Harvest for Bristol Channel Species List Created 22 Dec 22:59

Stage: completed
Fetched: 22 Dec 22:59
Validated: 22 Dec 22:59
Deltas Created 22 Dec 22:59
Units Normalized: 22 Dec 23:09
Ancestry Built: 22 Dec 23:00
Nodes Matched: 22 Dec 23:09
Names Parsed: 22 Dec 23:01
New Models Stored: 22 Dec 23:00
Indexed: 22 Dec 23:09
Completed: 22 Dec 23:11
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-22 22:59:56 -0500 by logger.rb/56815
[START] [2019-12-22 22:59:56] logged process
[START] [2019-12-22 22:59:56] create_harvest_instance
[STOP] [2019-12-22 22:59:57] create_harvest_instance
[START] [2019-12-22 22:59:57] fetch_files
[STOP] [2019-12-22 22:59:57] fetch_files
[START] [2019-12-22 22:59:57] validate_each_file
[STOP] [2019-12-22 22:59:57] validate_each_file
[START] [2019-12-22 22:59:57] convert_to_csv
[CMD] [2019-12-22 22:59:57] /usr/bin/sort /app/public/converted_csv/bristol_channel__refs_19146.csv > /app/public/converted_csv/bristol_channel__refs_19146.csv_sorted
[CMD] [2019-12-22 22:59:57] /usr/bin/sort /app/public/converted_csv/bristol_channel__nodes_19147.csv > /app/public/converted_csv/bristol_channel__nodes_19147.csv_sorted
[CMD] [2019-12-22 22:59:57] /usr/bin/sort /app/public/converted_csv/bristol_channel__occurrences_19148.csv > /app/public/converted_csv/bristol_channel__occurrences_19148.csv_sorted
[CMD] [2019-12-22 22:59:57] /usr/bin/sort /app/public/converted_csv/bristol_channel__measurements_19149.csv > /app/public/converted_csv/bristol_channel__measurements_19149.csv_sorted
[STOP] [2019-12-22 22:59:57] convert_to_csv
[START] [2019-12-22 22:59:57] calculate_delta
[CMD] [2019-12-22 22:59:57] echo "0a" > /app/public/diff/bristol_channel__refs_19146.diff
[CMD] [2019-12-22 22:59:58] tail -n +1 /app/public/converted_csv/bristol_channel__refs_19146.csv >> /app/public/diff/bristol_channel__refs_19146.diff
[CMD] [2019-12-22 22:59:58] echo "." >> /app/public/diff/bristol_channel__refs_19146.diff
[CMD] [2019-12-22 22:59:58] echo "0a" > /app/public/diff/bristol_channel__nodes_19147.diff
[CMD] [2019-12-22 22:59:58] tail -n +1 /app/public/converted_csv/bristol_channel__nodes_19147.csv >> /app/public/diff/bristol_channel__nodes_19147.diff
[CMD] [2019-12-22 22:59:58] echo "." >> /app/public/diff/bristol_channel__nodes_19147.diff
[CMD] [2019-12-22 22:59:58] echo "0a" > /app/public/diff/bristol_channel__occurrences_19148.diff
[CMD] [2019-12-22 22:59:58] tail -n +1 /app/public/converted_csv/bristol_channel__occurrences_19148.csv >> /app/public/diff/bristol_channel__occurrences_19148.diff
[CMD] [2019-12-22 22:59:58] echo "." >> /app/public/diff/bristol_channel__occurrences_19148.diff
[CMD] [2019-12-22 22:59:58] echo "0a" > /app/public/diff/bristol_channel__measurements_19149.diff
[CMD] [2019-12-22 22:59:58] tail -n +1 /app/public/converted_csv/bristol_channel__measurements_19149.csv >> /app/public/diff/bristol_channel__measurements_19149.diff
[CMD] [2019-12-22 22:59:58] echo "." >> /app/public/diff/bristol_channel__measurements_19149.diff
[STOP] [2019-12-22 22:59:58] calculate_delta
[START] [2019-12-22 22:59:58] parse_diff_and_store
[INFO] [2019-12-22 22:59:58] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 22:59:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 23:00:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 23:00:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 23:00:11] Storing 2 References
[INFO] [2019-12-22 23:00:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 23:00:12] Average Time: 0.0
[INFO] [2019-12-22 23:00:12] Total Time: 1s
[INFO] [2019-12-22 23:00:12] Storing 4292 ScientificNames
[INFO] [2019-12-22 23:00:12] Processing group of 4292 in 5 groups of 1000
[INFO] [2019-12-22 23:00:14] Average Time: 0.4
[INFO] [2019-12-22 23:00:14] Total Time: 3s
[INFO] [2019-12-22 23:00:14] Storing 4292 Nodes
[INFO] [2019-12-22 23:00:14] Processing group of 4292 in 5 groups of 1000
[INFO] [2019-12-22 23:00:15] Average Time: 0.348
[INFO] [2019-12-22 23:00:15] Total Time: 2s
[INFO] [2019-12-22 23:00:15] Storing 1927 Occurrences
[INFO] [2019-12-22 23:00:15] Processing group of 1927 in 2 groups of 1000
[INFO] [2019-12-22 23:00:16] Average Time: 0.12
[INFO] [2019-12-22 23:00:16] Total Time: 1s
[INFO] [2019-12-22 23:00:16] Storing 3854 TraitsReferences
[INFO] [2019-12-22 23:00:16] Processing group of 3854 in 4 groups of 1000
[INFO] [2019-12-22 23:00:16] Average Time: 0.103
[INFO] [2019-12-22 23:00:16] Total Time: 1s
[INFO] [2019-12-22 23:00:16] Storing 3854 Traits
[INFO] [2019-12-22 23:00:16] Processing group of 3854 in 4 groups of 1000
[INFO] [2019-12-22 23:00:18] Average Time: 0.368
[INFO] [2019-12-22 23:00:18] Total Time: 2s
[INFO] [2019-12-22 23:00:18] Storing 3854 MetaTraits
[INFO] [2019-12-22 23:00:18] Processing group of 3854 in 4 groups of 1000
[INFO] [2019-12-22 23:00:18] Average Time: 0.145
[INFO] [2019-12-22 23:00:18] Total Time: 1s
[STOP] [2019-12-22 23:00:18] parse_diff_and_store
[START] [2019-12-22 23:00:18] resolve_keys
[INFO] [2019-12-22 23:00:37] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 23:00:39] traits to occurrences...
[INFO] [2019-12-22 23:00:40] traits to nodes (through occurrences)...
[INFO] [2019-12-22 23:00:40] Traits to sex term...
[INFO] [2019-12-22 23:00:41] Traits to lifestage term...
[INFO] [2019-12-22 23:00:42] MetaTraits to traits...
[INFO] [2019-12-22 23:00:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 23:00:43] Assocs to occurrences...
[INFO] [2019-12-22 23:00:43] Assocs to nodes...
[INFO] [2019-12-22 23:00:43] Assoc to sex term...
[INFO] [2019-12-22 23:00:43] Assoc to lifestage term...
[STOP] [2019-12-22 23:00:43] resolve_keys
[START] [2019-12-22 23:00:43] hold_for_later_1
[STOP] [2019-12-22 23:00:43] hold_for_later_1
[START] [2019-12-22 23:00:43] hold_for_later_2
[STOP] [2019-12-22 23:00:43] hold_for_later_2
[START] [2019-12-22 23:00:43] resolve_missing_parents
[STOP] [2019-12-22 23:00:51] resolve_missing_parents
[START] [2019-12-22 23:00:51] rebuild_nodes
[START] [2019-12-22 23:00:51] Flattener#flatten
[START] [2019-12-22 23:00:51] Flattener#study_resource
[START] [2019-12-22 23:00:51] Flattener#build_ancestry
[STOP] [2019-12-22 23:00:51] Flattener#build_ancestry
[INFO] [2019-12-22 23:00:51] 4292 ancestry keys
[START] [2019-12-22 23:00:51] build_node_ancestors
[INFO] [2019-12-22 23:00:51] old ancestors deleted.
[STOP] [2019-12-22 23:00:53] build_node_ancestors
[START] [2019-12-22 23:00:55] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:00:55] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:00:55] Flattener#flatten
[STOP] [2019-12-22 23:00:55] rebuild_nodes
[START] [2019-12-22 23:00:55] resolve_missing_media_owners
[STOP] [2019-12-22 23:00:55] resolve_missing_media_owners
[START] [2019-12-22 23:00:55] sanitize_media_verbatims
[STOP] [2019-12-22 23:00:55] sanitize_media_verbatims
[START] [2019-12-22 23:00:55] queue_downloads
[STOP] [2019-12-22 23:00:55] queue_downloads
[START] [2019-12-22 23:00:55] parse_names
[WARN] [2019-12-22 23:00:55] I see 4292 names which still need to be parsed.
[STOP] [2019-12-22 23:01:00] parse_names
[START] [2019-12-22 23:01:00] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 23:01:00] denormalize_canonical_names_to_nodes
[START] [2019-12-22 23:01:00] match_nodes
[START] [2019-12-22 23:01:00] map_all_nodes_to_pages
[STOP] [2019-12-22 23:09:43] map_all_nodes_to_pages
[INFO] [2019-12-22 23:09:43] 217 Unmatched nodes (of 4292)! That's too many to output. First 10: Philomachus (#61780052); Philomachus pugnax (#61780051); Larus melanocephalus (#61779788); Anas penelope (#61778469); Anas clypeata (#61778505); Anas strepera (#61778786); Anas querquedula (#61779430); Chen (#61781413); Chen caerulescens (#61781412); Scorpaeniformes (#61778976)
[START] [2019-12-22 23:09:43] update_nodes
[STOP] [2019-12-22 23:09:45] update_nodes
[STOP] [2019-12-22 23:09:45] match_nodes
[START] [2019-12-22 23:09:45] reindex_search
[STOP] [2019-12-22 23:09:52] reindex_search
[START] [2019-12-22 23:09:52] normalize_units
[STOP] [2019-12-22 23:09:52] normalize_units
[START] [2019-12-22 23:09:52] calculate_statistics
[STOP] [2019-12-22 23:09:53] calculate_statistics
[START] [2019-12-22 23:09:53] complete_harvest_instance
[START] [2019-12-22 23:09:53] overall_tsv_creation
[INFO] [2019-12-22 23:09:53] Processing group of 4292 in 1 batches of 10000
[INFO] [2019-12-22 23:10:57] 1927 Traits (unfiltered)...
[INFO] [2019-12-22 23:11:10] 1927 Traits (filtered)...
[INFO] [2019-12-22 23:11:10] 0 Associations (filtered)...
[INFO] [2019-12-22 23:11:51] 9635 metadata added.
[INFO] [2019-12-22 23:11:51] 0 metadata added.
[INFO] [2019-12-22 23:11:51] Average Time: 93.04
[INFO] [2019-12-22 23:11:51] Total Time: 1m59s
[STOP] [2019-12-22 23:11:51] overall_tsv_creation
[INFO] [2019-12-22 23:11:51] Done. Check your files:
[INFO] [2019-12-22 23:11:51] (4292 lines) /app/public/data/bristol_channel_/publish_nodes.tsv
[INFO] [2019-12-22 23:11:51] (21104 lines) /app/public/data/bristol_channel_/publish_node_ancestors.tsv
[INFO] [2019-12-22 23:11:51] (4292 lines) /app/public/data/bristol_channel_/publish_scientific_names.tsv
[INFO] [2019-12-22 23:11:52] (1928 lines) /app/public/data/bristol_channel_/publish_traits.tsv
[INFO] [2019-12-22 23:11:52] (9636 lines) /app/public/data/bristol_channel_/publish_metadata.tsv
[STOP] [2019-12-22 23:11:52] complete_harvest_instance
[START] [2019-12-22 23:11:52] completed
[STOP] [2019-12-22 23:11:52] completed
[STOP] [2019-12-22 23:11:52] logged process, took 715.63
Latest Process

22 Dec 22:59 EXITED currently processing 0