Harvest for Switzerland Species List Created 16 Oct 09:38

Harvesting Log

# Logfile created on 2019-10-16 09:38:33 -0400 by logger.rb/56815
[START] [2019-10-16 09:38:33] logged process
[START] [2019-10-16 09:38:33] create_harvest_instance
[STOP] [2019-10-16 09:38:34] create_harvest_instance
[START] [2019-10-16 09:38:34] fetch_files
[STOP] [2019-10-16 09:38:34] fetch_files
[START] [2019-10-16 09:38:34] validate_each_file
[STOP] [2019-10-16 09:38:36] validate_each_file
[START] [2019-10-16 09:38:36] convert_to_csv
[CMD] [2019-10-16 09:38:36] /usr/bin/sort /app/public/converted_csv/switzerland_sp_l_refs_17369.csv > /app/public/converted_csv/switzerland_sp_l_refs_17369.csv_sorted
[CMD] [2019-10-16 09:38:37] /usr/bin/sort /app/public/converted_csv/switzerland_sp_l_nodes_17370.csv > /app/public/converted_csv/switzerland_sp_l_nodes_17370.csv_sorted
[CMD] [2019-10-16 09:38:37] /usr/bin/sort /app/public/converted_csv/switzerland_sp_l_occurrences_17371.csv > /app/public/converted_csv/switzerland_sp_l_occurrences_17371.csv_sorted
[CMD] [2019-10-16 09:38:37] /usr/bin/sort /app/public/converted_csv/switzerland_sp_l_measurements_17372.csv > /app/public/converted_csv/switzerland_sp_l_measurements_17372.csv_sorted
[STOP] [2019-10-16 09:38:37] convert_to_csv
[START] [2019-10-16 09:38:37] calculate_delta
[CMD] [2019-10-16 09:38:37] echo "0a" > /app/public/diff/switzerland_sp_l_refs_17369.diff
[CMD] [2019-10-16 09:38:38] tail -n +1 /app/public/converted_csv/switzerland_sp_l_refs_17369.csv >> /app/public/diff/switzerland_sp_l_refs_17369.diff
[CMD] [2019-10-16 09:38:38] echo "." >> /app/public/diff/switzerland_sp_l_refs_17369.diff
[CMD] [2019-10-16 09:38:38] echo "0a" > /app/public/diff/switzerland_sp_l_nodes_17370.diff
[CMD] [2019-10-16 09:38:38] tail -n +1 /app/public/converted_csv/switzerland_sp_l_nodes_17370.csv >> /app/public/diff/switzerland_sp_l_nodes_17370.diff
[CMD] [2019-10-16 09:38:39] echo "." >> /app/public/diff/switzerland_sp_l_nodes_17370.diff
[CMD] [2019-10-16 09:38:39] echo "0a" > /app/public/diff/switzerland_sp_l_occurrences_17371.diff
[CMD] [2019-10-16 09:38:39] tail -n +1 /app/public/converted_csv/switzerland_sp_l_occurrences_17371.csv >> /app/public/diff/switzerland_sp_l_occurrences_17371.diff
[CMD] [2019-10-16 09:38:40] echo "." >> /app/public/diff/switzerland_sp_l_occurrences_17371.diff
[CMD] [2019-10-16 09:38:40] echo "0a" > /app/public/diff/switzerland_sp_l_measurements_17372.diff
[CMD] [2019-10-16 09:38:40] tail -n +1 /app/public/converted_csv/switzerland_sp_l_measurements_17372.csv >> /app/public/diff/switzerland_sp_l_measurements_17372.diff
[CMD] [2019-10-16 09:38:40] echo "." >> /app/public/diff/switzerland_sp_l_measurements_17372.diff
[STOP] [2019-10-16 09:38:41] calculate_delta
[START] [2019-10-16 09:38:41] parse_diff_and_store
[INFO] [2019-10-16 09:38:41] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 09:38:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 09:38:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 09:38:52] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 09:40:09] Storing 2 References
[INFO] [2019-10-16 09:40:09] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 09:40:09] Average Time: 0.0
[INFO] [2019-10-16 09:40:09] Total Time: 1s
[INFO] [2019-10-16 09:40:09] Storing 20186 ScientificNames
[INFO] [2019-10-16 09:40:09] Processing group of 20186 in 21 groups of 1000
[INFO] [2019-10-16 09:40:16] Average Time: 0.345
[INFO] [2019-10-16 09:40:16] Total Time: 8s
[INFO] [2019-10-16 09:40:16] last 3 / first 3: 0.63
[INFO] [2019-10-16 09:40:16] Std.Dev: 0.07745966692414834; Max: 0.51
[INFO] [2019-10-16 09:40:16] Storing 20186 Nodes
[INFO] [2019-10-16 09:40:16] Processing group of 20186 in 21 groups of 1000
[INFO] [2019-10-16 09:40:22] Average Time: 0.29
[INFO] [2019-10-16 09:40:22] Total Time: 7s
[INFO] [2019-10-16 09:40:22] last 3 / first 3: 0.77
[INFO] [2019-10-16 09:40:22] Std.Dev: 0.05477225575051661; Max: 0.34
[INFO] [2019-10-16 09:40:22] Storing 13014 Occurrences
[INFO] [2019-10-16 09:40:22] Processing group of 13014 in 14 groups of 1000
[INFO] [2019-10-16 09:40:24] Average Time: 0.098
[INFO] [2019-10-16 09:40:24] Total Time: 2s
[INFO] [2019-10-16 09:40:24] last 3 / first 3: 0.63
[INFO] [2019-10-16 09:40:24] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-16 09:40:24] Storing 26190 TraitsReferences
[INFO] [2019-10-16 09:40:24] Processing group of 26190 in 27 groups of 1000
[INFO] [2019-10-16 09:40:27] Average Time: 0.106
[INFO] [2019-10-16 09:40:27] Total Time: 3s
[INFO] [2019-10-16 09:40:27] last 3 / first 3: 0.48
[INFO] [2019-10-16 09:40:27] Std.Dev: 0.06324555320336758; Max: 0.32
[INFO] [2019-10-16 09:40:27] Storing 26189 Traits
[INFO] [2019-10-16 09:40:27] Processing group of 26189 in 27 groups of 1000
[INFO] [2019-10-16 09:40:34] Average Time: 0.282
[INFO] [2019-10-16 09:40:34] Total Time: 8s
[INFO] [2019-10-16 09:40:34] last 3 / first 3: 0.66
[INFO] [2019-10-16 09:40:34] Std.Dev: 0.044721359549995794; Max: 0.36
[INFO] [2019-10-16 09:40:34] Storing 26170 MetaTraits
[INFO] [2019-10-16 09:40:34] Processing group of 26170 in 27 groups of 1000
[INFO] [2019-10-16 09:40:37] Average Time: 0.108
[INFO] [2019-10-16 09:40:37] Total Time: 4s
[INFO] [2019-10-16 09:40:37] last 3 / first 3: 0.69
[INFO] [2019-10-16 09:40:37] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-16 09:40:37] parse_diff_and_store
[START] [2019-10-16 09:40:37] resolve_keys
[INFO] [2019-10-16 09:41:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 09:41:50] traits to occurrences...
[INFO] [2019-10-16 09:41:55] traits to nodes (through occurrences)...
[INFO] [2019-10-16 09:41:55] Traits to sex term...
[INFO] [2019-10-16 09:41:59] Traits to lifestage term...
[INFO] [2019-10-16 09:42:03] MetaTraits to traits...
[INFO] [2019-10-16 09:42:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 09:42:09] Assocs to occurrences...
[INFO] [2019-10-16 09:42:09] Assocs to nodes...
[INFO] [2019-10-16 09:42:09] Assoc to sex term...
[INFO] [2019-10-16 09:42:09] Assoc to lifestage term...
[STOP] [2019-10-16 09:42:09] resolve_keys
[START] [2019-10-16 09:42:09] hold_for_later_1
[STOP] [2019-10-16 09:42:09] hold_for_later_1
[START] [2019-10-16 09:42:09] hold_for_later_2
[STOP] [2019-10-16 09:42:09] hold_for_later_2
[START] [2019-10-16 09:42:09] resolve_missing_parents
[STOP] [2019-10-16 09:42:45] resolve_missing_parents
[START] [2019-10-16 09:42:45] rebuild_nodes
[START] [2019-10-16 09:42:45] Flattener#flatten
[START] [2019-10-16 09:42:45] Flattener#study_resource
[START] [2019-10-16 09:42:45] Flattener#build_ancestry
[STOP] [2019-10-16 09:42:47] Flattener#build_ancestry
[INFO] [2019-10-16 09:42:47] 20186 ancestry keys
[START] [2019-10-16 09:42:47] build_node_ancestors
[INFO] [2019-10-16 09:42:47] old ancestors deleted.
[STOP] [2019-10-16 09:42:52] build_node_ancestors
[START] [2019-10-16 09:42:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 09:42:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 09:42:58] Flattener#flatten
[STOP] [2019-10-16 09:42:58] rebuild_nodes
[START] [2019-10-16 09:42:58] resolve_missing_media_owners
[STOP] [2019-10-16 09:42:58] resolve_missing_media_owners
[START] [2019-10-16 09:42:58] sanitize_media_verbatims
[STOP] [2019-10-16 09:42:58] sanitize_media_verbatims
[START] [2019-10-16 09:42:58] queue_downloads
[STOP] [2019-10-16 09:42:58] queue_downloads
[START] [2019-10-16 09:42:58] parse_names
[WARN] [2019-10-16 09:42:58] I see 20186 names which still need to be parsed.
[STOP] [2019-10-16 09:43:14] parse_names
[START] [2019-10-16 09:43:14] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 09:43:14] denormalize_canonical_names_to_nodes
[START] [2019-10-16 09:43:14] match_nodes
[START] [2019-10-16 09:43:14] map_all_nodes_to_pages
[STOP] [2019-10-16 10:08:13] map_all_nodes_to_pages
[INFO] [2019-10-16 10:08:13] 2952 Unmatched nodes (of 20186)! That's too many to output. First 10: Myrmica specioides (#52294018); Myrmica lonae (#52296749); Camponotus ligniperda (#52294332); Temnothorax (#52293974); Temnothorax affinis (#52293973); Tenthredo (#52288888); Tenthredo vespa (#52288887); Tenthredo balteata (#52290517); Tenthredo crassa (#52290549); Tenthredo temula (#52290658)
[START] [2019-10-16 10:08:13] update_nodes
[STOP] [2019-10-16 10:08:20] update_nodes
[STOP] [2019-10-16 10:08:20] match_nodes
[START] [2019-10-16 10:08:20] reindex_search
[STOP] [2019-10-16 10:09:20] reindex_search
[START] [2019-10-16 10:09:20] normalize_units
[STOP] [2019-10-16 10:09:20] normalize_units
[START] [2019-10-16 10:09:20] calculate_statistics
[STOP] [2019-10-16 10:09:20] calculate_statistics
[START] [2019-10-16 10:09:20] complete_harvest_instance
[START] [2019-10-16 10:09:20] overall_tsv_creation
[INFO] [2019-10-16 10:09:20] Processing group of 20186 in 3 batches of 10000
[INFO] [2019-10-16 10:10:48] 6182 Traits (unfiltered)...
[INFO] [2019-10-16 10:11:02] 6182 Traits (filtered)...
[INFO] [2019-10-16 10:11:02] 0 Associations (filtered)...
[INFO] [2019-10-16 10:11:51] 30909 metadata added.
[INFO] [2019-10-16 10:11:51] 0 metadata added.
[INFO] [2019-10-16 10:13:22] 6778 Traits (unfiltered)...
[INFO] [2019-10-16 10:13:37] 6778 Traits (filtered)...
[INFO] [2019-10-16 10:13:37] 0 Associations (filtered)...
[INFO] [2019-10-16 10:14:33] 33872 metadata added.
[INFO] [2019-10-16 10:14:33] 0 metadata added.
[INFO] [2019-10-16 10:15:18] 54 Traits (unfiltered)...
[INFO] [2019-10-16 10:15:31] 54 Traits (filtered)...
[INFO] [2019-10-16 10:15:31] 0 Associations (filtered)...
[INFO] [2019-10-16 10:16:10] 270 metadata added.
[INFO] [2019-10-16 10:16:10] 0 metadata added.
[INFO] [2019-10-16 10:16:10] Average Time: 111.203
[INFO] [2019-10-16 10:16:10] Total Time: 6m50s
[STOP] [2019-10-16 10:16:10] overall_tsv_creation
[INFO] [2019-10-16 10:16:10] Done. Check your files:
[INFO] [2019-10-16 10:16:10] (20186 lines) /app/public/data/switzerland_sp_l/publish_nodes.tsv
[INFO] [2019-10-16 10:16:10] (64697 lines) /app/public/data/switzerland_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-16 10:16:11] (20186 lines) /app/public/data/switzerland_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-16 10:16:11] (13015 lines) /app/public/data/switzerland_sp_l/publish_traits.tsv
[INFO] [2019-10-16 10:16:11] (65052 lines) /app/public/data/switzerland_sp_l/publish_metadata.tsv
[STOP] [2019-10-16 10:16:12] complete_harvest_instance
[START] [2019-10-16 10:16:12] completed
[STOP] [2019-10-16 10:16:12] completed
[STOP] [2019-10-16 10:16:12] logged process, took 2258.8

Latest Process

16 Oct 09:38 EXITED currently processing 0