Harvest for Gulf of Riga Species List Created 23 Dec 09:33

Stage: completed
Fetched: 23 Dec 09:33
Validated: 23 Dec 09:33
Deltas Created 23 Dec 09:33
Units Normalized: 23 Dec 09:36
Ancestry Built: 23 Dec 09:33
Nodes Matched: 23 Dec 09:36
Names Parsed: 23 Dec 09:33
New Models Stored: 23 Dec 09:33
Indexed: 23 Dec 09:36
Completed: 23 Dec 09:38
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 09:33:28 -0500 by logger.rb/56815
[START] [2019-12-23 09:33:28] logged process
[START] [2019-12-23 09:33:28] create_harvest_instance
[STOP] [2019-12-23 09:33:29] create_harvest_instance
[START] [2019-12-23 09:33:29] fetch_files
[STOP] [2019-12-23 09:33:29] fetch_files
[START] [2019-12-23 09:33:29] validate_each_file
[STOP] [2019-12-23 09:33:29] validate_each_file
[START] [2019-12-23 09:33:29] convert_to_csv
[CMD] [2019-12-23 09:33:29] /usr/bin/sort /app/public/converted_csv/gulf_riga_sp_lis_refs_19338.csv > /app/public/converted_csv/gulf_riga_sp_lis_refs_19338.csv_sorted
[CMD] [2019-12-23 09:33:30] /usr/bin/sort /app/public/converted_csv/gulf_riga_sp_lis_nodes_19339.csv > /app/public/converted_csv/gulf_riga_sp_lis_nodes_19339.csv_sorted
[CMD] [2019-12-23 09:33:30] /usr/bin/sort /app/public/converted_csv/gulf_riga_sp_lis_occurrences_19340.csv > /app/public/converted_csv/gulf_riga_sp_lis_occurrences_19340.csv_sorted
[CMD] [2019-12-23 09:33:31] /usr/bin/sort /app/public/converted_csv/gulf_riga_sp_lis_measurements_19341.csv > /app/public/converted_csv/gulf_riga_sp_lis_measurements_19341.csv_sorted
[STOP] [2019-12-23 09:33:32] convert_to_csv
[START] [2019-12-23 09:33:32] calculate_delta
[CMD] [2019-12-23 09:33:32] echo "0a" > /app/public/diff/gulf_riga_sp_lis_refs_19338.diff
[CMD] [2019-12-23 09:33:32] tail -n +1 /app/public/converted_csv/gulf_riga_sp_lis_refs_19338.csv >> /app/public/diff/gulf_riga_sp_lis_refs_19338.diff
[CMD] [2019-12-23 09:33:33] echo "." >> /app/public/diff/gulf_riga_sp_lis_refs_19338.diff
[CMD] [2019-12-23 09:33:34] echo "0a" > /app/public/diff/gulf_riga_sp_lis_nodes_19339.diff
[CMD] [2019-12-23 09:33:34] tail -n +1 /app/public/converted_csv/gulf_riga_sp_lis_nodes_19339.csv >> /app/public/diff/gulf_riga_sp_lis_nodes_19339.diff
[CMD] [2019-12-23 09:33:35] echo "." >> /app/public/diff/gulf_riga_sp_lis_nodes_19339.diff
[CMD] [2019-12-23 09:33:36] echo "0a" > /app/public/diff/gulf_riga_sp_lis_occurrences_19340.diff
[CMD] [2019-12-23 09:33:36] tail -n +1 /app/public/converted_csv/gulf_riga_sp_lis_occurrences_19340.csv >> /app/public/diff/gulf_riga_sp_lis_occurrences_19340.diff
[CMD] [2019-12-23 09:33:37] echo "." >> /app/public/diff/gulf_riga_sp_lis_occurrences_19340.diff
[CMD] [2019-12-23 09:33:38] echo "0a" > /app/public/diff/gulf_riga_sp_lis_measurements_19341.diff
[CMD] [2019-12-23 09:33:38] tail -n +1 /app/public/converted_csv/gulf_riga_sp_lis_measurements_19341.csv >> /app/public/diff/gulf_riga_sp_lis_measurements_19341.diff
[CMD] [2019-12-23 09:33:39] echo "." >> /app/public/diff/gulf_riga_sp_lis_measurements_19341.diff
[STOP] [2019-12-23 09:33:40] calculate_delta
[START] [2019-12-23 09:33:40] parse_diff_and_store
[INFO] [2019-12-23 09:33:40] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 09:33:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 09:33:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 09:33:43] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 09:33:44] Storing 2 References
[INFO] [2019-12-23 09:33:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 09:33:44] Average Time: 0.0
[INFO] [2019-12-23 09:33:44] Total Time: 1s
[INFO] [2019-12-23 09:33:44] Storing 561 ScientificNames
[INFO] [2019-12-23 09:33:44] Processing group of 561 in 1 groups of 1000
[INFO] [2019-12-23 09:33:44] Average Time: 0.29
[INFO] [2019-12-23 09:33:44] Total Time: 1s
[INFO] [2019-12-23 09:33:44] Storing 561 Nodes
[INFO] [2019-12-23 09:33:44] Processing group of 561 in 1 groups of 1000
[INFO] [2019-12-23 09:33:44] Average Time: 0.2
[INFO] [2019-12-23 09:33:44] Total Time: 1s
[INFO] [2019-12-23 09:33:44] Storing 221 Occurrences
[INFO] [2019-12-23 09:33:44] Processing group of 221 in 1 groups of 1000
[INFO] [2019-12-23 09:33:44] Average Time: 0.06
[INFO] [2019-12-23 09:33:44] Total Time: 1s
[INFO] [2019-12-23 09:33:44] Storing 442 TraitsReferences
[INFO] [2019-12-23 09:33:44] Processing group of 442 in 1 groups of 1000
[INFO] [2019-12-23 09:33:45] Average Time: 0.13
[INFO] [2019-12-23 09:33:45] Total Time: 1s
[INFO] [2019-12-23 09:33:45] Storing 442 Traits
[INFO] [2019-12-23 09:33:45] Processing group of 442 in 1 groups of 1000
[INFO] [2019-12-23 09:33:45] Average Time: 0.28
[INFO] [2019-12-23 09:33:45] Total Time: 1s
[INFO] [2019-12-23 09:33:45] Storing 442 MetaTraits
[INFO] [2019-12-23 09:33:45] Processing group of 442 in 1 groups of 1000
[INFO] [2019-12-23 09:33:45] Average Time: 0.1
[INFO] [2019-12-23 09:33:45] Total Time: 1s
[STOP] [2019-12-23 09:33:45] parse_diff_and_store
[START] [2019-12-23 09:33:45] resolve_keys
[INFO] [2019-12-23 09:33:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 09:33:50] traits to occurrences...
[INFO] [2019-12-23 09:33:50] traits to nodes (through occurrences)...
[INFO] [2019-12-23 09:33:50] Traits to sex term...
[INFO] [2019-12-23 09:33:50] Traits to lifestage term...
[INFO] [2019-12-23 09:33:50] MetaTraits to traits...
[INFO] [2019-12-23 09:33:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 09:33:50] Assocs to occurrences...
[INFO] [2019-12-23 09:33:50] Assocs to nodes...
[INFO] [2019-12-23 09:33:50] Assoc to sex term...
[INFO] [2019-12-23 09:33:51] Assoc to lifestage term...
[STOP] [2019-12-23 09:33:51] resolve_keys
[START] [2019-12-23 09:33:51] hold_for_later_1
[STOP] [2019-12-23 09:33:51] hold_for_later_1
[START] [2019-12-23 09:33:51] hold_for_later_2
[STOP] [2019-12-23 09:33:51] hold_for_later_2
[START] [2019-12-23 09:33:51] resolve_missing_parents
[STOP] [2019-12-23 09:33:51] resolve_missing_parents
[START] [2019-12-23 09:33:51] rebuild_nodes
[START] [2019-12-23 09:33:51] Flattener#flatten
[START] [2019-12-23 09:33:51] Flattener#study_resource
[START] [2019-12-23 09:33:51] Flattener#build_ancestry
[STOP] [2019-12-23 09:33:51] Flattener#build_ancestry
[INFO] [2019-12-23 09:33:51] 561 ancestry keys
[START] [2019-12-23 09:33:51] build_node_ancestors
[INFO] [2019-12-23 09:33:51] old ancestors deleted.
[STOP] [2019-12-23 09:33:51] build_node_ancestors
[START] [2019-12-23 09:33:51] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:33:51] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:33:51] Flattener#flatten
[STOP] [2019-12-23 09:33:51] rebuild_nodes
[START] [2019-12-23 09:33:51] resolve_missing_media_owners
[STOP] [2019-12-23 09:33:51] resolve_missing_media_owners
[START] [2019-12-23 09:33:51] sanitize_media_verbatims
[STOP] [2019-12-23 09:33:51] sanitize_media_verbatims
[START] [2019-12-23 09:33:51] queue_downloads
[STOP] [2019-12-23 09:33:51] queue_downloads
[START] [2019-12-23 09:33:51] parse_names
[WARN] [2019-12-23 09:33:51] I see 561 names which still need to be parsed.
[STOP] [2019-12-23 09:33:53] parse_names
[START] [2019-12-23 09:33:53] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 09:33:53] denormalize_canonical_names_to_nodes
[START] [2019-12-23 09:33:53] match_nodes
[START] [2019-12-23 09:33:53] map_all_nodes_to_pages
[STOP] [2019-12-23 09:36:55] map_all_nodes_to_pages
[INFO] [2019-12-23 09:36:55] 54 Unmatched nodes (of 561)! That's too many to output. First 10: Anas strepera (#61957552); Anas clypeata (#61957564); Anas penelope (#61957588); Anas querquedula (#61957605); Chen (#61957924); Chen caerulescens (#61957923); Philomachus (#61957670); Philomachus pugnax (#61957669); Limicola (#61957759); Limicola falcinellus (#61957758)
[START] [2019-12-23 09:36:55] update_nodes
[STOP] [2019-12-23 09:36:55] update_nodes
[STOP] [2019-12-23 09:36:55] match_nodes
[START] [2019-12-23 09:36:55] reindex_search
[STOP] [2019-12-23 09:36:56] reindex_search
[START] [2019-12-23 09:36:56] normalize_units
[STOP] [2019-12-23 09:36:56] normalize_units
[START] [2019-12-23 09:36:56] calculate_statistics
[STOP] [2019-12-23 09:36:56] calculate_statistics
[START] [2019-12-23 09:36:56] complete_harvest_instance
[START] [2019-12-23 09:36:56] overall_tsv_creation
[INFO] [2019-12-23 09:36:56] Processing group of 561 in 1 batches of 10000
[INFO] [2019-12-23 09:37:43] 221 Traits (unfiltered)...
[INFO] [2019-12-23 09:37:56] 221 Traits (filtered)...
[INFO] [2019-12-23 09:37:56] 0 Associations (filtered)...
[INFO] [2019-12-23 09:38:34] 1105 metadata added.
[INFO] [2019-12-23 09:38:34] 0 metadata added.
[INFO] [2019-12-23 09:38:34] Average Time: 75.04
[INFO] [2019-12-23 09:38:34] Total Time: 1m38s
[STOP] [2019-12-23 09:38:34] overall_tsv_creation
[INFO] [2019-12-23 09:38:34] Done. Check your files:
[INFO] [2019-12-23 09:38:35] (561 lines) /app/public/data/gulf_riga_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 09:38:35] (2611 lines) /app/public/data/gulf_riga_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 09:38:36] (561 lines) /app/public/data/gulf_riga_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 09:38:37] (222 lines) /app/public/data/gulf_riga_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 09:38:37] (1106 lines) /app/public/data/gulf_riga_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 09:38:37] complete_harvest_instance
[START] [2019-12-23 09:38:37] completed
[STOP] [2019-12-23 09:38:37] completed
[STOP] [2019-12-23 09:38:37] logged process, took 309.28
Latest Process

23 Dec 09:33 EXITED currently processing 0