Harvest for Saint Lucia Species List Created 15 Oct 16:21

Stage: completed
Fetched: 15 Oct 16:21
Validated: 15 Oct 16:21
Deltas Created 15 Oct 16:21
Units Normalized: 15 Oct 16:23
Ancestry Built: 15 Oct 16:22
Nodes Matched: 15 Oct 16:23
Names Parsed: 15 Oct 16:22
New Models Stored: 15 Oct 16:22
Indexed: 15 Oct 16:23
Completed: 15 Oct 16:25
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:21:46 -0400 by logger.rb/56815
[START] [2019-10-15 16:21:46] logged process
[START] [2019-10-15 16:21:46] create_harvest_instance
[STOP] [2019-10-15 16:21:47] create_harvest_instance
[START] [2019-10-15 16:21:47] fetch_files
[STOP] [2019-10-15 16:21:47] fetch_files
[START] [2019-10-15 16:21:47] validate_each_file
[STOP] [2019-10-15 16:21:47] validate_each_file
[START] [2019-10-15 16:21:47] convert_to_csv
[CMD] [2019-10-15 16:21:47] /usr/bin/sort /app/public/converted_csv/saint_lucia_sp_l_refs_17045.csv > /app/public/converted_csv/saint_lucia_sp_l_refs_17045.csv_sorted
[CMD] [2019-10-15 16:21:47] /usr/bin/sort /app/public/converted_csv/saint_lucia_sp_l_nodes_17046.csv > /app/public/converted_csv/saint_lucia_sp_l_nodes_17046.csv_sorted
[CMD] [2019-10-15 16:21:48] /usr/bin/sort /app/public/converted_csv/saint_lucia_sp_l_occurrences_17047.csv > /app/public/converted_csv/saint_lucia_sp_l_occurrences_17047.csv_sorted
[CMD] [2019-10-15 16:21:48] /usr/bin/sort /app/public/converted_csv/saint_lucia_sp_l_measurements_17048.csv > /app/public/converted_csv/saint_lucia_sp_l_measurements_17048.csv_sorted
[STOP] [2019-10-15 16:21:48] convert_to_csv
[START] [2019-10-15 16:21:48] calculate_delta
[CMD] [2019-10-15 16:21:48] echo "0a" > /app/public/diff/saint_lucia_sp_l_refs_17045.diff
[CMD] [2019-10-15 16:21:48] tail -n +1 /app/public/converted_csv/saint_lucia_sp_l_refs_17045.csv >> /app/public/diff/saint_lucia_sp_l_refs_17045.diff
[CMD] [2019-10-15 16:21:49] echo "." >> /app/public/diff/saint_lucia_sp_l_refs_17045.diff
[CMD] [2019-10-15 16:21:49] echo "0a" > /app/public/diff/saint_lucia_sp_l_nodes_17046.diff
[CMD] [2019-10-15 16:21:49] tail -n +1 /app/public/converted_csv/saint_lucia_sp_l_nodes_17046.csv >> /app/public/diff/saint_lucia_sp_l_nodes_17046.diff
[CMD] [2019-10-15 16:21:50] echo "." >> /app/public/diff/saint_lucia_sp_l_nodes_17046.diff
[CMD] [2019-10-15 16:21:50] echo "0a" > /app/public/diff/saint_lucia_sp_l_occurrences_17047.diff
[CMD] [2019-10-15 16:21:50] tail -n +1 /app/public/converted_csv/saint_lucia_sp_l_occurrences_17047.csv >> /app/public/diff/saint_lucia_sp_l_occurrences_17047.diff
[CMD] [2019-10-15 16:21:50] echo "." >> /app/public/diff/saint_lucia_sp_l_occurrences_17047.diff
[CMD] [2019-10-15 16:21:51] echo "0a" > /app/public/diff/saint_lucia_sp_l_measurements_17048.diff
[CMD] [2019-10-15 16:21:51] tail -n +1 /app/public/converted_csv/saint_lucia_sp_l_measurements_17048.csv >> /app/public/diff/saint_lucia_sp_l_measurements_17048.diff
[CMD] [2019-10-15 16:21:51] echo "." >> /app/public/diff/saint_lucia_sp_l_measurements_17048.diff
[STOP] [2019-10-15 16:21:52] calculate_delta
[START] [2019-10-15 16:21:52] parse_diff_and_store
[INFO] [2019-10-15 16:21:52] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:21:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:21:53] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:21:53] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:21:57] Storing 2 References
[INFO] [2019-10-15 16:21:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:21:57] Average Time: 0.0
[INFO] [2019-10-15 16:21:57] Total Time: 1s
[INFO] [2019-10-15 16:21:57] Storing 1535 ScientificNames
[INFO] [2019-10-15 16:21:57] Processing group of 1535 in 2 groups of 1000
[INFO] [2019-10-15 16:21:58] Average Time: 0.31
[INFO] [2019-10-15 16:21:58] Total Time: 1s
[INFO] [2019-10-15 16:21:58] Storing 1535 Nodes
[INFO] [2019-10-15 16:21:58] Processing group of 1535 in 2 groups of 1000
[INFO] [2019-10-15 16:21:59] Average Time: 0.24
[INFO] [2019-10-15 16:21:59] Total Time: 1s
[INFO] [2019-10-15 16:21:59] Storing 482 Occurrences
[INFO] [2019-10-15 16:21:59] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-15 16:21:59] Average Time: 0.07
[INFO] [2019-10-15 16:21:59] Total Time: 1s
[INFO] [2019-10-15 16:21:59] Storing 1450 TraitsReferences
[INFO] [2019-10-15 16:21:59] Processing group of 1450 in 2 groups of 1000
[INFO] [2019-10-15 16:21:59] Average Time: 0.08
[INFO] [2019-10-15 16:21:59] Total Time: 1s
[INFO] [2019-10-15 16:21:59] Storing 1449 Traits
[INFO] [2019-10-15 16:21:59] Processing group of 1449 in 2 groups of 1000
[INFO] [2019-10-15 16:21:59] Average Time: 0.275
[INFO] [2019-10-15 16:21:59] Total Time: 1s
[INFO] [2019-10-15 16:21:59] Storing 1450 MetaTraits
[INFO] [2019-10-15 16:21:59] Processing group of 1450 in 2 groups of 1000
[INFO] [2019-10-15 16:22:00] Average Time: 0.1
[INFO] [2019-10-15 16:22:00] Total Time: 1s
[STOP] [2019-10-15 16:22:00] parse_diff_and_store
[START] [2019-10-15 16:22:00] resolve_keys
[INFO] [2019-10-15 16:22:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:22:08] traits to occurrences...
[INFO] [2019-10-15 16:22:09] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:22:09] Traits to sex term...
[INFO] [2019-10-15 16:22:09] Traits to lifestage term...
[INFO] [2019-10-15 16:22:10] MetaTraits to traits...
[INFO] [2019-10-15 16:22:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:22:10] Assocs to occurrences...
[INFO] [2019-10-15 16:22:10] Assocs to nodes...
[INFO] [2019-10-15 16:22:10] Assoc to sex term...
[INFO] [2019-10-15 16:22:10] Assoc to lifestage term...
[STOP] [2019-10-15 16:22:10] resolve_keys
[START] [2019-10-15 16:22:10] hold_for_later_1
[STOP] [2019-10-15 16:22:10] hold_for_later_1
[START] [2019-10-15 16:22:10] hold_for_later_2
[STOP] [2019-10-15 16:22:10] hold_for_later_2
[START] [2019-10-15 16:22:10] resolve_missing_parents
[STOP] [2019-10-15 16:22:12] resolve_missing_parents
[START] [2019-10-15 16:22:12] rebuild_nodes
[START] [2019-10-15 16:22:12] Flattener#flatten
[START] [2019-10-15 16:22:12] Flattener#study_resource
[START] [2019-10-15 16:22:12] Flattener#build_ancestry
[STOP] [2019-10-15 16:22:12] Flattener#build_ancestry
[INFO] [2019-10-15 16:22:12] 1535 ancestry keys
[START] [2019-10-15 16:22:12] build_node_ancestors
[INFO] [2019-10-15 16:22:12] old ancestors deleted.
[STOP] [2019-10-15 16:22:12] build_node_ancestors
[START] [2019-10-15 16:22:12] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:22:12] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:22:12] Flattener#flatten
[STOP] [2019-10-15 16:22:12] rebuild_nodes
[START] [2019-10-15 16:22:12] resolve_missing_media_owners
[STOP] [2019-10-15 16:22:12] resolve_missing_media_owners
[START] [2019-10-15 16:22:12] sanitize_media_verbatims
[STOP] [2019-10-15 16:22:12] sanitize_media_verbatims
[START] [2019-10-15 16:22:12] queue_downloads
[STOP] [2019-10-15 16:22:12] queue_downloads
[START] [2019-10-15 16:22:12] parse_names
[WARN] [2019-10-15 16:22:12] I see 1535 names which still need to be parsed.
[STOP] [2019-10-15 16:22:14] parse_names
[START] [2019-10-15 16:22:14] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:22:14] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:22:14] match_nodes
[START] [2019-10-15 16:22:14] map_all_nodes_to_pages
[STOP] [2019-10-15 16:23:31] map_all_nodes_to_pages
[INFO] [2019-10-15 16:23:31] 58 Unmatched nodes (of 1535)! That's too many to output. First 10: Coerebidae (#51753318); Allenia fuscus (#51754069); Dendroica adelaidae (#51753629); Dendroica striata (#51753926); Dendroica petechia (#51753973); Strumigenys emmae (#51754284); Thalaseus (#51753444); Thalaseus maximus (#51753443); Thalaseus sandvicensis (#51754643); Thalaseus maxima (#51754828)
[START] [2019-10-15 16:23:31] update_nodes
[STOP] [2019-10-15 16:23:32] update_nodes
[STOP] [2019-10-15 16:23:32] match_nodes
[START] [2019-10-15 16:23:32] reindex_search
[STOP] [2019-10-15 16:23:35] reindex_search
[START] [2019-10-15 16:23:35] normalize_units
[STOP] [2019-10-15 16:23:35] normalize_units
[START] [2019-10-15 16:23:35] calculate_statistics
[STOP] [2019-10-15 16:23:35] calculate_statistics
[START] [2019-10-15 16:23:35] complete_harvest_instance
[START] [2019-10-15 16:23:35] overall_tsv_creation
[INFO] [2019-10-15 16:23:35] Processing group of 1535 in 1 batches of 10000
[INFO] [2019-10-15 16:24:26] 482 Traits (unfiltered)...
[INFO] [2019-10-15 16:24:41] 482 Traits (filtered)...
[INFO] [2019-10-15 16:24:41] 0 Associations (filtered)...
[INFO] [2019-10-15 16:25:20] 2410 metadata added.
[INFO] [2019-10-15 16:25:20] 0 metadata added.
[INFO] [2019-10-15 16:25:20] Average Time: 83.52
[INFO] [2019-10-15 16:25:20] Total Time: 1m46s
[STOP] [2019-10-15 16:25:20] overall_tsv_creation
[INFO] [2019-10-15 16:25:20] Done. Check your files:
[INFO] [2019-10-15 16:25:20] (1535 lines) /app/public/data/saint_lucia_sp_l/publish_nodes.tsv
[INFO] [2019-10-15 16:25:21] (1921 lines) /app/public/data/saint_lucia_sp_l/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:25:21] (1535 lines) /app/public/data/saint_lucia_sp_l/publish_scientific_names.tsv
[INFO] [2019-10-15 16:25:21] (483 lines) /app/public/data/saint_lucia_sp_l/publish_traits.tsv
[INFO] [2019-10-15 16:25:21] (2411 lines) /app/public/data/saint_lucia_sp_l/publish_metadata.tsv
[STOP] [2019-10-15 16:25:22] complete_harvest_instance
[START] [2019-10-15 16:25:22] completed
[STOP] [2019-10-15 16:25:22] completed
[STOP] [2019-10-15 16:25:22] logged process, took 215.28
Latest Process

15 Oct 16:21 EXITED currently processing 0