Harvest for Bermuda Species List Created 11 Oct 13:57

Stage: completed
Fetched: 11 Oct 13:57
Validated: 11 Oct 13:57
Deltas Created 11 Oct 13:57
Units Normalized: 11 Oct 13:59
Ancestry Built: 11 Oct 13:58
Nodes Matched: 11 Oct 13:59
Names Parsed: 11 Oct 13:58
New Models Stored: 11 Oct 13:57
Indexed: 11 Oct 13:59
Completed: 11 Oct 14:01
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-11 13:57:32 -0400 by logger.rb/56815
[START] [2019-10-11 13:57:32] logged process
[START] [2019-10-11 13:57:32] create_harvest_instance
[STOP] [2019-10-11 13:57:32] create_harvest_instance
[START] [2019-10-11 13:57:32] fetch_files
[STOP] [2019-10-11 13:57:32] fetch_files
[START] [2019-10-11 13:57:32] validate_each_file
[STOP] [2019-10-11 13:57:33] validate_each_file
[START] [2019-10-11 13:57:33] convert_to_csv
[CMD] [2019-10-11 13:57:33] /usr/bin/sort /app/public/converted_csv/bermuda_sp_list_refs_15132.csv > /app/public/converted_csv/bermuda_sp_list_refs_15132.csv_sorted
[CMD] [2019-10-11 13:57:33] /usr/bin/sort /app/public/converted_csv/bermuda_sp_list_nodes_15133.csv > /app/public/converted_csv/bermuda_sp_list_nodes_15133.csv_sorted
[CMD] [2019-10-11 13:57:33] /usr/bin/sort /app/public/converted_csv/bermuda_sp_list_occurrences_15134.csv > /app/public/converted_csv/bermuda_sp_list_occurrences_15134.csv_sorted
[CMD] [2019-10-11 13:57:33] /usr/bin/sort /app/public/converted_csv/bermuda_sp_list_measurements_15135.csv > /app/public/converted_csv/bermuda_sp_list_measurements_15135.csv_sorted
[STOP] [2019-10-11 13:57:33] convert_to_csv
[START] [2019-10-11 13:57:33] calculate_delta
[CMD] [2019-10-11 13:57:33] echo "0a" > /app/public/diff/bermuda_sp_list_refs_15132.diff
[CMD] [2019-10-11 13:57:33] tail -n +1 /app/public/converted_csv/bermuda_sp_list_refs_15132.csv >> /app/public/diff/bermuda_sp_list_refs_15132.diff
[CMD] [2019-10-11 13:57:33] echo "." >> /app/public/diff/bermuda_sp_list_refs_15132.diff
[CMD] [2019-10-11 13:57:33] echo "0a" > /app/public/diff/bermuda_sp_list_nodes_15133.diff
[CMD] [2019-10-11 13:57:33] tail -n +1 /app/public/converted_csv/bermuda_sp_list_nodes_15133.csv >> /app/public/diff/bermuda_sp_list_nodes_15133.diff
[CMD] [2019-10-11 13:57:33] echo "." >> /app/public/diff/bermuda_sp_list_nodes_15133.diff
[CMD] [2019-10-11 13:57:34] echo "0a" > /app/public/diff/bermuda_sp_list_occurrences_15134.diff
[CMD] [2019-10-11 13:57:34] tail -n +1 /app/public/converted_csv/bermuda_sp_list_occurrences_15134.csv >> /app/public/diff/bermuda_sp_list_occurrences_15134.diff
[CMD] [2019-10-11 13:57:34] echo "." >> /app/public/diff/bermuda_sp_list_occurrences_15134.diff
[CMD] [2019-10-11 13:57:34] echo "0a" > /app/public/diff/bermuda_sp_list_measurements_15135.diff
[CMD] [2019-10-11 13:57:34] tail -n +1 /app/public/converted_csv/bermuda_sp_list_measurements_15135.csv >> /app/public/diff/bermuda_sp_list_measurements_15135.diff
[CMD] [2019-10-11 13:57:34] echo "." >> /app/public/diff/bermuda_sp_list_measurements_15135.diff
[STOP] [2019-10-11 13:57:34] calculate_delta
[START] [2019-10-11 13:57:34] parse_diff_and_store
[INFO] [2019-10-11 13:57:34] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 13:57:34] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 13:57:35] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 13:57:36] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 13:57:42] Storing 2 References
[INFO] [2019-10-11 13:57:42] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 13:57:42] Average Time: 0.0
[INFO] [2019-10-11 13:57:42] Total Time: 1s
[INFO] [2019-10-11 13:57:42] Storing 2465 ScientificNames
[INFO] [2019-10-11 13:57:42] Processing group of 2465 in 3 groups of 1000
[INFO] [2019-10-11 13:57:43] Average Time: 0.33
[INFO] [2019-10-11 13:57:43] Total Time: 2s
[INFO] [2019-10-11 13:57:43] Storing 2465 Nodes
[INFO] [2019-10-11 13:57:43] Processing group of 2465 in 3 groups of 1000
[INFO] [2019-10-11 13:57:43] Average Time: 0.243
[INFO] [2019-10-11 13:57:43] Total Time: 1s
[INFO] [2019-10-11 13:57:43] Storing 964 Occurrences
[INFO] [2019-10-11 13:57:43] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-11 13:57:43] Average Time: 0.11
[INFO] [2019-10-11 13:57:43] Total Time: 1s
[INFO] [2019-10-11 13:57:43] Storing 2198 TraitsReferences
[INFO] [2019-10-11 13:57:43] Processing group of 2198 in 3 groups of 1000
[INFO] [2019-10-11 13:57:44] Average Time: 0.087
[INFO] [2019-10-11 13:57:44] Total Time: 1s
[INFO] [2019-10-11 13:57:44] Storing 2198 Traits
[INFO] [2019-10-11 13:57:44] Processing group of 2198 in 3 groups of 1000
[INFO] [2019-10-11 13:57:45] Average Time: 0.27
[INFO] [2019-10-11 13:57:45] Total Time: 1s
[INFO] [2019-10-11 13:57:45] Storing 2195 MetaTraits
[INFO] [2019-10-11 13:57:45] Processing group of 2195 in 3 groups of 1000
[INFO] [2019-10-11 13:57:45] Average Time: 0.127
[INFO] [2019-10-11 13:57:45] Total Time: 1s
[STOP] [2019-10-11 13:57:45] parse_diff_and_store
[START] [2019-10-11 13:57:45] resolve_keys
[INFO] [2019-10-11 13:57:56] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 13:57:57] traits to occurrences...
[INFO] [2019-10-11 13:57:58] traits to nodes (through occurrences)...
[INFO] [2019-10-11 13:57:58] Traits to sex term...
[INFO] [2019-10-11 13:57:59] Traits to lifestage term...
[INFO] [2019-10-11 13:58:00] MetaTraits to traits...
[INFO] [2019-10-11 13:58:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 13:58:01] Assocs to occurrences...
[INFO] [2019-10-11 13:58:01] Assocs to nodes...
[INFO] [2019-10-11 13:58:01] Assoc to sex term...
[INFO] [2019-10-11 13:58:01] Assoc to lifestage term...
[STOP] [2019-10-11 13:58:01] resolve_keys
[START] [2019-10-11 13:58:01] hold_for_later_1
[STOP] [2019-10-11 13:58:01] hold_for_later_1
[START] [2019-10-11 13:58:01] hold_for_later_2
[STOP] [2019-10-11 13:58:01] hold_for_later_2
[START] [2019-10-11 13:58:01] resolve_missing_parents
[STOP] [2019-10-11 13:58:04] resolve_missing_parents
[START] [2019-10-11 13:58:04] rebuild_nodes
[START] [2019-10-11 13:58:04] Flattener#flatten
[START] [2019-10-11 13:58:04] Flattener#study_resource
[START] [2019-10-11 13:58:04] Flattener#build_ancestry
[STOP] [2019-10-11 13:58:04] Flattener#build_ancestry
[INFO] [2019-10-11 13:58:04] 2465 ancestry keys
[START] [2019-10-11 13:58:04] build_node_ancestors
[INFO] [2019-10-11 13:58:04] old ancestors deleted.
[STOP] [2019-10-11 13:58:05] build_node_ancestors
[START] [2019-10-11 13:58:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 13:58:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 13:58:06] Flattener#flatten
[STOP] [2019-10-11 13:58:06] rebuild_nodes
[START] [2019-10-11 13:58:06] resolve_missing_media_owners
[STOP] [2019-10-11 13:58:06] resolve_missing_media_owners
[START] [2019-10-11 13:58:06] sanitize_media_verbatims
[STOP] [2019-10-11 13:58:06] sanitize_media_verbatims
[START] [2019-10-11 13:58:06] queue_downloads
[STOP] [2019-10-11 13:58:06] queue_downloads
[START] [2019-10-11 13:58:06] parse_names
[WARN] [2019-10-11 13:58:06] I see 2465 names which still need to be parsed.
[STOP] [2019-10-11 13:58:09] parse_names
[START] [2019-10-11 13:58:09] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 13:58:09] denormalize_canonical_names_to_nodes
[START] [2019-10-11 13:58:09] match_nodes
[START] [2019-10-11 13:58:09] map_all_nodes_to_pages
[STOP] [2019-10-11 13:59:31] map_all_nodes_to_pages
[INFO] [2019-10-11 13:59:31] 176 Unmatched nodes (of 2465)! That's too many to output. First 10: Fulica caribaea (#48767607); Porphyrio martinicus (#48767947); Grus canadensis (#48767537); Anas discors (#48767233); Anas americana (#48767353); Anas clypeata (#48767385); Anas penelope (#48767426); Anas strepera (#48767431); Anas querquedula (#48767588); Chen (#48767423)
[START] [2019-10-11 13:59:31] update_nodes
[STOP] [2019-10-11 13:59:32] update_nodes
[STOP] [2019-10-11 13:59:32] match_nodes
[START] [2019-10-11 13:59:32] reindex_search
[STOP] [2019-10-11 13:59:36] reindex_search
[START] [2019-10-11 13:59:36] normalize_units
[STOP] [2019-10-11 13:59:36] normalize_units
[START] [2019-10-11 13:59:36] calculate_statistics
[STOP] [2019-10-11 13:59:36] calculate_statistics
[START] [2019-10-11 13:59:36] complete_harvest_instance
[START] [2019-10-11 13:59:36] overall_tsv_creation
[INFO] [2019-10-11 13:59:36] Processing group of 2465 in 1 batches of 10000
[INFO] [2019-10-11 14:00:34] 964 Traits (unfiltered)...
[INFO] [2019-10-11 14:00:48] 964 Traits (filtered)...
[INFO] [2019-10-11 14:00:48] 0 Associations (filtered)...
[INFO] [2019-10-11 14:01:27] 4817 metadata added.
[INFO] [2019-10-11 14:01:27] 0 metadata added.
[INFO] [2019-10-11 14:01:27] Average Time: 86.98
[INFO] [2019-10-11 14:01:27] Total Time: 1m52s
[STOP] [2019-10-11 14:01:27] overall_tsv_creation
[INFO] [2019-10-11 14:01:27] Done. Check your files:
[INFO] [2019-10-11 14:01:27] (2465 lines) /app/public/data/bermuda_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 14:01:27] (9522 lines) /app/public/data/bermuda_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 14:01:27] (2465 lines) /app/public/data/bermuda_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 14:01:27] (965 lines) /app/public/data/bermuda_sp_list/publish_traits.tsv
[INFO] [2019-10-11 14:01:28] (4818 lines) /app/public/data/bermuda_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 14:01:28] complete_harvest_instance
[START] [2019-10-11 14:01:28] completed
[STOP] [2019-10-11 14:01:28] completed
[STOP] [2019-10-11 14:01:28] logged process, took 235.82
Latest Process

11 Oct 13:57 EXITED currently processing 0