Harvest for Tuvalu Species List Created 16 Oct 19:14

Stage: completed
Fetched: 16 Oct 19:14
Validated: 16 Oct 19:14
Deltas Created 16 Oct 19:14
Units Normalized: 16 Oct 19:14
Ancestry Built: 16 Oct 19:14
Nodes Matched: 16 Oct 19:14
Names Parsed: 16 Oct 19:14
New Models Stored: 16 Oct 19:14
Indexed: 16 Oct 19:14
Completed: 16 Oct 19:16
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 19:14:32 -0400 by logger.rb/56815
[START] [2019-10-16 19:14:32] logged process
[START] [2019-10-16 19:14:32] create_harvest_instance
[STOP] [2019-10-16 19:14:33] create_harvest_instance
[START] [2019-10-16 19:14:33] fetch_files
[STOP] [2019-10-16 19:14:33] fetch_files
[START] [2019-10-16 19:14:33] validate_each_file
[STOP] [2019-10-16 19:14:33] validate_each_file
[START] [2019-10-16 19:14:33] convert_to_csv
[CMD] [2019-10-16 19:14:33] /usr/bin/sort /app/public/converted_csv/tuvalu_sp_list_refs_17569.csv > /app/public/converted_csv/tuvalu_sp_list_refs_17569.csv_sorted
[CMD] [2019-10-16 19:14:33] /usr/bin/sort /app/public/converted_csv/tuvalu_sp_list_nodes_17570.csv > /app/public/converted_csv/tuvalu_sp_list_nodes_17570.csv_sorted
[CMD] [2019-10-16 19:14:33] /usr/bin/sort /app/public/converted_csv/tuvalu_sp_list_occurrences_17571.csv > /app/public/converted_csv/tuvalu_sp_list_occurrences_17571.csv_sorted
[CMD] [2019-10-16 19:14:33] /usr/bin/sort /app/public/converted_csv/tuvalu_sp_list_measurements_17572.csv > /app/public/converted_csv/tuvalu_sp_list_measurements_17572.csv_sorted
[STOP] [2019-10-16 19:14:33] convert_to_csv
[START] [2019-10-16 19:14:33] calculate_delta
[CMD] [2019-10-16 19:14:33] echo "0a" > /app/public/diff/tuvalu_sp_list_refs_17569.diff
[CMD] [2019-10-16 19:14:33] tail -n +1 /app/public/converted_csv/tuvalu_sp_list_refs_17569.csv >> /app/public/diff/tuvalu_sp_list_refs_17569.diff
[CMD] [2019-10-16 19:14:33] echo "." >> /app/public/diff/tuvalu_sp_list_refs_17569.diff
[CMD] [2019-10-16 19:14:33] echo "0a" > /app/public/diff/tuvalu_sp_list_nodes_17570.diff
[CMD] [2019-10-16 19:14:33] tail -n +1 /app/public/converted_csv/tuvalu_sp_list_nodes_17570.csv >> /app/public/diff/tuvalu_sp_list_nodes_17570.diff
[CMD] [2019-10-16 19:14:33] echo "." >> /app/public/diff/tuvalu_sp_list_nodes_17570.diff
[CMD] [2019-10-16 19:14:33] echo "0a" > /app/public/diff/tuvalu_sp_list_occurrences_17571.diff
[CMD] [2019-10-16 19:14:33] tail -n +1 /app/public/converted_csv/tuvalu_sp_list_occurrences_17571.csv >> /app/public/diff/tuvalu_sp_list_occurrences_17571.diff
[CMD] [2019-10-16 19:14:33] echo "." >> /app/public/diff/tuvalu_sp_list_occurrences_17571.diff
[CMD] [2019-10-16 19:14:34] echo "0a" > /app/public/diff/tuvalu_sp_list_measurements_17572.diff
[CMD] [2019-10-16 19:14:34] tail -n +1 /app/public/converted_csv/tuvalu_sp_list_measurements_17572.csv >> /app/public/diff/tuvalu_sp_list_measurements_17572.diff
[CMD] [2019-10-16 19:14:34] echo "." >> /app/public/diff/tuvalu_sp_list_measurements_17572.diff
[STOP] [2019-10-16 19:14:34] calculate_delta
[START] [2019-10-16 19:14:34] parse_diff_and_store
[INFO] [2019-10-16 19:14:34] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 19:14:34] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 19:14:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 19:14:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 19:14:34] Storing 2 References
[INFO] [2019-10-16 19:14:34] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.0
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[INFO] [2019-10-16 19:14:34] Storing 38 ScientificNames
[INFO] [2019-10-16 19:14:34] Processing group of 38 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.02
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[INFO] [2019-10-16 19:14:34] Storing 38 Nodes
[INFO] [2019-10-16 19:14:34] Processing group of 38 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.02
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[INFO] [2019-10-16 19:14:34] Storing 9 Occurrences
[INFO] [2019-10-16 19:14:34] Processing group of 9 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.0
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[INFO] [2019-10-16 19:14:34] Storing 18 TraitsReferences
[INFO] [2019-10-16 19:14:34] Processing group of 18 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.0
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[INFO] [2019-10-16 19:14:34] Storing 18 Traits
[INFO] [2019-10-16 19:14:34] Processing group of 18 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.01
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[INFO] [2019-10-16 19:14:34] Storing 18 MetaTraits
[INFO] [2019-10-16 19:14:34] Processing group of 18 in 1 groups of 1000
[INFO] [2019-10-16 19:14:34] Average Time: 0.0
[INFO] [2019-10-16 19:14:34] Total Time: 1s
[STOP] [2019-10-16 19:14:34] parse_diff_and_store
[START] [2019-10-16 19:14:34] resolve_keys
[INFO] [2019-10-16 19:14:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 19:14:38] traits to occurrences...
[INFO] [2019-10-16 19:14:38] traits to nodes (through occurrences)...
[INFO] [2019-10-16 19:14:38] Traits to sex term...
[INFO] [2019-10-16 19:14:38] Traits to lifestage term...
[INFO] [2019-10-16 19:14:38] MetaTraits to traits...
[INFO] [2019-10-16 19:14:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 19:14:38] Assocs to occurrences...
[INFO] [2019-10-16 19:14:38] Assocs to nodes...
[INFO] [2019-10-16 19:14:38] Assoc to sex term...
[INFO] [2019-10-16 19:14:38] Assoc to lifestage term...
[STOP] [2019-10-16 19:14:38] resolve_keys
[START] [2019-10-16 19:14:38] hold_for_later_1
[STOP] [2019-10-16 19:14:38] hold_for_later_1
[START] [2019-10-16 19:14:38] hold_for_later_2
[STOP] [2019-10-16 19:14:38] hold_for_later_2
[START] [2019-10-16 19:14:38] resolve_missing_parents
[STOP] [2019-10-16 19:14:38] resolve_missing_parents
[START] [2019-10-16 19:14:38] rebuild_nodes
[START] [2019-10-16 19:14:38] Flattener#flatten
[START] [2019-10-16 19:14:38] Flattener#study_resource
[START] [2019-10-16 19:14:38] Flattener#build_ancestry
[STOP] [2019-10-16 19:14:38] Flattener#build_ancestry
[INFO] [2019-10-16 19:14:38] 38 ancestry keys
[START] [2019-10-16 19:14:38] build_node_ancestors
[INFO] [2019-10-16 19:14:38] old ancestors deleted.
[STOP] [2019-10-16 19:14:38] build_node_ancestors
[START] [2019-10-16 19:14:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 19:14:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 19:14:38] Flattener#flatten
[STOP] [2019-10-16 19:14:38] rebuild_nodes
[START] [2019-10-16 19:14:38] resolve_missing_media_owners
[STOP] [2019-10-16 19:14:38] resolve_missing_media_owners
[START] [2019-10-16 19:14:38] sanitize_media_verbatims
[STOP] [2019-10-16 19:14:38] sanitize_media_verbatims
[START] [2019-10-16 19:14:38] queue_downloads
[STOP] [2019-10-16 19:14:38] queue_downloads
[START] [2019-10-16 19:14:38] parse_names
[WARN] [2019-10-16 19:14:38] I see 38 names which still need to be parsed.
[STOP] [2019-10-16 19:14:39] parse_names
[START] [2019-10-16 19:14:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 19:14:39] denormalize_canonical_names_to_nodes
[START] [2019-10-16 19:14:39] match_nodes
[START] [2019-10-16 19:14:39] map_all_nodes_to_pages
[STOP] [2019-10-16 19:14:44] map_all_nodes_to_pages
[INFO] [2019-10-16 19:14:44] ZERO unmatched nodes (of 38)! Nicely done.
[START] [2019-10-16 19:14:44] update_nodes
[STOP] [2019-10-16 19:14:44] update_nodes
[STOP] [2019-10-16 19:14:44] match_nodes
[START] [2019-10-16 19:14:44] reindex_search
[STOP] [2019-10-16 19:14:44] reindex_search
[START] [2019-10-16 19:14:44] normalize_units
[STOP] [2019-10-16 19:14:44] normalize_units
[START] [2019-10-16 19:14:44] calculate_statistics
[STOP] [2019-10-16 19:14:44] calculate_statistics
[START] [2019-10-16 19:14:44] complete_harvest_instance
[START] [2019-10-16 19:14:44] overall_tsv_creation
[INFO] [2019-10-16 19:14:44] Processing group of 38 in 1 batches of 10000
[INFO] [2019-10-16 19:15:27] 9 Traits (unfiltered)...
[INFO] [2019-10-16 19:15:40] 9 Traits (filtered)...
[INFO] [2019-10-16 19:15:40] 0 Associations (filtered)...
[INFO] [2019-10-16 19:16:17] 45 metadata added.
[INFO] [2019-10-16 19:16:17] 0 metadata added.
[INFO] [2019-10-16 19:16:17] Average Time: 72.07
[INFO] [2019-10-16 19:16:17] Total Time: 1m33s
[STOP] [2019-10-16 19:16:17] overall_tsv_creation
[INFO] [2019-10-16 19:16:17] Done. Check your files:
[INFO] [2019-10-16 19:16:17] (38 lines) /app/public/data/tuvalu_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 19:16:17] (148 lines) /app/public/data/tuvalu_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 19:16:17] (38 lines) /app/public/data/tuvalu_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 19:16:17] (10 lines) /app/public/data/tuvalu_sp_list/publish_traits.tsv
[INFO] [2019-10-16 19:16:17] (46 lines) /app/public/data/tuvalu_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 19:16:17] complete_harvest_instance
[START] [2019-10-16 19:16:17] completed
[STOP] [2019-10-16 19:16:17] completed
[STOP] [2019-10-16 19:16:17] logged process, took 104.81
Latest Process

16 Oct 19:14 EXITED currently processing 0