Harvest for Cape Verde Species List Created 12 Oct 02:12

Stage: completed
Fetched: 12 Oct 02:12
Validated: 12 Oct 02:12
Deltas Created 12 Oct 02:12
Units Normalized: 12 Oct 02:14
Ancestry Built: 12 Oct 02:13
Nodes Matched: 12 Oct 02:14
Names Parsed: 12 Oct 02:13
New Models Stored: 12 Oct 02:13
Indexed: 12 Oct 02:14
Completed: 12 Oct 02:15
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 02:12:57 -0400 by logger.rb/56815
[START] [2019-10-12 02:12:57] logged process
[START] [2019-10-12 02:12:57] create_harvest_instance
[STOP] [2019-10-12 02:12:58] create_harvest_instance
[START] [2019-10-12 02:12:58] fetch_files
[STOP] [2019-10-12 02:12:58] fetch_files
[START] [2019-10-12 02:12:58] validate_each_file
[STOP] [2019-10-12 02:12:58] validate_each_file
[START] [2019-10-12 02:12:58] convert_to_csv
[CMD] [2019-10-12 02:12:58] /usr/bin/sort /app/public/converted_csv/cape_verde_sp_li_refs_15379.csv > /app/public/converted_csv/cape_verde_sp_li_refs_15379.csv_sorted
[CMD] [2019-10-12 02:12:58] /usr/bin/sort /app/public/converted_csv/cape_verde_sp_li_nodes_15380.csv > /app/public/converted_csv/cape_verde_sp_li_nodes_15380.csv_sorted
[CMD] [2019-10-12 02:12:58] /usr/bin/sort /app/public/converted_csv/cape_verde_sp_li_occurrences_15381.csv > /app/public/converted_csv/cape_verde_sp_li_occurrences_15381.csv_sorted
[CMD] [2019-10-12 02:12:58] /usr/bin/sort /app/public/converted_csv/cape_verde_sp_li_measurements_15382.csv > /app/public/converted_csv/cape_verde_sp_li_measurements_15382.csv_sorted
[STOP] [2019-10-12 02:12:58] convert_to_csv
[START] [2019-10-12 02:12:58] calculate_delta
[CMD] [2019-10-12 02:12:58] echo "0a" > /app/public/diff/cape_verde_sp_li_refs_15379.diff
[CMD] [2019-10-12 02:12:58] tail -n +1 /app/public/converted_csv/cape_verde_sp_li_refs_15379.csv >> /app/public/diff/cape_verde_sp_li_refs_15379.diff
[CMD] [2019-10-12 02:12:58] echo "." >> /app/public/diff/cape_verde_sp_li_refs_15379.diff
[CMD] [2019-10-12 02:12:58] echo "0a" > /app/public/diff/cape_verde_sp_li_nodes_15380.diff
[CMD] [2019-10-12 02:12:59] tail -n +1 /app/public/converted_csv/cape_verde_sp_li_nodes_15380.csv >> /app/public/diff/cape_verde_sp_li_nodes_15380.diff
[CMD] [2019-10-12 02:12:59] echo "." >> /app/public/diff/cape_verde_sp_li_nodes_15380.diff
[CMD] [2019-10-12 02:12:59] echo "0a" > /app/public/diff/cape_verde_sp_li_occurrences_15381.diff
[CMD] [2019-10-12 02:12:59] tail -n +1 /app/public/converted_csv/cape_verde_sp_li_occurrences_15381.csv >> /app/public/diff/cape_verde_sp_li_occurrences_15381.diff
[CMD] [2019-10-12 02:12:59] echo "." >> /app/public/diff/cape_verde_sp_li_occurrences_15381.diff
[CMD] [2019-10-12 02:12:59] echo "0a" > /app/public/diff/cape_verde_sp_li_measurements_15382.diff
[CMD] [2019-10-12 02:12:59] tail -n +1 /app/public/converted_csv/cape_verde_sp_li_measurements_15382.csv >> /app/public/diff/cape_verde_sp_li_measurements_15382.diff
[CMD] [2019-10-12 02:12:59] echo "." >> /app/public/diff/cape_verde_sp_li_measurements_15382.diff
[STOP] [2019-10-12 02:12:59] calculate_delta
[START] [2019-10-12 02:12:59] parse_diff_and_store
[INFO] [2019-10-12 02:12:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 02:13:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 02:13:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 02:13:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 02:13:03] Storing 2 References
[INFO] [2019-10-12 02:13:03] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 02:13:03] Average Time: 0.0
[INFO] [2019-10-12 02:13:03] Total Time: 1s
[INFO] [2019-10-12 02:13:03] Storing 1115 ScientificNames
[INFO] [2019-10-12 02:13:03] Processing group of 1115 in 2 groups of 1000
[INFO] [2019-10-12 02:13:04] Average Time: 0.325
[INFO] [2019-10-12 02:13:04] Total Time: 1s
[INFO] [2019-10-12 02:13:04] Storing 1115 Nodes
[INFO] [2019-10-12 02:13:04] Processing group of 1115 in 2 groups of 1000
[INFO] [2019-10-12 02:13:04] Average Time: 0.235
[INFO] [2019-10-12 02:13:04] Total Time: 1s
[INFO] [2019-10-12 02:13:04] Storing 482 Occurrences
[INFO] [2019-10-12 02:13:04] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-12 02:13:04] Average Time: 0.08
[INFO] [2019-10-12 02:13:04] Total Time: 1s
[INFO] [2019-10-12 02:13:04] Storing 1050 TraitsReferences
[INFO] [2019-10-12 02:13:04] Processing group of 1050 in 2 groups of 1000
[INFO] [2019-10-12 02:13:05] Average Time: 0.085
[INFO] [2019-10-12 02:13:05] Total Time: 1s
[INFO] [2019-10-12 02:13:05] Storing 1049 Traits
[INFO] [2019-10-12 02:13:05] Processing group of 1049 in 2 groups of 1000
[INFO] [2019-10-12 02:13:05] Average Time: 0.24
[INFO] [2019-10-12 02:13:05] Total Time: 1s
[INFO] [2019-10-12 02:13:05] Storing 1049 MetaTraits
[INFO] [2019-10-12 02:13:05] Processing group of 1049 in 2 groups of 1000
[INFO] [2019-10-12 02:13:05] Average Time: 0.09
[INFO] [2019-10-12 02:13:05] Total Time: 1s
[STOP] [2019-10-12 02:13:05] parse_diff_and_store
[START] [2019-10-12 02:13:05] resolve_keys
[INFO] [2019-10-12 02:13:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 02:13:12] traits to occurrences...
[INFO] [2019-10-12 02:13:13] traits to nodes (through occurrences)...
[INFO] [2019-10-12 02:13:13] Traits to sex term...
[INFO] [2019-10-12 02:13:13] Traits to lifestage term...
[INFO] [2019-10-12 02:13:13] MetaTraits to traits...
[INFO] [2019-10-12 02:13:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 02:13:13] Assocs to occurrences...
[INFO] [2019-10-12 02:13:13] Assocs to nodes...
[INFO] [2019-10-12 02:13:13] Assoc to sex term...
[INFO] [2019-10-12 02:13:13] Assoc to lifestage term...
[STOP] [2019-10-12 02:13:13] resolve_keys
[START] [2019-10-12 02:13:13] hold_for_later_1
[STOP] [2019-10-12 02:13:13] hold_for_later_1
[START] [2019-10-12 02:13:13] hold_for_later_2
[STOP] [2019-10-12 02:13:13] hold_for_later_2
[START] [2019-10-12 02:13:13] resolve_missing_parents
[STOP] [2019-10-12 02:13:14] resolve_missing_parents
[START] [2019-10-12 02:13:14] rebuild_nodes
[START] [2019-10-12 02:13:14] Flattener#flatten
[START] [2019-10-12 02:13:14] Flattener#study_resource
[START] [2019-10-12 02:13:14] Flattener#build_ancestry
[STOP] [2019-10-12 02:13:14] Flattener#build_ancestry
[INFO] [2019-10-12 02:13:14] 1115 ancestry keys
[START] [2019-10-12 02:13:14] build_node_ancestors
[INFO] [2019-10-12 02:13:14] old ancestors deleted.
[STOP] [2019-10-12 02:13:14] build_node_ancestors
[START] [2019-10-12 02:13:15] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:13:15] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:13:15] Flattener#flatten
[STOP] [2019-10-12 02:13:15] rebuild_nodes
[START] [2019-10-12 02:13:15] resolve_missing_media_owners
[STOP] [2019-10-12 02:13:15] resolve_missing_media_owners
[START] [2019-10-12 02:13:15] sanitize_media_verbatims
[STOP] [2019-10-12 02:13:15] sanitize_media_verbatims
[START] [2019-10-12 02:13:15] queue_downloads
[STOP] [2019-10-12 02:13:15] queue_downloads
[START] [2019-10-12 02:13:15] parse_names
[WARN] [2019-10-12 02:13:15] I see 1115 names which still need to be parsed.
[STOP] [2019-10-12 02:13:17] parse_names
[START] [2019-10-12 02:13:17] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 02:13:17] denormalize_canonical_names_to_nodes
[START] [2019-10-12 02:13:17] match_nodes
[START] [2019-10-12 02:13:17] map_all_nodes_to_pages
[STOP] [2019-10-12 02:14:00] map_all_nodes_to_pages
[INFO] [2019-10-12 02:14:00] 77 Unmatched nodes (of 1115)! That's too many to output. First 10: Strumigenys emmae (#49085387); Caloplaca carphinea (#49085262); Egretta intermedia (#49085289); Philomachus (#49085192); Philomachus pugnax (#49085191); Isturgia catalaunaria (#49086030); Phaiogramma (#49086020); Phaiogramma faustinata (#49086019); Rocella canariensis (#49085085); Rocella vicentina (#49085096)
[START] [2019-10-12 02:14:00] update_nodes
[STOP] [2019-10-12 02:14:00] update_nodes
[STOP] [2019-10-12 02:14:00] match_nodes
[START] [2019-10-12 02:14:00] reindex_search
[STOP] [2019-10-12 02:14:02] reindex_search
[START] [2019-10-12 02:14:02] normalize_units
[STOP] [2019-10-12 02:14:02] normalize_units
[START] [2019-10-12 02:14:02] calculate_statistics
[STOP] [2019-10-12 02:14:02] calculate_statistics
[START] [2019-10-12 02:14:02] complete_harvest_instance
[START] [2019-10-12 02:14:02] overall_tsv_creation
[INFO] [2019-10-12 02:14:02] Processing group of 1115 in 1 batches of 10000
[INFO] [2019-10-12 02:14:53] 482 Traits (unfiltered)...
[INFO] [2019-10-12 02:15:07] 482 Traits (filtered)...
[INFO] [2019-10-12 02:15:07] 0 Associations (filtered)...
[INFO] [2019-10-12 02:15:44] 2409 metadata added.
[INFO] [2019-10-12 02:15:44] 0 metadata added.
[INFO] [2019-10-12 02:15:44] Average Time: 79.83
[INFO] [2019-10-12 02:15:44] Total Time: 1m43s
[STOP] [2019-10-12 02:15:44] overall_tsv_creation
[INFO] [2019-10-12 02:15:44] Done. Check your files:
[INFO] [2019-10-12 02:15:45] (1115 lines) /app/public/data/cape_verde_sp_li/publish_nodes.tsv
[INFO] [2019-10-12 02:15:45] (1376 lines) /app/public/data/cape_verde_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-12 02:15:45] (1115 lines) /app/public/data/cape_verde_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-12 02:15:45] (483 lines) /app/public/data/cape_verde_sp_li/publish_traits.tsv
[INFO] [2019-10-12 02:15:45] (2410 lines) /app/public/data/cape_verde_sp_li/publish_metadata.tsv
[STOP] [2019-10-12 02:15:45] complete_harvest_instance
[START] [2019-10-12 02:15:45] completed
[STOP] [2019-10-12 02:15:45] completed
[STOP] [2019-10-12 02:15:45] logged process, took 167.83
Latest Process

12 Oct 02:12 EXITED currently processing 0