Harvest for Serbia Species List Created 15 Oct 17:44

Stage: completed
Fetched: 15 Oct 17:44
Validated: 15 Oct 17:44
Deltas Created 15 Oct 17:44
Units Normalized: 15 Oct 17:51
Ancestry Built: 15 Oct 17:45
Nodes Matched: 15 Oct 17:51
Names Parsed: 15 Oct 17:46
New Models Stored: 15 Oct 17:45
Indexed: 15 Oct 17:51
Completed: 15 Oct 17:54
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 17:44:53 -0400 by logger.rb/56815
[START] [2019-10-15 17:44:53] logged process
[START] [2019-10-15 17:44:53] create_harvest_instance
[STOP] [2019-10-15 17:44:53] create_harvest_instance
[START] [2019-10-15 17:44:53] fetch_files
[STOP] [2019-10-15 17:44:53] fetch_files
[START] [2019-10-15 17:44:53] validate_each_file
[STOP] [2019-10-15 17:44:54] validate_each_file
[START] [2019-10-15 17:44:54] convert_to_csv
[CMD] [2019-10-15 17:44:54] /usr/bin/sort /app/public/converted_csv/serbia_sp_list_refs_17157.csv > /app/public/converted_csv/serbia_sp_list_refs_17157.csv_sorted
[CMD] [2019-10-15 17:44:54] /usr/bin/sort /app/public/converted_csv/serbia_sp_list_nodes_17158.csv > /app/public/converted_csv/serbia_sp_list_nodes_17158.csv_sorted
[CMD] [2019-10-15 17:44:54] /usr/bin/sort /app/public/converted_csv/serbia_sp_list_occurrences_17159.csv > /app/public/converted_csv/serbia_sp_list_occurrences_17159.csv_sorted
[CMD] [2019-10-15 17:44:55] /usr/bin/sort /app/public/converted_csv/serbia_sp_list_measurements_17160.csv > /app/public/converted_csv/serbia_sp_list_measurements_17160.csv_sorted
[STOP] [2019-10-15 17:44:55] convert_to_csv
[START] [2019-10-15 17:44:55] calculate_delta
[CMD] [2019-10-15 17:44:55] echo "0a" > /app/public/diff/serbia_sp_list_refs_17157.diff
[CMD] [2019-10-15 17:44:55] tail -n +1 /app/public/converted_csv/serbia_sp_list_refs_17157.csv >> /app/public/diff/serbia_sp_list_refs_17157.diff
[CMD] [2019-10-15 17:44:55] echo "." >> /app/public/diff/serbia_sp_list_refs_17157.diff
[CMD] [2019-10-15 17:44:56] echo "0a" > /app/public/diff/serbia_sp_list_nodes_17158.diff
[CMD] [2019-10-15 17:44:56] tail -n +1 /app/public/converted_csv/serbia_sp_list_nodes_17158.csv >> /app/public/diff/serbia_sp_list_nodes_17158.diff
[CMD] [2019-10-15 17:44:56] echo "." >> /app/public/diff/serbia_sp_list_nodes_17158.diff
[CMD] [2019-10-15 17:44:57] echo "0a" > /app/public/diff/serbia_sp_list_occurrences_17159.diff
[CMD] [2019-10-15 17:44:57] tail -n +1 /app/public/converted_csv/serbia_sp_list_occurrences_17159.csv >> /app/public/diff/serbia_sp_list_occurrences_17159.diff
[CMD] [2019-10-15 17:44:57] echo "." >> /app/public/diff/serbia_sp_list_occurrences_17159.diff
[CMD] [2019-10-15 17:44:57] echo "0a" > /app/public/diff/serbia_sp_list_measurements_17160.diff
[CMD] [2019-10-15 17:44:58] tail -n +1 /app/public/converted_csv/serbia_sp_list_measurements_17160.csv >> /app/public/diff/serbia_sp_list_measurements_17160.diff
[CMD] [2019-10-15 17:44:58] echo "." >> /app/public/diff/serbia_sp_list_measurements_17160.diff
[STOP] [2019-10-15 17:44:58] calculate_delta
[START] [2019-10-15 17:44:58] parse_diff_and_store
[INFO] [2019-10-15 17:44:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 17:44:59] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 17:45:01] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 17:45:01] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 17:45:16] Storing 2 References
[INFO] [2019-10-15 17:45:16] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 17:45:16] Average Time: 0.0
[INFO] [2019-10-15 17:45:16] Total Time: 1s
[INFO] [2019-10-15 17:45:16] Storing 4601 ScientificNames
[INFO] [2019-10-15 17:45:16] Processing group of 4601 in 5 groups of 1000
[INFO] [2019-10-15 17:45:18] Average Time: 0.39
[INFO] [2019-10-15 17:45:18] Total Time: 2s
[INFO] [2019-10-15 17:45:18] Storing 4601 Nodes
[INFO] [2019-10-15 17:45:18] Processing group of 4601 in 5 groups of 1000
[INFO] [2019-10-15 17:45:20] Average Time: 0.308
[INFO] [2019-10-15 17:45:20] Total Time: 2s
[INFO] [2019-10-15 17:45:20] Storing 2410 Occurrences
[INFO] [2019-10-15 17:45:20] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-15 17:45:20] Average Time: 0.183
[INFO] [2019-10-15 17:45:20] Total Time: 1s
[INFO] [2019-10-15 17:45:20] Storing 4950 TraitsReferences
[INFO] [2019-10-15 17:45:20] Processing group of 4950 in 5 groups of 1000
[INFO] [2019-10-15 17:45:21] Average Time: 0.08
[INFO] [2019-10-15 17:45:21] Total Time: 1s
[INFO] [2019-10-15 17:45:21] Storing 4949 Traits
[INFO] [2019-10-15 17:45:21] Processing group of 4949 in 5 groups of 1000
[INFO] [2019-10-15 17:45:22] Average Time: 0.31
[INFO] [2019-10-15 17:45:22] Total Time: 2s
[INFO] [2019-10-15 17:45:22] Storing 4950 MetaTraits
[INFO] [2019-10-15 17:45:22] Processing group of 4950 in 5 groups of 1000
[INFO] [2019-10-15 17:45:23] Average Time: 0.116
[INFO] [2019-10-15 17:45:23] Total Time: 1s
[STOP] [2019-10-15 17:45:23] parse_diff_and_store
[START] [2019-10-15 17:45:23] resolve_keys
[INFO] [2019-10-15 17:45:43] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 17:45:44] traits to occurrences...
[INFO] [2019-10-15 17:45:45] traits to nodes (through occurrences)...
[INFO] [2019-10-15 17:45:46] Traits to sex term...
[INFO] [2019-10-15 17:45:47] Traits to lifestage term...
[INFO] [2019-10-15 17:45:47] MetaTraits to traits...
[INFO] [2019-10-15 17:45:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 17:45:49] Assocs to occurrences...
[INFO] [2019-10-15 17:45:49] Assocs to nodes...
[INFO] [2019-10-15 17:45:49] Assoc to sex term...
[INFO] [2019-10-15 17:45:49] Assoc to lifestage term...
[STOP] [2019-10-15 17:45:49] resolve_keys
[START] [2019-10-15 17:45:49] hold_for_later_1
[STOP] [2019-10-15 17:45:49] hold_for_later_1
[START] [2019-10-15 17:45:49] hold_for_later_2
[STOP] [2019-10-15 17:45:49] hold_for_later_2
[START] [2019-10-15 17:45:49] resolve_missing_parents
[STOP] [2019-10-15 17:45:57] resolve_missing_parents
[START] [2019-10-15 17:45:57] rebuild_nodes
[START] [2019-10-15 17:45:57] Flattener#flatten
[START] [2019-10-15 17:45:57] Flattener#study_resource
[START] [2019-10-15 17:45:57] Flattener#build_ancestry
[STOP] [2019-10-15 17:45:57] Flattener#build_ancestry
[INFO] [2019-10-15 17:45:57] 4601 ancestry keys
[START] [2019-10-15 17:45:57] build_node_ancestors
[INFO] [2019-10-15 17:45:57] old ancestors deleted.
[STOP] [2019-10-15 17:45:58] build_node_ancestors
[START] [2019-10-15 17:45:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 17:45:59] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 17:45:59] Flattener#flatten
[STOP] [2019-10-15 17:45:59] rebuild_nodes
[START] [2019-10-15 17:45:59] resolve_missing_media_owners
[STOP] [2019-10-15 17:45:59] resolve_missing_media_owners
[START] [2019-10-15 17:45:59] sanitize_media_verbatims
[STOP] [2019-10-15 17:45:59] sanitize_media_verbatims
[START] [2019-10-15 17:45:59] queue_downloads
[STOP] [2019-10-15 17:45:59] queue_downloads
[START] [2019-10-15 17:45:59] parse_names
[WARN] [2019-10-15 17:45:59] I see 4601 names which still need to be parsed.
[STOP] [2019-10-15 17:46:03] parse_names
[START] [2019-10-15 17:46:03] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 17:46:03] denormalize_canonical_names_to_nodes
[START] [2019-10-15 17:46:03] match_nodes
[START] [2019-10-15 17:46:03] map_all_nodes_to_pages
[STOP] [2019-10-15 17:51:44] map_all_nodes_to_pages
[INFO] [2019-10-15 17:51:44] 554 Unmatched nodes (of 4601)! That's too many to output. First 10: Corvus monedula (#51786497); Parus palustris (#51789051); Delichon urbica (#51786969); Carduelis cannabina (#51787317); Carduelis spinus (#51787715); Carduelis chloris (#51790271); Phylloscopus sibillatrix (#51786501); Anas querquedula (#51786481); Anas clypeata (#51786490); Anas strepera (#51786502)
[START] [2019-10-15 17:51:44] update_nodes
[STOP] [2019-10-15 17:51:45] update_nodes
[STOP] [2019-10-15 17:51:45] match_nodes
[START] [2019-10-15 17:51:45] reindex_search
[STOP] [2019-10-15 17:51:58] reindex_search
[START] [2019-10-15 17:51:58] normalize_units
[STOP] [2019-10-15 17:51:58] normalize_units
[START] [2019-10-15 17:51:58] calculate_statistics
[STOP] [2019-10-15 17:51:58] calculate_statistics
[START] [2019-10-15 17:51:58] complete_harvest_instance
[START] [2019-10-15 17:51:58] overall_tsv_creation
[INFO] [2019-10-15 17:51:58] Processing group of 4601 in 1 batches of 10000
[INFO] [2019-10-15 17:53:02] 2410 Traits (unfiltered)...
[INFO] [2019-10-15 17:53:16] 2410 Traits (filtered)...
[INFO] [2019-10-15 17:53:16] 0 Associations (filtered)...
[INFO] [2019-10-15 17:53:58] 12050 metadata added.
[INFO] [2019-10-15 17:53:58] 0 metadata added.
[INFO] [2019-10-15 17:53:58] Average Time: 96.21
[INFO] [2019-10-15 17:53:58] Total Time: 1m60s
[STOP] [2019-10-15 17:53:58] overall_tsv_creation
[INFO] [2019-10-15 17:53:58] Done. Check your files:
[INFO] [2019-10-15 17:53:58] (4601 lines) /app/public/data/serbia_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 17:53:59] (9930 lines) /app/public/data/serbia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 17:53:59] (4601 lines) /app/public/data/serbia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 17:53:59] (2411 lines) /app/public/data/serbia_sp_list/publish_traits.tsv
[INFO] [2019-10-15 17:53:59] (12051 lines) /app/public/data/serbia_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 17:54:00] complete_harvest_instance
[START] [2019-10-15 17:54:00] completed
[STOP] [2019-10-15 17:54:00] completed
[STOP] [2019-10-15 17:54:00] logged process, took 547.16
Latest Process

15 Oct 17:44 EXITED currently processing 0