Harvest for Bouvet Island Species List Created 11 Oct 16:41

Stage: completed
Fetched: 11 Oct 16:41
Validated: 11 Oct 16:41
Deltas Created 11 Oct 16:41
Units Normalized: 11 Oct 16:42
Ancestry Built: 11 Oct 16:42
Nodes Matched: 11 Oct 16:42
Names Parsed: 11 Oct 16:42
New Models Stored: 11 Oct 16:41
Indexed: 11 Oct 16:42
Completed: 11 Oct 16:43
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-11 16:41:55 -0400 by logger.rb/56815
[START] [2019-10-11 16:41:55] logged process
[START] [2019-10-11 16:41:55] create_harvest_instance
[STOP] [2019-10-11 16:41:55] create_harvest_instance
[START] [2019-10-11 16:41:55] fetch_files
[STOP] [2019-10-11 16:41:55] fetch_files
[START] [2019-10-11 16:41:55] validate_each_file
[STOP] [2019-10-11 16:41:55] validate_each_file
[START] [2019-10-11 16:41:55] convert_to_csv
[CMD] [2019-10-11 16:41:55] /usr/bin/sort /app/public/converted_csv/bouvet_island_sp_refs_15249.csv > /app/public/converted_csv/bouvet_island_sp_refs_15249.csv_sorted
[CMD] [2019-10-11 16:41:55] /usr/bin/sort /app/public/converted_csv/bouvet_island_sp_nodes_15250.csv > /app/public/converted_csv/bouvet_island_sp_nodes_15250.csv_sorted
[CMD] [2019-10-11 16:41:56] /usr/bin/sort /app/public/converted_csv/bouvet_island_sp_occurrences_15251.csv > /app/public/converted_csv/bouvet_island_sp_occurrences_15251.csv_sorted
[CMD] [2019-10-11 16:41:56] /usr/bin/sort /app/public/converted_csv/bouvet_island_sp_measurements_15252.csv > /app/public/converted_csv/bouvet_island_sp_measurements_15252.csv_sorted
[STOP] [2019-10-11 16:41:56] convert_to_csv
[START] [2019-10-11 16:41:56] calculate_delta
[CMD] [2019-10-11 16:41:56] echo "0a" > /app/public/diff/bouvet_island_sp_refs_15249.diff
[CMD] [2019-10-11 16:41:56] tail -n +1 /app/public/converted_csv/bouvet_island_sp_refs_15249.csv >> /app/public/diff/bouvet_island_sp_refs_15249.diff
[CMD] [2019-10-11 16:41:56] echo "." >> /app/public/diff/bouvet_island_sp_refs_15249.diff
[CMD] [2019-10-11 16:41:56] echo "0a" > /app/public/diff/bouvet_island_sp_nodes_15250.diff
[CMD] [2019-10-11 16:41:56] tail -n +1 /app/public/converted_csv/bouvet_island_sp_nodes_15250.csv >> /app/public/diff/bouvet_island_sp_nodes_15250.diff
[CMD] [2019-10-11 16:41:56] echo "." >> /app/public/diff/bouvet_island_sp_nodes_15250.diff
[CMD] [2019-10-11 16:41:56] echo "0a" > /app/public/diff/bouvet_island_sp_occurrences_15251.diff
[CMD] [2019-10-11 16:41:56] tail -n +1 /app/public/converted_csv/bouvet_island_sp_occurrences_15251.csv >> /app/public/diff/bouvet_island_sp_occurrences_15251.diff
[CMD] [2019-10-11 16:41:56] echo "." >> /app/public/diff/bouvet_island_sp_occurrences_15251.diff
[CMD] [2019-10-11 16:41:56] echo "0a" > /app/public/diff/bouvet_island_sp_measurements_15252.diff
[CMD] [2019-10-11 16:41:56] tail -n +1 /app/public/converted_csv/bouvet_island_sp_measurements_15252.csv >> /app/public/diff/bouvet_island_sp_measurements_15252.diff
[CMD] [2019-10-11 16:41:56] echo "." >> /app/public/diff/bouvet_island_sp_measurements_15252.diff
[STOP] [2019-10-11 16:41:56] calculate_delta
[START] [2019-10-11 16:41:56] parse_diff_and_store
[INFO] [2019-10-11 16:41:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 16:41:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 16:41:56] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 16:41:56] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 16:41:57] Storing 2 References
[INFO] [2019-10-11 16:41:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.0
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[INFO] [2019-10-11 16:41:57] Storing 194 ScientificNames
[INFO] [2019-10-11 16:41:57] Processing group of 194 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.15
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[INFO] [2019-10-11 16:41:57] Storing 194 Nodes
[INFO] [2019-10-11 16:41:57] Processing group of 194 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.06
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[INFO] [2019-10-11 16:41:57] Storing 53 Occurrences
[INFO] [2019-10-11 16:41:57] Processing group of 53 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.01
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[INFO] [2019-10-11 16:41:57] Storing 106 TraitsReferences
[INFO] [2019-10-11 16:41:57] Processing group of 106 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.05
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[INFO] [2019-10-11 16:41:57] Storing 106 Traits
[INFO] [2019-10-11 16:41:57] Processing group of 106 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.07
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[INFO] [2019-10-11 16:41:57] Storing 106 MetaTraits
[INFO] [2019-10-11 16:41:57] Processing group of 106 in 1 groups of 1000
[INFO] [2019-10-11 16:41:57] Average Time: 0.03
[INFO] [2019-10-11 16:41:57] Total Time: 1s
[STOP] [2019-10-11 16:41:57] parse_diff_and_store
[START] [2019-10-11 16:41:57] resolve_keys
[INFO] [2019-10-11 16:42:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 16:42:01] traits to occurrences...
[INFO] [2019-10-11 16:42:01] traits to nodes (through occurrences)...
[INFO] [2019-10-11 16:42:01] Traits to sex term...
[INFO] [2019-10-11 16:42:01] Traits to lifestage term...
[INFO] [2019-10-11 16:42:01] MetaTraits to traits...
[INFO] [2019-10-11 16:42:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 16:42:01] Assocs to occurrences...
[INFO] [2019-10-11 16:42:01] Assocs to nodes...
[INFO] [2019-10-11 16:42:01] Assoc to sex term...
[INFO] [2019-10-11 16:42:01] Assoc to lifestage term...
[STOP] [2019-10-11 16:42:01] resolve_keys
[START] [2019-10-11 16:42:01] hold_for_later_1
[STOP] [2019-10-11 16:42:01] hold_for_later_1
[START] [2019-10-11 16:42:01] hold_for_later_2
[STOP] [2019-10-11 16:42:01] hold_for_later_2
[START] [2019-10-11 16:42:01] resolve_missing_parents
[STOP] [2019-10-11 16:42:01] resolve_missing_parents
[START] [2019-10-11 16:42:01] rebuild_nodes
[START] [2019-10-11 16:42:01] Flattener#flatten
[START] [2019-10-11 16:42:01] Flattener#study_resource
[START] [2019-10-11 16:42:01] Flattener#build_ancestry
[STOP] [2019-10-11 16:42:01] Flattener#build_ancestry
[INFO] [2019-10-11 16:42:01] 194 ancestry keys
[START] [2019-10-11 16:42:01] build_node_ancestors
[INFO] [2019-10-11 16:42:01] old ancestors deleted.
[STOP] [2019-10-11 16:42:01] build_node_ancestors
[START] [2019-10-11 16:42:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:42:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:42:01] Flattener#flatten
[STOP] [2019-10-11 16:42:01] rebuild_nodes
[START] [2019-10-11 16:42:01] resolve_missing_media_owners
[STOP] [2019-10-11 16:42:01] resolve_missing_media_owners
[START] [2019-10-11 16:42:01] sanitize_media_verbatims
[STOP] [2019-10-11 16:42:01] sanitize_media_verbatims
[START] [2019-10-11 16:42:01] queue_downloads
[STOP] [2019-10-11 16:42:01] queue_downloads
[START] [2019-10-11 16:42:01] parse_names
[WARN] [2019-10-11 16:42:01] I see 194 names which still need to be parsed.
[STOP] [2019-10-11 16:42:03] parse_names
[START] [2019-10-11 16:42:03] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 16:42:03] denormalize_canonical_names_to_nodes
[START] [2019-10-11 16:42:03] match_nodes
[START] [2019-10-11 16:42:03] map_all_nodes_to_pages
[STOP] [2019-10-11 16:42:12] map_all_nodes_to_pages
[INFO] [2019-10-11 16:42:12] Unmatched nodes (7 of 194): Tortula princeps (#48842686); Chiloscyphus dissitifolia (#48842652); Pygoscelis antarctica (#48842542); Romancheina martiali (#48842665); Semiceidae (#48842639); Carditoida (#48842626); Arcoida (#48842715)
[START] [2019-10-11 16:42:12] update_nodes
[STOP] [2019-10-11 16:42:13] update_nodes
[STOP] [2019-10-11 16:42:13] match_nodes
[START] [2019-10-11 16:42:13] reindex_search
[STOP] [2019-10-11 16:42:13] reindex_search
[START] [2019-10-11 16:42:13] normalize_units
[STOP] [2019-10-11 16:42:13] normalize_units
[START] [2019-10-11 16:42:13] calculate_statistics
[STOP] [2019-10-11 16:42:13] calculate_statistics
[START] [2019-10-11 16:42:13] complete_harvest_instance
[START] [2019-10-11 16:42:13] overall_tsv_creation
[INFO] [2019-10-11 16:42:13] Processing group of 194 in 1 batches of 10000
[INFO] [2019-10-11 16:42:58] 53 Traits (unfiltered)...
[INFO] [2019-10-11 16:43:12] 53 Traits (filtered)...
[INFO] [2019-10-11 16:43:12] 0 Associations (filtered)...
[INFO] [2019-10-11 16:43:49] 265 metadata added.
[INFO] [2019-10-11 16:43:49] 0 metadata added.
[INFO] [2019-10-11 16:43:49] Average Time: 75.21
[INFO] [2019-10-11 16:43:49] Total Time: 1m36s
[STOP] [2019-10-11 16:43:49] overall_tsv_creation
[INFO] [2019-10-11 16:43:49] Done. Check your files:
[INFO] [2019-10-11 16:43:49] (194 lines) /app/public/data/bouvet_island_sp/publish_nodes.tsv
[INFO] [2019-10-11 16:43:49] (808 lines) /app/public/data/bouvet_island_sp/publish_node_ancestors.tsv
[INFO] [2019-10-11 16:43:49] (194 lines) /app/public/data/bouvet_island_sp/publish_scientific_names.tsv
[INFO] [2019-10-11 16:43:49] (54 lines) /app/public/data/bouvet_island_sp/publish_traits.tsv
[INFO] [2019-10-11 16:43:49] (266 lines) /app/public/data/bouvet_island_sp/publish_metadata.tsv
[STOP] [2019-10-11 16:43:49] complete_harvest_instance
[START] [2019-10-11 16:43:49] completed
[STOP] [2019-10-11 16:43:49] completed
[STOP] [2019-10-11 16:43:49] logged process, took 114.2

Latest Process