Harvest for Timor Leste Species List Created 16 Oct 17:30

Stage: completed
Fetched: 16 Oct 17:30
Validated: 16 Oct 17:30
Deltas Created 16 Oct 17:30
Units Normalized: 16 Oct 17:33
Ancestry Built: 16 Oct 17:31
Nodes Matched: 16 Oct 17:33
Names Parsed: 16 Oct 17:31
New Models Stored: 16 Oct 17:30
Indexed: 16 Oct 17:33
Completed: 16 Oct 17:35
Time to Harvest: less than a minute

Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 17:30:29 -0400 by logger.rb/56815
[START] [2019-10-16 17:30:29] logged process
[START] [2019-10-16 17:30:29] create_harvest_instance
[STOP] [2019-10-16 17:30:30] create_harvest_instance
[START] [2019-10-16 17:30:30] fetch_files
[STOP] [2019-10-16 17:30:30] fetch_files
[START] [2019-10-16 17:30:30] validate_each_file
[STOP] [2019-10-16 17:30:30] validate_each_file
[START] [2019-10-16 17:30:30] convert_to_csv
[CMD] [2019-10-16 17:30:30] /usr/bin/sort /app/public/converted_csv/timor_leste_sp_l_refs_17497.csv > /app/public/converted_csv/timor_leste_sp_l_refs_17497.csv_sorted
[CMD] [2019-10-16 17:30:30] /usr/bin/sort /app/public/converted_csv/timor_leste_sp_l_nodes_17498.csv > /app/public/converted_csv/timor_leste_sp_l_nodes_17498.csv_sorted
[CMD] [2019-10-16 17:30:30] /usr/bin/sort /app/public/converted_csv/timor_leste_sp_l_occurrences_17499.csv > /app/public/converted_csv/timor_leste_sp_l_occurrences_17499.csv_sorted
[CMD] [2019-10-16 17:30:30] /usr/bin/sort /app/public/converted_csv/timor_leste_sp_l_measurements_17500.csv > /app/public/converted_csv/timor_leste_sp_l_measurements_17500.csv_sorted
[STOP] [2019-10-16 17:30:30] convert_to_csv
[START] [2019-10-16 17:30:30] calculate_delta
[CMD] [2019-10-16 17:30:30] echo "0a" > /app/public/diff/timor_leste_sp_l_refs_17497.diff
[CMD] [2019-10-16 17:30:30] tail -n +1 /app/public/converted_csv/timor_leste_sp_l_refs_17497.csv >> /app/public/diff/timor_leste_sp_l_refs_17497.diff
[CMD] [2019-10-16 17:30:30] echo "." >> /app/public/diff/timor_leste_sp_l_refs_17497.diff
[CMD] [2019-10-16 17:30:30] echo "0a" > /app/public/diff/timor_leste_sp_l_nodes_17498.diff
[CMD] [2019-10-16 17:30:31] tail -n +1 /app/public/converted_csv/timor_leste_sp_l_nodes_17498.csv >> /app/public/diff/timor_leste_sp_l_nodes_17498.diff
[CMD] [2019-10-16 17:30:31] echo "." >> /app/public/diff/timor_leste_sp_l_nodes_17498.diff
[CMD] [2019-10-16 17:30:31] echo "0a" > /app/public/diff/timor_leste_sp_l_occurrences_17499.diff
[CMD] [2019-10-16 17:30:31] tail -n +1 /app/public/converted_csv/timor_leste_sp_l_occurrences_17499.csv >> /app/public/diff/timor_leste_sp_l_occurrences_17499.diff
[CMD] [2019-10-16 17:30:31] echo "." >> /app/public/diff/timor_leste_sp_l_occurrences_17499.diff
[CMD] [2019-10-16 17:30:31] echo "0a" > /app/public/diff/timor_leste_sp_l_measurements_17500.diff
[CMD] [2019-10-16 17:30:31] tail -n +1 /app/public/converted_csv/timor_leste_sp_l_measurements_17500.csv >> /app/public/diff/timor_leste_sp_l_measurements_17500.diff
[CMD] [2019-10-16 17:30:31] echo "." >> /app/public/diff/timor_leste_sp_l_measurements_17500.diff
[STOP] [2019-10-16 17:30:31] calculate_delta
[START] [2019-10-16 17:30:31] parse_diff_and_store
[INFO] [2019-10-16 17:30:31] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 17:30:31] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 17:30:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 17:30:32] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 17:30:39] Storing 2 References
[INFO] [2019-10-16 17:30:39] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 17:30:39] Average Time: 0.0
[INFO] [2019-10-16 17:30:39] Total Time: 1s
[INFO] [2019-10-16 17:30:39] Storing 2397 ScientificNames
[INFO] [2019-10-16 17:30:39] Processing group of 2397 in 3 groups of 1000
[INFO] [2019-10-16 17:30:40] Average Time: 0.313
[INFO] [2019-10-16 17:30:40] Total Time: 1s
[INFO] [2019-10-16 17:30:40] Storing 2397 Nodes
[INFO] [2019-10-16 17:30:40] Processing group of 2397 in 3 groups of 1000
[INFO] [2019-10-16 17:30:41] Average Time: 0.227
[INFO] [2019-10-16 17:30:41] Total Time: 1s
[INFO] [2019-10-16 17:30:41] Storing 964 Occurrences
[INFO] [2019-10-16 17:30:41] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-16 17:30:41] Average Time: 0.12
[INFO] [2019-10-16 17:30:41] Total Time: 1s
[INFO] [2019-10-16 17:30:41] Storing 2500 TraitsReferences
[INFO] [2019-10-16 17:30:41] Processing group of 2500 in 3 groups of 1000
[INFO] [2019-10-16 17:30:41] Average Time: 0.073
[INFO] [2019-10-16 17:30:41] Total Time: 1s
[INFO] [2019-10-16 17:30:41] Storing 2499 Traits
[INFO] [2019-10-16 17:30:41] Processing group of 2499 in 3 groups of 1000
[INFO] [2019-10-16 17:30:42] Average Time: 0.253
[INFO] [2019-10-16 17:30:42] Total Time: 1s
[INFO] [2019-10-16 17:30:42] Storing 2499 MetaTraits
[INFO] [2019-10-16 17:30:42] Processing group of 2499 in 3 groups of 1000
[INFO] [2019-10-16 17:30:42] Average Time: 0.133
[INFO] [2019-10-16 17:30:42] Total Time: 1s
[STOP] [2019-10-16 17:30:42] parse_diff_and_store
[START] [2019-10-16 17:30:42] resolve_keys
[INFO] [2019-10-16 17:30:54] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 17:30:55] traits to occurrences...
[INFO] [2019-10-16 17:30:56] traits to nodes (through occurrences)...
[INFO] [2019-10-16 17:30:56] Traits to sex term...
[INFO] [2019-10-16 17:30:57] Traits to lifestage term...
[INFO] [2019-10-16 17:30:58] MetaTraits to traits...
[INFO] [2019-10-16 17:30:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 17:30:58] Assocs to occurrences...
[INFO] [2019-10-16 17:30:58] Assocs to nodes...
[INFO] [2019-10-16 17:30:58] Assoc to sex term...
[INFO] [2019-10-16 17:30:58] Assoc to lifestage term...
[STOP] [2019-10-16 17:30:58] resolve_keys
[START] [2019-10-16 17:30:58] hold_for_later_1
[STOP] [2019-10-16 17:30:58] hold_for_later_1
[START] [2019-10-16 17:30:58] hold_for_later_2
[STOP] [2019-10-16 17:30:58] hold_for_later_2
[START] [2019-10-16 17:30:58] resolve_missing_parents
[STOP] [2019-10-16 17:31:02] resolve_missing_parents
[START] [2019-10-16 17:31:02] rebuild_nodes
[START] [2019-10-16 17:31:02] Flattener#flatten
[START] [2019-10-16 17:31:02] Flattener#study_resource
[START] [2019-10-16 17:31:02] Flattener#build_ancestry
[STOP] [2019-10-16 17:31:02] Flattener#build_ancestry
[INFO] [2019-10-16 17:31:02] 2397 ancestry keys
[START] [2019-10-16 17:31:02] build_node_ancestors
[INFO] [2019-10-16 17:31:02] old ancestors deleted.
[STOP] [2019-10-16 17:31:02] build_node_ancestors
[START] [2019-10-16 17:31:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 17:31:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 17:31:02] Flattener#flatten
[STOP] [2019-10-16 17:31:02] rebuild_nodes
[START] [2019-10-16 17:31:02] resolve_missing_media_owners
[STOP] [2019-10-16 17:31:02] resolve_missing_media_owners
[START] [2019-10-16 17:31:02] sanitize_media_verbatims
[STOP] [2019-10-16 17:31:02] sanitize_media_verbatims
[START] [2019-10-16 17:31:02] queue_downloads
[STOP] [2019-10-16 17:31:02] queue_downloads
[START] [2019-10-16 17:31:02] parse_names
[WARN] [2019-10-16 17:31:02] I see 2397 names which still need to be parsed.
[STOP] [2019-10-16 17:31:05] parse_names
[START] [2019-10-16 17:31:05] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 17:31:05] denormalize_canonical_names_to_nodes
[START] [2019-10-16 17:31:05] match_nodes
[START] [2019-10-16 17:31:05] map_all_nodes_to_pages
[STOP] [2019-10-16 17:33:52] map_all_nodes_to_pages
[INFO] [2019-10-16 17:33:52] 134 Unmatched nodes (of 2397)! That's too many to output. First 10: Lichenostomus reticulata (#52480944); Streptopelia chinensis (#52480115); Geopelia maugei (#52480297); Trapezostigma (#52481248); Acmella iabadicensis (#52480517); Euchiton japonicum (#52482339); Adenophyllum lavenia (#52481742); Wedelia acerba (#52481988); Talipariti tiliaceus (#52480338); Fioria vitifolius (#52480786)
[START] [2019-10-16 17:33:52] update_nodes
[STOP] [2019-10-16 17:33:53] update_nodes
[STOP] [2019-10-16 17:33:53] match_nodes
[START] [2019-10-16 17:33:53] reindex_search
[STOP] [2019-10-16 17:33:58] reindex_search
[START] [2019-10-16 17:33:58] normalize_units
[STOP] [2019-10-16 17:33:58] normalize_units
[START] [2019-10-16 17:33:58] calculate_statistics
[STOP] [2019-10-16 17:33:58] calculate_statistics
[START] [2019-10-16 17:33:58] complete_harvest_instance
[START] [2019-10-16 17:33:58] overall_tsv_creation
[INFO] [2019-10-16 17:33:58] Processing group of 2397 in 1 batches of 10000
[INFO] [2019-10-16 17:34:52] 964 Traits (unfiltered)...
[INFO] [2019-10-16 17:35:05] 964 Traits (filtered)...
[INFO] [2019-10-16 17:35:05] 0 Associations (filtered)...
[INFO] [2019-10-16 17:35:44] 4819 metadata added.
[INFO] [2019-10-16 17:35:44] 0 metadata added.
[INFO] [2019-10-16 17:35:44] Average Time: 82.59
[INFO] [2019-10-16 17:35:44] Total Time: 1m46s
[STOP] [2019-10-16 17:35:44] overall_tsv_creation
[INFO] [2019-10-16 17:35:44] Done. Check your files:
[INFO] [2019-10-16 17:35:44] (2397 lines) /app/public/data/timor_leste_sp_l/publish_nodes.tsv
[INFO] [2019-10-16 17:35:44] (3324 lines) /app/public/data/timor_leste_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-16 17:35:44] (2397 lines) /app/public/data/timor_leste_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-16 17:35:44] (965 lines) /app/public/data/timor_leste_sp_l/publish_traits.tsv
[INFO] [2019-10-16 17:35:44] (4820 lines) /app/public/data/timor_leste_sp_l/publish_metadata.tsv
[STOP] [2019-10-16 17:35:44] complete_harvest_instance
[START] [2019-10-16 17:35:44] completed
[STOP] [2019-10-16 17:35:44] completed
[STOP] [2019-10-16 17:35:44] logged process, took 314.93

Latest Process