Harvest for Saint Barthelemy Species List Created 15 Oct 16:10

Stage: completed
Fetched: 15 Oct 16:10
Validated: 15 Oct 16:10
Deltas Created 15 Oct 16:10
Units Normalized: 15 Oct 16:11
Ancestry Built: 15 Oct 16:11
Nodes Matched: 15 Oct 16:11
Names Parsed: 15 Oct 16:11
New Models Stored: 15 Oct 16:11
Indexed: 15 Oct 16:11
Completed: 15 Oct 16:13
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:10:53 -0400 by logger.rb/56815
[START] [2019-10-15 16:10:53] logged process
[START] [2019-10-15 16:10:53] create_harvest_instance
[STOP] [2019-10-15 16:10:54] create_harvest_instance
[START] [2019-10-15 16:10:54] fetch_files
[STOP] [2019-10-15 16:10:54] fetch_files
[START] [2019-10-15 16:10:54] validate_each_file
[STOP] [2019-10-15 16:10:54] validate_each_file
[START] [2019-10-15 16:10:54] convert_to_csv
[CMD] [2019-10-15 16:10:54] /usr/bin/sort /app/public/converted_csv/saint_barthelemy_refs_17021.csv > /app/public/converted_csv/saint_barthelemy_refs_17021.csv_sorted
[CMD] [2019-10-15 16:10:54] /usr/bin/sort /app/public/converted_csv/saint_barthelemy_nodes_17022.csv > /app/public/converted_csv/saint_barthelemy_nodes_17022.csv_sorted
[CMD] [2019-10-15 16:10:55] /usr/bin/sort /app/public/converted_csv/saint_barthelemy_occurrences_17023.csv > /app/public/converted_csv/saint_barthelemy_occurrences_17023.csv_sorted
[CMD] [2019-10-15 16:10:55] /usr/bin/sort /app/public/converted_csv/saint_barthelemy_measurements_17024.csv > /app/public/converted_csv/saint_barthelemy_measurements_17024.csv_sorted
[STOP] [2019-10-15 16:10:55] convert_to_csv
[START] [2019-10-15 16:10:55] calculate_delta
[CMD] [2019-10-15 16:10:55] echo "0a" > /app/public/diff/saint_barthelemy_refs_17021.diff
[CMD] [2019-10-15 16:10:55] tail -n +1 /app/public/converted_csv/saint_barthelemy_refs_17021.csv >> /app/public/diff/saint_barthelemy_refs_17021.diff
[CMD] [2019-10-15 16:10:56] echo "." >> /app/public/diff/saint_barthelemy_refs_17021.diff
[CMD] [2019-10-15 16:10:56] echo "0a" > /app/public/diff/saint_barthelemy_nodes_17022.diff
[CMD] [2019-10-15 16:10:56] tail -n +1 /app/public/converted_csv/saint_barthelemy_nodes_17022.csv >> /app/public/diff/saint_barthelemy_nodes_17022.diff
[CMD] [2019-10-15 16:10:57] echo "." >> /app/public/diff/saint_barthelemy_nodes_17022.diff
[CMD] [2019-10-15 16:10:57] echo "0a" > /app/public/diff/saint_barthelemy_occurrences_17023.diff
[CMD] [2019-10-15 16:10:57] tail -n +1 /app/public/converted_csv/saint_barthelemy_occurrences_17023.csv >> /app/public/diff/saint_barthelemy_occurrences_17023.diff
[CMD] [2019-10-15 16:10:57] echo "." >> /app/public/diff/saint_barthelemy_occurrences_17023.diff
[CMD] [2019-10-15 16:10:58] echo "0a" > /app/public/diff/saint_barthelemy_measurements_17024.diff
[CMD] [2019-10-15 16:10:58] tail -n +1 /app/public/converted_csv/saint_barthelemy_measurements_17024.csv >> /app/public/diff/saint_barthelemy_measurements_17024.diff
[CMD] [2019-10-15 16:10:58] echo "." >> /app/public/diff/saint_barthelemy_measurements_17024.diff
[STOP] [2019-10-15 16:10:59] calculate_delta
[START] [2019-10-15 16:10:59] parse_diff_and_store
[INFO] [2019-10-15 16:10:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:10:59] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:11:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:11:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:11:01] Storing 2 References
[INFO] [2019-10-15 16:11:01] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:11:01] Average Time: 0.0
[INFO] [2019-10-15 16:11:01] Total Time: 1s
[INFO] [2019-10-15 16:11:01] Storing 477 ScientificNames
[INFO] [2019-10-15 16:11:01] Processing group of 477 in 1 groups of 1000
[INFO] [2019-10-15 16:11:01] Average Time: 0.23
[INFO] [2019-10-15 16:11:01] Total Time: 1s
[INFO] [2019-10-15 16:11:01] Storing 477 Nodes
[INFO] [2019-10-15 16:11:01] Processing group of 477 in 1 groups of 1000
[INFO] [2019-10-15 16:11:01] Average Time: 0.18
[INFO] [2019-10-15 16:11:01] Total Time: 1s
[INFO] [2019-10-15 16:11:01] Storing 178 Occurrences
[INFO] [2019-10-15 16:11:01] Processing group of 178 in 1 groups of 1000
[INFO] [2019-10-15 16:11:01] Average Time: 0.04
[INFO] [2019-10-15 16:11:01] Total Time: 1s
[INFO] [2019-10-15 16:11:01] Storing 356 TraitsReferences
[INFO] [2019-10-15 16:11:01] Processing group of 356 in 1 groups of 1000
[INFO] [2019-10-15 16:11:02] Average Time: 0.11
[INFO] [2019-10-15 16:11:02] Total Time: 1s
[INFO] [2019-10-15 16:11:02] Storing 356 Traits
[INFO] [2019-10-15 16:11:02] Processing group of 356 in 1 groups of 1000
[INFO] [2019-10-15 16:11:02] Average Time: 0.2
[INFO] [2019-10-15 16:11:02] Total Time: 1s
[INFO] [2019-10-15 16:11:02] Storing 356 MetaTraits
[INFO] [2019-10-15 16:11:02] Processing group of 356 in 1 groups of 1000
[INFO] [2019-10-15 16:11:02] Average Time: 0.07
[INFO] [2019-10-15 16:11:02] Total Time: 1s
[STOP] [2019-10-15 16:11:02] parse_diff_and_store
[START] [2019-10-15 16:11:02] resolve_keys
[INFO] [2019-10-15 16:11:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:11:07] traits to occurrences...
[INFO] [2019-10-15 16:11:07] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:11:07] Traits to sex term...
[INFO] [2019-10-15 16:11:07] Traits to lifestage term...
[INFO] [2019-10-15 16:11:07] MetaTraits to traits...
[INFO] [2019-10-15 16:11:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:11:07] Assocs to occurrences...
[INFO] [2019-10-15 16:11:07] Assocs to nodes...
[INFO] [2019-10-15 16:11:07] Assoc to sex term...
[INFO] [2019-10-15 16:11:07] Assoc to lifestage term...
[STOP] [2019-10-15 16:11:07] resolve_keys
[START] [2019-10-15 16:11:07] hold_for_later_1
[STOP] [2019-10-15 16:11:07] hold_for_later_1
[START] [2019-10-15 16:11:07] hold_for_later_2
[STOP] [2019-10-15 16:11:07] hold_for_later_2
[START] [2019-10-15 16:11:07] resolve_missing_parents
[STOP] [2019-10-15 16:11:07] resolve_missing_parents
[START] [2019-10-15 16:11:07] rebuild_nodes
[START] [2019-10-15 16:11:07] Flattener#flatten
[START] [2019-10-15 16:11:07] Flattener#study_resource
[START] [2019-10-15 16:11:07] Flattener#build_ancestry
[STOP] [2019-10-15 16:11:07] Flattener#build_ancestry
[INFO] [2019-10-15 16:11:07] 477 ancestry keys
[START] [2019-10-15 16:11:07] build_node_ancestors
[INFO] [2019-10-15 16:11:07] old ancestors deleted.
[STOP] [2019-10-15 16:11:07] build_node_ancestors
[START] [2019-10-15 16:11:08] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:11:08] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:11:08] Flattener#flatten
[STOP] [2019-10-15 16:11:08] rebuild_nodes
[START] [2019-10-15 16:11:08] resolve_missing_media_owners
[STOP] [2019-10-15 16:11:08] resolve_missing_media_owners
[START] [2019-10-15 16:11:08] sanitize_media_verbatims
[STOP] [2019-10-15 16:11:08] sanitize_media_verbatims
[START] [2019-10-15 16:11:08] queue_downloads
[STOP] [2019-10-15 16:11:08] queue_downloads
[START] [2019-10-15 16:11:08] parse_names
[WARN] [2019-10-15 16:11:08] I see 477 names which still need to be parsed.
[STOP] [2019-10-15 16:11:09] parse_names
[START] [2019-10-15 16:11:09] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:11:09] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:11:09] match_nodes
[START] [2019-10-15 16:11:09] map_all_nodes_to_pages
[STOP] [2019-10-15 16:11:47] map_all_nodes_to_pages
[INFO] [2019-10-15 16:11:47] 15 Unmatched nodes (of 477)! That's too many to output. First 10: Coerebidae (#51749715); Thalaseus (#51749777); Thalaseus maximus (#51749776); Limnodromus (#51750121); Fulica caribaea (#51750162); Anas discors (#51749805); Magnoliophyta (#51749824); Magnoliopsida (#51749823); Beloperone (#51749820); Astraea lobatus (#51750001)
[START] [2019-10-15 16:11:47] update_nodes
[STOP] [2019-10-15 16:11:47] update_nodes
[STOP] [2019-10-15 16:11:47] match_nodes
[START] [2019-10-15 16:11:47] reindex_search
[STOP] [2019-10-15 16:11:48] reindex_search
[START] [2019-10-15 16:11:48] normalize_units
[STOP] [2019-10-15 16:11:48] normalize_units
[START] [2019-10-15 16:11:48] calculate_statistics
[STOP] [2019-10-15 16:11:48] calculate_statistics
[START] [2019-10-15 16:11:48] complete_harvest_instance
[START] [2019-10-15 16:11:48] overall_tsv_creation
[INFO] [2019-10-15 16:11:48] Processing group of 477 in 1 batches of 10000
[INFO] [2019-10-15 16:12:35] 178 Traits (unfiltered)...
[INFO] [2019-10-15 16:12:48] 178 Traits (filtered)...
[INFO] [2019-10-15 16:12:48] 0 Associations (filtered)...
[INFO] [2019-10-15 16:13:25] 890 metadata added.
[INFO] [2019-10-15 16:13:25] 0 metadata added.
[INFO] [2019-10-15 16:13:25] Average Time: 75.61
[INFO] [2019-10-15 16:13:25] Total Time: 1m37s
[STOP] [2019-10-15 16:13:25] overall_tsv_creation
[INFO] [2019-10-15 16:13:25] Done. Check your files:
[INFO] [2019-10-15 16:13:25] (477 lines) /app/public/data/saint_barthelemy/publish_nodes.tsv
[INFO] [2019-10-15 16:13:26] (2266 lines) /app/public/data/saint_barthelemy/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:13:26] (477 lines) /app/public/data/saint_barthelemy/publish_scientific_names.tsv
[INFO] [2019-10-15 16:13:26] (179 lines) /app/public/data/saint_barthelemy/publish_traits.tsv
[INFO] [2019-10-15 16:13:26] (891 lines) /app/public/data/saint_barthelemy/publish_metadata.tsv
[STOP] [2019-10-15 16:13:26] complete_harvest_instance
[START] [2019-10-15 16:13:26] completed
[STOP] [2019-10-15 16:13:26] completed
[STOP] [2019-10-15 16:13:26] logged process, took 153.07
Latest Process

15 Oct 16:10 EXITED currently processing 0