Harvest for Czech Republic Species List Created 12 Oct 12:42

Stage: completed
Fetched: 12 Oct 12:42
Validated: 12 Oct 12:42
Deltas Created 12 Oct 12:42
Units Normalized: 12 Oct 13:00
Ancestry Built: 12 Oct 12:45
Nodes Matched: 12 Oct 12:59
Names Parsed: 12 Oct 12:45
New Models Stored: 12 Oct 12:43
Indexed: 12 Oct 13:00
Completed: 12 Oct 13:04
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-12 12:42:11 -0400 by logger.rb/56815
[START] [2019-10-12 12:42:11] logged process
[START] [2019-10-12 12:42:11] create_harvest_instance
[STOP] [2019-10-12 12:42:11] create_harvest_instance
[START] [2019-10-12 12:42:11] fetch_files
[STOP] [2019-10-12 12:42:12] fetch_files
[START] [2019-10-12 12:42:12] validate_each_file
[STOP] [2019-10-12 12:42:13] validate_each_file
[START] [2019-10-12 12:42:13] convert_to_csv
[CMD] [2019-10-12 12:42:13] /usr/bin/sort /app/public/converted_csv/czech_republic_s_refs_15563.csv > /app/public/converted_csv/czech_republic_s_refs_15563.csv_sorted
[CMD] [2019-10-12 12:42:14] /usr/bin/sort /app/public/converted_csv/czech_republic_s_nodes_15564.csv > /app/public/converted_csv/czech_republic_s_nodes_15564.csv_sorted
[CMD] [2019-10-12 12:42:14] /usr/bin/sort /app/public/converted_csv/czech_republic_s_occurrences_15565.csv > /app/public/converted_csv/czech_republic_s_occurrences_15565.csv_sorted
[CMD] [2019-10-12 12:42:14] /usr/bin/sort /app/public/converted_csv/czech_republic_s_measurements_15566.csv > /app/public/converted_csv/czech_republic_s_measurements_15566.csv_sorted
[STOP] [2019-10-12 12:42:14] convert_to_csv
[START] [2019-10-12 12:42:14] calculate_delta
[CMD] [2019-10-12 12:42:14] echo "0a" > /app/public/diff/czech_republic_s_refs_15563.diff
[CMD] [2019-10-12 12:42:14] tail -n +1 /app/public/converted_csv/czech_republic_s_refs_15563.csv >> /app/public/diff/czech_republic_s_refs_15563.diff
[CMD] [2019-10-12 12:42:14] echo "." >> /app/public/diff/czech_republic_s_refs_15563.diff
[CMD] [2019-10-12 12:42:14] echo "0a" > /app/public/diff/czech_republic_s_nodes_15564.diff
[CMD] [2019-10-12 12:42:14] tail -n +1 /app/public/converted_csv/czech_republic_s_nodes_15564.csv >> /app/public/diff/czech_republic_s_nodes_15564.diff
[CMD] [2019-10-12 12:42:14] echo "." >> /app/public/diff/czech_republic_s_nodes_15564.diff
[CMD] [2019-10-12 12:42:14] echo "0a" > /app/public/diff/czech_republic_s_occurrences_15565.diff
[CMD] [2019-10-12 12:42:15] tail -n +1 /app/public/converted_csv/czech_republic_s_occurrences_15565.csv >> /app/public/diff/czech_republic_s_occurrences_15565.diff
[CMD] [2019-10-12 12:42:15] echo "." >> /app/public/diff/czech_republic_s_occurrences_15565.diff
[CMD] [2019-10-12 12:42:15] echo "0a" > /app/public/diff/czech_republic_s_measurements_15566.diff
[CMD] [2019-10-12 12:42:15] tail -n +1 /app/public/converted_csv/czech_republic_s_measurements_15566.csv >> /app/public/diff/czech_republic_s_measurements_15566.diff
[CMD] [2019-10-12 12:42:15] echo "." >> /app/public/diff/czech_republic_s_measurements_15566.diff
[STOP] [2019-10-12 12:42:15] calculate_delta
[START] [2019-10-12 12:42:15] parse_diff_and_store
[INFO] [2019-10-12 12:42:15] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 12:42:15] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 12:42:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 12:42:23] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 12:43:20] Storing 2 References
[INFO] [2019-10-12 12:43:20] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 12:43:20] Average Time: 0.0
[INFO] [2019-10-12 12:43:20] Total Time: 1s
[INFO] [2019-10-12 12:43:20] Storing 16196 ScientificNames
[INFO] [2019-10-12 12:43:20] Processing group of 16196 in 17 groups of 1000
[INFO] [2019-10-12 12:43:27] Average Time: 0.374
[INFO] [2019-10-12 12:43:27] Total Time: 7s
[INFO] [2019-10-12 12:43:27] last 3 / first 3: 0.61
[INFO] [2019-10-12 12:43:27] Std.Dev: 0.11401754250991379; Max: 0.6
[INFO] [2019-10-12 12:43:27] Storing 16196 Nodes
[INFO] [2019-10-12 12:43:27] Processing group of 16196 in 17 groups of 1000
[INFO] [2019-10-12 12:43:32] Average Time: 0.281
[INFO] [2019-10-12 12:43:32] Total Time: 5s
[INFO] [2019-10-12 12:43:32] last 3 / first 3: 0.79
[INFO] [2019-10-12 12:43:32] Std.Dev: 0.06324555320336758; Max: 0.34
[INFO] [2019-10-12 12:43:32] Storing 9640 Occurrences
[INFO] [2019-10-12 12:43:32] Processing group of 9640 in 10 groups of 1000
[INFO] [2019-10-12 12:43:33] Average Time: 0.097
[INFO] [2019-10-12 12:43:33] Total Time: 2s
[INFO] [2019-10-12 12:43:33] last 3 / first 3: 0.87
[INFO] [2019-10-12 12:43:33] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-12 12:43:33] Storing 19872 TraitsReferences
[INFO] [2019-10-12 12:43:33] Processing group of 19872 in 20 groups of 1000
[INFO] [2019-10-12 12:43:34] Average Time: 0.076
[INFO] [2019-10-12 12:43:34] Total Time: 2s
[INFO] [2019-10-12 12:43:34] last 3 / first 3: 0.77
[INFO] [2019-10-12 12:43:34] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-12 12:43:34] Storing 19871 Traits
[INFO] [2019-10-12 12:43:34] Processing group of 19871 in 20 groups of 1000
[INFO] [2019-10-12 12:43:41] Average Time: 0.355
[INFO] [2019-10-12 12:43:41] Total Time: 8s
[INFO] [2019-10-12 12:43:41] last 3 / first 3: 0.83
[INFO] [2019-10-12 12:43:41] Std.Dev: 0.08366600265340755; Max: 0.58
[INFO] [2019-10-12 12:43:41] Storing 19841 MetaTraits
[INFO] [2019-10-12 12:43:41] Processing group of 19841 in 20 groups of 1000
[INFO] [2019-10-12 12:43:44] Average Time: 0.138
[INFO] [2019-10-12 12:43:44] Total Time: 3s
[INFO] [2019-10-12 12:43:44] last 3 / first 3: 0.81
[INFO] [2019-10-12 12:43:44] Std.Dev: 0.0; Max: 0.18
[STOP] [2019-10-12 12:43:44] parse_diff_and_store
[START] [2019-10-12 12:43:44] resolve_keys
[INFO] [2019-10-12 12:44:39] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 12:44:44] traits to occurrences...
[INFO] [2019-10-12 12:44:51] traits to nodes (through occurrences)...
[INFO] [2019-10-12 12:44:51] Traits to sex term...
[INFO] [2019-10-12 12:44:57] Traits to lifestage term...
[INFO] [2019-10-12 12:45:02] MetaTraits to traits...
[INFO] [2019-10-12 12:45:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 12:45:06] Assocs to occurrences...
[INFO] [2019-10-12 12:45:06] Assocs to nodes...
[INFO] [2019-10-12 12:45:06] Assoc to sex term...
[INFO] [2019-10-12 12:45:06] Assoc to lifestage term...
[STOP] [2019-10-12 12:45:06] resolve_keys
[START] [2019-10-12 12:45:06] hold_for_later_1
[STOP] [2019-10-12 12:45:06] hold_for_later_1
[START] [2019-10-12 12:45:06] hold_for_later_2
[STOP] [2019-10-12 12:45:06] hold_for_later_2
[START] [2019-10-12 12:45:06] resolve_missing_parents
[STOP] [2019-10-12 12:45:33] resolve_missing_parents
[START] [2019-10-12 12:45:33] rebuild_nodes
[START] [2019-10-12 12:45:33] Flattener#flatten
[START] [2019-10-12 12:45:33] Flattener#study_resource
[START] [2019-10-12 12:45:34] Flattener#build_ancestry
[STOP] [2019-10-12 12:45:34] Flattener#build_ancestry
[INFO] [2019-10-12 12:45:34] 16196 ancestry keys
[START] [2019-10-12 12:45:34] build_node_ancestors
[INFO] [2019-10-12 12:45:34] old ancestors deleted.
[STOP] [2019-10-12 12:45:38] build_node_ancestors
[START] [2019-10-12 12:45:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:45:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:45:43] Flattener#flatten
[STOP] [2019-10-12 12:45:43] rebuild_nodes
[START] [2019-10-12 12:45:43] resolve_missing_media_owners
[STOP] [2019-10-12 12:45:43] resolve_missing_media_owners
[START] [2019-10-12 12:45:43] sanitize_media_verbatims
[STOP] [2019-10-12 12:45:43] sanitize_media_verbatims
[START] [2019-10-12 12:45:43] queue_downloads
[STOP] [2019-10-12 12:45:43] queue_downloads
[START] [2019-10-12 12:45:43] parse_names
[WARN] [2019-10-12 12:45:43] I see 16196 names which still need to be parsed.
[STOP] [2019-10-12 12:45:56] parse_names
[START] [2019-10-12 12:45:56] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 12:45:57] denormalize_canonical_names_to_nodes
[START] [2019-10-12 12:45:57] match_nodes
[START] [2019-10-12 12:45:57] map_all_nodes_to_pages
[STOP] [2019-10-12 12:59:22] map_all_nodes_to_pages
[INFO] [2019-10-12 12:59:22] 2371 Unmatched nodes (of 16196)! That's too many to output. First 10: Parus caeruleus (#49386302); Parus cristatus (#49387518); Parus palustris (#49387754); Parus ater (#49389019); Parus montanus (#49391596); Corvus monedula (#49383881); Carduelis spinus (#49385010); Carduelis cannabina (#49385580); Carduelis chloris (#49387194); Carduelis flammea (#49390987)
[START] [2019-10-12 12:59:22] update_nodes
[STOP] [2019-10-12 12:59:28] update_nodes
[STOP] [2019-10-12 12:59:28] match_nodes
[START] [2019-10-12 12:59:28] reindex_search
[STOP] [2019-10-12 13:00:02] reindex_search
[START] [2019-10-12 13:00:02] normalize_units
[STOP] [2019-10-12 13:00:02] normalize_units
[START] [2019-10-12 13:00:02] calculate_statistics
[STOP] [2019-10-12 13:00:02] calculate_statistics
[START] [2019-10-12 13:00:02] complete_harvest_instance
[START] [2019-10-12 13:00:02] overall_tsv_creation
[INFO] [2019-10-12 13:00:02] Processing group of 16196 in 2 batches of 10000
[INFO] [2019-10-12 13:01:32] 5811 Traits (unfiltered)...
[INFO] [2019-10-12 13:01:46] 5811 Traits (filtered)...
[INFO] [2019-10-12 13:01:46] 0 Associations (filtered)...
[INFO] [2019-10-12 13:02:36] 29036 metadata added.
[INFO] [2019-10-12 13:02:36] 0 metadata added.
[INFO] [2019-10-12 13:03:48] 3829 Traits (unfiltered)...
[INFO] [2019-10-12 13:04:02] 3829 Traits (filtered)...
[INFO] [2019-10-12 13:04:02] 0 Associations (filtered)...
[INFO] [2019-10-12 13:04:47] 19134 metadata added.
[INFO] [2019-10-12 13:04:47] 0 metadata added.
[INFO] [2019-10-12 13:04:47] Average Time: 116.71
[INFO] [2019-10-12 13:04:47] Total Time: 4m46s
[STOP] [2019-10-12 13:04:47] overall_tsv_creation
[INFO] [2019-10-12 13:04:47] Done. Check your files:
[INFO] [2019-10-12 13:04:47] (16196 lines) /app/public/data/czech_republic_s/publish_nodes.tsv
[INFO] [2019-10-12 13:04:48] (53201 lines) /app/public/data/czech_republic_s/publish_node_ancestors.tsv
[INFO] [2019-10-12 13:04:48] (16196 lines) /app/public/data/czech_republic_s/publish_scientific_names.tsv
[INFO] [2019-10-12 13:04:48] (9641 lines) /app/public/data/czech_republic_s/publish_traits.tsv
[INFO] [2019-10-12 13:04:48] (48171 lines) /app/public/data/czech_republic_s/publish_metadata.tsv
[STOP] [2019-10-12 13:04:48] complete_harvest_instance
[START] [2019-10-12 13:04:48] completed
[STOP] [2019-10-12 13:04:48] completed
[STOP] [2019-10-12 13:04:48] logged process, took 1357.09
Latest Process

12 Oct 12:42 EXITED currently processing 0