Harvest for Belize Species List Created 10 Oct 15:23

Stage: completed
Fetched: 10 Oct 15:23
Validated: 10 Oct 15:23
Deltas Created 10 Oct 15:23
Units Normalized: 10 Oct 15:31
Ancestry Built: 10 Oct 15:26
Nodes Matched: 10 Oct 15:30
Names Parsed: 10 Oct 15:26
New Models Stored: 10 Oct 15:24
Indexed: 10 Oct 15:31
Completed: 10 Oct 15:33
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-10 15:23:40 -0400 by logger.rb/56815
[START] [2019-10-10 15:23:40] logged process
[START] [2019-10-10 15:23:40] create_harvest_instance
[STOP] [2019-10-10 15:23:40] create_harvest_instance
[START] [2019-10-10 15:23:40] fetch_files
[STOP] [2019-10-10 15:23:40] fetch_files
[START] [2019-10-10 15:23:40] validate_each_file
[STOP] [2019-10-10 15:23:43] validate_each_file
[START] [2019-10-10 15:23:43] convert_to_csv
[CMD] [2019-10-10 15:23:43] /usr/bin/sort /app/public/converted_csv/belize_sp_list_refs_15114.csv > /app/public/converted_csv/belize_sp_list_refs_15114.csv_sorted
[CMD] [2019-10-10 15:23:43] /usr/bin/sort /app/public/converted_csv/belize_sp_list_nodes_15115.csv > /app/public/converted_csv/belize_sp_list_nodes_15115.csv_sorted
[CMD] [2019-10-10 15:23:43] /usr/bin/sort /app/public/converted_csv/belize_sp_list_occurrences_15116.csv > /app/public/converted_csv/belize_sp_list_occurrences_15116.csv_sorted
[CMD] [2019-10-10 15:23:43] /usr/bin/sort /app/public/converted_csv/belize_sp_list_measurements_15117.csv > /app/public/converted_csv/belize_sp_list_measurements_15117.csv_sorted
[STOP] [2019-10-10 15:23:43] convert_to_csv
[START] [2019-10-10 15:23:43] calculate_delta
[CMD] [2019-10-10 15:23:43] echo "0a" > /app/public/diff/belize_sp_list_refs_15114.diff
[CMD] [2019-10-10 15:23:43] tail -n +1 /app/public/converted_csv/belize_sp_list_refs_15114.csv >> /app/public/diff/belize_sp_list_refs_15114.diff
[CMD] [2019-10-10 15:23:44] echo "." >> /app/public/diff/belize_sp_list_refs_15114.diff
[CMD] [2019-10-10 15:23:44] echo "0a" > /app/public/diff/belize_sp_list_nodes_15115.diff
[CMD] [2019-10-10 15:23:44] tail -n +1 /app/public/converted_csv/belize_sp_list_nodes_15115.csv >> /app/public/diff/belize_sp_list_nodes_15115.diff
[CMD] [2019-10-10 15:23:44] echo "." >> /app/public/diff/belize_sp_list_nodes_15115.diff
[CMD] [2019-10-10 15:23:44] echo "0a" > /app/public/diff/belize_sp_list_occurrences_15116.diff
[CMD] [2019-10-10 15:23:44] tail -n +1 /app/public/converted_csv/belize_sp_list_occurrences_15116.csv >> /app/public/diff/belize_sp_list_occurrences_15116.diff
[CMD] [2019-10-10 15:23:44] echo "." >> /app/public/diff/belize_sp_list_occurrences_15116.diff
[CMD] [2019-10-10 15:23:44] echo "0a" > /app/public/diff/belize_sp_list_measurements_15117.diff
[CMD] [2019-10-10 15:23:44] tail -n +1 /app/public/converted_csv/belize_sp_list_measurements_15117.csv >> /app/public/diff/belize_sp_list_measurements_15117.diff
[CMD] [2019-10-10 15:23:44] echo "." >> /app/public/diff/belize_sp_list_measurements_15117.diff
[STOP] [2019-10-10 15:23:45] calculate_delta
[START] [2019-10-10 15:23:45] parse_diff_and_store
[INFO] [2019-10-10 15:23:45] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-10 15:23:45] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-10 15:23:48] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-10 15:23:49] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-10 15:24:26] Storing 2 References
[INFO] [2019-10-10 15:24:26] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-10 15:24:26] Average Time: 0.0
[INFO] [2019-10-10 15:24:26] Total Time: 1s
[INFO] [2019-10-10 15:24:26] Storing 9882 ScientificNames
[INFO] [2019-10-10 15:24:26] Processing group of 9882 in 10 groups of 1000
[INFO] [2019-10-10 15:24:30] Average Time: 0.348
[INFO] [2019-10-10 15:24:30] Total Time: 4s
[INFO] [2019-10-10 15:24:30] last 3 / first 3: 0.89
[INFO] [2019-10-10 15:24:30] Std.Dev: 0.03162277660168379; Max: 0.4
[INFO] [2019-10-10 15:24:30] Storing 9882 Nodes
[INFO] [2019-10-10 15:24:30] Processing group of 9882 in 10 groups of 1000
[INFO] [2019-10-10 15:24:33] Average Time: 0.321
[INFO] [2019-10-10 15:24:33] Total Time: 4s
[INFO] [2019-10-10 15:24:33] last 3 / first 3: 1.15
[INFO] [2019-10-10 15:24:33] Std.Dev: 0.03162277660168379; Max: 0.39
[INFO] [2019-10-10 15:24:33] Storing 6266 Occurrences
[INFO] [2019-10-10 15:24:33] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-10 15:24:34] Average Time: 0.111
[INFO] [2019-10-10 15:24:34] Total Time: 1s
[INFO] [2019-10-10 15:24:34] last 3 / first 3: 0.55
[INFO] [2019-10-10 15:24:34] Std.Dev: 0.044721359549995794; Max: 0.19
[INFO] [2019-10-10 15:24:34] Storing 13060 TraitsReferences
[INFO] [2019-10-10 15:24:34] Processing group of 13060 in 14 groups of 1000
[INFO] [2019-10-10 15:24:35] Average Time: 0.072
[INFO] [2019-10-10 15:24:35] Total Time: 2s
[INFO] [2019-10-10 15:24:35] last 3 / first 3: 0.57
[INFO] [2019-10-10 15:24:35] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-10 15:24:35] Storing 13059 Traits
[INFO] [2019-10-10 15:24:35] Processing group of 13059 in 14 groups of 1000
[INFO] [2019-10-10 15:24:39] Average Time: 0.284
[INFO] [2019-10-10 15:24:39] Total Time: 5s
[INFO] [2019-10-10 15:24:39] last 3 / first 3: 0.64
[INFO] [2019-10-10 15:24:39] Std.Dev: 0.07745966692414834; Max: 0.39
[INFO] [2019-10-10 15:24:39] Storing 13052 MetaTraits
[INFO] [2019-10-10 15:24:39] Processing group of 13052 in 14 groups of 1000
[INFO] [2019-10-10 15:24:41] Average Time: 0.117
[INFO] [2019-10-10 15:24:41] Total Time: 2s
[INFO] [2019-10-10 15:24:41] last 3 / first 3: 0.63
[INFO] [2019-10-10 15:24:41] Std.Dev: 0.03162277660168379; Max: 0.16
[STOP] [2019-10-10 15:24:41] parse_diff_and_store
[START] [2019-10-10 15:24:41] resolve_keys
[INFO] [2019-10-10 15:25:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-10 15:25:23] traits to occurrences...
[INFO] [2019-10-10 15:25:27] traits to nodes (through occurrences)...
[INFO] [2019-10-10 15:25:28] Traits to sex term...
[INFO] [2019-10-10 15:25:31] Traits to lifestage term...
[INFO] [2019-10-10 15:25:35] MetaTraits to traits...
[INFO] [2019-10-10 15:25:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-10 15:25:38] Assocs to occurrences...
[INFO] [2019-10-10 15:25:38] Assocs to nodes...
[INFO] [2019-10-10 15:25:38] Assoc to sex term...
[INFO] [2019-10-10 15:25:38] Assoc to lifestage term...
[STOP] [2019-10-10 15:25:38] resolve_keys
[START] [2019-10-10 15:25:38] hold_for_later_1
[STOP] [2019-10-10 15:25:38] hold_for_later_1
[START] [2019-10-10 15:25:38] hold_for_later_2
[STOP] [2019-10-10 15:25:38] hold_for_later_2
[START] [2019-10-10 15:25:38] resolve_missing_parents
[STOP] [2019-10-10 15:25:58] resolve_missing_parents
[START] [2019-10-10 15:25:58] rebuild_nodes
[START] [2019-10-10 15:25:58] Flattener#flatten
[START] [2019-10-10 15:25:58] Flattener#study_resource
[START] [2019-10-10 15:25:58] Flattener#build_ancestry
[STOP] [2019-10-10 15:25:58] Flattener#build_ancestry
[INFO] [2019-10-10 15:25:58] 9882 ancestry keys
[START] [2019-10-10 15:25:58] build_node_ancestors
[INFO] [2019-10-10 15:25:58] old ancestors deleted.
[STOP] [2019-10-10 15:26:00] build_node_ancestors
[START] [2019-10-10 15:26:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-10 15:26:03] Flattener#propagate_ancestor_ids
[STOP] [2019-10-10 15:26:03] Flattener#flatten
[STOP] [2019-10-10 15:26:03] rebuild_nodes
[START] [2019-10-10 15:26:03] resolve_missing_media_owners
[STOP] [2019-10-10 15:26:03] resolve_missing_media_owners
[START] [2019-10-10 15:26:03] sanitize_media_verbatims
[STOP] [2019-10-10 15:26:03] sanitize_media_verbatims
[START] [2019-10-10 15:26:03] queue_downloads
[STOP] [2019-10-10 15:26:03] queue_downloads
[START] [2019-10-10 15:26:03] parse_names
[WARN] [2019-10-10 15:26:03] I see 9882 names which still need to be parsed.
[STOP] [2019-10-10 15:26:11] parse_names
[START] [2019-10-10 15:26:11] denormalize_canonical_names_to_nodes
[STOP] [2019-10-10 15:26:11] denormalize_canonical_names_to_nodes
[START] [2019-10-10 15:26:11] match_nodes
[START] [2019-10-10 15:26:11] map_all_nodes_to_pages
[STOP] [2019-10-10 15:30:45] map_all_nodes_to_pages
[INFO] [2019-10-10 15:30:45] 529 Unmatched nodes (of 9882)! That's too many to output. First 10: Seiurus noveboracensis (#48754761); Seiurus motacilla (#48755054); Seiurus aurocapillus (#48755673); Helmitheros vermivorus (#48757099); Vermivora peregrina (#48753145); Oreothlypis peregrina (#48749921); Oreothlypis celata (#48756593); Dendroica (#48751141); Dendroica magnolia (#48751140); Dendroica petechia (#48752826)
[START] [2019-10-10 15:30:45] update_nodes
[STOP] [2019-10-10 15:30:48] update_nodes
[STOP] [2019-10-10 15:30:48] match_nodes
[START] [2019-10-10 15:30:48] reindex_search
[STOP] [2019-10-10 15:31:05] reindex_search
[START] [2019-10-10 15:31:05] normalize_units
[STOP] [2019-10-10 15:31:05] normalize_units
[START] [2019-10-10 15:31:05] calculate_statistics
[STOP] [2019-10-10 15:31:05] calculate_statistics
[START] [2019-10-10 15:31:05] complete_harvest_instance
[START] [2019-10-10 15:31:05] overall_tsv_creation
[INFO] [2019-10-10 15:31:05] Processing group of 9882 in 1 batches of 10000
[INFO] [2019-10-10 15:32:35] 6266 Traits (unfiltered)...
[INFO] [2019-10-10 15:32:49] 6266 Traits (filtered)...
[INFO] [2019-10-10 15:32:50] 0 Associations (filtered)...
[INFO] [2019-10-10 15:33:40] 31324 metadata added.
[INFO] [2019-10-10 15:33:40] 0 metadata added.
[INFO] [2019-10-10 15:33:40] Average Time: 125.75
[INFO] [2019-10-10 15:33:40] Total Time: 2m36s
[STOP] [2019-10-10 15:33:40] overall_tsv_creation
[INFO] [2019-10-10 15:33:40] Done. Check your files:
[INFO] [2019-10-10 15:33:41] (9882 lines) /app/public/data/belize_sp_list/publish_nodes.tsv
[INFO] [2019-10-10 15:33:41] (24756 lines) /app/public/data/belize_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-10 15:33:41] (9882 lines) /app/public/data/belize_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-10 15:33:41] (6267 lines) /app/public/data/belize_sp_list/publish_traits.tsv
[INFO] [2019-10-10 15:33:41] (31325 lines) /app/public/data/belize_sp_list/publish_metadata.tsv
[STOP] [2019-10-10 15:33:41] complete_harvest_instance
[START] [2019-10-10 15:33:41] completed
[STOP] [2019-10-10 15:33:41] completed
[STOP] [2019-10-10 15:33:41] logged process, took 601.35

Latest Process