Harvest for Poland Species List Created 15 Oct 12:22

Stage: completed
Fetched: 15 Oct 12:22
Validated: 15 Oct 12:22
Deltas Created 15 Oct 12:22
Units Normalized: 15 Oct 12:50
Ancestry Built: 15 Oct 12:27
Nodes Matched: 15 Oct 12:50
Names Parsed: 15 Oct 12:27
New Models Stored: 15 Oct 12:24
Indexed: 15 Oct 12:50
Completed: 15 Oct 12:58
Time to Harvest: 1 minute
Harvesting Log

(161 lines)
# Logfile created on 2019-10-15 12:22:29 -0400 by logger.rb/56815
[START] [2019-10-15 12:22:29] logged process
[START] [2019-10-15 12:22:29] create_harvest_instance
[STOP] [2019-10-15 12:22:30] create_harvest_instance
[START] [2019-10-15 12:22:30] fetch_files
[STOP] [2019-10-15 12:22:30] fetch_files
[START] [2019-10-15 12:22:30] validate_each_file
[STOP] [2019-10-15 12:22:32] validate_each_file
[START] [2019-10-15 12:22:32] convert_to_csv
[CMD] [2019-10-15 12:22:32] /usr/bin/sort /app/public/converted_csv/poland_sp_list_refs_16933.csv > /app/public/converted_csv/poland_sp_list_refs_16933.csv_sorted
[CMD] [2019-10-15 12:22:33] /usr/bin/sort /app/public/converted_csv/poland_sp_list_nodes_16934.csv > /app/public/converted_csv/poland_sp_list_nodes_16934.csv_sorted
[CMD] [2019-10-15 12:22:33] /usr/bin/sort /app/public/converted_csv/poland_sp_list_occurrences_16935.csv > /app/public/converted_csv/poland_sp_list_occurrences_16935.csv_sorted
[CMD] [2019-10-15 12:22:33] /usr/bin/sort /app/public/converted_csv/poland_sp_list_measurements_16936.csv > /app/public/converted_csv/poland_sp_list_measurements_16936.csv_sorted
[STOP] [2019-10-15 12:22:34] convert_to_csv
[START] [2019-10-15 12:22:34] calculate_delta
[CMD] [2019-10-15 12:22:34] echo "0a" > /app/public/diff/poland_sp_list_refs_16933.diff
[CMD] [2019-10-15 12:22:34] tail -n +1 /app/public/converted_csv/poland_sp_list_refs_16933.csv >> /app/public/diff/poland_sp_list_refs_16933.diff
[CMD] [2019-10-15 12:22:34] echo "." >> /app/public/diff/poland_sp_list_refs_16933.diff
[CMD] [2019-10-15 12:22:35] echo "0a" > /app/public/diff/poland_sp_list_nodes_16934.diff
[CMD] [2019-10-15 12:22:35] tail -n +1 /app/public/converted_csv/poland_sp_list_nodes_16934.csv >> /app/public/diff/poland_sp_list_nodes_16934.diff
[CMD] [2019-10-15 12:22:35] echo "." >> /app/public/diff/poland_sp_list_nodes_16934.diff
[CMD] [2019-10-15 12:22:35] echo "0a" > /app/public/diff/poland_sp_list_occurrences_16935.diff
[CMD] [2019-10-15 12:22:36] tail -n +1 /app/public/converted_csv/poland_sp_list_occurrences_16935.csv >> /app/public/diff/poland_sp_list_occurrences_16935.diff
[CMD] [2019-10-15 12:22:36] echo "." >> /app/public/diff/poland_sp_list_occurrences_16935.diff
[CMD] [2019-10-15 12:22:36] echo "0a" > /app/public/diff/poland_sp_list_measurements_16936.diff
[CMD] [2019-10-15 12:22:36] tail -n +1 /app/public/converted_csv/poland_sp_list_measurements_16936.csv >> /app/public/diff/poland_sp_list_measurements_16936.diff
[CMD] [2019-10-15 12:22:37] echo "." >> /app/public/diff/poland_sp_list_measurements_16936.diff
[STOP] [2019-10-15 12:22:37] calculate_delta
[START] [2019-10-15 12:22:37] parse_diff_and_store
[INFO] [2019-10-15 12:22:37] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 12:22:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 12:22:47] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 12:22:49] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 12:24:17] Storing 2 References
[INFO] [2019-10-15 12:24:17] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 12:24:17] Average Time: 0.0
[INFO] [2019-10-15 12:24:17] Total Time: 1s
[INFO] [2019-10-15 12:24:17] Storing 23023 ScientificNames
[INFO] [2019-10-15 12:24:17] Processing group of 23023 in 24 groups of 1000
[INFO] [2019-10-15 12:24:26] Average Time: 0.383
[INFO] [2019-10-15 12:24:26] Total Time: 10s
[INFO] [2019-10-15 12:24:26] last 3 / first 3: 0.6
[INFO] [2019-10-15 12:24:26] Std.Dev: 0.1414213562373095; Max: 0.86
[INFO] [2019-10-15 12:24:26] Storing 23023 Nodes
[INFO] [2019-10-15 12:24:26] Processing group of 23023 in 24 groups of 1000
[INFO] [2019-10-15 12:24:33] Average Time: 0.284
[INFO] [2019-10-15 12:24:33] Total Time: 7s
[INFO] [2019-10-15 12:24:33] last 3 / first 3: 0.75
[INFO] [2019-10-15 12:24:33] Std.Dev: 0.06324555320336758; Max: 0.35
[INFO] [2019-10-15 12:24:33] Storing 14942 Occurrences
[INFO] [2019-10-15 12:24:33] Processing group of 14942 in 15 groups of 1000
[INFO] [2019-10-15 12:24:35] Average Time: 0.102
[INFO] [2019-10-15 12:24:35] Total Time: 2s
[INFO] [2019-10-15 12:24:35] last 3 / first 3: 0.97
[INFO] [2019-10-15 12:24:35] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-15 12:24:35] Storing 30050 TraitsReferences
[INFO] [2019-10-15 12:24:35] Processing group of 30050 in 31 groups of 1000
[INFO] [2019-10-15 12:24:37] Average Time: 0.073
[INFO] [2019-10-15 12:24:37] Total Time: 3s
[INFO] [2019-10-15 12:24:37] last 3 / first 3: 0.41
[INFO] [2019-10-15 12:24:37] Std.Dev: 0.03162277660168379; Max: 0.18
[INFO] [2019-10-15 12:24:37] Storing 30049 Traits
[INFO] [2019-10-15 12:24:37] Processing group of 30049 in 31 groups of 1000
[INFO] [2019-10-15 12:24:47] Average Time: 0.323
[INFO] [2019-10-15 12:24:47] Total Time: 11s
[INFO] [2019-10-15 12:24:47] last 3 / first 3: 0.66
[INFO] [2019-10-15 12:24:47] Std.Dev: 0.1224744871391589; Max: 0.77
[INFO] [2019-10-15 12:24:47] Storing 30038 MetaTraits
[INFO] [2019-10-15 12:24:47] Processing group of 30038 in 31 groups of 1000
[INFO] [2019-10-15 12:24:51] Average Time: 0.106
[INFO] [2019-10-15 12:24:51] Total Time: 4s
[INFO] [2019-10-15 12:24:51] last 3 / first 3: 0.57
[INFO] [2019-10-15 12:24:51] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-15 12:24:51] parse_diff_and_store
[START] [2019-10-15 12:24:51] resolve_keys
[INFO] [2019-10-15 12:26:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 12:26:08] traits to occurrences...
[INFO] [2019-10-15 12:26:13] traits to nodes (through occurrences)...
[INFO] [2019-10-15 12:26:13] Traits to sex term...
[INFO] [2019-10-15 12:26:18] Traits to lifestage term...
[INFO] [2019-10-15 12:26:23] MetaTraits to traits...
[INFO] [2019-10-15 12:26:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 12:26:29] Assocs to occurrences...
[INFO] [2019-10-15 12:26:29] Assocs to nodes...
[INFO] [2019-10-15 12:26:29] Assoc to sex term...
[INFO] [2019-10-15 12:26:29] Assoc to lifestage term...
[STOP] [2019-10-15 12:26:29] resolve_keys
[START] [2019-10-15 12:26:29] hold_for_later_1
[STOP] [2019-10-15 12:26:29] hold_for_later_1
[START] [2019-10-15 12:26:29] hold_for_later_2
[STOP] [2019-10-15 12:26:29] hold_for_later_2
[START] [2019-10-15 12:26:29] resolve_missing_parents
[STOP] [2019-10-15 12:27:09] resolve_missing_parents
[START] [2019-10-15 12:27:09] rebuild_nodes
[START] [2019-10-15 12:27:09] Flattener#flatten
[START] [2019-10-15 12:27:09] Flattener#study_resource
[START] [2019-10-15 12:27:09] Flattener#build_ancestry
[STOP] [2019-10-15 12:27:11] Flattener#build_ancestry
[INFO] [2019-10-15 12:27:11] 23023 ancestry keys
[START] [2019-10-15 12:27:11] build_node_ancestors
[INFO] [2019-10-15 12:27:11] old ancestors deleted.
[STOP] [2019-10-15 12:27:15] build_node_ancestors
[START] [2019-10-15 12:27:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 12:27:20] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 12:27:20] Flattener#flatten
[STOP] [2019-10-15 12:27:20] rebuild_nodes
[START] [2019-10-15 12:27:20] resolve_missing_media_owners
[STOP] [2019-10-15 12:27:20] resolve_missing_media_owners
[START] [2019-10-15 12:27:20] sanitize_media_verbatims
[STOP] [2019-10-15 12:27:20] sanitize_media_verbatims
[START] [2019-10-15 12:27:20] queue_downloads
[STOP] [2019-10-15 12:27:20] queue_downloads
[START] [2019-10-15 12:27:20] parse_names
[WARN] [2019-10-15 12:27:20] I see 23023 names which still need to be parsed.
[STOP] [2019-10-15 12:27:39] parse_names
[START] [2019-10-15 12:27:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 12:27:39] denormalize_canonical_names_to_nodes
[START] [2019-10-15 12:27:39] match_nodes
[START] [2019-10-15 12:27:39] map_all_nodes_to_pages
[STOP] [2019-10-15 12:49:57] map_all_nodes_to_pages
[INFO] [2019-10-15 12:49:57] 3825 Unmatched nodes (of 23023)! That's too many to output. First 10: Regulus ignicapillus (#51626535); Parus caeruleus (#51626171); Parus ater (#51626252); Parus montanus (#51626421); Parus palustris (#51626650); Parus cristatus (#51627222); Turdus ericetorum (#51643455); Carduelis spinus (#51626284); Carduelis flammea (#51626501); Carduelis cannabina (#51626800)
[START] [2019-10-15 12:49:57] update_nodes
[STOP] [2019-10-15 12:50:05] update_nodes
[STOP] [2019-10-15 12:50:05] match_nodes
[START] [2019-10-15 12:50:05] reindex_search
[STOP] [2019-10-15 12:50:59] reindex_search
[START] [2019-10-15 12:50:59] normalize_units
[STOP] [2019-10-15 12:50:59] normalize_units
[START] [2019-10-15 12:50:59] calculate_statistics
[STOP] [2019-10-15 12:50:59] calculate_statistics
[START] [2019-10-15 12:50:59] complete_harvest_instance
[START] [2019-10-15 12:50:59] overall_tsv_creation
[INFO] [2019-10-15 12:51:00] Processing group of 23023 in 3 batches of 10000
[INFO] [2019-10-15 12:52:28] 6036 Traits (unfiltered)...
[INFO] [2019-10-15 12:52:41] 6036 Traits (filtered)...
[INFO] [2019-10-15 12:52:41] 0 Associations (filtered)...
[INFO] [2019-10-15 12:53:32] 30174 metadata added.
[INFO] [2019-10-15 12:53:32] 0 metadata added.
[INFO] [2019-10-15 12:55:03] 6791 Traits (unfiltered)...
[INFO] [2019-10-15 12:55:17] 6791 Traits (filtered)...
[INFO] [2019-10-15 12:55:17] 0 Associations (filtered)...
[INFO] [2019-10-15 12:56:10] 33952 metadata added.
[INFO] [2019-10-15 12:56:10] 0 metadata added.
[INFO] [2019-10-15 12:57:10] 2115 Traits (unfiltered)...
[INFO] [2019-10-15 12:57:24] 2115 Traits (filtered)...
[INFO] [2019-10-15 12:57:24] 0 Associations (filtered)...
[INFO] [2019-10-15 12:58:05] 10572 metadata added.
[INFO] [2019-10-15 12:58:05] 0 metadata added.
[INFO] [2019-10-15 12:58:05] Average Time: 117.36
[INFO] [2019-10-15 12:58:05] Total Time: 7m6s
[STOP] [2019-10-15 12:58:05] overall_tsv_creation
[INFO] [2019-10-15 12:58:05] Done. Check your files:
[INFO] [2019-10-15 12:58:06] (23023 lines) /app/public/data/poland_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 12:58:06] (57124 lines) /app/public/data/poland_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 12:58:06] (23023 lines) /app/public/data/poland_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 12:58:06] (14943 lines) /app/public/data/poland_sp_list/publish_traits.tsv
[INFO] [2019-10-15 12:58:07] (74699 lines) /app/public/data/poland_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 12:58:07] complete_harvest_instance
[START] [2019-10-15 12:58:07] completed
[STOP] [2019-10-15 12:58:07] completed
[STOP] [2019-10-15 12:58:07] logged process, took 2137.74
Latest Process

15 Oct 12:22 EXITED currently processing 0