Harvest for Bosnia and Herzegovina Species List Created 11 Oct 16:30

Stage: completed
Fetched: 11 Oct 16:30
Validated: 11 Oct 16:30
Deltas Created 11 Oct 16:30
Units Normalized: 11 Oct 16:32
Ancestry Built: 11 Oct 16:31
Nodes Matched: 11 Oct 16:32
Names Parsed: 11 Oct 16:31
New Models Stored: 11 Oct 16:30
Indexed: 11 Oct 16:32
Completed: 11 Oct 16:34
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-11 16:30:37 -0400 by logger.rb/56815
[START] [2019-10-11 16:30:37] logged process
[START] [2019-10-11 16:30:37] create_harvest_instance
[STOP] [2019-10-11 16:30:37] create_harvest_instance
[START] [2019-10-11 16:30:37] fetch_files
[STOP] [2019-10-11 16:30:37] fetch_files
[START] [2019-10-11 16:30:37] validate_each_file
[STOP] [2019-10-11 16:30:38] validate_each_file
[START] [2019-10-11 16:30:38] convert_to_csv
[CMD] [2019-10-11 16:30:38] /usr/bin/sort /app/public/converted_csv/bosnia_herzegovi_refs_15228.csv > /app/public/converted_csv/bosnia_herzegovi_refs_15228.csv_sorted
[CMD] [2019-10-11 16:30:38] /usr/bin/sort /app/public/converted_csv/bosnia_herzegovi_nodes_15229.csv > /app/public/converted_csv/bosnia_herzegovi_nodes_15229.csv_sorted
[CMD] [2019-10-11 16:30:38] /usr/bin/sort /app/public/converted_csv/bosnia_herzegovi_occurrences_15230.csv > /app/public/converted_csv/bosnia_herzegovi_occurrences_15230.csv_sorted
[CMD] [2019-10-11 16:30:38] /usr/bin/sort /app/public/converted_csv/bosnia_herzegovi_measurements_15231.csv > /app/public/converted_csv/bosnia_herzegovi_measurements_15231.csv_sorted
[STOP] [2019-10-11 16:30:38] convert_to_csv
[START] [2019-10-11 16:30:38] calculate_delta
[CMD] [2019-10-11 16:30:38] echo "0a" > /app/public/diff/bosnia_herzegovi_refs_15228.diff
[CMD] [2019-10-11 16:30:38] tail -n +1 /app/public/converted_csv/bosnia_herzegovi_refs_15228.csv >> /app/public/diff/bosnia_herzegovi_refs_15228.diff
[CMD] [2019-10-11 16:30:38] echo "." >> /app/public/diff/bosnia_herzegovi_refs_15228.diff
[CMD] [2019-10-11 16:30:38] echo "0a" > /app/public/diff/bosnia_herzegovi_nodes_15229.diff
[CMD] [2019-10-11 16:30:38] tail -n +1 /app/public/converted_csv/bosnia_herzegovi_nodes_15229.csv >> /app/public/diff/bosnia_herzegovi_nodes_15229.diff
[CMD] [2019-10-11 16:30:38] echo "." >> /app/public/diff/bosnia_herzegovi_nodes_15229.diff
[CMD] [2019-10-11 16:30:38] echo "0a" > /app/public/diff/bosnia_herzegovi_occurrences_15230.diff
[CMD] [2019-10-11 16:30:38] tail -n +1 /app/public/converted_csv/bosnia_herzegovi_occurrences_15230.csv >> /app/public/diff/bosnia_herzegovi_occurrences_15230.diff
[CMD] [2019-10-11 16:30:38] echo "." >> /app/public/diff/bosnia_herzegovi_occurrences_15230.diff
[CMD] [2019-10-11 16:30:38] echo "0a" > /app/public/diff/bosnia_herzegovi_measurements_15231.diff
[CMD] [2019-10-11 16:30:38] tail -n +1 /app/public/converted_csv/bosnia_herzegovi_measurements_15231.csv >> /app/public/diff/bosnia_herzegovi_measurements_15231.diff
[CMD] [2019-10-11 16:30:38] echo "." >> /app/public/diff/bosnia_herzegovi_measurements_15231.diff
[STOP] [2019-10-11 16:30:38] calculate_delta
[START] [2019-10-11 16:30:38] parse_diff_and_store
[INFO] [2019-10-11 16:30:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 16:30:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 16:30:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 16:30:39] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 16:30:47] Storing 2 References
[INFO] [2019-10-11 16:30:47] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 16:30:47] Average Time: 0.0
[INFO] [2019-10-11 16:30:47] Total Time: 1s
[INFO] [2019-10-11 16:30:47] Storing 2399 ScientificNames
[INFO] [2019-10-11 16:30:47] Processing group of 2399 in 3 groups of 1000
[INFO] [2019-10-11 16:30:48] Average Time: 0.31
[INFO] [2019-10-11 16:30:48] Total Time: 1s
[INFO] [2019-10-11 16:30:48] Storing 2399 Nodes
[INFO] [2019-10-11 16:30:48] Processing group of 2399 in 3 groups of 1000
[INFO] [2019-10-11 16:30:49] Average Time: 0.263
[INFO] [2019-10-11 16:30:49] Total Time: 1s
[INFO] [2019-10-11 16:30:49] Storing 964 Occurrences
[INFO] [2019-10-11 16:30:49] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-11 16:30:49] Average Time: 0.12
[INFO] [2019-10-11 16:30:49] Total Time: 1s
[INFO] [2019-10-11 16:30:49] Storing 2608 TraitsReferences
[INFO] [2019-10-11 16:30:49] Processing group of 2608 in 3 groups of 1000
[INFO] [2019-10-11 16:30:49] Average Time: 0.09
[INFO] [2019-10-11 16:30:49] Total Time: 1s
[INFO] [2019-10-11 16:30:49] Storing 2607 Traits
[INFO] [2019-10-11 16:30:49] Processing group of 2607 in 3 groups of 1000
[INFO] [2019-10-11 16:30:50] Average Time: 0.35
[INFO] [2019-10-11 16:30:50] Total Time: 2s
[INFO] [2019-10-11 16:30:50] Storing 2608 MetaTraits
[INFO] [2019-10-11 16:30:50] Processing group of 2608 in 3 groups of 1000
[INFO] [2019-10-11 16:30:51] Average Time: 0.117
[INFO] [2019-10-11 16:30:51] Total Time: 1s
[STOP] [2019-10-11 16:30:51] parse_diff_and_store
[START] [2019-10-11 16:30:51] resolve_keys
[INFO] [2019-10-11 16:31:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 16:31:03] traits to occurrences...
[INFO] [2019-10-11 16:31:04] traits to nodes (through occurrences)...
[INFO] [2019-10-11 16:31:04] Traits to sex term...
[INFO] [2019-10-11 16:31:05] Traits to lifestage term...
[INFO] [2019-10-11 16:31:05] MetaTraits to traits...
[INFO] [2019-10-11 16:31:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 16:31:06] Assocs to occurrences...
[INFO] [2019-10-11 16:31:06] Assocs to nodes...
[INFO] [2019-10-11 16:31:06] Assoc to sex term...
[INFO] [2019-10-11 16:31:06] Assoc to lifestage term...
[STOP] [2019-10-11 16:31:06] resolve_keys
[START] [2019-10-11 16:31:06] hold_for_later_1
[STOP] [2019-10-11 16:31:06] hold_for_later_1
[START] [2019-10-11 16:31:06] hold_for_later_2
[STOP] [2019-10-11 16:31:06] hold_for_later_2
[START] [2019-10-11 16:31:06] resolve_missing_parents
[STOP] [2019-10-11 16:31:10] resolve_missing_parents
[START] [2019-10-11 16:31:10] rebuild_nodes
[START] [2019-10-11 16:31:10] Flattener#flatten
[START] [2019-10-11 16:31:10] Flattener#study_resource
[START] [2019-10-11 16:31:10] Flattener#build_ancestry
[STOP] [2019-10-11 16:31:10] Flattener#build_ancestry
[INFO] [2019-10-11 16:31:10] 2399 ancestry keys
[START] [2019-10-11 16:31:10] build_node_ancestors
[INFO] [2019-10-11 16:31:10] old ancestors deleted.
[STOP] [2019-10-11 16:31:10] build_node_ancestors
[START] [2019-10-11 16:31:10] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:31:11] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:31:11] Flattener#flatten
[STOP] [2019-10-11 16:31:11] rebuild_nodes
[START] [2019-10-11 16:31:11] resolve_missing_media_owners
[STOP] [2019-10-11 16:31:11] resolve_missing_media_owners
[START] [2019-10-11 16:31:11] sanitize_media_verbatims
[STOP] [2019-10-11 16:31:11] sanitize_media_verbatims
[START] [2019-10-11 16:31:11] queue_downloads
[STOP] [2019-10-11 16:31:11] queue_downloads
[START] [2019-10-11 16:31:11] parse_names
[WARN] [2019-10-11 16:31:11] I see 2399 names which still need to be parsed.
[STOP] [2019-10-11 16:31:13] parse_names
[START] [2019-10-11 16:31:13] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 16:31:13] denormalize_canonical_names_to_nodes
[START] [2019-10-11 16:31:13] match_nodes
[START] [2019-10-11 16:31:13] map_all_nodes_to_pages
[STOP] [2019-10-11 16:32:24] map_all_nodes_to_pages
[INFO] [2019-10-11 16:32:24] 158 Unmatched nodes (of 2399)! That's too many to output. First 10: Odyssea pungens (#48835783); Corvus monedula (#48833718); Parus caeruleus (#48835007); Anas querquedula (#48833767); Anas clypeata (#48834068); Anas penelope (#48834506); Anas strepera (#48834737); Delminichthys pstrossii (#48835138); Monticola (#48834199); Carduelis cannabina (#48833884)
[START] [2019-10-11 16:32:24] update_nodes
[STOP] [2019-10-11 16:32:25] update_nodes
[STOP] [2019-10-11 16:32:25] match_nodes
[START] [2019-10-11 16:32:25] reindex_search
[STOP] [2019-10-11 16:32:28] reindex_search
[START] [2019-10-11 16:32:28] normalize_units
[STOP] [2019-10-11 16:32:28] normalize_units
[START] [2019-10-11 16:32:28] calculate_statistics
[STOP] [2019-10-11 16:32:28] calculate_statistics
[START] [2019-10-11 16:32:28] complete_harvest_instance
[START] [2019-10-11 16:32:28] overall_tsv_creation
[INFO] [2019-10-11 16:32:28] Processing group of 2399 in 1 batches of 10000
[INFO] [2019-10-11 16:33:24] 964 Traits (unfiltered)...
[INFO] [2019-10-11 16:33:38] 964 Traits (filtered)...
[INFO] [2019-10-11 16:33:38] 0 Associations (filtered)...
[INFO] [2019-10-11 16:34:17] 4820 metadata added.
[INFO] [2019-10-11 16:34:17] 0 metadata added.
[INFO] [2019-10-11 16:34:17] Average Time: 86.21
[INFO] [2019-10-11 16:34:17] Total Time: 1m49s
[STOP] [2019-10-11 16:34:17] overall_tsv_creation
[INFO] [2019-10-11 16:34:17] Done. Check your files:
[INFO] [2019-10-11 16:34:17] (2399 lines) /app/public/data/bosnia_herzegovi/publish_nodes.tsv
[INFO] [2019-10-11 16:34:17] (3296 lines) /app/public/data/bosnia_herzegovi/publish_node_ancestors.tsv
[INFO] [2019-10-11 16:34:17] (2399 lines) /app/public/data/bosnia_herzegovi/publish_scientific_names.tsv
[INFO] [2019-10-11 16:34:17] (965 lines) /app/public/data/bosnia_herzegovi/publish_traits.tsv
[INFO] [2019-10-11 16:34:17] (4821 lines) /app/public/data/bosnia_herzegovi/publish_metadata.tsv
[STOP] [2019-10-11 16:34:17] complete_harvest_instance
[START] [2019-10-11 16:34:17] completed
[STOP] [2019-10-11 16:34:17] completed
[STOP] [2019-10-11 16:34:17] logged process, took 220.34

Latest Process