Harvest for Bonaire Saint Eustatius and Saba Species List Created 11 Oct 16:27

Stage: completed
Fetched: 11 Oct 16:27
Validated: 11 Oct 16:27
Deltas Created 11 Oct 16:27
Units Normalized: 11 Oct 16:28
Ancestry Built: 11 Oct 16:27
Nodes Matched: 11 Oct 16:28
Names Parsed: 11 Oct 16:27
New Models Stored: 11 Oct 16:27
Indexed: 11 Oct 16:28
Completed: 11 Oct 16:30
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-11 16:27:10 -0400 by logger.rb/56815
[START] [2019-10-11 16:27:10] logged process
[START] [2019-10-11 16:27:10] create_harvest_instance
[STOP] [2019-10-11 16:27:11] create_harvest_instance
[START] [2019-10-11 16:27:11] fetch_files
[STOP] [2019-10-11 16:27:11] fetch_files
[START] [2019-10-11 16:27:11] validate_each_file
[STOP] [2019-10-11 16:27:11] validate_each_file
[START] [2019-10-11 16:27:11] convert_to_csv
[CMD] [2019-10-11 16:27:11] /usr/bin/sort /app/public/converted_csv/bsessl_refs_15220.csv > /app/public/converted_csv/bsessl_refs_15220.csv_sorted
[CMD] [2019-10-11 16:27:11] /usr/bin/sort /app/public/converted_csv/bsessl_nodes_15221.csv > /app/public/converted_csv/bsessl_nodes_15221.csv_sorted
[CMD] [2019-10-11 16:27:11] /usr/bin/sort /app/public/converted_csv/bsessl_occurrences_15222.csv > /app/public/converted_csv/bsessl_occurrences_15222.csv_sorted
[CMD] [2019-10-11 16:27:11] /usr/bin/sort /app/public/converted_csv/bsessl_measurements_15223.csv > /app/public/converted_csv/bsessl_measurements_15223.csv_sorted
[STOP] [2019-10-11 16:27:11] convert_to_csv
[START] [2019-10-11 16:27:11] calculate_delta
[CMD] [2019-10-11 16:27:11] echo "0a" > /app/public/diff/bsessl_refs_15220.diff
[CMD] [2019-10-11 16:27:11] tail -n +1 /app/public/converted_csv/bsessl_refs_15220.csv >> /app/public/diff/bsessl_refs_15220.diff
[CMD] [2019-10-11 16:27:11] echo "." >> /app/public/diff/bsessl_refs_15220.diff
[CMD] [2019-10-11 16:27:11] echo "0a" > /app/public/diff/bsessl_nodes_15221.diff
[CMD] [2019-10-11 16:27:11] tail -n +1 /app/public/converted_csv/bsessl_nodes_15221.csv >> /app/public/diff/bsessl_nodes_15221.diff
[CMD] [2019-10-11 16:27:11] echo "." >> /app/public/diff/bsessl_nodes_15221.diff
[CMD] [2019-10-11 16:27:11] echo "0a" > /app/public/diff/bsessl_occurrences_15222.diff
[CMD] [2019-10-11 16:27:11] tail -n +1 /app/public/converted_csv/bsessl_occurrences_15222.csv >> /app/public/diff/bsessl_occurrences_15222.diff
[CMD] [2019-10-11 16:27:11] echo "." >> /app/public/diff/bsessl_occurrences_15222.diff
[CMD] [2019-10-11 16:27:11] echo "0a" > /app/public/diff/bsessl_measurements_15223.diff
[CMD] [2019-10-11 16:27:11] tail -n +1 /app/public/converted_csv/bsessl_measurements_15223.csv >> /app/public/diff/bsessl_measurements_15223.diff
[CMD] [2019-10-11 16:27:12] echo "." >> /app/public/diff/bsessl_measurements_15223.diff
[STOP] [2019-10-11 16:27:12] calculate_delta
[START] [2019-10-11 16:27:12] parse_diff_and_store
[INFO] [2019-10-11 16:27:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 16:27:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 16:27:13] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 16:27:13] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 16:27:19] Storing 2 References
[INFO] [2019-10-11 16:27:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 16:27:19] Average Time: 0.14
[INFO] [2019-10-11 16:27:19] Total Time: 1s
[INFO] [2019-10-11 16:27:19] Storing 2179 ScientificNames
[INFO] [2019-10-11 16:27:19] Processing group of 2179 in 3 groups of 1000
[INFO] [2019-10-11 16:27:20] Average Time: 0.397
[INFO] [2019-10-11 16:27:20] Total Time: 2s
[INFO] [2019-10-11 16:27:20] Storing 2179 Nodes
[INFO] [2019-10-11 16:27:20] Processing group of 2179 in 3 groups of 1000
[INFO] [2019-10-11 16:27:21] Average Time: 0.22
[INFO] [2019-10-11 16:27:21] Total Time: 1s
[INFO] [2019-10-11 16:27:21] Storing 964 Occurrences
[INFO] [2019-10-11 16:27:21] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-11 16:27:21] Average Time: 0.12
[INFO] [2019-10-11 16:27:21] Total Time: 1s
[INFO] [2019-10-11 16:27:21] Storing 2140 TraitsReferences
[INFO] [2019-10-11 16:27:21] Processing group of 2140 in 3 groups of 1000
[INFO] [2019-10-11 16:27:21] Average Time: 0.077
[INFO] [2019-10-11 16:27:21] Total Time: 1s
[INFO] [2019-10-11 16:27:21] Storing 2139 Traits
[INFO] [2019-10-11 16:27:21] Processing group of 2139 in 3 groups of 1000
[INFO] [2019-10-11 16:27:22] Average Time: 0.217
[INFO] [2019-10-11 16:27:22] Total Time: 1s
[INFO] [2019-10-11 16:27:22] Storing 2140 MetaTraits
[INFO] [2019-10-11 16:27:22] Processing group of 2140 in 3 groups of 1000
[INFO] [2019-10-11 16:27:22] Average Time: 0.087
[INFO] [2019-10-11 16:27:22] Total Time: 1s
[STOP] [2019-10-11 16:27:22] parse_diff_and_store
[START] [2019-10-11 16:27:22] resolve_keys
[INFO] [2019-10-11 16:27:33] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 16:27:34] traits to occurrences...
[INFO] [2019-10-11 16:27:35] traits to nodes (through occurrences)...
[INFO] [2019-10-11 16:27:35] Traits to sex term...
[INFO] [2019-10-11 16:27:36] Traits to lifestage term...
[INFO] [2019-10-11 16:27:37] MetaTraits to traits...
[INFO] [2019-10-11 16:27:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 16:27:37] Assocs to occurrences...
[INFO] [2019-10-11 16:27:37] Assocs to nodes...
[INFO] [2019-10-11 16:27:37] Assoc to sex term...
[INFO] [2019-10-11 16:27:37] Assoc to lifestage term...
[STOP] [2019-10-11 16:27:37] resolve_keys
[START] [2019-10-11 16:27:37] hold_for_later_1
[STOP] [2019-10-11 16:27:37] hold_for_later_1
[START] [2019-10-11 16:27:37] hold_for_later_2
[STOP] [2019-10-11 16:27:37] hold_for_later_2
[START] [2019-10-11 16:27:37] resolve_missing_parents
[STOP] [2019-10-11 16:27:41] resolve_missing_parents
[START] [2019-10-11 16:27:41] rebuild_nodes
[START] [2019-10-11 16:27:41] Flattener#flatten
[START] [2019-10-11 16:27:41] Flattener#study_resource
[START] [2019-10-11 16:27:41] Flattener#build_ancestry
[STOP] [2019-10-11 16:27:41] Flattener#build_ancestry
[INFO] [2019-10-11 16:27:41] 2179 ancestry keys
[START] [2019-10-11 16:27:41] build_node_ancestors
[INFO] [2019-10-11 16:27:41] old ancestors deleted.
[STOP] [2019-10-11 16:27:41] build_node_ancestors
[START] [2019-10-11 16:27:41] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:27:41] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 16:27:41] Flattener#flatten
[STOP] [2019-10-11 16:27:41] rebuild_nodes
[START] [2019-10-11 16:27:41] resolve_missing_media_owners
[STOP] [2019-10-11 16:27:41] resolve_missing_media_owners
[START] [2019-10-11 16:27:41] sanitize_media_verbatims
[STOP] [2019-10-11 16:27:41] sanitize_media_verbatims
[START] [2019-10-11 16:27:41] queue_downloads
[STOP] [2019-10-11 16:27:41] queue_downloads
[START] [2019-10-11 16:27:41] parse_names
[WARN] [2019-10-11 16:27:41] I see 2179 names which still need to be parsed.
[STOP] [2019-10-11 16:27:44] parse_names
[START] [2019-10-11 16:27:44] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 16:27:44] denormalize_canonical_names_to_nodes
[START] [2019-10-11 16:27:44] match_nodes
[START] [2019-10-11 16:27:44] map_all_nodes_to_pages
[STOP] [2019-10-11 16:28:40] map_all_nodes_to_pages
[INFO] [2019-10-11 16:28:40] 93 Unmatched nodes (of 2179)! That's too many to output. First 10: Mussidae (#48831872); Madracis mirabilis (#48832832); Pectiniidae (#48832379); Amphelikturus dendritica (#48833482); Arthonia cyrtodes (#48831531); Arthonia caribaea (#48831743); Arthonia minuta (#48832865); Arthonia scriblitella (#48833118); Arthothelium cyrtodes (#48831672); Arthothelium megalocarpa (#48831802)
[START] [2019-10-11 16:28:40] update_nodes
[STOP] [2019-10-11 16:28:43] update_nodes
[STOP] [2019-10-11 16:28:43] match_nodes
[START] [2019-10-11 16:28:43] reindex_search
[STOP] [2019-10-11 16:28:46] reindex_search
[START] [2019-10-11 16:28:46] normalize_units
[STOP] [2019-10-11 16:28:46] normalize_units
[START] [2019-10-11 16:28:46] calculate_statistics
[STOP] [2019-10-11 16:28:46] calculate_statistics
[START] [2019-10-11 16:28:46] complete_harvest_instance
[START] [2019-10-11 16:28:46] overall_tsv_creation
[INFO] [2019-10-11 16:28:46] Processing group of 2179 in 1 batches of 10000
[INFO] [2019-10-11 16:29:41] 964 Traits (unfiltered)...
[INFO] [2019-10-11 16:29:55] 964 Traits (filtered)...
[INFO] [2019-10-11 16:29:55] 0 Associations (filtered)...
[INFO] [2019-10-11 16:30:34] 4820 metadata added.
[INFO] [2019-10-11 16:30:34] 0 metadata added.
[INFO] [2019-10-11 16:30:34] Average Time: 84.85
[INFO] [2019-10-11 16:30:34] Total Time: 1m48s
[STOP] [2019-10-11 16:30:34] overall_tsv_creation
[INFO] [2019-10-11 16:30:34] Done. Check your files:
[INFO] [2019-10-11 16:30:34] (2179 lines) /app/public/data/bsessl/publish_nodes.tsv
[INFO] [2019-10-11 16:30:34] (3496 lines) /app/public/data/bsessl/publish_node_ancestors.tsv
[INFO] [2019-10-11 16:30:34] (2179 lines) /app/public/data/bsessl/publish_scientific_names.tsv
[INFO] [2019-10-11 16:30:34] (965 lines) /app/public/data/bsessl/publish_traits.tsv
[INFO] [2019-10-11 16:30:34] (4821 lines) /app/public/data/bsessl/publish_metadata.tsv
[STOP] [2019-10-11 16:30:34] complete_harvest_instance
[START] [2019-10-11 16:30:34] completed
[STOP] [2019-10-11 16:30:34] completed
[STOP] [2019-10-11 16:30:34] logged process, took 203.62

Latest Process