Harvest for Lebanon Species List Created 14 Oct 01:36

Stage: completed
Fetched: 14 Oct 01:36
Validated: 14 Oct 01:36
Deltas Created 14 Oct 01:36
Units Normalized: 14 Oct 01:39
Ancestry Built: 14 Oct 01:36
Nodes Matched: 14 Oct 01:38
Names Parsed: 14 Oct 01:36
New Models Stored: 14 Oct 01:36
Indexed: 14 Oct 01:39
Completed: 14 Oct 01:41
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 01:36:03 -0400 by logger.rb/56815
[START] [2019-10-14 01:36:03] logged process
[START] [2019-10-14 01:36:03] create_harvest_instance
[STOP] [2019-10-14 01:36:03] create_harvest_instance
[START] [2019-10-14 01:36:03] fetch_files
[STOP] [2019-10-14 01:36:03] fetch_files
[START] [2019-10-14 01:36:03] validate_each_file
[STOP] [2019-10-14 01:36:04] validate_each_file
[START] [2019-10-14 01:36:04] convert_to_csv
[CMD] [2019-10-14 01:36:04] /usr/bin/sort /app/public/converted_csv/lebanon_sp_list_refs_16379.csv > /app/public/converted_csv/lebanon_sp_list_refs_16379.csv_sorted
[CMD] [2019-10-14 01:36:04] /usr/bin/sort /app/public/converted_csv/lebanon_sp_list_nodes_16380.csv > /app/public/converted_csv/lebanon_sp_list_nodes_16380.csv_sorted
[CMD] [2019-10-14 01:36:04] /usr/bin/sort /app/public/converted_csv/lebanon_sp_list_occurrences_16381.csv > /app/public/converted_csv/lebanon_sp_list_occurrences_16381.csv_sorted
[CMD] [2019-10-14 01:36:04] /usr/bin/sort /app/public/converted_csv/lebanon_sp_list_measurements_16382.csv > /app/public/converted_csv/lebanon_sp_list_measurements_16382.csv_sorted
[STOP] [2019-10-14 01:36:04] convert_to_csv
[START] [2019-10-14 01:36:04] calculate_delta
[CMD] [2019-10-14 01:36:04] echo "0a" > /app/public/diff/lebanon_sp_list_refs_16379.diff
[CMD] [2019-10-14 01:36:04] tail -n +1 /app/public/converted_csv/lebanon_sp_list_refs_16379.csv >> /app/public/diff/lebanon_sp_list_refs_16379.diff
[CMD] [2019-10-14 01:36:04] echo "." >> /app/public/diff/lebanon_sp_list_refs_16379.diff
[CMD] [2019-10-14 01:36:04] echo "0a" > /app/public/diff/lebanon_sp_list_nodes_16380.diff
[CMD] [2019-10-14 01:36:05] tail -n +1 /app/public/converted_csv/lebanon_sp_list_nodes_16380.csv >> /app/public/diff/lebanon_sp_list_nodes_16380.diff
[CMD] [2019-10-14 01:36:05] echo "." >> /app/public/diff/lebanon_sp_list_nodes_16380.diff
[CMD] [2019-10-14 01:36:05] echo "0a" > /app/public/diff/lebanon_sp_list_occurrences_16381.diff
[CMD] [2019-10-14 01:36:05] tail -n +1 /app/public/converted_csv/lebanon_sp_list_occurrences_16381.csv >> /app/public/diff/lebanon_sp_list_occurrences_16381.diff
[CMD] [2019-10-14 01:36:05] echo "." >> /app/public/diff/lebanon_sp_list_occurrences_16381.diff
[CMD] [2019-10-14 01:36:05] echo "0a" > /app/public/diff/lebanon_sp_list_measurements_16382.diff
[CMD] [2019-10-14 01:36:05] tail -n +1 /app/public/converted_csv/lebanon_sp_list_measurements_16382.csv >> /app/public/diff/lebanon_sp_list_measurements_16382.diff
[CMD] [2019-10-14 01:36:05] echo "." >> /app/public/diff/lebanon_sp_list_measurements_16382.diff
[STOP] [2019-10-14 01:36:05] calculate_delta
[START] [2019-10-14 01:36:05] parse_diff_and_store
[INFO] [2019-10-14 01:36:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 01:36:05] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 01:36:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 01:36:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 01:36:14] Storing 2 References
[INFO] [2019-10-14 01:36:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 01:36:14] Average Time: 0.0
[INFO] [2019-10-14 01:36:14] Total Time: 1s
[INFO] [2019-10-14 01:36:14] Storing 2392 ScientificNames
[INFO] [2019-10-14 01:36:14] Processing group of 2392 in 3 groups of 1000
[INFO] [2019-10-14 01:36:15] Average Time: 0.31
[INFO] [2019-10-14 01:36:15] Total Time: 1s
[INFO] [2019-10-14 01:36:15] Storing 2392 Nodes
[INFO] [2019-10-14 01:36:15] Processing group of 2392 in 3 groups of 1000
[INFO] [2019-10-14 01:36:16] Average Time: 0.233
[INFO] [2019-10-14 01:36:16] Total Time: 1s
[INFO] [2019-10-14 01:36:16] Storing 964 Occurrences
[INFO] [2019-10-14 01:36:16] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-14 01:36:16] Average Time: 0.12
[INFO] [2019-10-14 01:36:16] Total Time: 1s
[INFO] [2019-10-14 01:36:16] Storing 2720 TraitsReferences
[INFO] [2019-10-14 01:36:16] Processing group of 2720 in 3 groups of 1000
[INFO] [2019-10-14 01:36:17] Average Time: 0.087
[INFO] [2019-10-14 01:36:17] Total Time: 1s
[INFO] [2019-10-14 01:36:17] Storing 2719 Traits
[INFO] [2019-10-14 01:36:17] Processing group of 2719 in 3 groups of 1000
[INFO] [2019-10-14 01:36:17] Average Time: 0.307
[INFO] [2019-10-14 01:36:17] Total Time: 1s
[INFO] [2019-10-14 01:36:17] Storing 2718 MetaTraits
[INFO] [2019-10-14 01:36:17] Processing group of 2718 in 3 groups of 1000
[INFO] [2019-10-14 01:36:18] Average Time: 0.11
[INFO] [2019-10-14 01:36:18] Total Time: 1s
[STOP] [2019-10-14 01:36:18] parse_diff_and_store
[START] [2019-10-14 01:36:18] resolve_keys
[INFO] [2019-10-14 01:36:30] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 01:36:30] traits to occurrences...
[INFO] [2019-10-14 01:36:32] traits to nodes (through occurrences)...
[INFO] [2019-10-14 01:36:32] Traits to sex term...
[INFO] [2019-10-14 01:36:32] Traits to lifestage term...
[INFO] [2019-10-14 01:36:33] MetaTraits to traits...
[INFO] [2019-10-14 01:36:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 01:36:34] Assocs to occurrences...
[INFO] [2019-10-14 01:36:34] Assocs to nodes...
[INFO] [2019-10-14 01:36:34] Assoc to sex term...
[INFO] [2019-10-14 01:36:34] Assoc to lifestage term...
[STOP] [2019-10-14 01:36:34] resolve_keys
[START] [2019-10-14 01:36:34] hold_for_later_1
[STOP] [2019-10-14 01:36:34] hold_for_later_1
[START] [2019-10-14 01:36:34] hold_for_later_2
[STOP] [2019-10-14 01:36:34] hold_for_later_2
[START] [2019-10-14 01:36:34] resolve_missing_parents
[STOP] [2019-10-14 01:36:38] resolve_missing_parents
[START] [2019-10-14 01:36:38] rebuild_nodes
[START] [2019-10-14 01:36:38] Flattener#flatten
[START] [2019-10-14 01:36:38] Flattener#study_resource
[START] [2019-10-14 01:36:38] Flattener#build_ancestry
[STOP] [2019-10-14 01:36:38] Flattener#build_ancestry
[INFO] [2019-10-14 01:36:38] 2392 ancestry keys
[START] [2019-10-14 01:36:38] build_node_ancestors
[INFO] [2019-10-14 01:36:38] old ancestors deleted.
[STOP] [2019-10-14 01:36:38] build_node_ancestors
[START] [2019-10-14 01:36:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:36:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:36:38] Flattener#flatten
[STOP] [2019-10-14 01:36:38] rebuild_nodes
[START] [2019-10-14 01:36:38] resolve_missing_media_owners
[STOP] [2019-10-14 01:36:38] resolve_missing_media_owners
[START] [2019-10-14 01:36:38] sanitize_media_verbatims
[STOP] [2019-10-14 01:36:38] sanitize_media_verbatims
[START] [2019-10-14 01:36:38] queue_downloads
[STOP] [2019-10-14 01:36:38] queue_downloads
[START] [2019-10-14 01:36:38] parse_names
[WARN] [2019-10-14 01:36:38] I see 2392 names which still need to be parsed.
[STOP] [2019-10-14 01:36:41] parse_names
[START] [2019-10-14 01:36:41] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 01:36:41] denormalize_canonical_names_to_nodes
[START] [2019-10-14 01:36:41] match_nodes
[START] [2019-10-14 01:36:41] map_all_nodes_to_pages
[STOP] [2019-10-14 01:38:57] map_all_nodes_to_pages
[INFO] [2019-10-14 01:38:57] 160 Unmatched nodes (of 2392)! That's too many to output. First 10: Achnatherum thomasii (#50533669); Oryzopsis miliaceum (#50533774); Oryzopsis holciforme (#50534356); Oryzopsis blancheanum (#50534468); Cenchrus caput-medusae (#50534694); Saccharum hostii (#50534716); Crypsis (#50534786); Crypsis schoenoides (#50534785); Pycreus (#50534512); Nectarinia osea (#50532733)
[START] [2019-10-14 01:38:57] update_nodes
[STOP] [2019-10-14 01:38:58] update_nodes
[STOP] [2019-10-14 01:38:58] match_nodes
[START] [2019-10-14 01:38:58] reindex_search
[STOP] [2019-10-14 01:39:03] reindex_search
[START] [2019-10-14 01:39:03] normalize_units
[STOP] [2019-10-14 01:39:03] normalize_units
[START] [2019-10-14 01:39:03] calculate_statistics
[STOP] [2019-10-14 01:39:03] calculate_statistics
[START] [2019-10-14 01:39:03] complete_harvest_instance
[START] [2019-10-14 01:39:03] overall_tsv_creation
[INFO] [2019-10-14 01:39:03] Processing group of 2392 in 1 batches of 10000
[INFO] [2019-10-14 01:40:00] 964 Traits (unfiltered)...
[INFO] [2019-10-14 01:40:13] 964 Traits (filtered)...
[INFO] [2019-10-14 01:40:13] 0 Associations (filtered)...
[INFO] [2019-10-14 01:40:59] 4819 metadata added.
[INFO] [2019-10-14 01:40:59] 0 metadata added.
[INFO] [2019-10-14 01:40:59] Average Time: 93.78
[INFO] [2019-10-14 01:40:59] Total Time: 1m57s
[STOP] [2019-10-14 01:40:59] overall_tsv_creation
[INFO] [2019-10-14 01:40:59] Done. Check your files:
[INFO] [2019-10-14 01:41:00] (2392 lines) /app/public/data/lebanon_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 01:41:00] (3811 lines) /app/public/data/lebanon_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 01:41:00] (2392 lines) /app/public/data/lebanon_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 01:41:00] (965 lines) /app/public/data/lebanon_sp_list/publish_traits.tsv
[INFO] [2019-10-14 01:41:00] (4820 lines) /app/public/data/lebanon_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 01:41:00] complete_harvest_instance
[START] [2019-10-14 01:41:00] completed
[STOP] [2019-10-14 01:41:00] completed
[STOP] [2019-10-14 01:41:00] logged process, took 297.06
Latest Process

14 Oct 01:36 EXITED currently processing 0