Harvest for Panama Species List Created 15 Oct 06:28

Harvesting Log

# Logfile created on 2019-10-15 06:28:39 -0400 by logger.rb/56815
[START] [2019-10-15 06:28:39] logged process
[START] [2019-10-15 06:28:39] create_harvest_instance
[STOP] [2019-10-15 06:28:39] create_harvest_instance
[START] [2019-10-15 06:28:39] fetch_files
[STOP] [2019-10-15 06:28:39] fetch_files
[START] [2019-10-15 06:28:39] validate_each_file
[STOP] [2019-10-15 06:28:43] validate_each_file
[START] [2019-10-15 06:28:43] convert_to_csv
[CMD] [2019-10-15 06:28:43] /usr/bin/sort /app/public/converted_csv/panama_sp_list_refs_16869.csv > /app/public/converted_csv/panama_sp_list_refs_16869.csv_sorted
[CMD] [2019-10-15 06:28:44] /usr/bin/sort /app/public/converted_csv/panama_sp_list_nodes_16870.csv > /app/public/converted_csv/panama_sp_list_nodes_16870.csv_sorted
[CMD] [2019-10-15 06:28:44] /usr/bin/sort /app/public/converted_csv/panama_sp_list_occurrences_16871.csv > /app/public/converted_csv/panama_sp_list_occurrences_16871.csv_sorted
[CMD] [2019-10-15 06:28:44] /usr/bin/sort /app/public/converted_csv/panama_sp_list_measurements_16872.csv > /app/public/converted_csv/panama_sp_list_measurements_16872.csv_sorted
[STOP] [2019-10-15 06:28:44] convert_to_csv
[START] [2019-10-15 06:28:44] calculate_delta
[CMD] [2019-10-15 06:28:44] echo "0a" > /app/public/diff/panama_sp_list_refs_16869.diff
[CMD] [2019-10-15 06:28:45] tail -n +1 /app/public/converted_csv/panama_sp_list_refs_16869.csv >> /app/public/diff/panama_sp_list_refs_16869.diff
[CMD] [2019-10-15 06:28:45] echo "." >> /app/public/diff/panama_sp_list_refs_16869.diff
[CMD] [2019-10-15 06:28:45] echo "0a" > /app/public/diff/panama_sp_list_nodes_16870.diff
[CMD] [2019-10-15 06:28:46] tail -n +1 /app/public/converted_csv/panama_sp_list_nodes_16870.csv >> /app/public/diff/panama_sp_list_nodes_16870.diff
[CMD] [2019-10-15 06:28:46] echo "." >> /app/public/diff/panama_sp_list_nodes_16870.diff
[CMD] [2019-10-15 06:28:46] echo "0a" > /app/public/diff/panama_sp_list_occurrences_16871.diff
[CMD] [2019-10-15 06:28:46] tail -n +1 /app/public/converted_csv/panama_sp_list_occurrences_16871.csv >> /app/public/diff/panama_sp_list_occurrences_16871.diff
[CMD] [2019-10-15 06:28:47] echo "." >> /app/public/diff/panama_sp_list_occurrences_16871.diff
[CMD] [2019-10-15 06:28:47] echo "0a" > /app/public/diff/panama_sp_list_measurements_16872.diff
[CMD] [2019-10-15 06:28:47] tail -n +1 /app/public/converted_csv/panama_sp_list_measurements_16872.csv >> /app/public/diff/panama_sp_list_measurements_16872.diff
[CMD] [2019-10-15 06:28:48] echo "." >> /app/public/diff/panama_sp_list_measurements_16872.diff
[STOP] [2019-10-15 06:28:48] calculate_delta
[START] [2019-10-15 06:28:48] parse_diff_and_store
[INFO] [2019-10-15 06:28:48] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 06:28:48] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 06:29:02] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 06:29:05] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 06:31:29] Storing 2 References
[INFO] [2019-10-15 06:31:29] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 06:31:29] Average Time: 0.0
[INFO] [2019-10-15 06:31:29] Total Time: 1s
[INFO] [2019-10-15 06:31:29] Storing 33803 ScientificNames
[INFO] [2019-10-15 06:31:29] Processing group of 33803 in 34 groups of 1000
[INFO] [2019-10-15 06:31:42] Average Time: 0.395
[INFO] [2019-10-15 06:31:42] Total Time: 14s
[INFO] [2019-10-15 06:31:42] last 3 / first 3: 0.8
[INFO] [2019-10-15 06:31:42] Std.Dev: 0.12649110640673517; Max: 0.89
[INFO] [2019-10-15 06:31:42] Storing 33803 Nodes
[INFO] [2019-10-15 06:31:42] Processing group of 33803 in 34 groups of 1000
[INFO] [2019-10-15 06:31:54] Average Time: 0.344
[INFO] [2019-10-15 06:31:54] Total Time: 12s
[INFO] [2019-10-15 06:31:54] last 3 / first 3: 0.92
[INFO] [2019-10-15 06:31:54] Std.Dev: 0.13784048752090222; Max: 1.0
[INFO] [2019-10-15 06:31:54] Storing 24100 Occurrences
[INFO] [2019-10-15 06:31:54] Processing group of 24100 in 25 groups of 1000
[INFO] [2019-10-15 06:31:57] Average Time: 0.102
[INFO] [2019-10-15 06:31:57] Total Time: 3s
[INFO] [2019-10-15 06:31:57] last 3 / first 3: 0.83
[INFO] [2019-10-15 06:31:57] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-15 06:31:57] Storing 48850 TraitsReferences
[INFO] [2019-10-15 06:31:57] Processing group of 48850 in 49 groups of 1000
[INFO] [2019-10-15 06:32:00] Average Time: 0.074
[INFO] [2019-10-15 06:32:00] Total Time: 4s
[INFO] [2019-10-15 06:32:00] last 3 / first 3: 0.67
[INFO] [2019-10-15 06:32:00] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-15 06:32:00] Storing 48849 Traits
[INFO] [2019-10-15 06:32:00] Processing group of 48849 in 49 groups of 1000
[INFO] [2019-10-15 06:32:17] Average Time: 0.332
[INFO] [2019-10-15 06:32:17] Total Time: 17s
[INFO] [2019-10-15 06:32:17] last 3 / first 3: 0.77
[INFO] [2019-10-15 06:32:17] Std.Dev: 0.10954451150103323; Max: 0.76
[INFO] [2019-10-15 06:32:17] Storing 48818 MetaTraits
[INFO] [2019-10-15 06:32:17] Processing group of 48818 in 49 groups of 1000
[INFO] [2019-10-15 06:32:23] Average Time: 0.108
[INFO] [2019-10-15 06:32:23] Total Time: 6s
[INFO] [2019-10-15 06:32:23] last 3 / first 3: 0.68
[INFO] [2019-10-15 06:32:23] Std.Dev: 0.03162277660168379; Max: 0.2
[STOP] [2019-10-15 06:32:23] parse_diff_and_store
[START] [2019-10-15 06:32:23] resolve_keys
[INFO] [2019-10-15 06:34:04] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 06:34:12] traits to occurrences...
[INFO] [2019-10-15 06:34:17] traits to nodes (through occurrences)...
[INFO] [2019-10-15 06:34:18] Traits to sex term...
[INFO] [2019-10-15 06:34:24] Traits to lifestage term...
[INFO] [2019-10-15 06:34:31] MetaTraits to traits...
[INFO] [2019-10-15 06:34:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 06:34:41] Assocs to occurrences...
[INFO] [2019-10-15 06:34:41] Assocs to nodes...
[INFO] [2019-10-15 06:34:41] Assoc to sex term...
[INFO] [2019-10-15 06:34:41] Assoc to lifestage term...
[STOP] [2019-10-15 06:34:41] resolve_keys
[START] [2019-10-15 06:34:41] hold_for_later_1
[STOP] [2019-10-15 06:34:41] hold_for_later_1
[START] [2019-10-15 06:34:41] hold_for_later_2
[STOP] [2019-10-15 06:34:41] hold_for_later_2
[START] [2019-10-15 06:34:41] resolve_missing_parents
[STOP] [2019-10-15 06:35:42] resolve_missing_parents
[START] [2019-10-15 06:35:42] rebuild_nodes
[START] [2019-10-15 06:35:42] Flattener#flatten
[START] [2019-10-15 06:35:42] Flattener#study_resource
[START] [2019-10-15 06:35:42] Flattener#build_ancestry
[STOP] [2019-10-15 06:35:46] Flattener#build_ancestry
[INFO] [2019-10-15 06:35:46] 33803 ancestry keys
[START] [2019-10-15 06:35:46] build_node_ancestors
[INFO] [2019-10-15 06:35:46] old ancestors deleted.
[STOP] [2019-10-15 06:36:05] build_node_ancestors
[START] [2019-10-15 06:36:10] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 06:36:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 06:36:14] Flattener#flatten
[STOP] [2019-10-15 06:36:14] rebuild_nodes
[START] [2019-10-15 06:36:14] resolve_missing_media_owners
[STOP] [2019-10-15 06:36:14] resolve_missing_media_owners
[START] [2019-10-15 06:36:14] sanitize_media_verbatims
[STOP] [2019-10-15 06:36:14] sanitize_media_verbatims
[START] [2019-10-15 06:36:14] queue_downloads
[STOP] [2019-10-15 06:36:14] queue_downloads
[START] [2019-10-15 06:36:14] parse_names
[WARN] [2019-10-15 06:36:14] I see 33803 names which still need to be parsed.
[STOP] [2019-10-15 06:36:40] parse_names
[START] [2019-10-15 06:36:40] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 06:36:40] denormalize_canonical_names_to_nodes
[START] [2019-10-15 06:36:40] match_nodes
[START] [2019-10-15 06:36:40] map_all_nodes_to_pages
[STOP] [2019-10-15 07:05:55] map_all_nodes_to_pages
[INFO] [2019-10-15 07:05:55] 1844 Unmatched nodes (of 33803)! That's too many to output. First 10: Lycoperdon fuliginea (#51426136); Lycoperdon pyriformis (#51433093); Lycoperdon excipuliformis (#51437622); Lycoperdon velutina (#51455168); Marasmius leoninus (#51448491); Marasmius poecilus (#51453748); Gloeostereum incarnatus (#51430337); Callistosporium luteoolivaceum (#51445939); Entoloma serrulata (#51435774); Artomyces pyxidata (#51426850)
[START] [2019-10-15 07:05:55] update_nodes
[STOP] [2019-10-15 07:06:07] update_nodes
[STOP] [2019-10-15 07:06:07] match_nodes
[START] [2019-10-15 07:06:07] reindex_search
[STOP] [2019-10-15 07:07:29] reindex_search
[START] [2019-10-15 07:07:29] normalize_units
[STOP] [2019-10-15 07:07:29] normalize_units
[START] [2019-10-15 07:07:29] calculate_statistics
[STOP] [2019-10-15 07:07:29] calculate_statistics
[START] [2019-10-15 07:07:29] complete_harvest_instance
[START] [2019-10-15 07:07:29] overall_tsv_creation
[INFO] [2019-10-15 07:07:29] Processing group of 33803 in 4 batches of 10000
[INFO] [2019-10-15 07:08:58] 6412 Traits (unfiltered)...
[INFO] [2019-10-15 07:09:12] 6412 Traits (filtered)...
[INFO] [2019-10-15 07:09:12] 0 Associations (filtered)...
[INFO] [2019-10-15 07:10:02] 32056 metadata added.
[INFO] [2019-10-15 07:10:02] 0 metadata added.
[INFO] [2019-10-15 07:11:36] 7305 Traits (unfiltered)...
[INFO] [2019-10-15 07:11:51] 7305 Traits (filtered)...
[INFO] [2019-10-15 07:11:51] 0 Associations (filtered)...
[INFO] [2019-10-15 07:12:45] 36520 metadata added.
[INFO] [2019-10-15 07:12:45] 0 metadata added.
[INFO] [2019-10-15 07:14:22] 7591 Traits (unfiltered)...
[INFO] [2019-10-15 07:14:35] 7591 Traits (filtered)...
[INFO] [2019-10-15 07:14:36] 0 Associations (filtered)...
[INFO] [2019-10-15 07:15:31] 37942 metadata added.
[INFO] [2019-10-15 07:15:31] 0 metadata added.
[INFO] [2019-10-15 07:16:34] 2792 Traits (unfiltered)...
[INFO] [2019-10-15 07:16:48] 2792 Traits (filtered)...
[INFO] [2019-10-15 07:16:48] 0 Associations (filtered)...
[INFO] [2019-10-15 07:17:31] 13950 metadata added.
[INFO] [2019-10-15 07:17:31] 0 metadata added.
[INFO] [2019-10-15 07:17:31] Average Time: 124.81
[INFO] [2019-10-15 07:17:31] Total Time: 10m2s
[STOP] [2019-10-15 07:17:31] overall_tsv_creation
[INFO] [2019-10-15 07:17:31] Done. Check your files:
[INFO] [2019-10-15 07:17:31] (33803 lines) /app/public/data/panama_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 07:17:31] (156047 lines) /app/public/data/panama_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 07:17:32] (33803 lines) /app/public/data/panama_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 07:17:32] (24101 lines) /app/public/data/panama_sp_list/publish_traits.tsv
[INFO] [2019-10-15 07:17:32] (120469 lines) /app/public/data/panama_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 07:17:32] complete_harvest_instance
[START] [2019-10-15 07:17:32] completed
[STOP] [2019-10-15 07:17:32] completed
[STOP] [2019-10-15 07:17:32] logged process, took 2933.91

Latest Process

15 Oct 06:28 EXITED currently processing 0