Harvest for Kyrgyzstan Species List Created 14 Oct 00:45

Stage: completed
Fetched: 14 Oct 00:45
Validated: 14 Oct 00:45
Deltas Created 14 Oct 00:45
Units Normalized: 14 Oct 00:50
Ancestry Built: 14 Oct 00:46
Nodes Matched: 14 Oct 00:49
Names Parsed: 14 Oct 00:46
New Models Stored: 14 Oct 00:46
Indexed: 14 Oct 00:50
Completed: 14 Oct 00:52
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 00:45:53 -0400 by logger.rb/56815
[START] [2019-10-14 00:45:53] logged process
[START] [2019-10-14 00:45:53] create_harvest_instance
[STOP] [2019-10-14 00:45:53] create_harvest_instance
[START] [2019-10-14 00:45:53] fetch_files
[STOP] [2019-10-14 00:45:53] fetch_files
[START] [2019-10-14 00:45:53] validate_each_file
[STOP] [2019-10-14 00:45:54] validate_each_file
[START] [2019-10-14 00:45:54] convert_to_csv
[CMD] [2019-10-14 00:45:54] /usr/bin/sort /app/public/converted_csv/kyrgyzstan_sp_li_refs_16331.csv > /app/public/converted_csv/kyrgyzstan_sp_li_refs_16331.csv_sorted
[CMD] [2019-10-14 00:45:54] /usr/bin/sort /app/public/converted_csv/kyrgyzstan_sp_li_nodes_16332.csv > /app/public/converted_csv/kyrgyzstan_sp_li_nodes_16332.csv_sorted
[CMD] [2019-10-14 00:45:54] /usr/bin/sort /app/public/converted_csv/kyrgyzstan_sp_li_occurrences_16333.csv > /app/public/converted_csv/kyrgyzstan_sp_li_occurrences_16333.csv_sorted
[CMD] [2019-10-14 00:45:54] /usr/bin/sort /app/public/converted_csv/kyrgyzstan_sp_li_measurements_16334.csv > /app/public/converted_csv/kyrgyzstan_sp_li_measurements_16334.csv_sorted
[STOP] [2019-10-14 00:45:54] convert_to_csv
[START] [2019-10-14 00:45:54] calculate_delta
[CMD] [2019-10-14 00:45:54] echo "0a" > /app/public/diff/kyrgyzstan_sp_li_refs_16331.diff
[CMD] [2019-10-14 00:45:54] tail -n +1 /app/public/converted_csv/kyrgyzstan_sp_li_refs_16331.csv >> /app/public/diff/kyrgyzstan_sp_li_refs_16331.diff
[CMD] [2019-10-14 00:45:54] echo "." >> /app/public/diff/kyrgyzstan_sp_li_refs_16331.diff
[CMD] [2019-10-14 00:45:55] echo "0a" > /app/public/diff/kyrgyzstan_sp_li_nodes_16332.diff
[CMD] [2019-10-14 00:45:55] tail -n +1 /app/public/converted_csv/kyrgyzstan_sp_li_nodes_16332.csv >> /app/public/diff/kyrgyzstan_sp_li_nodes_16332.diff
[CMD] [2019-10-14 00:45:55] echo "." >> /app/public/diff/kyrgyzstan_sp_li_nodes_16332.diff
[CMD] [2019-10-14 00:45:55] echo "0a" > /app/public/diff/kyrgyzstan_sp_li_occurrences_16333.diff
[CMD] [2019-10-14 00:45:55] tail -n +1 /app/public/converted_csv/kyrgyzstan_sp_li_occurrences_16333.csv >> /app/public/diff/kyrgyzstan_sp_li_occurrences_16333.diff
[CMD] [2019-10-14 00:45:55] echo "." >> /app/public/diff/kyrgyzstan_sp_li_occurrences_16333.diff
[CMD] [2019-10-14 00:45:55] echo "0a" > /app/public/diff/kyrgyzstan_sp_li_measurements_16334.diff
[CMD] [2019-10-14 00:45:55] tail -n +1 /app/public/converted_csv/kyrgyzstan_sp_li_measurements_16334.csv >> /app/public/diff/kyrgyzstan_sp_li_measurements_16334.diff
[CMD] [2019-10-14 00:45:55] echo "." >> /app/public/diff/kyrgyzstan_sp_li_measurements_16334.diff
[STOP] [2019-10-14 00:45:55] calculate_delta
[START] [2019-10-14 00:45:55] parse_diff_and_store
[INFO] [2019-10-14 00:45:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 00:45:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 00:45:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 00:45:57] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 00:46:07] Storing 2 References
[INFO] [2019-10-14 00:46:07] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 00:46:07] Average Time: 0.0
[INFO] [2019-10-14 00:46:07] Total Time: 1s
[INFO] [2019-10-14 00:46:07] Storing 3001 ScientificNames
[INFO] [2019-10-14 00:46:07] Processing group of 3001 in 4 groups of 1000
[INFO] [2019-10-14 00:46:08] Average Time: 0.303
[INFO] [2019-10-14 00:46:08] Total Time: 2s
[INFO] [2019-10-14 00:46:08] Storing 3001 Nodes
[INFO] [2019-10-14 00:46:08] Processing group of 3001 in 4 groups of 1000
[INFO] [2019-10-14 00:46:09] Average Time: 0.222
[INFO] [2019-10-14 00:46:09] Total Time: 1s
[INFO] [2019-10-14 00:46:09] Storing 1446 Occurrences
[INFO] [2019-10-14 00:46:09] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-14 00:46:09] Average Time: 0.08
[INFO] [2019-10-14 00:46:09] Total Time: 1s
[INFO] [2019-10-14 00:46:09] Storing 3450 TraitsReferences
[INFO] [2019-10-14 00:46:09] Processing group of 3450 in 4 groups of 1000
[INFO] [2019-10-14 00:46:10] Average Time: 0.082
[INFO] [2019-10-14 00:46:10] Total Time: 1s
[INFO] [2019-10-14 00:46:10] Storing 3449 Traits
[INFO] [2019-10-14 00:46:10] Processing group of 3449 in 4 groups of 1000
[INFO] [2019-10-14 00:46:11] Average Time: 0.28
[INFO] [2019-10-14 00:46:11] Total Time: 2s
[INFO] [2019-10-14 00:46:11] Storing 3448 MetaTraits
[INFO] [2019-10-14 00:46:11] Processing group of 3448 in 4 groups of 1000
[INFO] [2019-10-14 00:46:11] Average Time: 0.105
[INFO] [2019-10-14 00:46:11] Total Time: 1s
[STOP] [2019-10-14 00:46:11] parse_diff_and_store
[START] [2019-10-14 00:46:11] resolve_keys
[INFO] [2019-10-14 00:46:25] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 00:46:26] traits to occurrences...
[INFO] [2019-10-14 00:46:27] traits to nodes (through occurrences)...
[INFO] [2019-10-14 00:46:27] Traits to sex term...
[INFO] [2019-10-14 00:46:27] Traits to lifestage term...
[INFO] [2019-10-14 00:46:28] MetaTraits to traits...
[INFO] [2019-10-14 00:46:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 00:46:28] Assocs to occurrences...
[INFO] [2019-10-14 00:46:28] Assocs to nodes...
[INFO] [2019-10-14 00:46:28] Assoc to sex term...
[INFO] [2019-10-14 00:46:28] Assoc to lifestage term...
[STOP] [2019-10-14 00:46:28] resolve_keys
[START] [2019-10-14 00:46:28] hold_for_later_1
[STOP] [2019-10-14 00:46:28] hold_for_later_1
[START] [2019-10-14 00:46:28] hold_for_later_2
[STOP] [2019-10-14 00:46:28] hold_for_later_2
[START] [2019-10-14 00:46:28] resolve_missing_parents
[STOP] [2019-10-14 00:46:34] resolve_missing_parents
[START] [2019-10-14 00:46:34] rebuild_nodes
[START] [2019-10-14 00:46:34] Flattener#flatten
[START] [2019-10-14 00:46:34] Flattener#study_resource
[START] [2019-10-14 00:46:34] Flattener#build_ancestry
[STOP] [2019-10-14 00:46:34] Flattener#build_ancestry
[INFO] [2019-10-14 00:46:34] 3001 ancestry keys
[START] [2019-10-14 00:46:34] build_node_ancestors
[INFO] [2019-10-14 00:46:34] old ancestors deleted.
[STOP] [2019-10-14 00:46:34] build_node_ancestors
[START] [2019-10-14 00:46:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:46:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:46:35] Flattener#flatten
[STOP] [2019-10-14 00:46:35] rebuild_nodes
[START] [2019-10-14 00:46:35] resolve_missing_media_owners
[STOP] [2019-10-14 00:46:35] resolve_missing_media_owners
[START] [2019-10-14 00:46:35] sanitize_media_verbatims
[STOP] [2019-10-14 00:46:35] sanitize_media_verbatims
[START] [2019-10-14 00:46:35] queue_downloads
[STOP] [2019-10-14 00:46:35] queue_downloads
[START] [2019-10-14 00:46:35] parse_names
[WARN] [2019-10-14 00:46:35] I see 3001 names which still need to be parsed.
[STOP] [2019-10-14 00:46:39] parse_names
[START] [2019-10-14 00:46:39] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 00:46:39] denormalize_canonical_names_to_nodes
[START] [2019-10-14 00:46:39] match_nodes
[START] [2019-10-14 00:46:39] map_all_nodes_to_pages
[STOP] [2019-10-14 00:49:56] map_all_nodes_to_pages
[INFO] [2019-10-14 00:49:56] 238 Unmatched nodes (of 3001)! That's too many to output. First 10: Psammotettix provincialis (#50509206); Cicadula quadrinotata (#50509118); Anaceratagallia brachyptera (#50509594); Evacanthus interruptus (#50509486); Macrosteles cristatus (#50509298); Macrosteles sexnotatus (#50510109); Macrosteles lividus (#50510166); Mocuellus (#50509155); Mocuellus collinus (#50509154); Rhopalopyx preyssleri (#50509364)
[START] [2019-10-14 00:49:56] update_nodes
[STOP] [2019-10-14 00:49:57] update_nodes
[STOP] [2019-10-14 00:49:57] match_nodes
[START] [2019-10-14 00:49:57] reindex_search
[STOP] [2019-10-14 00:50:07] reindex_search
[START] [2019-10-14 00:50:07] normalize_units
[STOP] [2019-10-14 00:50:07] normalize_units
[START] [2019-10-14 00:50:07] calculate_statistics
[STOP] [2019-10-14 00:50:07] calculate_statistics
[START] [2019-10-14 00:50:07] complete_harvest_instance
[START] [2019-10-14 00:50:07] overall_tsv_creation
[INFO] [2019-10-14 00:50:07] Processing group of 3001 in 1 batches of 10000
[INFO] [2019-10-14 00:51:04] 1446 Traits (unfiltered)...
[INFO] [2019-10-14 00:51:18] 1446 Traits (filtered)...
[INFO] [2019-10-14 00:51:18] 0 Associations (filtered)...
[INFO] [2019-10-14 00:52:02] 7229 metadata added.
[INFO] [2019-10-14 00:52:02] 0 metadata added.
[INFO] [2019-10-14 00:52:02] Average Time: 92.18
[INFO] [2019-10-14 00:52:02] Total Time: 1m55s
[STOP] [2019-10-14 00:52:02] overall_tsv_creation
[INFO] [2019-10-14 00:52:02] Done. Check your files:
[INFO] [2019-10-14 00:52:02] (3001 lines) /app/public/data/kyrgyzstan_sp_li/publish_nodes.tsv
[INFO] [2019-10-14 00:52:02] (6699 lines) /app/public/data/kyrgyzstan_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-14 00:52:02] (3001 lines) /app/public/data/kyrgyzstan_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-14 00:52:02] (1447 lines) /app/public/data/kyrgyzstan_sp_li/publish_traits.tsv
[INFO] [2019-10-14 00:52:02] (7230 lines) /app/public/data/kyrgyzstan_sp_li/publish_metadata.tsv
[STOP] [2019-10-14 00:52:02] complete_harvest_instance
[START] [2019-10-14 00:52:02] completed
[STOP] [2019-10-14 00:52:02] completed
[STOP] [2019-10-14 00:52:02] logged process, took 369.78
Latest Process

14 Oct 00:45 EXITED currently processing 0