Harvest for Cuba Species List Created 01 Nov 02:17

Stage: completed
Fetched: 01 Nov 02:17
Validated: 01 Nov 02:17
Deltas Created 01 Nov 02:17
Units Normalized: 01 Nov 02:28
Ancestry Built: 01 Nov 02:19
Nodes Matched: 01 Nov 02:28
Names Parsed: 01 Nov 02:19
New Models Stored: 01 Nov 02:18
Indexed: 01 Nov 02:28
Completed: 01 Nov 02:31
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-11-01 02:17:19 -0400 by logger.rb/56815
[START] [2019-11-01 02:17:19] logged process
[START] [2019-11-01 02:17:19] create_harvest_instance
[STOP] [2019-11-01 02:17:19] create_harvest_instance
[START] [2019-11-01 02:17:19] fetch_files
[STOP] [2019-11-01 02:17:19] fetch_files
[START] [2019-11-01 02:17:19] validate_each_file
[STOP] [2019-11-01 02:17:20] validate_each_file
[START] [2019-11-01 02:17:20] convert_to_csv
[CMD] [2019-11-01 02:17:20] /usr/bin/sort /app/public/converted_csv/cuba_sp_list_refs_17984.csv > /app/public/converted_csv/cuba_sp_list_refs_17984.csv_sorted
[CMD] [2019-11-01 02:17:20] /usr/bin/sort /app/public/converted_csv/cuba_sp_list_nodes_17985.csv > /app/public/converted_csv/cuba_sp_list_nodes_17985.csv_sorted
[CMD] [2019-11-01 02:17:21] /usr/bin/sort /app/public/converted_csv/cuba_sp_list_occurrences_17986.csv > /app/public/converted_csv/cuba_sp_list_occurrences_17986.csv_sorted
[CMD] [2019-11-01 02:17:21] /usr/bin/sort /app/public/converted_csv/cuba_sp_list_measurements_17987.csv > /app/public/converted_csv/cuba_sp_list_measurements_17987.csv_sorted
[STOP] [2019-11-01 02:17:21] convert_to_csv
[START] [2019-11-01 02:17:21] calculate_delta
[CMD] [2019-11-01 02:17:21] echo "0a" > /app/public/diff/cuba_sp_list_refs_17984.diff
[CMD] [2019-11-01 02:17:21] tail -n +1 /app/public/converted_csv/cuba_sp_list_refs_17984.csv >> /app/public/diff/cuba_sp_list_refs_17984.diff
[CMD] [2019-11-01 02:17:22] echo "." >> /app/public/diff/cuba_sp_list_refs_17984.diff
[CMD] [2019-11-01 02:17:22] echo "0a" > /app/public/diff/cuba_sp_list_nodes_17985.diff
[CMD] [2019-11-01 02:17:22] tail -n +1 /app/public/converted_csv/cuba_sp_list_nodes_17985.csv >> /app/public/diff/cuba_sp_list_nodes_17985.diff
[CMD] [2019-11-01 02:17:22] echo "." >> /app/public/diff/cuba_sp_list_nodes_17985.diff
[CMD] [2019-11-01 02:17:22] echo "0a" > /app/public/diff/cuba_sp_list_occurrences_17986.diff
[CMD] [2019-11-01 02:17:23] tail -n +1 /app/public/converted_csv/cuba_sp_list_occurrences_17986.csv >> /app/public/diff/cuba_sp_list_occurrences_17986.diff
[CMD] [2019-11-01 02:17:23] echo "." >> /app/public/diff/cuba_sp_list_occurrences_17986.diff
[CMD] [2019-11-01 02:17:23] echo "0a" > /app/public/diff/cuba_sp_list_measurements_17987.diff
[CMD] [2019-11-01 02:17:23] tail -n +1 /app/public/converted_csv/cuba_sp_list_measurements_17987.csv >> /app/public/diff/cuba_sp_list_measurements_17987.diff
[CMD] [2019-11-01 02:17:23] echo "." >> /app/public/diff/cuba_sp_list_measurements_17987.diff
[STOP] [2019-11-01 02:17:24] calculate_delta
[START] [2019-11-01 02:17:24] parse_diff_and_store
[INFO] [2019-11-01 02:17:24] Loading refs diff file into memory (true lines)...
[INFO] [2019-11-01 02:17:24] Loading nodes diff file into memory (true lines)...
[INFO] [2019-11-01 02:17:27] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-01 02:17:28] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-01 02:17:57] Storing 2 References
[INFO] [2019-11-01 02:17:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-11-01 02:17:57] Average Time: 0.0
[INFO] [2019-11-01 02:17:57] Total Time: 1s
[INFO] [2019-11-01 02:17:57] Storing 8162 ScientificNames
[INFO] [2019-11-01 02:17:57] Processing group of 8162 in 9 groups of 1000
[INFO] [2019-11-01 02:18:00] Average Time: 0.303
[INFO] [2019-11-01 02:18:00] Total Time: 3s
[INFO] [2019-11-01 02:18:00] last 3 / first 3: 0.63
[INFO] [2019-11-01 02:18:00] Std.Dev: 0.1; Max: 0.41
[INFO] [2019-11-01 02:18:00] Storing 8162 Nodes
[INFO] [2019-11-01 02:18:00] Processing group of 8162 in 9 groups of 1000
[INFO] [2019-11-01 02:18:02] Average Time: 0.26
[INFO] [2019-11-01 02:18:02] Total Time: 3s
[INFO] [2019-11-01 02:18:02] last 3 / first 3: 0.63
[INFO] [2019-11-01 02:18:02] Std.Dev: 0.08944271909999159; Max: 0.4
[INFO] [2019-11-01 02:18:02] Storing 4820 Occurrences
[INFO] [2019-11-01 02:18:02] Processing group of 4820 in 5 groups of 1000
[INFO] [2019-11-01 02:18:03] Average Time: 0.092
[INFO] [2019-11-01 02:18:03] Total Time: 1s
[INFO] [2019-11-01 02:18:03] Storing 9842 TraitsReferences
[INFO] [2019-11-01 02:18:03] Processing group of 9842 in 10 groups of 1000
[INFO] [2019-11-01 02:18:03] Average Time: 0.07
[INFO] [2019-11-01 02:18:03] Total Time: 1s
[INFO] [2019-11-01 02:18:03] last 3 / first 3: 0.63
[INFO] [2019-11-01 02:18:03] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-11-01 02:18:03] Storing 9841 Traits
[INFO] [2019-11-01 02:18:03] Processing group of 9841 in 10 groups of 1000
[INFO] [2019-11-01 02:18:06] Average Time: 0.291
[INFO] [2019-11-01 02:18:06] Total Time: 3s
[INFO] [2019-11-01 02:18:06] last 3 / first 3: 0.78
[INFO] [2019-11-01 02:18:06] Std.Dev: 0.03162277660168379; Max: 0.36
[INFO] [2019-11-01 02:18:06] Storing 9838 MetaTraits
[INFO] [2019-11-01 02:18:06] Processing group of 9838 in 10 groups of 1000
[INFO] [2019-11-01 02:18:08] Average Time: 0.107
[INFO] [2019-11-01 02:18:08] Total Time: 2s
[INFO] [2019-11-01 02:18:08] last 3 / first 3: 0.8
[INFO] [2019-11-01 02:18:08] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-11-01 02:18:08] parse_diff_and_store
[START] [2019-11-01 02:18:08] resolve_keys
[INFO] [2019-11-01 02:18:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-01 02:18:44] traits to occurrences...
[INFO] [2019-11-01 02:18:48] traits to nodes (through occurrences)...
[INFO] [2019-11-01 02:18:48] Traits to sex term...
[INFO] [2019-11-01 02:18:51] Traits to lifestage term...
[INFO] [2019-11-01 02:18:55] MetaTraits to traits...
[INFO] [2019-11-01 02:18:55] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-01 02:18:57] Assocs to occurrences...
[INFO] [2019-11-01 02:18:57] Assocs to nodes...
[INFO] [2019-11-01 02:18:57] Assoc to sex term...
[INFO] [2019-11-01 02:18:57] Assoc to lifestage term...
[STOP] [2019-11-01 02:18:57] resolve_keys
[START] [2019-11-01 02:18:57] hold_for_later_1
[STOP] [2019-11-01 02:18:57] hold_for_later_1
[START] [2019-11-01 02:18:57] hold_for_later_2
[STOP] [2019-11-01 02:18:57] hold_for_later_2
[START] [2019-11-01 02:18:57] resolve_missing_parents
[STOP] [2019-11-01 02:19:13] resolve_missing_parents
[START] [2019-11-01 02:19:13] rebuild_nodes
[START] [2019-11-01 02:19:13] Flattener#flatten
[START] [2019-11-01 02:19:13] Flattener#study_resource
[START] [2019-11-01 02:19:13] Flattener#build_ancestry
[STOP] [2019-11-01 02:19:15] Flattener#build_ancestry
[INFO] [2019-11-01 02:19:15] 8162 ancestry keys
[START] [2019-11-01 02:19:15] build_node_ancestors
[INFO] [2019-11-01 02:19:15] old ancestors deleted.
[STOP] [2019-11-01 02:19:16] build_node_ancestors
[START] [2019-11-01 02:19:19] Flattener#propagate_ancestor_ids
[STOP] [2019-11-01 02:19:19] Flattener#propagate_ancestor_ids
[STOP] [2019-11-01 02:19:19] Flattener#flatten
[STOP] [2019-11-01 02:19:19] rebuild_nodes
[START] [2019-11-01 02:19:19] resolve_missing_media_owners
[STOP] [2019-11-01 02:19:19] resolve_missing_media_owners
[START] [2019-11-01 02:19:19] sanitize_media_verbatims
[STOP] [2019-11-01 02:19:19] sanitize_media_verbatims
[START] [2019-11-01 02:19:19] queue_downloads
[STOP] [2019-11-01 02:19:19] queue_downloads
[START] [2019-11-01 02:19:19] parse_names
[WARN] [2019-11-01 02:19:19] I see 8162 names which still need to be parsed.
[STOP] [2019-11-01 02:19:26] parse_names
[START] [2019-11-01 02:19:26] denormalize_canonical_names_to_nodes
[STOP] [2019-11-01 02:19:26] denormalize_canonical_names_to_nodes
[START] [2019-11-01 02:19:26] match_nodes
[START] [2019-11-01 02:19:26] map_all_nodes_to_pages
[STOP] [2019-11-01 02:28:39] map_all_nodes_to_pages
[INFO] [2019-11-01 02:28:39] 530 Unmatched nodes (of 8162)! That's too many to output. First 10: Dives atroviolaceus (#54167394); Oreothlypis peregrina (#54168282); Dendroica (#54170528); Dendroica discolor (#54170527); Dendroica caerulescens (#54173646); Dendroica palmarum (#54173901); Dendroica dominica (#54174662); Parula (#54172837); Parula americana (#54172836); Tiaris olivacea (#54168698)
[START] [2019-11-01 02:28:39] update_nodes
[STOP] [2019-11-01 02:28:42] update_nodes
[STOP] [2019-11-01 02:28:42] match_nodes
[START] [2019-11-01 02:28:42] reindex_search
[STOP] [2019-11-01 02:28:57] reindex_search
[START] [2019-11-01 02:28:57] normalize_units
[STOP] [2019-11-01 02:28:57] normalize_units
[START] [2019-11-01 02:28:57] calculate_statistics
[STOP] [2019-11-01 02:28:58] calculate_statistics
[START] [2019-11-01 02:28:58] complete_harvest_instance
[START] [2019-11-01 02:28:58] overall_tsv_creation
[INFO] [2019-11-01 02:28:58] Processing group of 8162 in 1 batches of 10000
[INFO] [2019-11-01 02:30:18] 4820 Traits (unfiltered)...
[INFO] [2019-11-01 02:30:31] 4820 Traits (filtered)...
[INFO] [2019-11-01 02:30:32] 0 Associations (filtered)...
[INFO] [2019-11-01 02:31:17] 24096 metadata added.
[INFO] [2019-11-01 02:31:17] 0 metadata added.
[INFO] [2019-11-01 02:31:17] Average Time: 110.2
[INFO] [2019-11-01 02:31:17] Total Time: 2m20s
[STOP] [2019-11-01 02:31:17] overall_tsv_creation
[INFO] [2019-11-01 02:31:17] Done. Check your files:
[INFO] [2019-11-01 02:31:17] (8162 lines) /app/public/data/cuba_sp_list/publish_nodes.tsv
[INFO] [2019-11-01 02:31:17] (28936 lines) /app/public/data/cuba_sp_list/publish_node_ancestors.tsv
[INFO] [2019-11-01 02:31:18] (8162 lines) /app/public/data/cuba_sp_list/publish_scientific_names.tsv
[INFO] [2019-11-01 02:31:18] (4821 lines) /app/public/data/cuba_sp_list/publish_traits.tsv
[INFO] [2019-11-01 02:31:18] (24097 lines) /app/public/data/cuba_sp_list/publish_metadata.tsv
[STOP] [2019-11-01 02:31:18] complete_harvest_instance
[START] [2019-11-01 02:31:18] completed
[STOP] [2019-11-01 02:31:18] completed
[STOP] [2019-11-01 02:31:18] logged process, took 839.42
Latest Process

01 Nov 02:17 EXITED currently processing 0