Harvest for Togo Species List Created 16 Oct 18:08

Stage: completed
Fetched: 16 Oct 18:08
Validated: 16 Oct 18:08
Deltas Created 16 Oct 18:08
Units Normalized: 16 Oct 18:16
Ancestry Built: 16 Oct 18:10
Nodes Matched: 16 Oct 18:16
Names Parsed: 16 Oct 18:10
New Models Stored: 16 Oct 18:09
Indexed: 16 Oct 18:16
Completed: 16 Oct 18:18
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-16 18:08:41 -0400 by logger.rb/56815
[START] [2019-10-16 18:08:41] logged process
[START] [2019-10-16 18:08:41] create_harvest_instance
[STOP] [2019-10-16 18:08:41] create_harvest_instance
[START] [2019-10-16 18:08:41] fetch_files
[STOP] [2019-10-16 18:08:41] fetch_files
[START] [2019-10-16 18:08:41] validate_each_file
[STOP] [2019-10-16 18:08:42] validate_each_file
[START] [2019-10-16 18:08:42] convert_to_csv
[CMD] [2019-10-16 18:08:42] /usr/bin/sort /app/public/converted_csv/togo_sp_list_refs_17513.csv > /app/public/converted_csv/togo_sp_list_refs_17513.csv_sorted
[CMD] [2019-10-16 18:08:42] /usr/bin/sort /app/public/converted_csv/togo_sp_list_nodes_17514.csv > /app/public/converted_csv/togo_sp_list_nodes_17514.csv_sorted
[CMD] [2019-10-16 18:08:42] /usr/bin/sort /app/public/converted_csv/togo_sp_list_occurrences_17515.csv > /app/public/converted_csv/togo_sp_list_occurrences_17515.csv_sorted
[CMD] [2019-10-16 18:08:42] /usr/bin/sort /app/public/converted_csv/togo_sp_list_measurements_17516.csv > /app/public/converted_csv/togo_sp_list_measurements_17516.csv_sorted
[STOP] [2019-10-16 18:08:42] convert_to_csv
[START] [2019-10-16 18:08:42] calculate_delta
[CMD] [2019-10-16 18:08:42] echo "0a" > /app/public/diff/togo_sp_list_refs_17513.diff
[CMD] [2019-10-16 18:08:42] tail -n +1 /app/public/converted_csv/togo_sp_list_refs_17513.csv >> /app/public/diff/togo_sp_list_refs_17513.diff
[CMD] [2019-10-16 18:08:42] echo "." >> /app/public/diff/togo_sp_list_refs_17513.diff
[CMD] [2019-10-16 18:08:42] echo "0a" > /app/public/diff/togo_sp_list_nodes_17514.diff
[CMD] [2019-10-16 18:08:42] tail -n +1 /app/public/converted_csv/togo_sp_list_nodes_17514.csv >> /app/public/diff/togo_sp_list_nodes_17514.diff
[CMD] [2019-10-16 18:08:42] echo "." >> /app/public/diff/togo_sp_list_nodes_17514.diff
[CMD] [2019-10-16 18:08:42] echo "0a" > /app/public/diff/togo_sp_list_occurrences_17515.diff
[CMD] [2019-10-16 18:08:43] tail -n +1 /app/public/converted_csv/togo_sp_list_occurrences_17515.csv >> /app/public/diff/togo_sp_list_occurrences_17515.diff
[CMD] [2019-10-16 18:08:43] echo "." >> /app/public/diff/togo_sp_list_occurrences_17515.diff
[CMD] [2019-10-16 18:08:43] echo "0a" > /app/public/diff/togo_sp_list_measurements_17516.diff
[CMD] [2019-10-16 18:08:43] tail -n +1 /app/public/converted_csv/togo_sp_list_measurements_17516.csv >> /app/public/diff/togo_sp_list_measurements_17516.diff
[CMD] [2019-10-16 18:08:43] echo "." >> /app/public/diff/togo_sp_list_measurements_17516.diff
[STOP] [2019-10-16 18:08:43] calculate_delta
[START] [2019-10-16 18:08:43] parse_diff_and_store
[INFO] [2019-10-16 18:08:43] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 18:08:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 18:08:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 18:08:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 18:09:06] Storing 2 References
[INFO] [2019-10-16 18:09:06] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:09:06] Average Time: 0.0
[INFO] [2019-10-16 18:09:06] Total Time: 1s
[INFO] [2019-10-16 18:09:06] Storing 5645 ScientificNames
[INFO] [2019-10-16 18:09:06] Processing group of 5645 in 6 groups of 1000
[INFO] [2019-10-16 18:09:08] Average Time: 0.322
[INFO] [2019-10-16 18:09:08] Total Time: 2s
[INFO] [2019-10-16 18:09:08] Storing 5645 Nodes
[INFO] [2019-10-16 18:09:08] Processing group of 5645 in 6 groups of 1000
[INFO] [2019-10-16 18:09:10] Average Time: 0.267
[INFO] [2019-10-16 18:09:10] Total Time: 2s
[INFO] [2019-10-16 18:09:10] Storing 3374 Occurrences
[INFO] [2019-10-16 18:09:10] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-16 18:09:10] Average Time: 0.085
[INFO] [2019-10-16 18:09:10] Total Time: 1s
[INFO] [2019-10-16 18:09:10] Storing 7000 TraitsReferences
[INFO] [2019-10-16 18:09:10] Processing group of 7000 in 7 groups of 1000
[INFO] [2019-10-16 18:09:11] Average Time: 0.069
[INFO] [2019-10-16 18:09:11] Total Time: 1s
[INFO] [2019-10-16 18:09:11] last 3 / first 3: 0.75
[INFO] [2019-10-16 18:09:11] Std.Dev: 0.03162277660168379; Max: 0.12
[INFO] [2019-10-16 18:09:11] Storing 6999 Traits
[INFO] [2019-10-16 18:09:11] Processing group of 6999 in 7 groups of 1000
[INFO] [2019-10-16 18:09:13] Average Time: 0.296
[INFO] [2019-10-16 18:09:13] Total Time: 3s
[INFO] [2019-10-16 18:09:13] last 3 / first 3: 0.8
[INFO] [2019-10-16 18:09:13] Std.Dev: 0.05477225575051661; Max: 0.4
[INFO] [2019-10-16 18:09:13] Storing 6996 MetaTraits
[INFO] [2019-10-16 18:09:13] Processing group of 6996 in 7 groups of 1000
[INFO] [2019-10-16 18:09:14] Average Time: 0.107
[INFO] [2019-10-16 18:09:14] Total Time: 1s
[INFO] [2019-10-16 18:09:14] last 3 / first 3: 0.86
[INFO] [2019-10-16 18:09:14] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-10-16 18:09:14] parse_diff_and_store
[START] [2019-10-16 18:09:14] resolve_keys
[INFO] [2019-10-16 18:09:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 18:09:40] traits to occurrences...
[INFO] [2019-10-16 18:09:43] traits to nodes (through occurrences)...
[INFO] [2019-10-16 18:09:44] Traits to sex term...
[INFO] [2019-10-16 18:09:46] Traits to lifestage term...
[INFO] [2019-10-16 18:09:49] MetaTraits to traits...
[INFO] [2019-10-16 18:09:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 18:09:50] Assocs to occurrences...
[INFO] [2019-10-16 18:09:50] Assocs to nodes...
[INFO] [2019-10-16 18:09:50] Assoc to sex term...
[INFO] [2019-10-16 18:09:50] Assoc to lifestage term...
[STOP] [2019-10-16 18:09:50] resolve_keys
[START] [2019-10-16 18:09:50] hold_for_later_1
[STOP] [2019-10-16 18:09:50] hold_for_later_1
[START] [2019-10-16 18:09:50] hold_for_later_2
[STOP] [2019-10-16 18:09:50] hold_for_later_2
[START] [2019-10-16 18:09:50] resolve_missing_parents
[STOP] [2019-10-16 18:10:02] resolve_missing_parents
[START] [2019-10-16 18:10:02] rebuild_nodes
[START] [2019-10-16 18:10:02] Flattener#flatten
[START] [2019-10-16 18:10:02] Flattener#study_resource
[START] [2019-10-16 18:10:02] Flattener#build_ancestry
[STOP] [2019-10-16 18:10:02] Flattener#build_ancestry
[INFO] [2019-10-16 18:10:02] 5645 ancestry keys
[START] [2019-10-16 18:10:02] build_node_ancestors
[INFO] [2019-10-16 18:10:02] old ancestors deleted.
[STOP] [2019-10-16 18:10:03] build_node_ancestors
[START] [2019-10-16 18:10:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:10:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:10:04] Flattener#flatten
[STOP] [2019-10-16 18:10:04] rebuild_nodes
[START] [2019-10-16 18:10:04] resolve_missing_media_owners
[STOP] [2019-10-16 18:10:04] resolve_missing_media_owners
[START] [2019-10-16 18:10:04] sanitize_media_verbatims
[STOP] [2019-10-16 18:10:04] sanitize_media_verbatims
[START] [2019-10-16 18:10:04] queue_downloads
[STOP] [2019-10-16 18:10:04] queue_downloads
[START] [2019-10-16 18:10:04] parse_names
[WARN] [2019-10-16 18:10:04] I see 5645 names which still need to be parsed.
[STOP] [2019-10-16 18:10:10] parse_names
[START] [2019-10-16 18:10:10] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 18:10:10] denormalize_canonical_names_to_nodes
[START] [2019-10-16 18:10:10] match_nodes
[START] [2019-10-16 18:10:10] map_all_nodes_to_pages
[STOP] [2019-10-16 18:16:06] map_all_nodes_to_pages
[INFO] [2019-10-16 18:16:06] 305 Unmatched nodes (of 5645)! That's too many to output. First 10: Pennisetum uniseta (#52495902); Pennisetum polystachios (#52496565); Digitaria leptorrhachis (#52500013); Panicum maximus (#52499180); Chrysopogon nigritana (#52495605); Andropogon fastigiata (#52499451); Setaria pallidifusca (#52499880); Echinochloa colonum (#52497759); Centosteca (#52495777); Centosteca latifolia (#52495776)
[START] [2019-10-16 18:16:06] update_nodes
[STOP] [2019-10-16 18:16:07] update_nodes
[STOP] [2019-10-16 18:16:07] match_nodes
[START] [2019-10-16 18:16:07] reindex_search
[STOP] [2019-10-16 18:16:23] reindex_search
[START] [2019-10-16 18:16:23] normalize_units
[STOP] [2019-10-16 18:16:23] normalize_units
[START] [2019-10-16 18:16:23] calculate_statistics
[STOP] [2019-10-16 18:16:23] calculate_statistics
[START] [2019-10-16 18:16:23] complete_harvest_instance
[START] [2019-10-16 18:16:23] overall_tsv_creation
[INFO] [2019-10-16 18:16:23] Processing group of 5645 in 1 batches of 10000
[INFO] [2019-10-16 18:17:30] 3374 Traits (unfiltered)...
[INFO] [2019-10-16 18:17:43] 3374 Traits (filtered)...
[INFO] [2019-10-16 18:17:44] 0 Associations (filtered)...
[INFO] [2019-10-16 18:18:27] 16866 metadata added.
[INFO] [2019-10-16 18:18:27] 0 metadata added.
[INFO] [2019-10-16 18:18:27] Average Time: 100.17
[INFO] [2019-10-16 18:18:27] Total Time: 2m5s
[STOP] [2019-10-16 18:18:27] overall_tsv_creation
[INFO] [2019-10-16 18:18:27] Done. Check your files:
[INFO] [2019-10-16 18:18:27] (5645 lines) /app/public/data/togo_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 18:18:27] (13894 lines) /app/public/data/togo_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 18:18:27] (5645 lines) /app/public/data/togo_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 18:18:28] (3375 lines) /app/public/data/togo_sp_list/publish_traits.tsv
[INFO] [2019-10-16 18:18:28] (16867 lines) /app/public/data/togo_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 18:18:28] complete_harvest_instance
[START] [2019-10-16 18:18:28] completed
[STOP] [2019-10-16 18:18:28] completed
[STOP] [2019-10-16 18:18:28] logged process, took 587.21
Latest Process

16 Oct 18:08 EXITED currently processing 0