Harvest for Botswana Species List Created 11 Oct 16:34

Stage: completed
Fetched: 11 Oct 16:34
Validated: 11 Oct 16:34
Deltas Created 11 Oct 16:34
Units Normalized: 11 Oct 16:39
Ancestry Built: 11 Oct 16:36
Nodes Matched: 11 Oct 16:39
Names Parsed: 11 Oct 16:36
New Models Stored: 11 Oct 16:35
Indexed: 11 Oct 16:39
Completed: 11 Oct 16:41
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-11 16:34:25 -0400 by logger.rb/56815
[START] [2019-10-11 16:34:25] logged process
[START] [2019-10-11 16:34:25] create_harvest_instance
[STOP] [2019-10-11 16:34:26] create_harvest_instance
[START] [2019-10-11 16:34:26] fetch_files
[STOP] [2019-10-11 16:34:26] fetch_files
[START] [2019-10-11 16:34:26] validate_each_file
[STOP] [2019-10-11 16:34:27] validate_each_file
[START] [2019-10-11 16:34:27] convert_to_csv
[CMD] [2019-10-11 16:34:27] /usr/bin/sort /app/public/converted_csv/botswana_sp_list_refs_15236.csv > /app/public/converted_csv/botswana_sp_list_refs_15236.csv_sorted
[CMD] [2019-10-11 16:34:27] /usr/bin/sort /app/public/converted_csv/botswana_sp_list_nodes_15237.csv > /app/public/converted_csv/botswana_sp_list_nodes_15237.csv_sorted
[CMD] [2019-10-11 16:34:27] /usr/bin/sort /app/public/converted_csv/botswana_sp_list_occurrences_15238.csv > /app/public/converted_csv/botswana_sp_list_occurrences_15238.csv_sorted
[CMD] [2019-10-11 16:34:27] /usr/bin/sort /app/public/converted_csv/botswana_sp_list_measurements_15239.csv > /app/public/converted_csv/botswana_sp_list_measurements_15239.csv_sorted
[STOP] [2019-10-11 16:34:27] convert_to_csv
[START] [2019-10-11 16:34:27] calculate_delta
[CMD] [2019-10-11 16:34:27] echo "0a" > /app/public/diff/botswana_sp_list_refs_15236.diff
[CMD] [2019-10-11 16:34:27] tail -n +1 /app/public/converted_csv/botswana_sp_list_refs_15236.csv >> /app/public/diff/botswana_sp_list_refs_15236.diff
[CMD] [2019-10-11 16:34:27] echo "." >> /app/public/diff/botswana_sp_list_refs_15236.diff
[CMD] [2019-10-11 16:34:27] echo "0a" > /app/public/diff/botswana_sp_list_nodes_15237.diff
[CMD] [2019-10-11 16:34:27] tail -n +1 /app/public/converted_csv/botswana_sp_list_nodes_15237.csv >> /app/public/diff/botswana_sp_list_nodes_15237.diff
[CMD] [2019-10-11 16:34:27] echo "." >> /app/public/diff/botswana_sp_list_nodes_15237.diff
[CMD] [2019-10-11 16:34:27] echo "0a" > /app/public/diff/botswana_sp_list_occurrences_15238.diff
[CMD] [2019-10-11 16:34:27] tail -n +1 /app/public/converted_csv/botswana_sp_list_occurrences_15238.csv >> /app/public/diff/botswana_sp_list_occurrences_15238.diff
[CMD] [2019-10-11 16:34:27] echo "." >> /app/public/diff/botswana_sp_list_occurrences_15238.diff
[CMD] [2019-10-11 16:34:27] echo "0a" > /app/public/diff/botswana_sp_list_measurements_15239.diff
[CMD] [2019-10-11 16:34:27] tail -n +1 /app/public/converted_csv/botswana_sp_list_measurements_15239.csv >> /app/public/diff/botswana_sp_list_measurements_15239.diff
[CMD] [2019-10-11 16:34:27] echo "." >> /app/public/diff/botswana_sp_list_measurements_15239.diff
[STOP] [2019-10-11 16:34:27] calculate_delta
[START] [2019-10-11 16:34:27] parse_diff_and_store
[INFO] [2019-10-11 16:34:28] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 16:34:28] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 16:34:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 16:34:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 16:34:57] Storing 2 References
[INFO] [2019-10-11 16:34:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 16:34:57] Average Time: 0.0
[INFO] [2019-10-11 16:34:57] Total Time: 1s
[INFO] [2019-10-11 16:34:57] Storing 6602 ScientificNames
[INFO] [2019-10-11 16:34:57] Processing group of 6602 in 7 groups of 1000
[INFO] [2019-10-11 16:34:59] Average Time: 0.361
[INFO] [2019-10-11 16:34:59] Total Time: 3s
[INFO] [2019-10-11 16:34:59] last 3 / first 3: 0.75
[INFO] [2019-10-11 16:34:59] Std.Dev: 0.06324555320336758; Max: 0.45
[INFO] [2019-10-11 16:34:59] Storing 6602 Nodes
[INFO] [2019-10-11 16:34:59] Processing group of 6602 in 7 groups of 1000
[INFO] [2019-10-11 16:35:01] Average Time: 0.29
[INFO] [2019-10-11 16:35:01] Total Time: 3s
[INFO] [2019-10-11 16:35:01] last 3 / first 3: 0.89
[INFO] [2019-10-11 16:35:01] Std.Dev: 0.044721359549995794; Max: 0.35
[INFO] [2019-10-11 16:35:01] Storing 4338 Occurrences
[INFO] [2019-10-11 16:35:01] Processing group of 4338 in 5 groups of 1000
[INFO] [2019-10-11 16:35:02] Average Time: 0.088
[INFO] [2019-10-11 16:35:02] Total Time: 1s
[INFO] [2019-10-11 16:35:02] Storing 8700 TraitsReferences
[INFO] [2019-10-11 16:35:02] Processing group of 8700 in 9 groups of 1000
[INFO] [2019-10-11 16:35:03] Average Time: 0.082
[INFO] [2019-10-11 16:35:03] Total Time: 1s
[INFO] [2019-10-11 16:35:03] last 3 / first 3: 0.79
[INFO] [2019-10-11 16:35:03] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-11 16:35:03] Storing 8699 Traits
[INFO] [2019-10-11 16:35:03] Processing group of 8699 in 9 groups of 1000
[INFO] [2019-10-11 16:35:06] Average Time: 0.368
[INFO] [2019-10-11 16:35:06] Total Time: 4s
[INFO] [2019-10-11 16:35:06] last 3 / first 3: 0.82
[INFO] [2019-10-11 16:35:06] Std.Dev: 0.08366600265340755; Max: 0.49
[INFO] [2019-10-11 16:35:06] Storing 8696 MetaTraits
[INFO] [2019-10-11 16:35:06] Processing group of 8696 in 9 groups of 1000
[INFO] [2019-10-11 16:35:07] Average Time: 0.144
[INFO] [2019-10-11 16:35:07] Total Time: 2s
[INFO] [2019-10-11 16:35:07] last 3 / first 3: 0.83
[INFO] [2019-10-11 16:35:07] Std.Dev: 0.03162277660168379; Max: 0.17
[STOP] [2019-10-11 16:35:07] parse_diff_and_store
[START] [2019-10-11 16:35:07] resolve_keys
[INFO] [2019-10-11 16:35:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 16:35:38] traits to occurrences...
[INFO] [2019-10-11 16:35:42] traits to nodes (through occurrences)...
[INFO] [2019-10-11 16:35:42] Traits to sex term...
[INFO] [2019-10-11 16:35:45] Traits to lifestage term...
[INFO] [2019-10-11 16:35:48] MetaTraits to traits...
[INFO] [2019-10-11 16:35:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 16:35:50] Assocs to occurrences...
[INFO] [2019-10-11 16:35:50] Assocs to nodes...
[INFO] [2019-10-11 16:35:50] Assoc to sex term...
[INFO] [2019-10-11 16:35:50] Assoc to lifestage term...
[STOP] [2019-10-11 16:35:50] resolve_keys
[START] [2019-10-11 16:35:50] hold_for_later_1
[STOP] [2019-10-11 16:35:50] hold_for_later_1
[START] [2019-10-11 16:35:50] hold_for_later_2
[STOP] [2019-10-11 16:35:50] hold_for_later_2
[START] [2019-10-11 16:35:50] resolve_missing_parents
[STOP] [2019-10-11 16:36:04] resolve_missing_parents
[START] [2019-10-11 16:36:04] rebuild_nodes
[START] [2019-10-11 16:36:04] Flattener#flatten
[START] [2019-10-11 16:36:04] Flattener#study_resource
[START] [2019-10-11 16:36:04] Flattener#build_ancestry
[STOP] [2019-10-11 16:36:04] Flattener#build_ancestry
[INFO] [2019-10-11 16:36:04] 6602 ancestry keys
[START] [2019-10-11 16:36:04] build_node_ancestors
[INFO] [2019-10-11 16:36:04] old ancestors deleted.
[STOP] [2019-10-11 16:36:05] build_node_ancestors
[START] [2019-10-11 16:36:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:36:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:36:06] Flattener#flatten
[STOP] [2019-10-11 16:36:06] rebuild_nodes
[START] [2019-10-11 16:36:06] resolve_missing_media_owners
[STOP] [2019-10-11 16:36:06] resolve_missing_media_owners
[START] [2019-10-11 16:36:06] sanitize_media_verbatims
[STOP] [2019-10-11 16:36:06] sanitize_media_verbatims
[START] [2019-10-11 16:36:06] queue_downloads
[STOP] [2019-10-11 16:36:06] queue_downloads
[START] [2019-10-11 16:36:06] parse_names
[WARN] [2019-10-11 16:36:06] I see 6602 names which still need to be parsed.
[STOP] [2019-10-11 16:36:12] parse_names
[START] [2019-10-11 16:36:12] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 16:36:12] denormalize_canonical_names_to_nodes
[START] [2019-10-11 16:36:12] match_nodes
[START] [2019-10-11 16:36:12] map_all_nodes_to_pages
[STOP] [2019-10-11 16:39:25] map_all_nodes_to_pages
[INFO] [2019-10-11 16:39:25] 364 Unmatched nodes (of 6602)! That's too many to output. First 10: Hirundo semirufa (#48836731); Hirundo abyssinica (#48836803); Hirundo fuligula (#48837742); Hirundo cucullata (#48837980); Hirundo pyrrhonota (#48841488); Delichon urbica (#48840285); Ortygospiza fuscocrissa (#48838307); Tchagra senegala (#48840692); Telophorus sulfureopectus (#48836725); Urolestes melanoleuca (#48836249)
[START] [2019-10-11 16:39:25] update_nodes
[STOP] [2019-10-11 16:39:27] update_nodes
[STOP] [2019-10-11 16:39:27] match_nodes
[START] [2019-10-11 16:39:27] reindex_search
[STOP] [2019-10-11 16:39:38] reindex_search
[START] [2019-10-11 16:39:38] normalize_units
[STOP] [2019-10-11 16:39:38] normalize_units
[START] [2019-10-11 16:39:38] calculate_statistics
[STOP] [2019-10-11 16:39:38] calculate_statistics
[START] [2019-10-11 16:39:38] complete_harvest_instance
[START] [2019-10-11 16:39:38] overall_tsv_creation
[INFO] [2019-10-11 16:39:38] Processing group of 6602 in 1 batches of 10000
[INFO] [2019-10-11 16:40:53] 4338 Traits (unfiltered)...
[INFO] [2019-10-11 16:41:07] 4338 Traits (filtered)...
[INFO] [2019-10-11 16:41:07] 0 Associations (filtered)...
[INFO] [2019-10-11 16:41:53] 21686 metadata added.
[INFO] [2019-10-11 16:41:53] 0 metadata added.
[INFO] [2019-10-11 16:41:53] Average Time: 108.58
[INFO] [2019-10-11 16:41:53] Total Time: 2m16s
[STOP] [2019-10-11 16:41:53] overall_tsv_creation
[INFO] [2019-10-11 16:41:53] Done. Check your files:
[INFO] [2019-10-11 16:41:53] (6602 lines) /app/public/data/botswana_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 16:41:53] (11862 lines) /app/public/data/botswana_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 16:41:53] (6602 lines) /app/public/data/botswana_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 16:41:53] (4339 lines) /app/public/data/botswana_sp_list/publish_traits.tsv
[INFO] [2019-10-11 16:41:53] (21687 lines) /app/public/data/botswana_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 16:41:54] complete_harvest_instance
[START] [2019-10-11 16:41:54] completed
[STOP] [2019-10-11 16:41:54] completed
[STOP] [2019-10-11 16:41:54] logged process, took 448.39
Latest Process

11 Oct 16:34 EXITED currently processing 0