Harvest for Uganda Species List Created 16 Oct 19:51

Stage: completed
Fetched: 16 Oct 19:51
Validated: 16 Oct 19:51
Deltas Created 16 Oct 19:52
Units Normalized: 16 Oct 20:06
Ancestry Built: 16 Oct 19:54
Nodes Matched: 16 Oct 20:06
Names Parsed: 16 Oct 19:54
New Models Stored: 16 Oct 19:52
Indexed: 16 Oct 20:06
Completed: 16 Oct 20:11
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-16 19:51:57 -0400 by logger.rb/56815
[START] [2019-10-16 19:51:57] logged process
[START] [2019-10-16 19:51:57] create_harvest_instance
[STOP] [2019-10-16 19:51:57] create_harvest_instance
[START] [2019-10-16 19:51:57] fetch_files
[STOP] [2019-10-16 19:51:57] fetch_files
[START] [2019-10-16 19:51:57] validate_each_file
[STOP] [2019-10-16 19:51:59] validate_each_file
[START] [2019-10-16 19:51:59] convert_to_csv
[CMD] [2019-10-16 19:51:59] /usr/bin/sort /app/public/converted_csv/uganda_sp_list_refs_17601.csv > /app/public/converted_csv/uganda_sp_list_refs_17601.csv_sorted
[CMD] [2019-10-16 19:51:59] /usr/bin/sort /app/public/converted_csv/uganda_sp_list_nodes_17602.csv > /app/public/converted_csv/uganda_sp_list_nodes_17602.csv_sorted
[CMD] [2019-10-16 19:51:59] /usr/bin/sort /app/public/converted_csv/uganda_sp_list_occurrences_17603.csv > /app/public/converted_csv/uganda_sp_list_occurrences_17603.csv_sorted
[CMD] [2019-10-16 19:51:59] /usr/bin/sort /app/public/converted_csv/uganda_sp_list_measurements_17604.csv > /app/public/converted_csv/uganda_sp_list_measurements_17604.csv_sorted
[STOP] [2019-10-16 19:51:59] convert_to_csv
[START] [2019-10-16 19:51:59] calculate_delta
[CMD] [2019-10-16 19:51:59] echo "0a" > /app/public/diff/uganda_sp_list_refs_17601.diff
[CMD] [2019-10-16 19:51:59] tail -n +1 /app/public/converted_csv/uganda_sp_list_refs_17601.csv >> /app/public/diff/uganda_sp_list_refs_17601.diff
[CMD] [2019-10-16 19:51:59] echo "." >> /app/public/diff/uganda_sp_list_refs_17601.diff
[CMD] [2019-10-16 19:51:59] echo "0a" > /app/public/diff/uganda_sp_list_nodes_17602.diff
[CMD] [2019-10-16 19:51:59] tail -n +1 /app/public/converted_csv/uganda_sp_list_nodes_17602.csv >> /app/public/diff/uganda_sp_list_nodes_17602.diff
[CMD] [2019-10-16 19:51:59] echo "." >> /app/public/diff/uganda_sp_list_nodes_17602.diff
[CMD] [2019-10-16 19:51:59] echo "0a" > /app/public/diff/uganda_sp_list_occurrences_17603.diff
[CMD] [2019-10-16 19:51:59] tail -n +1 /app/public/converted_csv/uganda_sp_list_occurrences_17603.csv >> /app/public/diff/uganda_sp_list_occurrences_17603.diff
[CMD] [2019-10-16 19:51:59] echo "." >> /app/public/diff/uganda_sp_list_occurrences_17603.diff
[CMD] [2019-10-16 19:51:59] echo "0a" > /app/public/diff/uganda_sp_list_measurements_17604.diff
[CMD] [2019-10-16 19:51:59] tail -n +1 /app/public/converted_csv/uganda_sp_list_measurements_17604.csv >> /app/public/diff/uganda_sp_list_measurements_17604.diff
[CMD] [2019-10-16 19:51:59] echo "." >> /app/public/diff/uganda_sp_list_measurements_17604.diff
[STOP] [2019-10-16 19:52:00] calculate_delta
[START] [2019-10-16 19:52:00] parse_diff_and_store
[INFO] [2019-10-16 19:52:00] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 19:52:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 19:52:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 19:52:04] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 19:52:43] Storing 2 References
[INFO] [2019-10-16 19:52:43] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 19:52:43] Average Time: 0.0
[INFO] [2019-10-16 19:52:43] Total Time: 1s
[INFO] [2019-10-16 19:52:43] Storing 10457 ScientificNames
[INFO] [2019-10-16 19:52:43] Processing group of 10457 in 11 groups of 1000
[INFO] [2019-10-16 19:52:47] Average Time: 0.341
[INFO] [2019-10-16 19:52:47] Total Time: 4s
[INFO] [2019-10-16 19:52:47] last 3 / first 3: 0.82
[INFO] [2019-10-16 19:52:47] Std.Dev: 0.06324555320336758; Max: 0.43
[INFO] [2019-10-16 19:52:47] Storing 10457 Nodes
[INFO] [2019-10-16 19:52:47] Processing group of 10457 in 11 groups of 1000
[INFO] [2019-10-16 19:52:50] Average Time: 0.273
[INFO] [2019-10-16 19:52:50] Total Time: 4s
[INFO] [2019-10-16 19:52:50] last 3 / first 3: 0.87
[INFO] [2019-10-16 19:52:50] Std.Dev: 0.05477225575051661; Max: 0.35
[INFO] [2019-10-16 19:52:50] Storing 6748 Occurrences
[INFO] [2019-10-16 19:52:50] Processing group of 6748 in 7 groups of 1000
[INFO] [2019-10-16 19:52:50] Average Time: 0.097
[INFO] [2019-10-16 19:52:50] Total Time: 1s
[INFO] [2019-10-16 19:52:50] last 3 / first 3: 0.97
[INFO] [2019-10-16 19:52:50] Std.Dev: 0.0; Max: 0.11
[INFO] [2019-10-16 19:52:50] Storing 13920 TraitsReferences
[INFO] [2019-10-16 19:52:50] Processing group of 13920 in 14 groups of 1000
[INFO] [2019-10-16 19:52:51] Average Time: 0.07
[INFO] [2019-10-16 19:52:51] Total Time: 2s
[INFO] [2019-10-16 19:52:51] last 3 / first 3: 0.8
[INFO] [2019-10-16 19:52:51] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-16 19:52:51] Storing 13919 Traits
[INFO] [2019-10-16 19:52:51] Processing group of 13919 in 14 groups of 1000
[INFO] [2019-10-16 19:52:55] Average Time: 0.282
[INFO] [2019-10-16 19:52:55] Total Time: 5s
[INFO] [2019-10-16 19:52:55] last 3 / first 3: 0.86
[INFO] [2019-10-16 19:52:55] Std.Dev: 0.03162277660168379; Max: 0.36
[INFO] [2019-10-16 19:52:55] Storing 13916 MetaTraits
[INFO] [2019-10-16 19:52:55] Processing group of 13916 in 14 groups of 1000
[INFO] [2019-10-16 19:52:57] Average Time: 0.112
[INFO] [2019-10-16 19:52:57] Total Time: 2s
[INFO] [2019-10-16 19:52:57] last 3 / first 3: 0.88
[INFO] [2019-10-16 19:52:57] Std.Dev: 0.03162277660168379; Max: 0.19
[STOP] [2019-10-16 19:52:57] parse_diff_and_store
[START] [2019-10-16 19:52:57] resolve_keys
[INFO] [2019-10-16 19:53:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 19:53:44] traits to occurrences...
[INFO] [2019-10-16 19:53:48] traits to nodes (through occurrences)...
[INFO] [2019-10-16 19:53:49] Traits to sex term...
[INFO] [2019-10-16 19:53:53] Traits to lifestage term...
[INFO] [2019-10-16 19:53:57] MetaTraits to traits...
[INFO] [2019-10-16 19:53:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 19:53:59] Assocs to occurrences...
[INFO] [2019-10-16 19:53:59] Assocs to nodes...
[INFO] [2019-10-16 19:53:59] Assoc to sex term...
[INFO] [2019-10-16 19:53:59] Assoc to lifestage term...
[STOP] [2019-10-16 19:53:59] resolve_keys
[START] [2019-10-16 19:53:59] hold_for_later_1
[STOP] [2019-10-16 19:53:59] hold_for_later_1
[START] [2019-10-16 19:53:59] hold_for_later_2
[STOP] [2019-10-16 19:53:59] hold_for_later_2
[START] [2019-10-16 19:53:59] resolve_missing_parents
[STOP] [2019-10-16 19:54:20] resolve_missing_parents
[START] [2019-10-16 19:54:20] rebuild_nodes
[START] [2019-10-16 19:54:20] Flattener#flatten
[START] [2019-10-16 19:54:20] Flattener#study_resource
[START] [2019-10-16 19:54:20] Flattener#build_ancestry
[STOP] [2019-10-16 19:54:20] Flattener#build_ancestry
[INFO] [2019-10-16 19:54:20] 10457 ancestry keys
[START] [2019-10-16 19:54:20] build_node_ancestors
[INFO] [2019-10-16 19:54:20] old ancestors deleted.
[STOP] [2019-10-16 19:54:23] build_node_ancestors
[START] [2019-10-16 19:54:25] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 19:54:25] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 19:54:25] Flattener#flatten
[STOP] [2019-10-16 19:54:25] rebuild_nodes
[START] [2019-10-16 19:54:25] resolve_missing_media_owners
[STOP] [2019-10-16 19:54:25] resolve_missing_media_owners
[START] [2019-10-16 19:54:25] sanitize_media_verbatims
[STOP] [2019-10-16 19:54:25] sanitize_media_verbatims
[START] [2019-10-16 19:54:25] queue_downloads
[STOP] [2019-10-16 19:54:25] queue_downloads
[START] [2019-10-16 19:54:25] parse_names
[WARN] [2019-10-16 19:54:25] I see 10457 names which still need to be parsed.
[STOP] [2019-10-16 19:54:34] parse_names
[START] [2019-10-16 19:54:34] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 19:54:34] denormalize_canonical_names_to_nodes
[START] [2019-10-16 19:54:34] match_nodes
[START] [2019-10-16 19:54:34] map_all_nodes_to_pages
[STOP] [2019-10-16 20:06:18] map_all_nodes_to_pages
[INFO] [2019-10-16 20:06:18] 655 Unmatched nodes (of 10457)! That's too many to output. First 10: Bleda eximia (#52544752); Bleda syndactyla (#52547548); Andropadus latirostris (#52544740); Andropadus virens (#52544771); Andropadus curvirostris (#52544892); Andropadus gracilirostris (#52546135); Andropadus gracilis (#52546565); Hirundo semirufa (#52546588); Hirundo senegalensis (#52547295); Hirundo abyssinica (#52549515)
[START] [2019-10-16 20:06:18] update_nodes
[STOP] [2019-10-16 20:06:21] update_nodes
[STOP] [2019-10-16 20:06:21] match_nodes
[START] [2019-10-16 20:06:21] reindex_search
[STOP] [2019-10-16 20:06:51] reindex_search
[START] [2019-10-16 20:06:51] normalize_units
[STOP] [2019-10-16 20:06:51] normalize_units
[START] [2019-10-16 20:06:51] calculate_statistics
[STOP] [2019-10-16 20:06:51] calculate_statistics
[START] [2019-10-16 20:06:51] complete_harvest_instance
[START] [2019-10-16 20:06:51] overall_tsv_creation
[INFO] [2019-10-16 20:06:51] Processing group of 10457 in 2 batches of 10000
[INFO] [2019-10-16 20:08:37] 6622 Traits (unfiltered)...
[INFO] [2019-10-16 20:08:50] 6622 Traits (filtered)...
[INFO] [2019-10-16 20:08:50] 0 Associations (filtered)...
[INFO] [2019-10-16 20:09:41] 33107 metadata added.
[INFO] [2019-10-16 20:09:41] 0 metadata added.
[INFO] [2019-10-16 20:10:26] 126 Traits (unfiltered)...
[INFO] [2019-10-16 20:10:39] 126 Traits (filtered)...
[INFO] [2019-10-16 20:10:39] 0 Associations (filtered)...
[INFO] [2019-10-16 20:11:16] 630 metadata added.
[INFO] [2019-10-16 20:11:16] 0 metadata added.
[INFO] [2019-10-16 20:11:16] Average Time: 98.79
[INFO] [2019-10-16 20:11:16] Total Time: 4m26s
[STOP] [2019-10-16 20:11:16] overall_tsv_creation
[INFO] [2019-10-16 20:11:16] Done. Check your files:
[INFO] [2019-10-16 20:11:17] (10457 lines) /app/public/data/uganda_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 20:11:17] (26469 lines) /app/public/data/uganda_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 20:11:17] (10457 lines) /app/public/data/uganda_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 20:11:17] (6749 lines) /app/public/data/uganda_sp_list/publish_traits.tsv
[INFO] [2019-10-16 20:11:17] (33738 lines) /app/public/data/uganda_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 20:11:17] complete_harvest_instance
[START] [2019-10-16 20:11:17] completed
[STOP] [2019-10-16 20:11:17] completed
[STOP] [2019-10-16 20:11:17] logged process, took 1160.37
Latest Process

16 Oct 19:51 EXITED currently processing 0