Harvest for Somalia Species List Created 15 Oct 20:30

Stage: completed
Fetched: 15 Oct 20:30
Validated: 15 Oct 20:30
Deltas Created 15 Oct 20:30
Units Normalized: 15 Oct 20:36
Ancestry Built: 15 Oct 20:31
Nodes Matched: 15 Oct 20:36
Names Parsed: 15 Oct 20:31
New Models Stored: 15 Oct 20:31
Indexed: 15 Oct 20:36
Completed: 15 Oct 20:38
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-15 20:30:29 -0400 by logger.rb/56815
[START] [2019-10-15 20:30:29] logged process
[START] [2019-10-15 20:30:29] create_harvest_instance
[STOP] [2019-10-15 20:30:30] create_harvest_instance
[START] [2019-10-15 20:30:30] fetch_files
[STOP] [2019-10-15 20:30:30] fetch_files
[START] [2019-10-15 20:30:30] validate_each_file
[STOP] [2019-10-15 20:30:31] validate_each_file
[START] [2019-10-15 20:30:31] convert_to_csv
[CMD] [2019-10-15 20:30:31] /usr/bin/sort /app/public/converted_csv/somalia_sp_list_refs_17253.csv > /app/public/converted_csv/somalia_sp_list_refs_17253.csv_sorted
[CMD] [2019-10-15 20:30:31] /usr/bin/sort /app/public/converted_csv/somalia_sp_list_nodes_17254.csv > /app/public/converted_csv/somalia_sp_list_nodes_17254.csv_sorted
[CMD] [2019-10-15 20:30:31] /usr/bin/sort /app/public/converted_csv/somalia_sp_list_occurrences_17255.csv > /app/public/converted_csv/somalia_sp_list_occurrences_17255.csv_sorted
[CMD] [2019-10-15 20:30:31] /usr/bin/sort /app/public/converted_csv/somalia_sp_list_measurements_17256.csv > /app/public/converted_csv/somalia_sp_list_measurements_17256.csv_sorted
[STOP] [2019-10-15 20:30:32] convert_to_csv
[START] [2019-10-15 20:30:32] calculate_delta
[CMD] [2019-10-15 20:30:32] echo "0a" > /app/public/diff/somalia_sp_list_refs_17253.diff
[CMD] [2019-10-15 20:30:32] tail -n +1 /app/public/converted_csv/somalia_sp_list_refs_17253.csv >> /app/public/diff/somalia_sp_list_refs_17253.diff
[CMD] [2019-10-15 20:30:32] echo "." >> /app/public/diff/somalia_sp_list_refs_17253.diff
[CMD] [2019-10-15 20:30:33] echo "0a" > /app/public/diff/somalia_sp_list_nodes_17254.diff
[CMD] [2019-10-15 20:30:33] tail -n +1 /app/public/converted_csv/somalia_sp_list_nodes_17254.csv >> /app/public/diff/somalia_sp_list_nodes_17254.diff
[CMD] [2019-10-15 20:30:33] echo "." >> /app/public/diff/somalia_sp_list_nodes_17254.diff
[CMD] [2019-10-15 20:30:33] echo "0a" > /app/public/diff/somalia_sp_list_occurrences_17255.diff
[CMD] [2019-10-15 20:30:34] tail -n +1 /app/public/converted_csv/somalia_sp_list_occurrences_17255.csv >> /app/public/diff/somalia_sp_list_occurrences_17255.diff
[CMD] [2019-10-15 20:30:34] echo "." >> /app/public/diff/somalia_sp_list_occurrences_17255.diff
[CMD] [2019-10-15 20:30:34] echo "0a" > /app/public/diff/somalia_sp_list_measurements_17256.diff
[CMD] [2019-10-15 20:30:35] tail -n +1 /app/public/converted_csv/somalia_sp_list_measurements_17256.csv >> /app/public/diff/somalia_sp_list_measurements_17256.diff
[CMD] [2019-10-15 20:30:35] echo "." >> /app/public/diff/somalia_sp_list_measurements_17256.diff
[STOP] [2019-10-15 20:30:35] calculate_delta
[START] [2019-10-15 20:30:35] parse_diff_and_store
[INFO] [2019-10-15 20:30:35] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 20:30:36] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 20:30:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 20:30:38] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 20:30:56] Storing 2 References
[INFO] [2019-10-15 20:30:56] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 20:30:56] Average Time: 0.0
[INFO] [2019-10-15 20:30:56] Total Time: 1s
[INFO] [2019-10-15 20:30:56] Storing 4795 ScientificNames
[INFO] [2019-10-15 20:30:56] Processing group of 4795 in 5 groups of 1000
[INFO] [2019-10-15 20:30:58] Average Time: 0.35
[INFO] [2019-10-15 20:30:58] Total Time: 2s
[INFO] [2019-10-15 20:30:58] Storing 4795 Nodes
[INFO] [2019-10-15 20:30:58] Processing group of 4795 in 5 groups of 1000
[INFO] [2019-10-15 20:30:59] Average Time: 0.306
[INFO] [2019-10-15 20:30:59] Total Time: 2s
[INFO] [2019-10-15 20:30:59] Storing 2892 Occurrences
[INFO] [2019-10-15 20:30:59] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-15 20:31:00] Average Time: 0.097
[INFO] [2019-10-15 20:31:00] Total Time: 1s
[INFO] [2019-10-15 20:31:00] Storing 6060 TraitsReferences
[INFO] [2019-10-15 20:31:00] Processing group of 6060 in 7 groups of 1000
[INFO] [2019-10-15 20:31:00] Average Time: 0.071
[INFO] [2019-10-15 20:31:00] Total Time: 1s
[INFO] [2019-10-15 20:31:00] last 3 / first 3: 0.43
[INFO] [2019-10-15 20:31:00] Std.Dev: 0.044721359549995794; Max: 0.16
[INFO] [2019-10-15 20:31:00] Storing 6059 Traits
[INFO] [2019-10-15 20:31:00] Processing group of 6059 in 7 groups of 1000
[INFO] [2019-10-15 20:31:02] Average Time: 0.274
[INFO] [2019-10-15 20:31:02] Total Time: 2s
[INFO] [2019-10-15 20:31:02] last 3 / first 3: 0.74
[INFO] [2019-10-15 20:31:02] Std.Dev: 0.11832159566199232; Max: 0.38
[INFO] [2019-10-15 20:31:02] Storing 6060 MetaTraits
[INFO] [2019-10-15 20:31:02] Processing group of 6060 in 7 groups of 1000
[INFO] [2019-10-15 20:31:03] Average Time: 0.1
[INFO] [2019-10-15 20:31:03] Total Time: 1s
[INFO] [2019-10-15 20:31:03] last 3 / first 3: 0.64
[INFO] [2019-10-15 20:31:03] Std.Dev: 0.044721359549995794; Max: 0.14
[STOP] [2019-10-15 20:31:03] parse_diff_and_store
[START] [2019-10-15 20:31:03] resolve_keys
[INFO] [2019-10-15 20:31:23] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 20:31:26] traits to occurrences...
[INFO] [2019-10-15 20:31:27] traits to nodes (through occurrences)...
[INFO] [2019-10-15 20:31:27] Traits to sex term...
[INFO] [2019-10-15 20:31:28] Traits to lifestage term...
[INFO] [2019-10-15 20:31:29] MetaTraits to traits...
[INFO] [2019-10-15 20:31:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 20:31:31] Assocs to occurrences...
[INFO] [2019-10-15 20:31:31] Assocs to nodes...
[INFO] [2019-10-15 20:31:31] Assoc to sex term...
[INFO] [2019-10-15 20:31:31] Assoc to lifestage term...
[STOP] [2019-10-15 20:31:31] resolve_keys
[START] [2019-10-15 20:31:31] hold_for_later_1
[STOP] [2019-10-15 20:31:31] hold_for_later_1
[START] [2019-10-15 20:31:31] hold_for_later_2
[STOP] [2019-10-15 20:31:31] hold_for_later_2
[START] [2019-10-15 20:31:31] resolve_missing_parents
[STOP] [2019-10-15 20:31:40] resolve_missing_parents
[START] [2019-10-15 20:31:40] rebuild_nodes
[START] [2019-10-15 20:31:40] Flattener#flatten
[START] [2019-10-15 20:31:40] Flattener#study_resource
[START] [2019-10-15 20:31:40] Flattener#build_ancestry
[STOP] [2019-10-15 20:31:41] Flattener#build_ancestry
[INFO] [2019-10-15 20:31:41] 4795 ancestry keys
[START] [2019-10-15 20:31:41] build_node_ancestors
[INFO] [2019-10-15 20:31:41] old ancestors deleted.
[STOP] [2019-10-15 20:31:41] build_node_ancestors
[START] [2019-10-15 20:31:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 20:31:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 20:31:42] Flattener#flatten
[STOP] [2019-10-15 20:31:42] rebuild_nodes
[START] [2019-10-15 20:31:42] resolve_missing_media_owners
[STOP] [2019-10-15 20:31:42] resolve_missing_media_owners
[START] [2019-10-15 20:31:42] sanitize_media_verbatims
[STOP] [2019-10-15 20:31:42] sanitize_media_verbatims
[START] [2019-10-15 20:31:43] queue_downloads
[STOP] [2019-10-15 20:31:43] queue_downloads
[START] [2019-10-15 20:31:43] parse_names
[WARN] [2019-10-15 20:31:43] I see 4795 names which still need to be parsed.
[STOP] [2019-10-15 20:31:47] parse_names
[START] [2019-10-15 20:31:47] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 20:31:47] denormalize_canonical_names_to_nodes
[START] [2019-10-15 20:31:47] match_nodes
[START] [2019-10-15 20:31:47] map_all_nodes_to_pages
[STOP] [2019-10-15 20:36:15] map_all_nodes_to_pages
[INFO] [2019-10-15 20:36:15] 271 Unmatched nodes (of 4795)! That's too many to output. First 10: Pennisetum setaceus (#51865450); Bothriochloa insculptum (#51865886); Leptochloa obtusiflora (#51863846); Disakisperma obtusiflora (#51864246); Lintonia (#51865199); Cyperus hyalina (#51865460); Kyllinga odorata (#51863253); Kyllinga microstylus (#51865092); Kyllinga oblongus (#51865252); Kylinga welwitschii (#51864044)
[START] [2019-10-15 20:36:15] update_nodes
[STOP] [2019-10-15 20:36:17] update_nodes
[STOP] [2019-10-15 20:36:17] match_nodes
[START] [2019-10-15 20:36:17] reindex_search
[STOP] [2019-10-15 20:36:28] reindex_search
[START] [2019-10-15 20:36:28] normalize_units
[STOP] [2019-10-15 20:36:28] normalize_units
[START] [2019-10-15 20:36:28] calculate_statistics
[STOP] [2019-10-15 20:36:28] calculate_statistics
[START] [2019-10-15 20:36:28] complete_harvest_instance
[START] [2019-10-15 20:36:28] overall_tsv_creation
[INFO] [2019-10-15 20:36:28] Processing group of 4795 in 1 batches of 10000
[INFO] [2019-10-15 20:37:33] 2892 Traits (unfiltered)...
[INFO] [2019-10-15 20:37:48] 2892 Traits (filtered)...
[INFO] [2019-10-15 20:37:48] 0 Associations (filtered)...
[INFO] [2019-10-15 20:38:32] 14460 metadata added.
[INFO] [2019-10-15 20:38:32] 0 metadata added.
[INFO] [2019-10-15 20:38:32] Average Time: 100.1
[INFO] [2019-10-15 20:38:32] Total Time: 2m4s
[STOP] [2019-10-15 20:38:32] overall_tsv_creation
[INFO] [2019-10-15 20:38:32] Done. Check your files:
[INFO] [2019-10-15 20:38:32] (4795 lines) /app/public/data/somalia_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 20:38:33] (10768 lines) /app/public/data/somalia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 20:38:33] (4795 lines) /app/public/data/somalia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 20:38:33] (2893 lines) /app/public/data/somalia_sp_list/publish_traits.tsv
[INFO] [2019-10-15 20:38:34] (14461 lines) /app/public/data/somalia_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 20:38:34] complete_harvest_instance
[START] [2019-10-15 20:38:34] completed
[STOP] [2019-10-15 20:38:34] completed
[STOP] [2019-10-15 20:38:34] logged process, took 484.41
Latest Process

15 Oct 20:30 EXITED currently processing 0