Harvest for Tokelau Species List Created 16 Oct 18:18

Stage: completed
Fetched: 16 Oct 18:18
Validated: 16 Oct 18:18
Deltas Created 16 Oct 18:18
Units Normalized: 16 Oct 18:18
Ancestry Built: 16 Oct 18:18
Nodes Matched: 16 Oct 18:18
Names Parsed: 16 Oct 18:18
New Models Stored: 16 Oct 18:18
Indexed: 16 Oct 18:18
Completed: 16 Oct 18:20
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 18:18:29 -0400 by logger.rb/56815
[START] [2019-10-16 18:18:29] logged process
[START] [2019-10-16 18:18:29] create_harvest_instance
[STOP] [2019-10-16 18:18:30] create_harvest_instance
[START] [2019-10-16 18:18:30] fetch_files
[STOP] [2019-10-16 18:18:30] fetch_files
[START] [2019-10-16 18:18:30] validate_each_file
[STOP] [2019-10-16 18:18:30] validate_each_file
[START] [2019-10-16 18:18:30] convert_to_csv
[CMD] [2019-10-16 18:18:30] /usr/bin/sort /app/public/converted_csv/tokelau_sp_list_refs_17521.csv > /app/public/converted_csv/tokelau_sp_list_refs_17521.csv_sorted
[CMD] [2019-10-16 18:18:30] /usr/bin/sort /app/public/converted_csv/tokelau_sp_list_nodes_17522.csv > /app/public/converted_csv/tokelau_sp_list_nodes_17522.csv_sorted
[CMD] [2019-10-16 18:18:30] /usr/bin/sort /app/public/converted_csv/tokelau_sp_list_occurrences_17523.csv > /app/public/converted_csv/tokelau_sp_list_occurrences_17523.csv_sorted
[CMD] [2019-10-16 18:18:30] /usr/bin/sort /app/public/converted_csv/tokelau_sp_list_measurements_17524.csv > /app/public/converted_csv/tokelau_sp_list_measurements_17524.csv_sorted
[STOP] [2019-10-16 18:18:30] convert_to_csv
[START] [2019-10-16 18:18:30] calculate_delta
[CMD] [2019-10-16 18:18:30] echo "0a" > /app/public/diff/tokelau_sp_list_refs_17521.diff
[CMD] [2019-10-16 18:18:30] tail -n +1 /app/public/converted_csv/tokelau_sp_list_refs_17521.csv >> /app/public/diff/tokelau_sp_list_refs_17521.diff
[CMD] [2019-10-16 18:18:30] echo "." >> /app/public/diff/tokelau_sp_list_refs_17521.diff
[CMD] [2019-10-16 18:18:30] echo "0a" > /app/public/diff/tokelau_sp_list_nodes_17522.diff
[CMD] [2019-10-16 18:18:30] tail -n +1 /app/public/converted_csv/tokelau_sp_list_nodes_17522.csv >> /app/public/diff/tokelau_sp_list_nodes_17522.diff
[CMD] [2019-10-16 18:18:31] echo "." >> /app/public/diff/tokelau_sp_list_nodes_17522.diff
[CMD] [2019-10-16 18:18:31] echo "0a" > /app/public/diff/tokelau_sp_list_occurrences_17523.diff
[CMD] [2019-10-16 18:18:31] tail -n +1 /app/public/converted_csv/tokelau_sp_list_occurrences_17523.csv >> /app/public/diff/tokelau_sp_list_occurrences_17523.diff
[CMD] [2019-10-16 18:18:31] echo "." >> /app/public/diff/tokelau_sp_list_occurrences_17523.diff
[CMD] [2019-10-16 18:18:31] echo "0a" > /app/public/diff/tokelau_sp_list_measurements_17524.diff
[CMD] [2019-10-16 18:18:31] tail -n +1 /app/public/converted_csv/tokelau_sp_list_measurements_17524.csv >> /app/public/diff/tokelau_sp_list_measurements_17524.diff
[CMD] [2019-10-16 18:18:31] echo "." >> /app/public/diff/tokelau_sp_list_measurements_17524.diff
[STOP] [2019-10-16 18:18:31] calculate_delta
[START] [2019-10-16 18:18:31] parse_diff_and_store
[INFO] [2019-10-16 18:18:31] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 18:18:31] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 18:18:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 18:18:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 18:18:31] Storing 2 References
[INFO] [2019-10-16 18:18:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.0
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[INFO] [2019-10-16 18:18:31] Storing 7 ScientificNames
[INFO] [2019-10-16 18:18:31] Processing group of 7 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.01
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[INFO] [2019-10-16 18:18:31] Storing 7 Nodes
[INFO] [2019-10-16 18:18:31] Processing group of 7 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.0
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[INFO] [2019-10-16 18:18:31] Storing 1 Occurrences
[INFO] [2019-10-16 18:18:31] Processing group of 1 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.0
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[INFO] [2019-10-16 18:18:31] Storing 2 TraitsReferences
[INFO] [2019-10-16 18:18:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.0
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[INFO] [2019-10-16 18:18:31] Storing 2 Traits
[INFO] [2019-10-16 18:18:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.0
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[INFO] [2019-10-16 18:18:31] Storing 2 MetaTraits
[INFO] [2019-10-16 18:18:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:18:31] Average Time: 0.0
[INFO] [2019-10-16 18:18:31] Total Time: 1s
[STOP] [2019-10-16 18:18:31] parse_diff_and_store
[START] [2019-10-16 18:18:31] resolve_keys
[INFO] [2019-10-16 18:18:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 18:18:35] traits to occurrences...
[INFO] [2019-10-16 18:18:35] traits to nodes (through occurrences)...
[INFO] [2019-10-16 18:18:35] Traits to sex term...
[INFO] [2019-10-16 18:18:35] Traits to lifestage term...
[INFO] [2019-10-16 18:18:35] MetaTraits to traits...
[INFO] [2019-10-16 18:18:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 18:18:35] Assocs to occurrences...
[INFO] [2019-10-16 18:18:35] Assocs to nodes...
[INFO] [2019-10-16 18:18:35] Assoc to sex term...
[INFO] [2019-10-16 18:18:35] Assoc to lifestage term...
[STOP] [2019-10-16 18:18:35] resolve_keys
[START] [2019-10-16 18:18:35] hold_for_later_1
[STOP] [2019-10-16 18:18:35] hold_for_later_1
[START] [2019-10-16 18:18:35] hold_for_later_2
[STOP] [2019-10-16 18:18:35] hold_for_later_2
[START] [2019-10-16 18:18:35] resolve_missing_parents
[STOP] [2019-10-16 18:18:35] resolve_missing_parents
[START] [2019-10-16 18:18:35] rebuild_nodes
[START] [2019-10-16 18:18:35] Flattener#flatten
[START] [2019-10-16 18:18:35] Flattener#study_resource
[START] [2019-10-16 18:18:35] Flattener#build_ancestry
[STOP] [2019-10-16 18:18:35] Flattener#build_ancestry
[INFO] [2019-10-16 18:18:35] 7 ancestry keys
[START] [2019-10-16 18:18:35] build_node_ancestors
[INFO] [2019-10-16 18:18:35] old ancestors deleted.
[STOP] [2019-10-16 18:18:35] build_node_ancestors
[START] [2019-10-16 18:18:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:18:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:18:35] Flattener#flatten
[STOP] [2019-10-16 18:18:35] rebuild_nodes
[START] [2019-10-16 18:18:35] resolve_missing_media_owners
[STOP] [2019-10-16 18:18:35] resolve_missing_media_owners
[START] [2019-10-16 18:18:35] sanitize_media_verbatims
[STOP] [2019-10-16 18:18:35] sanitize_media_verbatims
[START] [2019-10-16 18:18:35] queue_downloads
[STOP] [2019-10-16 18:18:35] queue_downloads
[START] [2019-10-16 18:18:35] parse_names
[WARN] [2019-10-16 18:18:35] I see 7 names which still need to be parsed.
[STOP] [2019-10-16 18:18:36] parse_names
[START] [2019-10-16 18:18:36] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 18:18:36] denormalize_canonical_names_to_nodes
[START] [2019-10-16 18:18:36] match_nodes
[START] [2019-10-16 18:18:36] map_all_nodes_to_pages
[STOP] [2019-10-16 18:18:37] map_all_nodes_to_pages
[INFO] [2019-10-16 18:18:37] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2019-10-16 18:18:37] update_nodes
[STOP] [2019-10-16 18:18:37] update_nodes
[STOP] [2019-10-16 18:18:37] match_nodes
[START] [2019-10-16 18:18:37] reindex_search
[STOP] [2019-10-16 18:18:37] reindex_search
[START] [2019-10-16 18:18:37] normalize_units
[STOP] [2019-10-16 18:18:37] normalize_units
[START] [2019-10-16 18:18:37] calculate_statistics
[STOP] [2019-10-16 18:18:37] calculate_statistics
[START] [2019-10-16 18:18:37] complete_harvest_instance
[START] [2019-10-16 18:18:37] overall_tsv_creation
[INFO] [2019-10-16 18:18:37] Processing group of 7 in 1 batches of 10000
[INFO] [2019-10-16 18:19:18] 1 Traits (unfiltered)...
[INFO] [2019-10-16 18:19:31] 1 Traits (filtered)...
[INFO] [2019-10-16 18:19:31] 0 Associations (filtered)...
[INFO] [2019-10-16 18:20:08] 5 metadata added.
[INFO] [2019-10-16 18:20:08] 0 metadata added.
[INFO] [2019-10-16 18:20:08] Average Time: 71.5
[INFO] [2019-10-16 18:20:08] Total Time: 1m32s
[STOP] [2019-10-16 18:20:08] overall_tsv_creation
[INFO] [2019-10-16 18:20:09] Done. Check your files:
[INFO] [2019-10-16 18:20:09] (7 lines) /app/public/data/tokelau_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 18:20:09] (21 lines) /app/public/data/tokelau_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 18:20:09] (7 lines) /app/public/data/tokelau_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 18:20:09] (2 lines) /app/public/data/tokelau_sp_list/publish_traits.tsv
[INFO] [2019-10-16 18:20:09] (6 lines) /app/public/data/tokelau_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 18:20:09] complete_harvest_instance
[START] [2019-10-16 18:20:09] completed
[STOP] [2019-10-16 18:20:09] completed
[STOP] [2019-10-16 18:20:09] logged process, took 99.34
Latest Process

16 Oct 18:18 EXITED currently processing 0