Harvest for Mongolia Species List Created 14 Oct 09:12

Stage: completed
Fetched: 14 Oct 09:12
Validated: 14 Oct 09:12
Deltas Created 14 Oct 09:12
Units Normalized: 14 Oct 09:16
Ancestry Built: 14 Oct 09:13
Nodes Matched: 14 Oct 09:16
Names Parsed: 14 Oct 09:13
New Models Stored: 14 Oct 09:12
Indexed: 14 Oct 09:16
Completed: 14 Oct 09:18
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 09:12:02 -0400 by logger.rb/56815
[START] [2019-10-14 09:12:02] logged process
[START] [2019-10-14 09:12:02] create_harvest_instance
[STOP] [2019-10-14 09:12:02] create_harvest_instance
[START] [2019-10-14 09:12:02] fetch_files
[STOP] [2019-10-14 09:12:02] fetch_files
[START] [2019-10-14 09:12:02] validate_each_file
[STOP] [2019-10-14 09:12:03] validate_each_file
[START] [2019-10-14 09:12:03] convert_to_csv
[CMD] [2019-10-14 09:12:03] /usr/bin/sort /app/public/converted_csv/mongolia_sp_list_refs_16611.csv > /app/public/converted_csv/mongolia_sp_list_refs_16611.csv_sorted
[CMD] [2019-10-14 09:12:03] /usr/bin/sort /app/public/converted_csv/mongolia_sp_list_nodes_16612.csv > /app/public/converted_csv/mongolia_sp_list_nodes_16612.csv_sorted
[CMD] [2019-10-14 09:12:03] /usr/bin/sort /app/public/converted_csv/mongolia_sp_list_occurrences_16613.csv > /app/public/converted_csv/mongolia_sp_list_occurrences_16613.csv_sorted
[CMD] [2019-10-14 09:12:03] /usr/bin/sort /app/public/converted_csv/mongolia_sp_list_measurements_16614.csv > /app/public/converted_csv/mongolia_sp_list_measurements_16614.csv_sorted
[STOP] [2019-10-14 09:12:03] convert_to_csv
[START] [2019-10-14 09:12:03] calculate_delta
[CMD] [2019-10-14 09:12:03] echo "0a" > /app/public/diff/mongolia_sp_list_refs_16611.diff
[CMD] [2019-10-14 09:12:04] tail -n +1 /app/public/converted_csv/mongolia_sp_list_refs_16611.csv >> /app/public/diff/mongolia_sp_list_refs_16611.diff
[CMD] [2019-10-14 09:12:04] echo "." >> /app/public/diff/mongolia_sp_list_refs_16611.diff
[CMD] [2019-10-14 09:12:04] echo "0a" > /app/public/diff/mongolia_sp_list_nodes_16612.diff
[CMD] [2019-10-14 09:12:04] tail -n +1 /app/public/converted_csv/mongolia_sp_list_nodes_16612.csv >> /app/public/diff/mongolia_sp_list_nodes_16612.diff
[CMD] [2019-10-14 09:12:04] echo "." >> /app/public/diff/mongolia_sp_list_nodes_16612.diff
[CMD] [2019-10-14 09:12:04] echo "0a" > /app/public/diff/mongolia_sp_list_occurrences_16613.diff
[CMD] [2019-10-14 09:12:04] tail -n +1 /app/public/converted_csv/mongolia_sp_list_occurrences_16613.csv >> /app/public/diff/mongolia_sp_list_occurrences_16613.diff
[CMD] [2019-10-14 09:12:04] echo "." >> /app/public/diff/mongolia_sp_list_occurrences_16613.diff
[CMD] [2019-10-14 09:12:04] echo "0a" > /app/public/diff/mongolia_sp_list_measurements_16614.diff
[CMD] [2019-10-14 09:12:04] tail -n +1 /app/public/converted_csv/mongolia_sp_list_measurements_16614.csv >> /app/public/diff/mongolia_sp_list_measurements_16614.diff
[CMD] [2019-10-14 09:12:04] echo "." >> /app/public/diff/mongolia_sp_list_measurements_16614.diff
[STOP] [2019-10-14 09:12:05] calculate_delta
[START] [2019-10-14 09:12:05] parse_diff_and_store
[INFO] [2019-10-14 09:12:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 09:12:05] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 09:12:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 09:12:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 09:12:21] Storing 2 References
[INFO] [2019-10-14 09:12:21] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 09:12:21] Average Time: 0.0
[INFO] [2019-10-14 09:12:21] Total Time: 1s
[INFO] [2019-10-14 09:12:21] Storing 4299 ScientificNames
[INFO] [2019-10-14 09:12:21] Processing group of 4299 in 5 groups of 1000
[INFO] [2019-10-14 09:12:23] Average Time: 0.342
[INFO] [2019-10-14 09:12:23] Total Time: 2s
[INFO] [2019-10-14 09:12:23] Storing 4299 Nodes
[INFO] [2019-10-14 09:12:23] Processing group of 4299 in 5 groups of 1000
[INFO] [2019-10-14 09:12:24] Average Time: 0.274
[INFO] [2019-10-14 09:12:24] Total Time: 2s
[INFO] [2019-10-14 09:12:24] Storing 2410 Occurrences
[INFO] [2019-10-14 09:12:24] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-14 09:12:25] Average Time: 0.157
[INFO] [2019-10-14 09:12:25] Total Time: 1s
[INFO] [2019-10-14 09:12:25] Storing 4820 TraitsReferences
[INFO] [2019-10-14 09:12:25] Processing group of 4820 in 5 groups of 1000
[INFO] [2019-10-14 09:12:25] Average Time: 0.09
[INFO] [2019-10-14 09:12:25] Total Time: 1s
[INFO] [2019-10-14 09:12:25] Storing 4819 Traits
[INFO] [2019-10-14 09:12:25] Processing group of 4819 in 5 groups of 1000
[INFO] [2019-10-14 09:12:27] Average Time: 0.304
[INFO] [2019-10-14 09:12:27] Total Time: 2s
[INFO] [2019-10-14 09:12:27] Storing 4813 MetaTraits
[INFO] [2019-10-14 09:12:27] Processing group of 4813 in 5 groups of 1000
[INFO] [2019-10-14 09:12:27] Average Time: 0.126
[INFO] [2019-10-14 09:12:27] Total Time: 1s
[STOP] [2019-10-14 09:12:27] parse_diff_and_store
[START] [2019-10-14 09:12:27] resolve_keys
[INFO] [2019-10-14 09:12:47] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 09:12:49] traits to occurrences...
[INFO] [2019-10-14 09:12:50] traits to nodes (through occurrences)...
[INFO] [2019-10-14 09:12:50] Traits to sex term...
[INFO] [2019-10-14 09:12:51] Traits to lifestage term...
[INFO] [2019-10-14 09:12:52] MetaTraits to traits...
[INFO] [2019-10-14 09:12:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 09:12:53] Assocs to occurrences...
[INFO] [2019-10-14 09:12:53] Assocs to nodes...
[INFO] [2019-10-14 09:12:53] Assoc to sex term...
[INFO] [2019-10-14 09:12:53] Assoc to lifestage term...
[STOP] [2019-10-14 09:12:53] resolve_keys
[START] [2019-10-14 09:12:53] hold_for_later_1
[STOP] [2019-10-14 09:12:53] hold_for_later_1
[START] [2019-10-14 09:12:53] hold_for_later_2
[STOP] [2019-10-14 09:12:53] hold_for_later_2
[START] [2019-10-14 09:12:53] resolve_missing_parents
[STOP] [2019-10-14 09:13:00] resolve_missing_parents
[START] [2019-10-14 09:13:00] rebuild_nodes
[START] [2019-10-14 09:13:00] Flattener#flatten
[START] [2019-10-14 09:13:00] Flattener#study_resource
[START] [2019-10-14 09:13:00] Flattener#build_ancestry
[STOP] [2019-10-14 09:13:01] Flattener#build_ancestry
[INFO] [2019-10-14 09:13:01] 4299 ancestry keys
[START] [2019-10-14 09:13:01] build_node_ancestors
[INFO] [2019-10-14 09:13:01] old ancestors deleted.
[STOP] [2019-10-14 09:13:01] build_node_ancestors
[START] [2019-10-14 09:13:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:13:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:13:02] Flattener#flatten
[STOP] [2019-10-14 09:13:02] rebuild_nodes
[START] [2019-10-14 09:13:02] resolve_missing_media_owners
[STOP] [2019-10-14 09:13:02] resolve_missing_media_owners
[START] [2019-10-14 09:13:02] sanitize_media_verbatims
[STOP] [2019-10-14 09:13:02] sanitize_media_verbatims
[START] [2019-10-14 09:13:02] queue_downloads
[STOP] [2019-10-14 09:13:02] queue_downloads
[START] [2019-10-14 09:13:02] parse_names
[WARN] [2019-10-14 09:13:02] I see 4299 names which still need to be parsed.
[STOP] [2019-10-14 09:13:07] parse_names
[START] [2019-10-14 09:13:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 09:13:07] denormalize_canonical_names_to_nodes
[START] [2019-10-14 09:13:07] match_nodes
[START] [2019-10-14 09:13:07] map_all_nodes_to_pages
[STOP] [2019-10-14 09:16:37] map_all_nodes_to_pages
[INFO] [2019-10-14 09:16:37] 356 Unmatched nodes (of 4299)! That's too many to output. First 10: Philomachus pugnax (#50783858); Limnodromus (#50784115); Larus ichthyaetus (#50785015); Larus relictus (#50787536); Tribosphenomys secundus (#50786292); Adamisaurus (#50784162); Adamisaurus magnidentatus (#50784161); Erdenetesaurus (#50786058); Erdenetesaurus robinsonae (#50786057); Gobinatus (#50786110)
[START] [2019-10-14 09:16:37] update_nodes
[STOP] [2019-10-14 09:16:38] update_nodes
[STOP] [2019-10-14 09:16:38] match_nodes
[START] [2019-10-14 09:16:38] reindex_search
[STOP] [2019-10-14 09:16:47] reindex_search
[START] [2019-10-14 09:16:47] normalize_units
[STOP] [2019-10-14 09:16:47] normalize_units
[START] [2019-10-14 09:16:47] calculate_statistics
[STOP] [2019-10-14 09:16:47] calculate_statistics
[START] [2019-10-14 09:16:47] complete_harvest_instance
[START] [2019-10-14 09:16:47] overall_tsv_creation
[INFO] [2019-10-14 09:16:47] Processing group of 4299 in 1 batches of 10000
[INFO] [2019-10-14 09:17:51] 2410 Traits (unfiltered)...
[INFO] [2019-10-14 09:18:04] 2410 Traits (filtered)...
[INFO] [2019-10-14 09:18:04] 0 Associations (filtered)...
[INFO] [2019-10-14 09:18:46] 12042 metadata added.
[INFO] [2019-10-14 09:18:46] 0 metadata added.
[INFO] [2019-10-14 09:18:46] Average Time: 94.71
[INFO] [2019-10-14 09:18:46] Total Time: 1m60s
[STOP] [2019-10-14 09:18:46] overall_tsv_creation
[INFO] [2019-10-14 09:18:46] Done. Check your files:
[INFO] [2019-10-14 09:18:46] (4299 lines) /app/public/data/mongolia_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 09:18:46] (9723 lines) /app/public/data/mongolia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 09:18:46] (4299 lines) /app/public/data/mongolia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 09:18:46] (2411 lines) /app/public/data/mongolia_sp_list/publish_traits.tsv
[INFO] [2019-10-14 09:18:46] (12043 lines) /app/public/data/mongolia_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 09:18:47] complete_harvest_instance
[START] [2019-10-14 09:18:47] completed
[STOP] [2019-10-14 09:18:47] completed
[STOP] [2019-10-14 09:18:47] logged process, took 404.59
Latest Process

14 Oct 09:12 EXITED currently processing 0