Harvest for Ireland Species List Created 13 Oct 18:18

Harvesting Log

# Logfile created on 2019-10-13 18:18:02 -0400 by logger.rb/56815
[START] [2019-10-13 18:18:02] logged process
[START] [2019-10-13 18:18:02] create_harvest_instance
[STOP] [2019-10-13 18:18:02] create_harvest_instance
[START] [2019-10-13 18:18:02] fetch_files
[STOP] [2019-10-13 18:18:02] fetch_files
[START] [2019-10-13 18:18:02] validate_each_file
[STOP] [2019-10-13 18:18:05] validate_each_file
[START] [2019-10-13 18:18:05] convert_to_csv
[CMD] [2019-10-13 18:18:05] /usr/bin/sort /app/public/converted_csv/ireland_sp_list_refs_16195.csv > /app/public/converted_csv/ireland_sp_list_refs_16195.csv_sorted
[CMD] [2019-10-13 18:18:05] /usr/bin/sort /app/public/converted_csv/ireland_sp_list_nodes_16196.csv > /app/public/converted_csv/ireland_sp_list_nodes_16196.csv_sorted
[CMD] [2019-10-13 18:18:05] /usr/bin/sort /app/public/converted_csv/ireland_sp_list_occurrences_16197.csv > /app/public/converted_csv/ireland_sp_list_occurrences_16197.csv_sorted
[CMD] [2019-10-13 18:18:06] /usr/bin/sort /app/public/converted_csv/ireland_sp_list_measurements_16198.csv > /app/public/converted_csv/ireland_sp_list_measurements_16198.csv_sorted
[STOP] [2019-10-13 18:18:06] convert_to_csv
[START] [2019-10-13 18:18:06] calculate_delta
[CMD] [2019-10-13 18:18:06] echo "0a" > /app/public/diff/ireland_sp_list_refs_16195.diff
[CMD] [2019-10-13 18:18:06] tail -n +1 /app/public/converted_csv/ireland_sp_list_refs_16195.csv >> /app/public/diff/ireland_sp_list_refs_16195.diff
[CMD] [2019-10-13 18:18:06] echo "." >> /app/public/diff/ireland_sp_list_refs_16195.diff
[CMD] [2019-10-13 18:18:06] echo "0a" > /app/public/diff/ireland_sp_list_nodes_16196.diff
[CMD] [2019-10-13 18:18:06] tail -n +1 /app/public/converted_csv/ireland_sp_list_nodes_16196.csv >> /app/public/diff/ireland_sp_list_nodes_16196.diff
[CMD] [2019-10-13 18:18:06] echo "." >> /app/public/diff/ireland_sp_list_nodes_16196.diff
[CMD] [2019-10-13 18:18:06] echo "0a" > /app/public/diff/ireland_sp_list_occurrences_16197.diff
[CMD] [2019-10-13 18:18:06] tail -n +1 /app/public/converted_csv/ireland_sp_list_occurrences_16197.csv >> /app/public/diff/ireland_sp_list_occurrences_16197.diff
[CMD] [2019-10-13 18:18:06] echo "." >> /app/public/diff/ireland_sp_list_occurrences_16197.diff
[CMD] [2019-10-13 18:18:07] echo "0a" > /app/public/diff/ireland_sp_list_measurements_16198.diff
[CMD] [2019-10-13 18:18:07] tail -n +1 /app/public/converted_csv/ireland_sp_list_measurements_16198.csv >> /app/public/diff/ireland_sp_list_measurements_16198.diff
[CMD] [2019-10-13 18:18:07] echo "." >> /app/public/diff/ireland_sp_list_measurements_16198.diff
[STOP] [2019-10-13 18:18:07] calculate_delta
[START] [2019-10-13 18:18:07] parse_diff_and_store
[INFO] [2019-10-13 18:18:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 18:18:07] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 18:18:17] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 18:18:19] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 18:19:49] Storing 2 References
[INFO] [2019-10-13 18:19:49] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 18:19:49] Average Time: 0.0
[INFO] [2019-10-13 18:19:49] Total Time: 1s
[INFO] [2019-10-13 18:19:49] Storing 24581 ScientificNames
[INFO] [2019-10-13 18:19:49] Processing group of 24581 in 25 groups of 1000
[INFO] [2019-10-13 18:19:59] Average Time: 0.389
[INFO] [2019-10-13 18:19:59] Total Time: 10s
[INFO] [2019-10-13 18:19:59] last 3 / first 3: 1.09
[INFO] [2019-10-13 18:19:59] Std.Dev: 0.1224744871391589; Max: 0.78
[INFO] [2019-10-13 18:19:59] Storing 24581 Nodes
[INFO] [2019-10-13 18:19:59] Processing group of 24581 in 25 groups of 1000
[INFO] [2019-10-13 18:20:07] Average Time: 0.289
[INFO] [2019-10-13 18:20:07] Total Time: 8s
[INFO] [2019-10-13 18:20:07] last 3 / first 3: 0.82
[INFO] [2019-10-13 18:20:07] Std.Dev: 0.03162277660168379; Max: 0.36
[INFO] [2019-10-13 18:20:07] Storing 15424 Occurrences
[INFO] [2019-10-13 18:20:07] Processing group of 15424 in 16 groups of 1000
[INFO] [2019-10-13 18:20:08] Average Time: 0.101
[INFO] [2019-10-13 18:20:08] Total Time: 2s
[INFO] [2019-10-13 18:20:08] last 3 / first 3: 0.78
[INFO] [2019-10-13 18:20:08] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-13 18:20:08] Storing 31000 TraitsReferences
[INFO] [2019-10-13 18:20:08] Processing group of 31000 in 31 groups of 1000
[INFO] [2019-10-13 18:20:11] Average Time: 0.074
[INFO] [2019-10-13 18:20:11] Total Time: 3s
[INFO] [2019-10-13 18:20:11] last 3 / first 3: 0.72
[INFO] [2019-10-13 18:20:11] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-13 18:20:11] Storing 30999 Traits
[INFO] [2019-10-13 18:20:11] Processing group of 30999 in 31 groups of 1000
[INFO] [2019-10-13 18:20:21] Average Time: 0.333
[INFO] [2019-10-13 18:20:21] Total Time: 11s
[INFO] [2019-10-13 18:20:21] last 3 / first 3: 1.78
[INFO] [2019-10-13 18:20:21] Std.Dev: 0.09486832980505137; Max: 0.65
[INFO] [2019-10-13 18:20:21] Storing 30985 MetaTraits
[INFO] [2019-10-13 18:20:21] Processing group of 30985 in 31 groups of 1000
[INFO] [2019-10-13 18:20:25] Average Time: 0.109
[INFO] [2019-10-13 18:20:25] Total Time: 4s
[INFO] [2019-10-13 18:20:25] last 3 / first 3: 0.81
[INFO] [2019-10-13 18:20:25] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-10-13 18:20:25] parse_diff_and_store
[START] [2019-10-13 18:20:25] resolve_keys
[INFO] [2019-10-13 18:21:32] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 18:21:38] traits to occurrences...
[INFO] [2019-10-13 18:21:43] traits to nodes (through occurrences)...
[INFO] [2019-10-13 18:21:43] Traits to sex term...
[INFO] [2019-10-13 18:21:48] Traits to lifestage term...
[INFO] [2019-10-13 18:21:54] MetaTraits to traits...
[INFO] [2019-10-13 18:21:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 18:22:00] Assocs to occurrences...
[INFO] [2019-10-13 18:22:00] Assocs to nodes...
[INFO] [2019-10-13 18:22:00] Assoc to sex term...
[INFO] [2019-10-13 18:22:00] Assoc to lifestage term...
[STOP] [2019-10-13 18:22:00] resolve_keys
[START] [2019-10-13 18:22:00] hold_for_later_1
[STOP] [2019-10-13 18:22:00] hold_for_later_1
[START] [2019-10-13 18:22:00] hold_for_later_2
[STOP] [2019-10-13 18:22:00] hold_for_later_2
[START] [2019-10-13 18:22:00] resolve_missing_parents
[STOP] [2019-10-13 18:22:45] resolve_missing_parents
[START] [2019-10-13 18:22:45] rebuild_nodes
[START] [2019-10-13 18:22:45] Flattener#flatten
[START] [2019-10-13 18:22:45] Flattener#study_resource
[START] [2019-10-13 18:22:45] Flattener#build_ancestry
[STOP] [2019-10-13 18:22:47] Flattener#build_ancestry
[INFO] [2019-10-13 18:22:47] 24581 ancestry keys
[START] [2019-10-13 18:22:47] build_node_ancestors
[INFO] [2019-10-13 18:22:47] old ancestors deleted.
[STOP] [2019-10-13 18:22:53] build_node_ancestors
[START] [2019-10-13 18:23:00] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 18:23:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 18:23:02] Flattener#flatten
[STOP] [2019-10-13 18:23:02] rebuild_nodes
[START] [2019-10-13 18:23:02] resolve_missing_media_owners
[STOP] [2019-10-13 18:23:02] resolve_missing_media_owners
[START] [2019-10-13 18:23:02] sanitize_media_verbatims
[STOP] [2019-10-13 18:23:02] sanitize_media_verbatims
[START] [2019-10-13 18:23:02] queue_downloads
[STOP] [2019-10-13 18:23:02] queue_downloads
[START] [2019-10-13 18:23:02] parse_names
[WARN] [2019-10-13 18:23:02] I see 24581 names which still need to be parsed.
[STOP] [2019-10-13 18:23:21] parse_names
[START] [2019-10-13 18:23:21] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 18:23:21] denormalize_canonical_names_to_nodes
[START] [2019-10-13 18:23:21] match_nodes
[START] [2019-10-13 18:23:21] map_all_nodes_to_pages
[STOP] [2019-10-13 18:46:43] map_all_nodes_to_pages
[INFO] [2019-10-13 18:46:43] 2086 Unmatched nodes (of 24581)! That's too many to output. First 10: Mustela furo (#50306936); Ursus spelaeus (#50319938); Clethrionomys (#50309739); Myocastoridae (#50319429); Erinaceomorpha (#50302213); Mammut primigenius (#50321485); Elephas primigenius (#50322140); Aglais io (#50302021); Vanessa cardui (#50302804); Argynnis aglaja (#50303304)
[START] [2019-10-13 18:46:43] update_nodes
[STOP] [2019-10-13 18:46:52] update_nodes
[STOP] [2019-10-13 18:46:52] match_nodes
[START] [2019-10-13 18:46:52] reindex_search
[STOP] [2019-10-13 18:47:53] reindex_search
[START] [2019-10-13 18:47:53] normalize_units
[STOP] [2019-10-13 18:47:53] normalize_units
[START] [2019-10-13 18:47:53] calculate_statistics
[STOP] [2019-10-13 18:47:53] calculate_statistics
[START] [2019-10-13 18:47:53] complete_harvest_instance
[START] [2019-10-13 18:47:53] overall_tsv_creation
[INFO] [2019-10-13 18:47:53] Processing group of 24581 in 3 batches of 10000
[INFO] [2019-10-13 18:49:21] 5703 Traits (unfiltered)...
[INFO] [2019-10-13 18:49:34] 5703 Traits (filtered)...
[INFO] [2019-10-13 18:49:35] 0 Associations (filtered)...
[INFO] [2019-10-13 18:50:24] 28513 metadata added.
[INFO] [2019-10-13 18:50:24] 0 metadata added.
[INFO] [2019-10-13 18:51:55] 6558 Traits (unfiltered)...
[INFO] [2019-10-13 18:52:09] 6558 Traits (filtered)...
[INFO] [2019-10-13 18:52:09] 0 Associations (filtered)...
[INFO] [2019-10-13 18:53:00] 32784 metadata added.
[INFO] [2019-10-13 18:53:00] 0 metadata added.
[INFO] [2019-10-13 18:54:08] 3163 Traits (unfiltered)...
[INFO] [2019-10-13 18:54:21] 3163 Traits (filtered)...
[INFO] [2019-10-13 18:54:21] 0 Associations (filtered)...
[INFO] [2019-10-13 18:55:05] 15808 metadata added.
[INFO] [2019-10-13 18:55:05] 0 metadata added.
[INFO] [2019-10-13 18:55:05] Average Time: 119.037
[INFO] [2019-10-13 18:55:05] Total Time: 7m13s
[STOP] [2019-10-13 18:55:05] overall_tsv_creation
[INFO] [2019-10-13 18:55:05] Done. Check your files:
[INFO] [2019-10-13 18:55:05] (24581 lines) /app/public/data/ireland_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 18:55:05] (83763 lines) /app/public/data/ireland_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 18:55:06] (24581 lines) /app/public/data/ireland_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 18:55:06] (15425 lines) /app/public/data/ireland_sp_list/publish_traits.tsv
[INFO] [2019-10-13 18:55:06] (77106 lines) /app/public/data/ireland_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 18:55:06] complete_harvest_instance
[START] [2019-10-13 18:55:06] completed
[STOP] [2019-10-13 18:55:06] completed
[STOP] [2019-10-13 18:55:06] logged process, took 2224.18

Latest Process

13 Oct 18:18 EXITED currently processing 0