Harvest for Uruguay Species List Created 17 Oct 11:01

Stage: completed
Fetched: 17 Oct 11:01
Validated: 17 Oct 11:01
Deltas Created 17 Oct 11:01
Units Normalized: 17 Oct 11:05
Ancestry Built: 17 Oct 11:02
Nodes Matched: 17 Oct 11:05
Names Parsed: 17 Oct 11:02
New Models Stored: 17 Oct 11:01
Indexed: 17 Oct 11:05
Completed: 17 Oct 11:07
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2019-10-17 11:01:18 -0400 by logger.rb/56815
[START] [2019-10-17 11:01:18] logged process
[START] [2019-10-17 11:01:18] create_harvest_instance
[STOP] [2019-10-17 11:01:18] create_harvest_instance
[START] [2019-10-17 11:01:18] fetch_files
[STOP] [2019-10-17 11:01:18] fetch_files
[START] [2019-10-17 11:01:18] validate_each_file
[STOP] [2019-10-17 11:01:19] validate_each_file
[START] [2019-10-17 11:01:19] convert_to_csv
[CMD] [2019-10-17 11:01:19] /usr/bin/sort /app/public/converted_csv/uruguay_sp_list_refs_17697.csv > /app/public/converted_csv/uruguay_sp_list_refs_17697.csv_sorted
[CMD] [2019-10-17 11:01:19] /usr/bin/sort /app/public/converted_csv/uruguay_sp_list_nodes_17698.csv > /app/public/converted_csv/uruguay_sp_list_nodes_17698.csv_sorted
[CMD] [2019-10-17 11:01:19] /usr/bin/sort /app/public/converted_csv/uruguay_sp_list_occurrences_17699.csv > /app/public/converted_csv/uruguay_sp_list_occurrences_17699.csv_sorted
[CMD] [2019-10-17 11:01:19] /usr/bin/sort /app/public/converted_csv/uruguay_sp_list_measurements_17700.csv > /app/public/converted_csv/uruguay_sp_list_measurements_17700.csv_sorted
[STOP] [2019-10-17 11:01:19] convert_to_csv
[START] [2019-10-17 11:01:19] calculate_delta
[CMD] [2019-10-17 11:01:19] echo "0a" > /app/public/diff/uruguay_sp_list_refs_17697.diff
[CMD] [2019-10-17 11:01:20] tail -n +1 /app/public/converted_csv/uruguay_sp_list_refs_17697.csv >> /app/public/diff/uruguay_sp_list_refs_17697.diff
[CMD] [2019-10-17 11:01:20] echo "." >> /app/public/diff/uruguay_sp_list_refs_17697.diff
[CMD] [2019-10-17 11:01:20] echo "0a" > /app/public/diff/uruguay_sp_list_nodes_17698.diff
[CMD] [2019-10-17 11:01:20] tail -n +1 /app/public/converted_csv/uruguay_sp_list_nodes_17698.csv >> /app/public/diff/uruguay_sp_list_nodes_17698.diff
[CMD] [2019-10-17 11:01:20] echo "." >> /app/public/diff/uruguay_sp_list_nodes_17698.diff
[CMD] [2019-10-17 11:01:20] echo "0a" > /app/public/diff/uruguay_sp_list_occurrences_17699.diff
[CMD] [2019-10-17 11:01:20] tail -n +1 /app/public/converted_csv/uruguay_sp_list_occurrences_17699.csv >> /app/public/diff/uruguay_sp_list_occurrences_17699.diff
[CMD] [2019-10-17 11:01:20] echo "." >> /app/public/diff/uruguay_sp_list_occurrences_17699.diff
[CMD] [2019-10-17 11:01:20] echo "0a" > /app/public/diff/uruguay_sp_list_measurements_17700.diff
[CMD] [2019-10-17 11:01:20] tail -n +1 /app/public/converted_csv/uruguay_sp_list_measurements_17700.csv >> /app/public/diff/uruguay_sp_list_measurements_17700.diff
[CMD] [2019-10-17 11:01:20] echo "." >> /app/public/diff/uruguay_sp_list_measurements_17700.diff
[STOP] [2019-10-17 11:01:21] calculate_delta
[START] [2019-10-17 11:01:21] parse_diff_and_store
[INFO] [2019-10-17 11:01:21] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:01:21] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:01:24] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:01:25] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:01:41] Storing 2 References
[INFO] [2019-10-17 11:01:41] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:01:41] Average Time: 0.0
[INFO] [2019-10-17 11:01:41] Total Time: 1s
[INFO] [2019-10-17 11:01:41] Storing 5264 ScientificNames
[INFO] [2019-10-17 11:01:41] Processing group of 5264 in 6 groups of 1000
[INFO] [2019-10-17 11:01:43] Average Time: 0.293
[INFO] [2019-10-17 11:01:43] Total Time: 2s
[INFO] [2019-10-17 11:01:43] Storing 5264 Nodes
[INFO] [2019-10-17 11:01:43] Processing group of 5264 in 6 groups of 1000
[INFO] [2019-10-17 11:01:45] Average Time: 0.247
[INFO] [2019-10-17 11:01:45] Total Time: 2s
[INFO] [2019-10-17 11:01:45] Storing 2892 Occurrences
[INFO] [2019-10-17 11:01:45] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-17 11:01:45] Average Time: 0.087
[INFO] [2019-10-17 11:01:45] Total Time: 1s
[INFO] [2019-10-17 11:01:45] Storing 6150 TraitsReferences
[INFO] [2019-10-17 11:01:45] Processing group of 6150 in 7 groups of 1000
[INFO] [2019-10-17 11:01:45] Average Time: 0.073
[INFO] [2019-10-17 11:01:45] Total Time: 1s
[INFO] [2019-10-17 11:01:45] last 3 / first 3: 0.73
[INFO] [2019-10-17 11:01:45] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-17 11:01:45] Storing 6149 Traits
[INFO] [2019-10-17 11:01:45] Processing group of 6149 in 7 groups of 1000
[INFO] [2019-10-17 11:01:47] Average Time: 0.246
[INFO] [2019-10-17 11:01:47] Total Time: 2s
[INFO] [2019-10-17 11:01:47] last 3 / first 3: 0.62
[INFO] [2019-10-17 11:01:47] Std.Dev: 0.09486832980505137; Max: 0.35
[INFO] [2019-10-17 11:01:47] Storing 6147 MetaTraits
[INFO] [2019-10-17 11:01:47] Processing group of 6147 in 7 groups of 1000
[INFO] [2019-10-17 11:01:48] Average Time: 0.096
[INFO] [2019-10-17 11:01:48] Total Time: 1s
[INFO] [2019-10-17 11:01:48] last 3 / first 3: 0.63
[INFO] [2019-10-17 11:01:48] Std.Dev: 0.03162277660168379; Max: 0.14
[STOP] [2019-10-17 11:01:48] parse_diff_and_store
[START] [2019-10-17 11:01:48] resolve_keys
[INFO] [2019-10-17 11:02:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:02:13] traits to occurrences...
[INFO] [2019-10-17 11:02:16] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:02:16] Traits to sex term...
[INFO] [2019-10-17 11:02:18] Traits to lifestage term...
[INFO] [2019-10-17 11:02:20] MetaTraits to traits...
[INFO] [2019-10-17 11:02:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:02:22] Assocs to occurrences...
[INFO] [2019-10-17 11:02:22] Assocs to nodes...
[INFO] [2019-10-17 11:02:22] Assoc to sex term...
[INFO] [2019-10-17 11:02:22] Assoc to lifestage term...
[STOP] [2019-10-17 11:02:22] resolve_keys
[START] [2019-10-17 11:02:22] hold_for_later_1
[STOP] [2019-10-17 11:02:22] hold_for_later_1
[START] [2019-10-17 11:02:22] hold_for_later_2
[STOP] [2019-10-17 11:02:22] hold_for_later_2
[START] [2019-10-17 11:02:22] resolve_missing_parents
[STOP] [2019-10-17 11:02:32] resolve_missing_parents
[START] [2019-10-17 11:02:32] rebuild_nodes
[START] [2019-10-17 11:02:32] Flattener#flatten
[START] [2019-10-17 11:02:32] Flattener#study_resource
[START] [2019-10-17 11:02:32] Flattener#build_ancestry
[STOP] [2019-10-17 11:02:32] Flattener#build_ancestry
[INFO] [2019-10-17 11:02:32] 5264 ancestry keys
[START] [2019-10-17 11:02:32] build_node_ancestors
[INFO] [2019-10-17 11:02:32] old ancestors deleted.
[STOP] [2019-10-17 11:02:33] build_node_ancestors
[START] [2019-10-17 11:02:34] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:02:34] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:02:34] Flattener#flatten
[STOP] [2019-10-17 11:02:34] rebuild_nodes
[START] [2019-10-17 11:02:34] resolve_missing_media_owners
[STOP] [2019-10-17 11:02:34] resolve_missing_media_owners
[START] [2019-10-17 11:02:34] sanitize_media_verbatims
[STOP] [2019-10-17 11:02:34] sanitize_media_verbatims
[START] [2019-10-17 11:02:34] queue_downloads
[STOP] [2019-10-17 11:02:34] queue_downloads
[START] [2019-10-17 11:02:34] parse_names
[WARN] [2019-10-17 11:02:34] I see 5264 names which still need to be parsed.
[STOP] [2019-10-17 11:02:39] parse_names
[START] [2019-10-17 11:02:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:02:39] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:02:39] match_nodes
[START] [2019-10-17 11:02:39] map_all_nodes_to_pages
[STOP] [2019-10-17 11:05:26] map_all_nodes_to_pages
[INFO] [2019-10-17 11:05:26] 350 Unmatched nodes (of 5264)! That's too many to output. First 10: Stenella coeruleoalbus (#52710827); Limnornis rectirostris (#52710007); Xolmis dominicanus (#52708279); Xolmis cinerea (#52709770); Machetornis rixosus (#52709675); Hymenops perspicillata (#52709880); Euscarthmus (#52708368); Euscarthmus meloryphus (#52708367); Empidonomus aurantioatrocristatus (#52708563); Attila sulphuratus (#52713070)
[START] [2019-10-17 11:05:26] update_nodes
[STOP] [2019-10-17 11:05:28] update_nodes
[STOP] [2019-10-17 11:05:28] match_nodes
[START] [2019-10-17 11:05:28] reindex_search
[STOP] [2019-10-17 11:05:35] reindex_search
[START] [2019-10-17 11:05:35] normalize_units
[STOP] [2019-10-17 11:05:35] normalize_units
[START] [2019-10-17 11:05:35] calculate_statistics
[STOP] [2019-10-17 11:05:35] calculate_statistics
[START] [2019-10-17 11:05:35] complete_harvest_instance
[START] [2019-10-17 11:05:36] overall_tsv_creation
[INFO] [2019-10-17 11:05:36] Processing group of 5264 in 1 batches of 10000
[INFO] [2019-10-17 11:06:43] 2892 Traits (unfiltered)...
[INFO] [2019-10-17 11:06:56] 2892 Traits (filtered)...
[INFO] [2019-10-17 11:06:56] 0 Associations (filtered)...
[INFO] [2019-10-17 11:07:39] 14457 metadata added.
[INFO] [2019-10-17 11:07:39] 0 metadata added.
[INFO] [2019-10-17 11:07:39] Average Time: 97.47
[INFO] [2019-10-17 11:07:39] Total Time: 2m4s
[STOP] [2019-10-17 11:07:39] overall_tsv_creation
[INFO] [2019-10-17 11:07:39] Done. Check your files:
[INFO] [2019-10-17 11:07:39] (5264 lines) /app/public/data/uruguay_sp_list/publish_nodes.tsv
[INFO] [2019-10-17 11:07:39] (12406 lines) /app/public/data/uruguay_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:07:39] (5264 lines) /app/public/data/uruguay_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-17 11:07:39] (2893 lines) /app/public/data/uruguay_sp_list/publish_traits.tsv
[INFO] [2019-10-17 11:07:40] (14458 lines) /app/public/data/uruguay_sp_list/publish_metadata.tsv
[STOP] [2019-10-17 11:07:40] complete_harvest_instance
[START] [2019-10-17 11:07:40] completed
[STOP] [2019-10-17 11:07:40] completed
[STOP] [2019-10-17 11:07:40] logged process, took 382.03
Latest Process

17 Oct 11:01 EXITED currently processing 0