Harvest for Montenegro Species List Created 14 Oct 09:18

Stage: completed
Fetched: 14 Oct 09:18
Validated: 14 Oct 09:18
Deltas Created 14 Oct 09:18
Units Normalized: 14 Oct 09:22
Ancestry Built: 14 Oct 09:19
Nodes Matched: 14 Oct 09:22
Names Parsed: 14 Oct 09:19
New Models Stored: 14 Oct 09:19
Indexed: 14 Oct 09:22
Completed: 14 Oct 09:24
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 09:18:53 -0400 by logger.rb/56815
[START] [2019-10-14 09:18:53] logged process
[START] [2019-10-14 09:18:53] create_harvest_instance
[STOP] [2019-10-14 09:18:53] create_harvest_instance
[START] [2019-10-14 09:18:53] fetch_files
[STOP] [2019-10-14 09:18:53] fetch_files
[START] [2019-10-14 09:18:53] validate_each_file
[STOP] [2019-10-14 09:18:54] validate_each_file
[START] [2019-10-14 09:18:54] convert_to_csv
[CMD] [2019-10-14 09:18:54] /usr/bin/sort /app/public/converted_csv/montenegro_sp_li_refs_16619.csv > /app/public/converted_csv/montenegro_sp_li_refs_16619.csv_sorted
[CMD] [2019-10-14 09:18:54] /usr/bin/sort /app/public/converted_csv/montenegro_sp_li_nodes_16620.csv > /app/public/converted_csv/montenegro_sp_li_nodes_16620.csv_sorted
[CMD] [2019-10-14 09:18:54] /usr/bin/sort /app/public/converted_csv/montenegro_sp_li_occurrences_16621.csv > /app/public/converted_csv/montenegro_sp_li_occurrences_16621.csv_sorted
[CMD] [2019-10-14 09:18:54] /usr/bin/sort /app/public/converted_csv/montenegro_sp_li_measurements_16622.csv > /app/public/converted_csv/montenegro_sp_li_measurements_16622.csv_sorted
[STOP] [2019-10-14 09:18:54] convert_to_csv
[START] [2019-10-14 09:18:54] calculate_delta
[CMD] [2019-10-14 09:18:54] echo "0a" > /app/public/diff/montenegro_sp_li_refs_16619.diff
[CMD] [2019-10-14 09:18:54] tail -n +1 /app/public/converted_csv/montenegro_sp_li_refs_16619.csv >> /app/public/diff/montenegro_sp_li_refs_16619.diff
[CMD] [2019-10-14 09:18:54] echo "." >> /app/public/diff/montenegro_sp_li_refs_16619.diff
[CMD] [2019-10-14 09:18:54] echo "0a" > /app/public/diff/montenegro_sp_li_nodes_16620.diff
[CMD] [2019-10-14 09:18:54] tail -n +1 /app/public/converted_csv/montenegro_sp_li_nodes_16620.csv >> /app/public/diff/montenegro_sp_li_nodes_16620.diff
[CMD] [2019-10-14 09:18:55] echo "." >> /app/public/diff/montenegro_sp_li_nodes_16620.diff
[CMD] [2019-10-14 09:18:55] echo "0a" > /app/public/diff/montenegro_sp_li_occurrences_16621.diff
[CMD] [2019-10-14 09:18:55] tail -n +1 /app/public/converted_csv/montenegro_sp_li_occurrences_16621.csv >> /app/public/diff/montenegro_sp_li_occurrences_16621.diff
[CMD] [2019-10-14 09:18:55] echo "." >> /app/public/diff/montenegro_sp_li_occurrences_16621.diff
[CMD] [2019-10-14 09:18:55] echo "0a" > /app/public/diff/montenegro_sp_li_measurements_16622.diff
[CMD] [2019-10-14 09:18:55] tail -n +1 /app/public/converted_csv/montenegro_sp_li_measurements_16622.csv >> /app/public/diff/montenegro_sp_li_measurements_16622.diff
[CMD] [2019-10-14 09:18:55] echo "." >> /app/public/diff/montenegro_sp_li_measurements_16622.diff
[STOP] [2019-10-14 09:18:55] calculate_delta
[START] [2019-10-14 09:18:55] parse_diff_and_store
[INFO] [2019-10-14 09:18:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 09:18:55] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 09:18:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 09:18:57] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 09:19:07] Storing 2 References
[INFO] [2019-10-14 09:19:07] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 09:19:07] Average Time: 0.0
[INFO] [2019-10-14 09:19:07] Total Time: 1s
[INFO] [2019-10-14 09:19:07] Storing 3300 ScientificNames
[INFO] [2019-10-14 09:19:07] Processing group of 3300 in 4 groups of 1000
[INFO] [2019-10-14 09:19:08] Average Time: 0.323
[INFO] [2019-10-14 09:19:08] Total Time: 2s
[INFO] [2019-10-14 09:19:08] Storing 3300 Nodes
[INFO] [2019-10-14 09:19:08] Processing group of 3300 in 4 groups of 1000
[INFO] [2019-10-14 09:19:09] Average Time: 0.253
[INFO] [2019-10-14 09:19:09] Total Time: 2s
[INFO] [2019-10-14 09:19:09] Storing 1446 Occurrences
[INFO] [2019-10-14 09:19:09] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-14 09:19:09] Average Time: 0.09
[INFO] [2019-10-14 09:19:09] Total Time: 1s
[INFO] [2019-10-14 09:19:09] Storing 3440 TraitsReferences
[INFO] [2019-10-14 09:19:09] Processing group of 3440 in 4 groups of 1000
[INFO] [2019-10-14 09:19:10] Average Time: 0.083
[INFO] [2019-10-14 09:19:10] Total Time: 1s
[INFO] [2019-10-14 09:19:10] Storing 3439 Traits
[INFO] [2019-10-14 09:19:10] Processing group of 3439 in 4 groups of 1000
[INFO] [2019-10-14 09:19:11] Average Time: 0.333
[INFO] [2019-10-14 09:19:11] Total Time: 2s
[INFO] [2019-10-14 09:19:11] Storing 3440 MetaTraits
[INFO] [2019-10-14 09:19:11] Processing group of 3440 in 4 groups of 1000
[INFO] [2019-10-14 09:19:12] Average Time: 0.103
[INFO] [2019-10-14 09:19:12] Total Time: 1s
[STOP] [2019-10-14 09:19:12] parse_diff_and_store
[START] [2019-10-14 09:19:12] resolve_keys
[INFO] [2019-10-14 09:19:26] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 09:19:27] traits to occurrences...
[INFO] [2019-10-14 09:19:28] traits to nodes (through occurrences)...
[INFO] [2019-10-14 09:19:28] Traits to sex term...
[INFO] [2019-10-14 09:19:29] Traits to lifestage term...
[INFO] [2019-10-14 09:19:29] MetaTraits to traits...
[INFO] [2019-10-14 09:19:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 09:19:30] Assocs to occurrences...
[INFO] [2019-10-14 09:19:30] Assocs to nodes...
[INFO] [2019-10-14 09:19:30] Assoc to sex term...
[INFO] [2019-10-14 09:19:30] Assoc to lifestage term...
[STOP] [2019-10-14 09:19:30] resolve_keys
[START] [2019-10-14 09:19:30] hold_for_later_1
[STOP] [2019-10-14 09:19:30] hold_for_later_1
[START] [2019-10-14 09:19:30] hold_for_later_2
[STOP] [2019-10-14 09:19:30] hold_for_later_2
[START] [2019-10-14 09:19:30] resolve_missing_parents
[STOP] [2019-10-14 09:19:36] resolve_missing_parents
[START] [2019-10-14 09:19:36] rebuild_nodes
[START] [2019-10-14 09:19:36] Flattener#flatten
[START] [2019-10-14 09:19:36] Flattener#study_resource
[START] [2019-10-14 09:19:36] Flattener#build_ancestry
[STOP] [2019-10-14 09:19:37] Flattener#build_ancestry
[INFO] [2019-10-14 09:19:37] 3300 ancestry keys
[START] [2019-10-14 09:19:37] build_node_ancestors
[INFO] [2019-10-14 09:19:37] old ancestors deleted.
[STOP] [2019-10-14 09:19:38] build_node_ancestors
[START] [2019-10-14 09:19:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:19:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:19:39] Flattener#flatten
[STOP] [2019-10-14 09:19:39] rebuild_nodes
[START] [2019-10-14 09:19:39] resolve_missing_media_owners
[STOP] [2019-10-14 09:19:39] resolve_missing_media_owners
[START] [2019-10-14 09:19:39] sanitize_media_verbatims
[STOP] [2019-10-14 09:19:39] sanitize_media_verbatims
[START] [2019-10-14 09:19:39] queue_downloads
[STOP] [2019-10-14 09:19:39] queue_downloads
[START] [2019-10-14 09:19:39] parse_names
[WARN] [2019-10-14 09:19:39] I see 3300 names which still need to be parsed.
[STOP] [2019-10-14 09:19:42] parse_names
[START] [2019-10-14 09:19:42] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 09:19:42] denormalize_canonical_names_to_nodes
[START] [2019-10-14 09:19:42] match_nodes
[START] [2019-10-14 09:19:42] map_all_nodes_to_pages
[STOP] [2019-10-14 09:22:41] map_all_nodes_to_pages
[INFO] [2019-10-14 09:22:41] 204 Unmatched nodes (of 3300)! That's too many to output. First 10: Elymus caninum (#50789360); Thinopyrum farctus (#50790032); Carex gracilis (#50790056); Leopoldia comosum (#50788960); Xanthorrhoeaceae (#50790595); Asplenium officinarum (#50789171); Klukisporites (#50790426); Klukisporites variegatus (#50790679); Otozamites (#50790301); Duplexisporites (#50790191)
[START] [2019-10-14 09:22:41] update_nodes
[STOP] [2019-10-14 09:22:42] update_nodes
[STOP] [2019-10-14 09:22:42] match_nodes
[START] [2019-10-14 09:22:42] reindex_search
[STOP] [2019-10-14 09:22:49] reindex_search
[START] [2019-10-14 09:22:49] normalize_units
[STOP] [2019-10-14 09:22:49] normalize_units
[START] [2019-10-14 09:22:49] calculate_statistics
[STOP] [2019-10-14 09:22:49] calculate_statistics
[START] [2019-10-14 09:22:49] complete_harvest_instance
[START] [2019-10-14 09:22:49] overall_tsv_creation
[INFO] [2019-10-14 09:22:49] Processing group of 3300 in 1 batches of 10000
[INFO] [2019-10-14 09:23:49] 1446 Traits (unfiltered)...
[INFO] [2019-10-14 09:24:03] 1446 Traits (filtered)...
[INFO] [2019-10-14 09:24:03] 0 Associations (filtered)...
[INFO] [2019-10-14 09:24:42] 7230 metadata added.
[INFO] [2019-10-14 09:24:42] 0 metadata added.
[INFO] [2019-10-14 09:24:42] Average Time: 90.06
[INFO] [2019-10-14 09:24:42] Total Time: 1m54s
[STOP] [2019-10-14 09:24:42] overall_tsv_creation
[INFO] [2019-10-14 09:24:42] Done. Check your files:
[INFO] [2019-10-14 09:24:43] (3300 lines) /app/public/data/montenegro_sp_li/publish_nodes.tsv
[INFO] [2019-10-14 09:24:43] (13912 lines) /app/public/data/montenegro_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-14 09:24:43] (3300 lines) /app/public/data/montenegro_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-14 09:24:43] (1447 lines) /app/public/data/montenegro_sp_li/publish_traits.tsv
[INFO] [2019-10-14 09:24:43] (7231 lines) /app/public/data/montenegro_sp_li/publish_metadata.tsv
[STOP] [2019-10-14 09:24:43] complete_harvest_instance
[START] [2019-10-14 09:24:43] completed
[STOP] [2019-10-14 09:24:43] completed
[STOP] [2019-10-14 09:24:43] logged process, took 350.42
Latest Process

14 Oct 09:18 EXITED currently processing 0