Harvest for British Virgin Islands Species List Created 12 Oct 18:29

Stage: completed
Fetched: 12 Oct 18:29
Validated: 12 Oct 18:29
Deltas Created 12 Oct 18:29
Units Normalized: 12 Oct 18:30
Ancestry Built: 12 Oct 18:30
Nodes Matched: 12 Oct 18:30
Names Parsed: 12 Oct 18:30
New Models Stored: 12 Oct 18:30
Indexed: 12 Oct 18:30
Completed: 12 Oct 18:32
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-12 18:29:56 -0400 by logger.rb/56815
[START] [2019-10-12 18:29:56] logged process
[START] [2019-10-12 18:29:56] create_harvest_instance
[STOP] [2019-10-12 18:29:57] create_harvest_instance
[START] [2019-10-12 18:29:57] fetch_files
[STOP] [2019-10-12 18:29:57] fetch_files
[START] [2019-10-12 18:29:57] validate_each_file
[STOP] [2019-10-12 18:29:57] validate_each_file
[START] [2019-10-12 18:29:57] convert_to_csv
[CMD] [2019-10-12 18:29:57] /usr/bin/sort /app/public/converted_csv/bvisl_refs_15691.csv > /app/public/converted_csv/bvisl_refs_15691.csv_sorted
[CMD] [2019-10-12 18:29:57] /usr/bin/sort /app/public/converted_csv/bvisl_nodes_15692.csv > /app/public/converted_csv/bvisl_nodes_15692.csv_sorted
[CMD] [2019-10-12 18:29:57] /usr/bin/sort /app/public/converted_csv/bvisl_occurrences_15693.csv > /app/public/converted_csv/bvisl_occurrences_15693.csv_sorted
[CMD] [2019-10-12 18:29:57] /usr/bin/sort /app/public/converted_csv/bvisl_measurements_15694.csv > /app/public/converted_csv/bvisl_measurements_15694.csv_sorted
[STOP] [2019-10-12 18:29:57] convert_to_csv
[START] [2019-10-12 18:29:57] calculate_delta
[CMD] [2019-10-12 18:29:57] echo "0a" > /app/public/diff/bvisl_refs_15691.diff
[CMD] [2019-10-12 18:29:57] tail -n +1 /app/public/converted_csv/bvisl_refs_15691.csv >> /app/public/diff/bvisl_refs_15691.diff
[CMD] [2019-10-12 18:29:58] echo "." >> /app/public/diff/bvisl_refs_15691.diff
[CMD] [2019-10-12 18:29:58] echo "0a" > /app/public/diff/bvisl_nodes_15692.diff
[CMD] [2019-10-12 18:29:58] tail -n +1 /app/public/converted_csv/bvisl_nodes_15692.csv >> /app/public/diff/bvisl_nodes_15692.diff
[CMD] [2019-10-12 18:29:58] echo "." >> /app/public/diff/bvisl_nodes_15692.diff
[CMD] [2019-10-12 18:29:58] echo "0a" > /app/public/diff/bvisl_occurrences_15693.diff
[CMD] [2019-10-12 18:29:58] tail -n +1 /app/public/converted_csv/bvisl_occurrences_15693.csv >> /app/public/diff/bvisl_occurrences_15693.diff
[CMD] [2019-10-12 18:29:58] echo "." >> /app/public/diff/bvisl_occurrences_15693.diff
[CMD] [2019-10-12 18:29:58] echo "0a" > /app/public/diff/bvisl_measurements_15694.diff
[CMD] [2019-10-12 18:29:58] tail -n +1 /app/public/converted_csv/bvisl_measurements_15694.csv >> /app/public/diff/bvisl_measurements_15694.diff
[CMD] [2019-10-12 18:29:58] echo "." >> /app/public/diff/bvisl_measurements_15694.diff
[STOP] [2019-10-12 18:29:58] calculate_delta
[START] [2019-10-12 18:29:58] parse_diff_and_store
[INFO] [2019-10-12 18:29:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 18:29:59] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 18:29:59] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 18:29:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 18:29:59] Storing 2 References
[INFO] [2019-10-12 18:29:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 18:29:59] Average Time: 0.0
[INFO] [2019-10-12 18:29:59] Total Time: 1s
[INFO] [2019-10-12 18:29:59] Storing 203 ScientificNames
[INFO] [2019-10-12 18:29:59] Processing group of 203 in 1 groups of 1000
[INFO] [2019-10-12 18:30:00] Average Time: 0.17
[INFO] [2019-10-12 18:30:00] Total Time: 1s
[INFO] [2019-10-12 18:30:00] Storing 203 Nodes
[INFO] [2019-10-12 18:30:00] Processing group of 203 in 1 groups of 1000
[INFO] [2019-10-12 18:30:00] Average Time: 0.08
[INFO] [2019-10-12 18:30:00] Total Time: 1s
[INFO] [2019-10-12 18:30:00] Storing 73 Occurrences
[INFO] [2019-10-12 18:30:00] Processing group of 73 in 1 groups of 1000
[INFO] [2019-10-12 18:30:00] Average Time: 0.02
[INFO] [2019-10-12 18:30:00] Total Time: 1s
[INFO] [2019-10-12 18:30:00] Storing 146 TraitsReferences
[INFO] [2019-10-12 18:30:00] Processing group of 146 in 1 groups of 1000
[INFO] [2019-10-12 18:30:00] Average Time: 0.06
[INFO] [2019-10-12 18:30:00] Total Time: 1s
[INFO] [2019-10-12 18:30:00] Storing 146 Traits
[INFO] [2019-10-12 18:30:00] Processing group of 146 in 1 groups of 1000
[INFO] [2019-10-12 18:30:00] Average Time: 0.12
[INFO] [2019-10-12 18:30:00] Total Time: 1s
[INFO] [2019-10-12 18:30:00] Storing 146 MetaTraits
[INFO] [2019-10-12 18:30:00] Processing group of 146 in 1 groups of 1000
[INFO] [2019-10-12 18:30:00] Average Time: 0.03
[INFO] [2019-10-12 18:30:00] Total Time: 1s
[STOP] [2019-10-12 18:30:00] parse_diff_and_store
[START] [2019-10-12 18:30:00] resolve_keys
[INFO] [2019-10-12 18:30:04] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 18:30:04] traits to occurrences...
[INFO] [2019-10-12 18:30:04] traits to nodes (through occurrences)...
[INFO] [2019-10-12 18:30:04] Traits to sex term...
[INFO] [2019-10-12 18:30:04] Traits to lifestage term...
[INFO] [2019-10-12 18:30:04] MetaTraits to traits...
[INFO] [2019-10-12 18:30:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 18:30:04] Assocs to occurrences...
[INFO] [2019-10-12 18:30:04] Assocs to nodes...
[INFO] [2019-10-12 18:30:04] Assoc to sex term...
[INFO] [2019-10-12 18:30:04] Assoc to lifestage term...
[STOP] [2019-10-12 18:30:04] resolve_keys
[START] [2019-10-12 18:30:04] hold_for_later_1
[STOP] [2019-10-12 18:30:04] hold_for_later_1
[START] [2019-10-12 18:30:04] hold_for_later_2
[STOP] [2019-10-12 18:30:04] hold_for_later_2
[START] [2019-10-12 18:30:04] resolve_missing_parents
[STOP] [2019-10-12 18:30:04] resolve_missing_parents
[START] [2019-10-12 18:30:04] rebuild_nodes
[START] [2019-10-12 18:30:04] Flattener#flatten
[START] [2019-10-12 18:30:04] Flattener#study_resource
[START] [2019-10-12 18:30:04] Flattener#build_ancestry
[STOP] [2019-10-12 18:30:04] Flattener#build_ancestry
[INFO] [2019-10-12 18:30:04] 203 ancestry keys
[START] [2019-10-12 18:30:04] build_node_ancestors
[INFO] [2019-10-12 18:30:04] old ancestors deleted.
[STOP] [2019-10-12 18:30:04] build_node_ancestors
[START] [2019-10-12 18:30:05] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 18:30:05] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 18:30:05] Flattener#flatten
[STOP] [2019-10-12 18:30:05] rebuild_nodes
[START] [2019-10-12 18:30:05] resolve_missing_media_owners
[STOP] [2019-10-12 18:30:05] resolve_missing_media_owners
[START] [2019-10-12 18:30:05] sanitize_media_verbatims
[STOP] [2019-10-12 18:30:05] sanitize_media_verbatims
[START] [2019-10-12 18:30:05] queue_downloads
[STOP] [2019-10-12 18:30:05] queue_downloads
[START] [2019-10-12 18:30:05] parse_names
[WARN] [2019-10-12 18:30:05] I see 203 names which still need to be parsed.
[STOP] [2019-10-12 18:30:06] parse_names
[START] [2019-10-12 18:30:06] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 18:30:06] denormalize_canonical_names_to_nodes
[START] [2019-10-12 18:30:06] match_nodes
[START] [2019-10-12 18:30:06] map_all_nodes_to_pages
[STOP] [2019-10-12 18:30:30] map_all_nodes_to_pages
[INFO] [2019-10-12 18:30:30] Unmatched nodes (9 of 203): Coerebidae (#49577514); Thalaseus (#49577591); Thalaseus maximus (#49577590); Thalaseus sandvicensis (#49577692); Anas americana (#49577613); Anas discors (#49577679); Teuthida (#49577666); Magnoliophyta (#49577620); Magnoliopsida (#49577619)
[START] [2019-10-12 18:30:30] update_nodes
[STOP] [2019-10-12 18:30:30] update_nodes
[STOP] [2019-10-12 18:30:30] match_nodes
[START] [2019-10-12 18:30:30] reindex_search
[STOP] [2019-10-12 18:30:30] reindex_search
[START] [2019-10-12 18:30:30] normalize_units
[STOP] [2019-10-12 18:30:30] normalize_units
[START] [2019-10-12 18:30:30] calculate_statistics
[STOP] [2019-10-12 18:30:30] calculate_statistics
[START] [2019-10-12 18:30:30] complete_harvest_instance
[START] [2019-10-12 18:30:30] overall_tsv_creation
[INFO] [2019-10-12 18:30:30] Processing group of 203 in 1 batches of 10000
[INFO] [2019-10-12 18:31:15] 73 Traits (unfiltered)...
[INFO] [2019-10-12 18:31:29] 73 Traits (filtered)...
[INFO] [2019-10-12 18:31:29] 0 Associations (filtered)...
[INFO] [2019-10-12 18:32:07] 365 metadata added.
[INFO] [2019-10-12 18:32:07] 0 metadata added.
[INFO] [2019-10-12 18:32:07] Average Time: 76.36
[INFO] [2019-10-12 18:32:07] Total Time: 1m38s
[STOP] [2019-10-12 18:32:07] overall_tsv_creation
[INFO] [2019-10-12 18:32:07] Done. Check your files:
[INFO] [2019-10-12 18:32:08] (203 lines) /app/public/data/bvisl/publish_nodes.tsv
[INFO] [2019-10-12 18:32:09] (921 lines) /app/public/data/bvisl/publish_node_ancestors.tsv
[INFO] [2019-10-12 18:32:10] (203 lines) /app/public/data/bvisl/publish_scientific_names.tsv
[INFO] [2019-10-12 18:32:11] (74 lines) /app/public/data/bvisl/publish_traits.tsv
[INFO] [2019-10-12 18:32:11] (366 lines) /app/public/data/bvisl/publish_metadata.tsv
[STOP] [2019-10-12 18:32:11] complete_harvest_instance
[START] [2019-10-12 18:32:11] completed
[STOP] [2019-10-12 18:32:11] completed
[STOP] [2019-10-12 18:32:11] logged process, took 134.68

Latest Process