Harvest for Isle of Man Species List Created 13 Oct 19:13

Harvesting Log

# Logfile created on 2019-10-13 19:13:27 -0400 by logger.rb/56815
[START] [2019-10-13 19:13:27] logged process
[START] [2019-10-13 19:13:27] create_harvest_instance
[STOP] [2019-10-13 19:13:28] create_harvest_instance
[START] [2019-10-13 19:13:28] fetch_files
[STOP] [2019-10-13 19:13:28] fetch_files
[START] [2019-10-13 19:13:28] validate_each_file
[STOP] [2019-10-13 19:13:29] validate_each_file
[START] [2019-10-13 19:13:29] convert_to_csv
[CMD] [2019-10-13 19:13:29] /usr/bin/sort /app/public/converted_csv/isle_man_sp_list_refs_16211.csv > /app/public/converted_csv/isle_man_sp_list_refs_16211.csv_sorted
[CMD] [2019-10-13 19:13:29] /usr/bin/sort /app/public/converted_csv/isle_man_sp_list_nodes_16212.csv > /app/public/converted_csv/isle_man_sp_list_nodes_16212.csv_sorted
[CMD] [2019-10-13 19:13:29] /usr/bin/sort /app/public/converted_csv/isle_man_sp_list_occurrences_16213.csv > /app/public/converted_csv/isle_man_sp_list_occurrences_16213.csv_sorted
[CMD] [2019-10-13 19:13:29] /usr/bin/sort /app/public/converted_csv/isle_man_sp_list_measurements_16214.csv > /app/public/converted_csv/isle_man_sp_list_measurements_16214.csv_sorted
[STOP] [2019-10-13 19:13:29] convert_to_csv
[START] [2019-10-13 19:13:29] calculate_delta
[CMD] [2019-10-13 19:13:29] echo "0a" > /app/public/diff/isle_man_sp_list_refs_16211.diff
[CMD] [2019-10-13 19:13:29] tail -n +1 /app/public/converted_csv/isle_man_sp_list_refs_16211.csv >> /app/public/diff/isle_man_sp_list_refs_16211.diff
[CMD] [2019-10-13 19:13:29] echo "." >> /app/public/diff/isle_man_sp_list_refs_16211.diff
[CMD] [2019-10-13 19:13:29] echo "0a" > /app/public/diff/isle_man_sp_list_nodes_16212.diff
[CMD] [2019-10-13 19:13:29] tail -n +1 /app/public/converted_csv/isle_man_sp_list_nodes_16212.csv >> /app/public/diff/isle_man_sp_list_nodes_16212.diff
[CMD] [2019-10-13 19:13:30] echo "." >> /app/public/diff/isle_man_sp_list_nodes_16212.diff
[CMD] [2019-10-13 19:13:30] echo "0a" > /app/public/diff/isle_man_sp_list_occurrences_16213.diff
[CMD] [2019-10-13 19:13:30] tail -n +1 /app/public/converted_csv/isle_man_sp_list_occurrences_16213.csv >> /app/public/diff/isle_man_sp_list_occurrences_16213.diff
[CMD] [2019-10-13 19:13:30] echo "." >> /app/public/diff/isle_man_sp_list_occurrences_16213.diff
[CMD] [2019-10-13 19:13:30] echo "0a" > /app/public/diff/isle_man_sp_list_measurements_16214.diff
[CMD] [2019-10-13 19:13:30] tail -n +1 /app/public/converted_csv/isle_man_sp_list_measurements_16214.csv >> /app/public/diff/isle_man_sp_list_measurements_16214.diff
[CMD] [2019-10-13 19:13:30] echo "." >> /app/public/diff/isle_man_sp_list_measurements_16214.diff
[STOP] [2019-10-13 19:13:30] calculate_delta
[START] [2019-10-13 19:13:30] parse_diff_and_store
[INFO] [2019-10-13 19:13:30] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 19:13:30] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 19:13:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 19:13:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 19:14:03] Storing 2 References
[INFO] [2019-10-13 19:14:03] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 19:14:03] Average Time: 0.0
[INFO] [2019-10-13 19:14:03] Total Time: 1s
[INFO] [2019-10-13 19:14:03] Storing 8653 ScientificNames
[INFO] [2019-10-13 19:14:03] Processing group of 8653 in 9 groups of 1000
[INFO] [2019-10-13 19:14:06] Average Time: 0.347
[INFO] [2019-10-13 19:14:06] Total Time: 4s
[INFO] [2019-10-13 19:14:06] last 3 / first 3: 0.81
[INFO] [2019-10-13 19:14:06] Std.Dev: 0.05477225575051661; Max: 0.44
[INFO] [2019-10-13 19:14:06] Storing 8653 Nodes
[INFO] [2019-10-13 19:14:06] Processing group of 8653 in 9 groups of 1000
[INFO] [2019-10-13 19:14:09] Average Time: 0.288
[INFO] [2019-10-13 19:14:09] Total Time: 3s
[INFO] [2019-10-13 19:14:09] last 3 / first 3: 0.77
[INFO] [2019-10-13 19:14:09] Std.Dev: 0.05477225575051661; Max: 0.39
[INFO] [2019-10-13 19:14:09] Storing 4338 Occurrences
[INFO] [2019-10-13 19:14:09] Processing group of 4338 in 5 groups of 1000
[INFO] [2019-10-13 19:14:09] Average Time: 0.086
[INFO] [2019-10-13 19:14:09] Total Time: 1s
[INFO] [2019-10-13 19:14:09] Storing 9610 TraitsReferences
[INFO] [2019-10-13 19:14:09] Processing group of 9610 in 10 groups of 1000
[INFO] [2019-10-13 19:14:10] Average Time: 0.071
[INFO] [2019-10-13 19:14:10] Total Time: 1s
[INFO] [2019-10-13 19:14:10] last 3 / first 3: 0.67
[INFO] [2019-10-13 19:14:10] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-13 19:14:10] Storing 9609 Traits
[INFO] [2019-10-13 19:14:10] Processing group of 9609 in 10 groups of 1000
[INFO] [2019-10-13 19:14:13] Average Time: 0.306
[INFO] [2019-10-13 19:14:13] Total Time: 4s
[INFO] [2019-10-13 19:14:13] last 3 / first 3: 0.67
[INFO] [2019-10-13 19:14:13] Std.Dev: 0.07745966692414834; Max: 0.49
[INFO] [2019-10-13 19:14:13] Storing 9605 MetaTraits
[INFO] [2019-10-13 19:14:13] Processing group of 9605 in 10 groups of 1000
[INFO] [2019-10-13 19:14:14] Average Time: 0.118
[INFO] [2019-10-13 19:14:14] Total Time: 2s
[INFO] [2019-10-13 19:14:14] last 3 / first 3: 0.84
[INFO] [2019-10-13 19:14:14] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-13 19:14:14] parse_diff_and_store
[START] [2019-10-13 19:14:14] resolve_keys
[INFO] [2019-10-13 19:14:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 19:14:53] traits to occurrences...
[INFO] [2019-10-13 19:14:55] traits to nodes (through occurrences)...
[INFO] [2019-10-13 19:14:55] Traits to sex term...
[INFO] [2019-10-13 19:14:57] Traits to lifestage term...
[INFO] [2019-10-13 19:14:59] MetaTraits to traits...
[INFO] [2019-10-13 19:14:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 19:15:01] Assocs to occurrences...
[INFO] [2019-10-13 19:15:01] Assocs to nodes...
[INFO] [2019-10-13 19:15:01] Assoc to sex term...
[INFO] [2019-10-13 19:15:01] Assoc to lifestage term...
[STOP] [2019-10-13 19:15:01] resolve_keys
[START] [2019-10-13 19:15:01] hold_for_later_1
[STOP] [2019-10-13 19:15:01] hold_for_later_1
[START] [2019-10-13 19:15:01] hold_for_later_2
[STOP] [2019-10-13 19:15:01] hold_for_later_2
[START] [2019-10-13 19:15:01] resolve_missing_parents
[STOP] [2019-10-13 19:15:22] resolve_missing_parents
[START] [2019-10-13 19:15:22] rebuild_nodes
[START] [2019-10-13 19:15:22] Flattener#flatten
[START] [2019-10-13 19:15:22] Flattener#study_resource
[START] [2019-10-13 19:15:22] Flattener#build_ancestry
[STOP] [2019-10-13 19:15:23] Flattener#build_ancestry
[INFO] [2019-10-13 19:15:23] 8653 ancestry keys
[START] [2019-10-13 19:15:23] build_node_ancestors
[INFO] [2019-10-13 19:15:23] old ancestors deleted.
[STOP] [2019-10-13 19:15:24] build_node_ancestors
[START] [2019-10-13 19:15:26] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 19:15:27] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 19:15:27] Flattener#flatten
[STOP] [2019-10-13 19:15:27] rebuild_nodes
[START] [2019-10-13 19:15:27] resolve_missing_media_owners
[STOP] [2019-10-13 19:15:27] resolve_missing_media_owners
[START] [2019-10-13 19:15:27] sanitize_media_verbatims
[STOP] [2019-10-13 19:15:27] sanitize_media_verbatims
[START] [2019-10-13 19:15:27] queue_downloads
[STOP] [2019-10-13 19:15:27] queue_downloads
[START] [2019-10-13 19:15:27] parse_names
[WARN] [2019-10-13 19:15:27] I see 8653 names which still need to be parsed.
[STOP] [2019-10-13 19:15:34] parse_names
[START] [2019-10-13 19:15:34] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 19:15:34] denormalize_canonical_names_to_nodes
[START] [2019-10-13 19:15:34] match_nodes
[START] [2019-10-13 19:15:34] map_all_nodes_to_pages
[STOP] [2019-10-13 19:24:35] map_all_nodes_to_pages
[INFO] [2019-10-13 19:24:35] 559 Unmatched nodes (of 8653)! That's too many to output. First 10: Erinaceomorpha (#50334425); Mustela furo (#50335302); Magnoliopsida (#50334258); Bistorta bistorta (#50338228); Stellaria pallida (#50340726); Sagina subulata (#50338638); Silene maritima (#50339595); Silene alba (#50341612); Tetragonia tetragonioides (#50340758); Jacobaea aquaticus (#50336039)
[START] [2019-10-13 19:24:35] update_nodes
[STOP] [2019-10-13 19:24:38] update_nodes
[STOP] [2019-10-13 19:24:38] match_nodes
[START] [2019-10-13 19:24:38] reindex_search
[STOP] [2019-10-13 19:25:02] reindex_search
[START] [2019-10-13 19:25:02] normalize_units
[STOP] [2019-10-13 19:25:02] normalize_units
[START] [2019-10-13 19:25:02] calculate_statistics
[STOP] [2019-10-13 19:25:02] calculate_statistics
[START] [2019-10-13 19:25:02] complete_harvest_instance
[START] [2019-10-13 19:25:02] overall_tsv_creation
[INFO] [2019-10-13 19:25:02] Processing group of 8653 in 1 batches of 10000
[INFO] [2019-10-13 19:26:25] 4338 Traits (unfiltered)...
[INFO] [2019-10-13 19:26:39] 4338 Traits (filtered)...
[INFO] [2019-10-13 19:26:39] 0 Associations (filtered)...
[INFO] [2019-10-13 19:27:25] 21686 metadata added.
[INFO] [2019-10-13 19:27:25] 0 metadata added.
[INFO] [2019-10-13 19:27:25] Average Time: 116.37
[INFO] [2019-10-13 19:27:25] Total Time: 2m24s
[STOP] [2019-10-13 19:27:25] overall_tsv_creation
[INFO] [2019-10-13 19:27:25] Done. Check your files:
[INFO] [2019-10-13 19:27:25] (8653 lines) /app/public/data/isle_man_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 19:27:25] (21849 lines) /app/public/data/isle_man_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 19:27:25] (8653 lines) /app/public/data/isle_man_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 19:27:25] (4339 lines) /app/public/data/isle_man_sp_list/publish_traits.tsv
[INFO] [2019-10-13 19:27:25] (21687 lines) /app/public/data/isle_man_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 19:27:26] complete_harvest_instance
[START] [2019-10-13 19:27:26] completed
[STOP] [2019-10-13 19:27:26] completed
[STOP] [2019-10-13 19:27:26] logged process, took 838.48

Latest Process

13 Oct 19:13 EXITED currently processing 0