Harvest for Peru Species List Created 15 Oct 08:49

Harvesting Log

# Logfile created on 2019-10-15 08:49:59 -0400 by logger.rb/56815
[START] [2019-10-15 08:49:59] logged process
[START] [2019-10-15 08:49:59] create_harvest_instance
[STOP] [2019-10-15 08:50:00] create_harvest_instance
[START] [2019-10-15 08:50:00] fetch_files
[STOP] [2019-10-15 08:50:00] fetch_files
[START] [2019-10-15 08:50:00] validate_each_file
[STOP] [2019-10-15 08:50:06] validate_each_file
[START] [2019-10-15 08:50:06] convert_to_csv
[CMD] [2019-10-15 08:50:06] /usr/bin/sort /app/public/converted_csv/peru_sp_list_refs_16901.csv > /app/public/converted_csv/peru_sp_list_refs_16901.csv_sorted
[CMD] [2019-10-15 08:50:07] /usr/bin/sort /app/public/converted_csv/peru_sp_list_nodes_16902.csv > /app/public/converted_csv/peru_sp_list_nodes_16902.csv_sorted
[CMD] [2019-10-15 08:50:07] /usr/bin/sort /app/public/converted_csv/peru_sp_list_occurrences_16903.csv > /app/public/converted_csv/peru_sp_list_occurrences_16903.csv_sorted
[CMD] [2019-10-15 08:50:07] /usr/bin/sort /app/public/converted_csv/peru_sp_list_measurements_16904.csv > /app/public/converted_csv/peru_sp_list_measurements_16904.csv_sorted
[STOP] [2019-10-15 08:50:07] convert_to_csv
[START] [2019-10-15 08:50:07] calculate_delta
[CMD] [2019-10-15 08:50:07] echo "0a" > /app/public/diff/peru_sp_list_refs_16901.diff
[CMD] [2019-10-15 08:50:08] tail -n +1 /app/public/converted_csv/peru_sp_list_refs_16901.csv >> /app/public/diff/peru_sp_list_refs_16901.diff
[CMD] [2019-10-15 08:50:08] echo "." >> /app/public/diff/peru_sp_list_refs_16901.diff
[CMD] [2019-10-15 08:50:08] echo "0a" > /app/public/diff/peru_sp_list_nodes_16902.diff
[CMD] [2019-10-15 08:50:08] tail -n +1 /app/public/converted_csv/peru_sp_list_nodes_16902.csv >> /app/public/diff/peru_sp_list_nodes_16902.diff
[CMD] [2019-10-15 08:50:09] echo "." >> /app/public/diff/peru_sp_list_nodes_16902.diff
[CMD] [2019-10-15 08:50:09] echo "0a" > /app/public/diff/peru_sp_list_occurrences_16903.diff
[CMD] [2019-10-15 08:50:09] tail -n +1 /app/public/converted_csv/peru_sp_list_occurrences_16903.csv >> /app/public/diff/peru_sp_list_occurrences_16903.diff
[CMD] [2019-10-15 08:50:10] echo "." >> /app/public/diff/peru_sp_list_occurrences_16903.diff
[CMD] [2019-10-15 08:50:10] echo "0a" > /app/public/diff/peru_sp_list_measurements_16904.diff
[CMD] [2019-10-15 08:50:10] tail -n +1 /app/public/converted_csv/peru_sp_list_measurements_16904.csv >> /app/public/diff/peru_sp_list_measurements_16904.diff
[CMD] [2019-10-15 08:50:10] echo "." >> /app/public/diff/peru_sp_list_measurements_16904.diff
[STOP] [2019-10-15 08:50:11] calculate_delta
[START] [2019-10-15 08:50:11] parse_diff_and_store
[INFO] [2019-10-15 08:50:11] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 08:50:11] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 08:50:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 08:50:36] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 08:54:28] Storing 2 References
[INFO] [2019-10-15 08:54:28] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 08:54:28] Average Time: 0.0
[INFO] [2019-10-15 08:54:28] Total Time: 1s
[INFO] [2019-10-15 08:54:28] Storing 48714 ScientificNames
[INFO] [2019-10-15 08:54:28] Processing group of 48714 in 49 groups of 1000
[INFO] [2019-10-15 08:54:50] Average Time: 0.443
[INFO] [2019-10-15 08:54:50] Total Time: 22s
[INFO] [2019-10-15 08:54:50] last 3 / first 3: 0.84
[INFO] [2019-10-15 08:54:50] Std.Dev: 0.3; Max: 2.26
[INFO] [2019-10-15 08:54:50] Storing 48714 Nodes
[INFO] [2019-10-15 08:54:50] Processing group of 48714 in 49 groups of 1000
[INFO] [2019-10-15 08:55:06] Average Time: 0.327
[INFO] [2019-10-15 08:55:06] Total Time: 17s
[INFO] [2019-10-15 08:55:06] last 3 / first 3: 1.63
[INFO] [2019-10-15 08:55:06] Std.Dev: 0.05477225575051661; Max: 0.57
[INFO] [2019-10-15 08:55:06] Storing 39042 Occurrences
[INFO] [2019-10-15 08:55:06] Processing group of 39042 in 40 groups of 1000
[INFO] [2019-10-15 08:55:15] Average Time: 0.206
[INFO] [2019-10-15 08:55:15] Total Time: 9s
[INFO] [2019-10-15 08:55:15] last 3 / first 3: 0.12
[INFO] [2019-10-15 08:55:15] Std.Dev: 0.43703546766824314; Max: 2.43
[INFO] [2019-10-15 08:55:15] Storing 78590 TraitsReferences
[INFO] [2019-10-15 08:55:15] Processing group of 78590 in 79 groups of 1000
[INFO] [2019-10-15 08:55:20] Average Time: 0.068
[INFO] [2019-10-15 08:55:20] Total Time: 6s
[INFO] [2019-10-15 08:55:20] last 3 / first 3: 0.49
[INFO] [2019-10-15 08:55:20] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-15 08:55:20] Storing 78589 Traits
[INFO] [2019-10-15 08:55:20] Processing group of 78589 in 79 groups of 1000
[INFO] [2019-10-15 08:55:47] Average Time: 0.329
[INFO] [2019-10-15 08:55:47] Total Time: 27s
[INFO] [2019-10-15 08:55:47] last 3 / first 3: 0.83
[INFO] [2019-10-15 08:55:47] Std.Dev: 0.17606816861659008; Max: 1.78
[INFO] [2019-10-15 08:55:47] Storing 78500 MetaTraits
[INFO] [2019-10-15 08:55:47] Processing group of 78500 in 79 groups of 1000
[INFO] [2019-10-15 08:55:59] Average Time: 0.145
[INFO] [2019-10-15 08:55:59] Total Time: 12s
[INFO] [2019-10-15 08:55:59] last 3 / first 3: 0.7
[INFO] [2019-10-15 08:55:59] Std.Dev: 0.12649110640673517; Max: 1.12
[STOP] [2019-10-15 08:55:59] parse_diff_and_store
[START] [2019-10-15 08:55:59] resolve_keys
[INFO] [2019-10-15 08:58:05] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 08:58:14] traits to occurrences...
[INFO] [2019-10-15 08:58:21] traits to nodes (through occurrences)...
[INFO] [2019-10-15 08:58:22] Traits to sex term...
[INFO] [2019-10-15 08:58:28] Traits to lifestage term...
[INFO] [2019-10-15 08:58:35] MetaTraits to traits...
[INFO] [2019-10-15 08:58:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 08:58:51] Assocs to occurrences...
[INFO] [2019-10-15 08:58:51] Assocs to nodes...
[INFO] [2019-10-15 08:58:51] Assoc to sex term...
[INFO] [2019-10-15 08:58:51] Assoc to lifestage term...
[STOP] [2019-10-15 08:58:51] resolve_keys
[START] [2019-10-15 08:58:51] hold_for_later_1
[STOP] [2019-10-15 08:58:51] hold_for_later_1
[START] [2019-10-15 08:58:51] hold_for_later_2
[STOP] [2019-10-15 08:58:51] hold_for_later_2
[START] [2019-10-15 08:58:51] resolve_missing_parents
[STOP] [2019-10-15 09:00:05] resolve_missing_parents
[START] [2019-10-15 09:00:05] rebuild_nodes
[START] [2019-10-15 09:00:05] Flattener#flatten
[START] [2019-10-15 09:00:05] Flattener#study_resource
[START] [2019-10-15 09:00:05] Flattener#build_ancestry
[STOP] [2019-10-15 09:00:23] Flattener#build_ancestry
[INFO] [2019-10-15 09:00:23] 48714 ancestry keys
[START] [2019-10-15 09:00:23] build_node_ancestors
[INFO] [2019-10-15 09:00:23] old ancestors deleted.
[STOP] [2019-10-15 09:00:43] build_node_ancestors
[START] [2019-10-15 09:00:45] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 09:00:49] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 09:00:49] Flattener#flatten
[STOP] [2019-10-15 09:00:49] rebuild_nodes
[START] [2019-10-15 09:00:49] resolve_missing_media_owners
[STOP] [2019-10-15 09:00:49] resolve_missing_media_owners
[START] [2019-10-15 09:00:49] sanitize_media_verbatims
[STOP] [2019-10-15 09:00:49] sanitize_media_verbatims
[START] [2019-10-15 09:00:49] queue_downloads
[STOP] [2019-10-15 09:00:49] queue_downloads
[START] [2019-10-15 09:00:49] parse_names
[WARN] [2019-10-15 09:00:49] I see 48714 names which still need to be parsed.
[STOP] [2019-10-15 09:01:28] parse_names
[START] [2019-10-15 09:01:28] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 09:01:28] denormalize_canonical_names_to_nodes
[START] [2019-10-15 09:01:28] match_nodes
[START] [2019-10-15 09:01:28] map_all_nodes_to_pages
[STOP] [2019-10-15 09:47:06] map_all_nodes_to_pages
[INFO] [2019-10-15 09:47:06] 3736 Unmatched nodes (of 48714)! That's too many to output. First 10: Oenocarpus weberbaueri (#51561014); Geonoma acaulis (#51518657); Geonoma oligosticha (#51542480); Attalea stenorhyncha (#51551213); Astrocaryum ruizii (#51558067); Desmoncus macroacantha (#51515403); Desmoncus acanthospatha (#51536143); Desmoncus longifolius (#51539879); Chelyocarpus longibracteata (#51560156); Cyphorhinus aradus (#51538393)
[START] [2019-10-15 09:47:06] update_nodes
[STOP] [2019-10-15 09:47:24] update_nodes
[STOP] [2019-10-15 09:47:24] match_nodes
[START] [2019-10-15 09:47:24] reindex_search
[STOP] [2019-10-15 09:49:33] reindex_search
[START] [2019-10-15 09:49:33] normalize_units
[STOP] [2019-10-15 09:49:33] normalize_units
[START] [2019-10-15 09:49:33] calculate_statistics
[STOP] [2019-10-15 09:49:33] calculate_statistics
[START] [2019-10-15 09:49:33] complete_harvest_instance
[START] [2019-10-15 09:49:33] overall_tsv_creation
[INFO] [2019-10-15 09:49:33] Processing group of 48714 in 5 batches of 10000
[INFO] [2019-10-15 09:51:01] 6747 Traits (unfiltered)...
[INFO] [2019-10-15 09:51:15] 6747 Traits (filtered)...
[INFO] [2019-10-15 09:51:15] 0 Associations (filtered)...
[INFO] [2019-10-15 09:52:06] 33733 metadata added.
[INFO] [2019-10-15 09:52:06] 0 metadata added.
[INFO] [2019-10-15 09:53:38] 8181 Traits (unfiltered)...
[INFO] [2019-10-15 09:53:52] 8181 Traits (filtered)...
[INFO] [2019-10-15 09:53:52] 0 Associations (filtered)...
[INFO] [2019-10-15 09:54:48] 40899 metadata added.
[INFO] [2019-10-15 09:54:48] 0 metadata added.
[INFO] [2019-10-15 09:56:21] 8285 Traits (unfiltered)...
[INFO] [2019-10-15 09:56:35] 8285 Traits (filtered)...
[INFO] [2019-10-15 09:56:35] 0 Associations (filtered)...
[INFO] [2019-10-15 09:57:31] 41399 metadata added.
[INFO] [2019-10-15 09:57:31] 0 metadata added.
[INFO] [2019-10-15 09:59:04] 8392 Traits (unfiltered)...
[INFO] [2019-10-15 09:59:18] 8392 Traits (filtered)...
[INFO] [2019-10-15 09:59:18] 0 Associations (filtered)...
[INFO] [2019-10-15 10:00:14] 41936 metadata added.
[INFO] [2019-10-15 10:00:14] 0 metadata added.
[INFO] [2019-10-15 10:01:42] 7437 Traits (unfiltered)...
[INFO] [2019-10-15 10:01:56] 7437 Traits (filtered)...
[INFO] [2019-10-15 10:01:56] 0 Associations (filtered)...
[INFO] [2019-10-15 10:02:51] 37154 metadata added.
[INFO] [2019-10-15 10:02:51] 0 metadata added.
[INFO] [2019-10-15 10:02:51] Average Time: 133.344
[INFO] [2019-10-15 10:02:51] Total Time: 13m18s
[STOP] [2019-10-15 10:02:51] overall_tsv_creation
[INFO] [2019-10-15 10:02:51] Done. Check your files:
[INFO] [2019-10-15 10:02:51] (48714 lines) /app/public/data/peru_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 10:02:52] (132929 lines) /app/public/data/peru_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 10:02:52] (48714 lines) /app/public/data/peru_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 10:02:52] (39043 lines) /app/public/data/peru_sp_list/publish_traits.tsv
[INFO] [2019-10-15 10:02:53] (195122 lines) /app/public/data/peru_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 10:02:53] complete_harvest_instance
[START] [2019-10-15 10:02:53] completed
[STOP] [2019-10-15 10:02:53] completed
[STOP] [2019-10-15 10:02:53] logged process, took 4373.58

Latest Process

15 Oct 08:49 EXITED currently processing 0