Harvest for Ethiopia Species List Created 12 Oct 20:18

Stage: completed
Fetched: 12 Oct 20:18
Validated: 12 Oct 20:18
Deltas Created 12 Oct 20:18
Units Normalized: 12 Oct 20:34
Ancestry Built: 12 Oct 20:21
Nodes Matched: 12 Oct 20:33
Names Parsed: 12 Oct 20:21
New Models Stored: 12 Oct 20:20
Indexed: 12 Oct 20:34
Completed: 12 Oct 20:38
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-12 20:18:48 -0400 by logger.rb/56815
[START] [2019-10-12 20:18:48] logged process
[START] [2019-10-12 20:18:48] create_harvest_instance
[STOP] [2019-10-12 20:18:48] create_harvest_instance
[START] [2019-10-12 20:18:49] fetch_files
[STOP] [2019-10-12 20:18:49] fetch_files
[START] [2019-10-12 20:18:49] validate_each_file
[STOP] [2019-10-12 20:18:50] validate_each_file
[START] [2019-10-12 20:18:50] convert_to_csv
[CMD] [2019-10-12 20:18:50] /usr/bin/sort /app/public/converted_csv/ethiopia_sp_list_refs_15723.csv > /app/public/converted_csv/ethiopia_sp_list_refs_15723.csv_sorted
[CMD] [2019-10-12 20:18:50] /usr/bin/sort /app/public/converted_csv/ethiopia_sp_list_nodes_15724.csv > /app/public/converted_csv/ethiopia_sp_list_nodes_15724.csv_sorted
[CMD] [2019-10-12 20:18:50] /usr/bin/sort /app/public/converted_csv/ethiopia_sp_list_occurrences_15725.csv > /app/public/converted_csv/ethiopia_sp_list_occurrences_15725.csv_sorted
[CMD] [2019-10-12 20:18:51] /usr/bin/sort /app/public/converted_csv/ethiopia_sp_list_measurements_15726.csv > /app/public/converted_csv/ethiopia_sp_list_measurements_15726.csv_sorted
[STOP] [2019-10-12 20:18:51] convert_to_csv
[START] [2019-10-12 20:18:51] calculate_delta
[CMD] [2019-10-12 20:18:51] echo "0a" > /app/public/diff/ethiopia_sp_list_refs_15723.diff
[CMD] [2019-10-12 20:18:51] tail -n +1 /app/public/converted_csv/ethiopia_sp_list_refs_15723.csv >> /app/public/diff/ethiopia_sp_list_refs_15723.diff
[CMD] [2019-10-12 20:18:51] echo "." >> /app/public/diff/ethiopia_sp_list_refs_15723.diff
[CMD] [2019-10-12 20:18:51] echo "0a" > /app/public/diff/ethiopia_sp_list_nodes_15724.diff
[CMD] [2019-10-12 20:18:51] tail -n +1 /app/public/converted_csv/ethiopia_sp_list_nodes_15724.csv >> /app/public/diff/ethiopia_sp_list_nodes_15724.diff
[CMD] [2019-10-12 20:18:51] echo "." >> /app/public/diff/ethiopia_sp_list_nodes_15724.diff
[CMD] [2019-10-12 20:18:51] echo "0a" > /app/public/diff/ethiopia_sp_list_occurrences_15725.diff
[CMD] [2019-10-12 20:18:51] tail -n +1 /app/public/converted_csv/ethiopia_sp_list_occurrences_15725.csv >> /app/public/diff/ethiopia_sp_list_occurrences_15725.diff
[CMD] [2019-10-12 20:18:51] echo "." >> /app/public/diff/ethiopia_sp_list_occurrences_15725.diff
[CMD] [2019-10-12 20:18:52] echo "0a" > /app/public/diff/ethiopia_sp_list_measurements_15726.diff
[CMD] [2019-10-12 20:18:52] tail -n +1 /app/public/converted_csv/ethiopia_sp_list_measurements_15726.csv >> /app/public/diff/ethiopia_sp_list_measurements_15726.diff
[CMD] [2019-10-12 20:18:52] echo "." >> /app/public/diff/ethiopia_sp_list_measurements_15726.diff
[STOP] [2019-10-12 20:18:52] calculate_delta
[START] [2019-10-12 20:18:52] parse_diff_and_store
[INFO] [2019-10-12 20:18:52] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 20:18:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 20:18:56] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 20:18:58] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 20:19:46] Storing 2 References
[INFO] [2019-10-12 20:19:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 20:19:46] Average Time: 0.0
[INFO] [2019-10-12 20:19:46] Total Time: 1s
[INFO] [2019-10-12 20:19:46] Storing 11609 ScientificNames
[INFO] [2019-10-12 20:19:46] Processing group of 11609 in 12 groups of 1000
[INFO] [2019-10-12 20:19:50] Average Time: 0.352
[INFO] [2019-10-12 20:19:50] Total Time: 5s
[INFO] [2019-10-12 20:19:50] last 3 / first 3: 0.87
[INFO] [2019-10-12 20:19:50] Std.Dev: 0.05477225575051661; Max: 0.46
[INFO] [2019-10-12 20:19:50] Storing 11609 Nodes
[INFO] [2019-10-12 20:19:50] Processing group of 11609 in 12 groups of 1000
[INFO] [2019-10-12 20:19:54] Average Time: 0.291
[INFO] [2019-10-12 20:19:54] Total Time: 4s
[INFO] [2019-10-12 20:19:54] last 3 / first 3: 1.01
[INFO] [2019-10-12 20:19:54] Std.Dev: 0.044721359549995794; Max: 0.38
[INFO] [2019-10-12 20:19:54] Storing 8194 Occurrences
[INFO] [2019-10-12 20:19:54] Processing group of 8194 in 9 groups of 1000
[INFO] [2019-10-12 20:19:55] Average Time: 0.097
[INFO] [2019-10-12 20:19:55] Total Time: 1s
[INFO] [2019-10-12 20:19:55] last 3 / first 3: 0.65
[INFO] [2019-10-12 20:19:55] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-12 20:19:55] Storing 16420 TraitsReferences
[INFO] [2019-10-12 20:19:55] Processing group of 16420 in 17 groups of 1000
[INFO] [2019-10-12 20:19:56] Average Time: 0.074
[INFO] [2019-10-12 20:19:56] Total Time: 2s
[INFO] [2019-10-12 20:19:56] last 3 / first 3: 0.73
[INFO] [2019-10-12 20:19:56] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-12 20:19:56] Storing 16419 Traits
[INFO] [2019-10-12 20:19:56] Processing group of 16419 in 17 groups of 1000
[INFO] [2019-10-12 20:20:03] Average Time: 0.389
[INFO] [2019-10-12 20:20:03] Total Time: 7s
[INFO] [2019-10-12 20:20:03] last 3 / first 3: 0.46
[INFO] [2019-10-12 20:20:03] Std.Dev: 0.20976176963403032; Max: 0.95
[INFO] [2019-10-12 20:20:03] Storing 16414 MetaTraits
[INFO] [2019-10-12 20:20:03] Processing group of 16414 in 17 groups of 1000
[INFO] [2019-10-12 20:20:05] Average Time: 0.141
[INFO] [2019-10-12 20:20:05] Total Time: 3s
[INFO] [2019-10-12 20:20:05] last 3 / first 3: 0.72
[INFO] [2019-10-12 20:20:05] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-12 20:20:05] parse_diff_and_store
[START] [2019-10-12 20:20:05] resolve_keys
[INFO] [2019-10-12 20:20:53] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 20:20:57] traits to occurrences...
[INFO] [2019-10-12 20:21:03] traits to nodes (through occurrences)...
[INFO] [2019-10-12 20:21:03] Traits to sex term...
[INFO] [2019-10-12 20:21:08] Traits to lifestage term...
[INFO] [2019-10-12 20:21:14] MetaTraits to traits...
[INFO] [2019-10-12 20:21:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 20:21:17] Assocs to occurrences...
[INFO] [2019-10-12 20:21:17] Assocs to nodes...
[INFO] [2019-10-12 20:21:17] Assoc to sex term...
[INFO] [2019-10-12 20:21:17] Assoc to lifestage term...
[STOP] [2019-10-12 20:21:17] resolve_keys
[START] [2019-10-12 20:21:17] hold_for_later_1
[STOP] [2019-10-12 20:21:17] hold_for_later_1
[START] [2019-10-12 20:21:17] hold_for_later_2
[STOP] [2019-10-12 20:21:17] hold_for_later_2
[START] [2019-10-12 20:21:17] resolve_missing_parents
[STOP] [2019-10-12 20:21:40] resolve_missing_parents
[START] [2019-10-12 20:21:40] rebuild_nodes
[START] [2019-10-12 20:21:40] Flattener#flatten
[START] [2019-10-12 20:21:40] Flattener#study_resource
[START] [2019-10-12 20:21:40] Flattener#build_ancestry
[STOP] [2019-10-12 20:21:42] Flattener#build_ancestry
[INFO] [2019-10-12 20:21:42] 11609 ancestry keys
[START] [2019-10-12 20:21:42] build_node_ancestors
[INFO] [2019-10-12 20:21:42] old ancestors deleted.
[STOP] [2019-10-12 20:21:44] build_node_ancestors
[START] [2019-10-12 20:21:46] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:21:47] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 20:21:47] Flattener#flatten
[STOP] [2019-10-12 20:21:47] rebuild_nodes
[START] [2019-10-12 20:21:47] resolve_missing_media_owners
[STOP] [2019-10-12 20:21:47] resolve_missing_media_owners
[START] [2019-10-12 20:21:47] sanitize_media_verbatims
[STOP] [2019-10-12 20:21:47] sanitize_media_verbatims
[START] [2019-10-12 20:21:47] queue_downloads
[STOP] [2019-10-12 20:21:47] queue_downloads
[START] [2019-10-12 20:21:47] parse_names
[WARN] [2019-10-12 20:21:47] I see 11609 names which still need to be parsed.
[STOP] [2019-10-12 20:21:56] parse_names
[START] [2019-10-12 20:21:56] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 20:21:56] denormalize_canonical_names_to_nodes
[START] [2019-10-12 20:21:56] match_nodes
[START] [2019-10-12 20:21:56] map_all_nodes_to_pages
[STOP] [2019-10-12 20:33:31] map_all_nodes_to_pages
[INFO] [2019-10-12 20:33:31] 871 Unmatched nodes (of 11609)! That's too many to output. First 10: Brachiaria semiundulatum (#49635380); Eragrostis poaeoides (#49632849); Sorghum purpureosericea (#49633966); Sorghum purpureosericeus (#49635159); Panicum maximus (#49629450); Melinis roseum (#49629019); Pennisetum ramosum (#49627176); Pennisetum uniseta (#49628772); Pennisetum adoense (#49630244); Pennisetum polystachios (#49630581)
[START] [2019-10-12 20:33:31] update_nodes
[STOP] [2019-10-12 20:33:35] update_nodes
[STOP] [2019-10-12 20:33:35] match_nodes
[START] [2019-10-12 20:33:35] reindex_search
[STOP] [2019-10-12 20:34:08] reindex_search
[START] [2019-10-12 20:34:08] normalize_units
[STOP] [2019-10-12 20:34:08] normalize_units
[START] [2019-10-12 20:34:08] calculate_statistics
[STOP] [2019-10-12 20:34:08] calculate_statistics
[START] [2019-10-12 20:34:08] complete_harvest_instance
[START] [2019-10-12 20:34:08] overall_tsv_creation
[INFO] [2019-10-12 20:34:08] Processing group of 11609 in 2 batches of 10000
[INFO] [2019-10-12 20:35:36] 6961 Traits (unfiltered)...
[INFO] [2019-10-12 20:35:50] 6961 Traits (filtered)...
[INFO] [2019-10-12 20:35:50] 0 Associations (filtered)...
[INFO] [2019-10-12 20:36:46] 34801 metadata added.
[INFO] [2019-10-12 20:36:46] 0 metadata added.
[INFO] [2019-10-12 20:37:38] 1233 Traits (unfiltered)...
[INFO] [2019-10-12 20:37:52] 1233 Traits (filtered)...
[INFO] [2019-10-12 20:37:52] 0 Associations (filtered)...
[INFO] [2019-10-12 20:38:31] 6163 metadata added.
[INFO] [2019-10-12 20:38:31] 0 metadata added.
[INFO] [2019-10-12 20:38:31] Average Time: 107.27
[INFO] [2019-10-12 20:38:31] Total Time: 4m23s
[STOP] [2019-10-12 20:38:31] overall_tsv_creation
[INFO] [2019-10-12 20:38:31] Done. Check your files:
[INFO] [2019-10-12 20:38:31] (11609 lines) /app/public/data/ethiopia_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 20:38:31] (29935 lines) /app/public/data/ethiopia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 20:38:31] (11609 lines) /app/public/data/ethiopia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 20:38:31] (8195 lines) /app/public/data/ethiopia_sp_list/publish_traits.tsv
[INFO] [2019-10-12 20:38:31] (40965 lines) /app/public/data/ethiopia_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 20:38:32] complete_harvest_instance
[START] [2019-10-12 20:38:32] completed
[STOP] [2019-10-12 20:38:32] completed
[STOP] [2019-10-12 20:38:32] logged process, took 1183.56
Latest Process

12 Oct 20:18 EXITED currently processing 0