Harvest for The Bahamas Species List Created 16 Oct 12:44

Stage: completed
Fetched: 16 Oct 12:44
Validated: 16 Oct 12:44
Deltas Created 16 Oct 12:44
Units Normalized: 16 Oct 13:00
Ancestry Built: 16 Oct 12:47
Nodes Matched: 16 Oct 13:00
Names Parsed: 16 Oct 12:47
New Models Stored: 16 Oct 12:45
Indexed: 16 Oct 13:00
Completed: 16 Oct 13:05
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-16 12:44:32 -0400 by logger.rb/56815
[START] [2019-10-16 12:44:32] logged process
[START] [2019-10-16 12:44:32] create_harvest_instance
[STOP] [2019-10-16 12:44:32] create_harvest_instance
[START] [2019-10-16 12:44:32] fetch_files
[STOP] [2019-10-16 12:44:32] fetch_files
[START] [2019-10-16 12:44:32] validate_each_file
[STOP] [2019-10-16 12:44:34] validate_each_file
[START] [2019-10-16 12:44:34] convert_to_csv
[CMD] [2019-10-16 12:44:34] /usr/bin/sort /app/public/converted_csv/bahamas_sp_list_refs_17433.csv > /app/public/converted_csv/bahamas_sp_list_refs_17433.csv_sorted
[CMD] [2019-10-16 12:44:34] /usr/bin/sort /app/public/converted_csv/bahamas_sp_list_nodes_17434.csv > /app/public/converted_csv/bahamas_sp_list_nodes_17434.csv_sorted
[CMD] [2019-10-16 12:44:34] /usr/bin/sort /app/public/converted_csv/bahamas_sp_list_occurrences_17435.csv > /app/public/converted_csv/bahamas_sp_list_occurrences_17435.csv_sorted
[CMD] [2019-10-16 12:44:34] /usr/bin/sort /app/public/converted_csv/bahamas_sp_list_measurements_17436.csv > /app/public/converted_csv/bahamas_sp_list_measurements_17436.csv_sorted
[STOP] [2019-10-16 12:44:35] convert_to_csv
[START] [2019-10-16 12:44:35] calculate_delta
[CMD] [2019-10-16 12:44:35] echo "0a" > /app/public/diff/bahamas_sp_list_refs_17433.diff
[CMD] [2019-10-16 12:44:35] tail -n +1 /app/public/converted_csv/bahamas_sp_list_refs_17433.csv >> /app/public/diff/bahamas_sp_list_refs_17433.diff
[CMD] [2019-10-16 12:44:35] echo "." >> /app/public/diff/bahamas_sp_list_refs_17433.diff
[CMD] [2019-10-16 12:44:36] echo "0a" > /app/public/diff/bahamas_sp_list_nodes_17434.diff
[CMD] [2019-10-16 12:44:36] tail -n +1 /app/public/converted_csv/bahamas_sp_list_nodes_17434.csv >> /app/public/diff/bahamas_sp_list_nodes_17434.diff
[CMD] [2019-10-16 12:44:36] echo "." >> /app/public/diff/bahamas_sp_list_nodes_17434.diff
[CMD] [2019-10-16 12:44:36] echo "0a" > /app/public/diff/bahamas_sp_list_occurrences_17435.diff
[CMD] [2019-10-16 12:44:37] tail -n +1 /app/public/converted_csv/bahamas_sp_list_occurrences_17435.csv >> /app/public/diff/bahamas_sp_list_occurrences_17435.diff
[CMD] [2019-10-16 12:44:37] echo "." >> /app/public/diff/bahamas_sp_list_occurrences_17435.diff
[CMD] [2019-10-16 12:44:37] echo "0a" > /app/public/diff/bahamas_sp_list_measurements_17436.diff
[CMD] [2019-10-16 12:44:37] tail -n +1 /app/public/converted_csv/bahamas_sp_list_measurements_17436.csv >> /app/public/diff/bahamas_sp_list_measurements_17436.diff
[CMD] [2019-10-16 12:44:38] echo "." >> /app/public/diff/bahamas_sp_list_measurements_17436.diff
[STOP] [2019-10-16 12:44:38] calculate_delta
[START] [2019-10-16 12:44:38] parse_diff_and_store
[INFO] [2019-10-16 12:44:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 12:44:39] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 12:44:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 12:44:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 12:45:25] Storing 2 References
[INFO] [2019-10-16 12:45:25] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 12:45:25] Average Time: 0.0
[INFO] [2019-10-16 12:45:25] Total Time: 1s
[INFO] [2019-10-16 12:45:25] Storing 11439 ScientificNames
[INFO] [2019-10-16 12:45:25] Processing group of 11439 in 12 groups of 1000
[INFO] [2019-10-16 12:45:29] Average Time: 0.391
[INFO] [2019-10-16 12:45:29] Total Time: 5s
[INFO] [2019-10-16 12:45:29] last 3 / first 3: 1.36
[INFO] [2019-10-16 12:45:29] Std.Dev: 0.21908902300206645; Max: 1.05
[INFO] [2019-10-16 12:45:29] Storing 11439 Nodes
[INFO] [2019-10-16 12:45:29] Processing group of 11439 in 12 groups of 1000
[INFO] [2019-10-16 12:45:33] Average Time: 0.288
[INFO] [2019-10-16 12:45:33] Total Time: 4s
[INFO] [2019-10-16 12:45:33] last 3 / first 3: 0.87
[INFO] [2019-10-16 12:45:33] Std.Dev: 0.05477225575051661; Max: 0.38
[INFO] [2019-10-16 12:45:33] Storing 6266 Occurrences
[INFO] [2019-10-16 12:45:33] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-16 12:45:33] Average Time: 0.093
[INFO] [2019-10-16 12:45:33] Total Time: 1s
[INFO] [2019-10-16 12:45:33] last 3 / first 3: 0.72
[INFO] [2019-10-16 12:45:33] Std.Dev: 0.03162277660168379; Max: 0.12
[INFO] [2019-10-16 12:45:33] Storing 12910 TraitsReferences
[INFO] [2019-10-16 12:45:33] Processing group of 12910 in 13 groups of 1000
[INFO] [2019-10-16 12:45:34] Average Time: 0.068
[INFO] [2019-10-16 12:45:34] Total Time: 1s
[INFO] [2019-10-16 12:45:34] last 3 / first 3: 0.67
[INFO] [2019-10-16 12:45:34] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-16 12:45:34] Storing 12909 Traits
[INFO] [2019-10-16 12:45:34] Processing group of 12909 in 13 groups of 1000
[INFO] [2019-10-16 12:45:38] Average Time: 0.299
[INFO] [2019-10-16 12:45:38] Total Time: 4s
[INFO] [2019-10-16 12:45:38] last 3 / first 3: 0.8
[INFO] [2019-10-16 12:45:38] Std.Dev: 0.044721359549995794; Max: 0.4
[INFO] [2019-10-16 12:45:38] Storing 12901 MetaTraits
[INFO] [2019-10-16 12:45:38] Processing group of 12901 in 13 groups of 1000
[INFO] [2019-10-16 12:45:40] Average Time: 0.122
[INFO] [2019-10-16 12:45:40] Total Time: 2s
[INFO] [2019-10-16 12:45:40] last 3 / first 3: 0.97
[INFO] [2019-10-16 12:45:40] Std.Dev: 0.03162277660168379; Max: 0.22
[STOP] [2019-10-16 12:45:40] parse_diff_and_store
[START] [2019-10-16 12:45:40] resolve_keys
[INFO] [2019-10-16 12:46:22] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 12:46:26] traits to occurrences...
[INFO] [2019-10-16 12:46:31] traits to nodes (through occurrences)...
[INFO] [2019-10-16 12:46:31] Traits to sex term...
[INFO] [2019-10-16 12:46:36] Traits to lifestage term...
[INFO] [2019-10-16 12:46:40] MetaTraits to traits...
[INFO] [2019-10-16 12:46:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 12:46:43] Assocs to occurrences...
[INFO] [2019-10-16 12:46:43] Assocs to nodes...
[INFO] [2019-10-16 12:46:43] Assoc to sex term...
[INFO] [2019-10-16 12:46:43] Assoc to lifestage term...
[STOP] [2019-10-16 12:46:43] resolve_keys
[START] [2019-10-16 12:46:43] hold_for_later_1
[STOP] [2019-10-16 12:46:43] hold_for_later_1
[START] [2019-10-16 12:46:43] hold_for_later_2
[STOP] [2019-10-16 12:46:43] hold_for_later_2
[START] [2019-10-16 12:46:43] resolve_missing_parents
[STOP] [2019-10-16 12:47:04] resolve_missing_parents
[START] [2019-10-16 12:47:04] rebuild_nodes
[START] [2019-10-16 12:47:04] Flattener#flatten
[START] [2019-10-16 12:47:04] Flattener#study_resource
[START] [2019-10-16 12:47:04] Flattener#build_ancestry
[STOP] [2019-10-16 12:47:05] Flattener#build_ancestry
[INFO] [2019-10-16 12:47:05] 11439 ancestry keys
[START] [2019-10-16 12:47:05] build_node_ancestors
[INFO] [2019-10-16 12:47:05] old ancestors deleted.
[STOP] [2019-10-16 12:47:09] build_node_ancestors
[START] [2019-10-16 12:47:12] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 12:47:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 12:47:14] Flattener#flatten
[STOP] [2019-10-16 12:47:14] rebuild_nodes
[START] [2019-10-16 12:47:14] resolve_missing_media_owners
[STOP] [2019-10-16 12:47:14] resolve_missing_media_owners
[START] [2019-10-16 12:47:14] sanitize_media_verbatims
[STOP] [2019-10-16 12:47:14] sanitize_media_verbatims
[START] [2019-10-16 12:47:14] queue_downloads
[STOP] [2019-10-16 12:47:14] queue_downloads
[START] [2019-10-16 12:47:14] parse_names
[WARN] [2019-10-16 12:47:14] I see 11439 names which still need to be parsed.
[STOP] [2019-10-16 12:47:23] parse_names
[START] [2019-10-16 12:47:23] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 12:47:23] denormalize_canonical_names_to_nodes
[START] [2019-10-16 12:47:23] match_nodes
[START] [2019-10-16 12:47:23] map_all_nodes_to_pages
[STOP] [2019-10-16 13:00:09] map_all_nodes_to_pages
[INFO] [2019-10-16 13:00:09] 733 Unmatched nodes (of 11439)! That's too many to output. First 10: Acropora saludensis (#52395318); Acropora panamensis (#52397743); Caulastraea portoricensis (#52394661); Caulastrea (#52394682); Caulastrea portoricensis (#52394681); Montastrea canalis (#52396723); Goniastrea canalis (#52397533); Porites baracoaensis (#52393983); Porites portoricensis (#52394391); Porites waylandi (#52395989)
[START] [2019-10-16 13:00:09] update_nodes
[STOP] [2019-10-16 13:00:13] update_nodes
[STOP] [2019-10-16 13:00:13] match_nodes
[START] [2019-10-16 13:00:13] reindex_search
[STOP] [2019-10-16 13:00:56] reindex_search
[START] [2019-10-16 13:00:56] normalize_units
[STOP] [2019-10-16 13:00:56] normalize_units
[START] [2019-10-16 13:00:56] calculate_statistics
[STOP] [2019-10-16 13:00:56] calculate_statistics
[START] [2019-10-16 13:00:56] complete_harvest_instance
[START] [2019-10-16 13:00:56] overall_tsv_creation
[INFO] [2019-10-16 13:00:56] Processing group of 11439 in 2 batches of 10000
[INFO] [2019-10-16 13:02:24] 5503 Traits (unfiltered)...
[INFO] [2019-10-16 13:02:38] 5503 Traits (filtered)...
[INFO] [2019-10-16 13:02:38] 0 Associations (filtered)...
[INFO] [2019-10-16 13:03:26] 27506 metadata added.
[INFO] [2019-10-16 13:03:26] 0 metadata added.
[INFO] [2019-10-16 13:04:16] 763 Traits (unfiltered)...
[INFO] [2019-10-16 13:04:29] 763 Traits (filtered)...
[INFO] [2019-10-16 13:04:29] 0 Associations (filtered)...
[INFO] [2019-10-16 13:05:07] 3815 metadata added.
[INFO] [2019-10-16 13:05:07] 0 metadata added.
[INFO] [2019-10-16 13:05:07] Average Time: 101.46
[INFO] [2019-10-16 13:05:07] Total Time: 4m12s
[STOP] [2019-10-16 13:05:07] overall_tsv_creation
[INFO] [2019-10-16 13:05:07] Done. Check your files:
[INFO] [2019-10-16 13:05:08] (11439 lines) /app/public/data/bahamas_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 13:05:08] (47877 lines) /app/public/data/bahamas_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 13:05:08] (11439 lines) /app/public/data/bahamas_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 13:05:08] (6267 lines) /app/public/data/bahamas_sp_list/publish_traits.tsv
[INFO] [2019-10-16 13:05:09] (31322 lines) /app/public/data/bahamas_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 13:05:09] complete_harvest_instance
[START] [2019-10-16 13:05:09] completed
[STOP] [2019-10-16 13:05:09] completed
[STOP] [2019-10-16 13:05:09] logged process, took 1237.24
Latest Process

16 Oct 12:44 EXITED currently processing 0