 11:56:15] Assoc to lifestage term...
[STOP] [2019-10-02 11:56:15] resolve_keys
[START] [2019-10-02 11:56:15] hold_for_later_1
[STOP] [2019-10-02 11:56:15] hold_for_later_1
[START] [2019-10-02 11:56:15] hold_for_later_2
[STOP] [2019-10-02 11:56:15] hold_for_later_2
[START] [2019-10-02 11:56:15] resolve_missing_parents
[STOP] [2019-10-02 11:56:20] resolve_missing_parents
[START] [2019-10-02 11:56:20] rebuild_nodes
[START] [2019-10-02 11:56:20] Flattener#flatten
[START] [2019-10-02 11:56:20] Flattener#study_resource
[START] [2019-10-02 11:56:20] Flattener#build_ancestry
[STOP] [2019-10-02 11:56:20] Flattener#build_ancestry
[INFO] [2019-10-02 11:56:20] 3098 ancestry keys
[START] [2019-10-02 11:56:20] build_node_ancestors
[INFO] [2019-10-02 11:56:20] old ancestors deleted.
[STOP] [2019-10-02 11:56:21] build_node_ancestors
[START] [2019-10-02 11:56:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 11:56:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 11:56:21] Flattener#flatten
[STOP] [2019-10-02 11:56:21] rebuild_nodes
[START] [2019-10-02 11:56:21] resolve_missing_media_owners
[STOP] [2019-10-02 11:56:21] resolve_missing_media_owners
[START] [2019-10-02 11:56:21] sanitize_media_verbatims
[STOP] [2019-10-02 11:56:21] sanitize_media_verbatims
[START] [2019-10-02 11:56:21] queue_downloads
[STOP] [2019-10-02 11:56:21] queue_downloads
[START] [2019-10-02 11:56:21] parse_names
[WARN] [2019-10-02 11:56:21] I see 3098 names which still need to be parsed.
[STOP] [2019-10-02 11:56:24] parse_names
[START] [2019-10-02 11:56:24] denormalize_canonical_names_to_nodes
[STOP] [2019-10-02 11:56:24] denormalize_canonical_names_to_nodes
[START] [2019-10-02 11:56:24] match_nodes
[START] [2019-10-02 11:56:24] map_all_nodes_to_pages
[STOP] [2019-10-02 12:00:09] map_all_nodes_to_pages
[INFO] [2019-10-02 12:00:09] 295 Unmatched nodes (of 3098)! That's too many to output. First 10: Pelophylax esculentus (#47735320); Pelophylax esculenta (#47735343); Anas querquedula (#47734990); Anas clypeata (#47735105); Anas strepera (#47735487); Anas penelope (#47735565); Delichon urbica (#47735482); Parus caeruleus (#47735272); Parus cyanus (#47735858); Parus montanus (#47735957)
[START] [2019-10-02 12:00:09] update_nodes
[STOP] [2019-10-02 12:00:10] update_nodes
[STOP] [2019-10-02 12:00:10] match_nodes
[START] [2019-10-02 12:00:10] reindex_search
[STOP] [2019-10-02 12:00:20] reindex_search
[START] [2019-10-02 12:00:20] normalize_units
[STOP] [2019-10-02 12:00:20] normalize_units
[START] [2019-10-02 12:00:20] calculate_statistics
[STOP] [2019-10-02 12:00:20] calculate_statistics
[START] [2019-10-02 12:00:20] complete_harvest_instance
[START] [2019-10-02 12:00:20] overall_tsv_creation
[INFO] [2019-10-02 12:00:20] Processing group of 3098 in 1 batches of 10000
[INFO] [2019-10-02 12:01:16] 1446 Traits (unfiltered)...
[INFO] [2019-10-02 12:01:29] 1446 Traits (filtered)...
[INFO] [2019-10-02 12:01:29] 0 Associations (filtered)...
[INFO] [2019-10-02 12:02:07] 7229 metadata added.
[INFO] [2019-10-02 12:02:07] 0 metadata added.
[INFO] [2019-10-02 12:02:07] Average Time: 84.65
[INFO] [2019-10-02 12:02:07] Total Time: 1m48s
[STOP] [2019-10-02 12:02:07] overall_tsv_creation
[INFO] [2019-10-02 12:02:07] Done. Check your files:
[INFO] [2019-10-02 12:02:09] (3098 lines) /app/public/data/belarus_sp_list/publish_nodes.tsv
[INFO] [2019-10-02 12:02:10] (5999 lines) /app/public/data/belarus_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-02 12:02:12] (3098 lines) /app/public/data/belarus_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-02 12:02:13] (1447 lines) /app/public/data/belarus_sp_list/publish_traits.tsv
[INFO] [2019-10-02 12:02:15] (7230 lines) /app/public/data/belarus_sp_list/publish_metadata.tsv
[STOP] [2019-10-02 12:02:15] complete_harvest_instance
[START] [2019-10-02 12:02:15] completed
[STOP] [2019-10-02 12:02:15] completed
[STOP] [2019-10-02 12:02:15] logged process, took 426.89
Latest Process

02 Oct 11:55 EXITED currently processing 0