Harvest for Gambia Species List Created 13 Oct 01:10

Stage: completed
Fetched: 13 Oct 01:10
Validated: 13 Oct 01:10
Deltas Created 13 Oct 01:10
Units Normalized: 13 Oct 01:12
Ancestry Built: 13 Oct 01:11
Nodes Matched: 13 Oct 01:12
Names Parsed: 13 Oct 01:11
New Models Stored: 13 Oct 01:10
Indexed: 13 Oct 01:12
Completed: 13 Oct 01:14
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 01:10:42 -0400 by logger.rb/56815
[START] [2019-10-13 01:10:42] logged process
[START] [2019-10-13 01:10:42] create_harvest_instance
[STOP] [2019-10-13 01:10:42] create_harvest_instance
[START] [2019-10-13 01:10:42] fetch_files
[STOP] [2019-10-13 01:10:42] fetch_files
[START] [2019-10-13 01:10:42] validate_each_file
[STOP] [2019-10-13 01:10:43] validate_each_file
[START] [2019-10-13 01:10:43] convert_to_csv
[CMD] [2019-10-13 01:10:43] /usr/bin/sort /app/public/converted_csv/gambia_sp_list_refs_15811.csv > /app/public/converted_csv/gambia_sp_list_refs_15811.csv_sorted
[CMD] [2019-10-13 01:10:43] /usr/bin/sort /app/public/converted_csv/gambia_sp_list_nodes_15812.csv > /app/public/converted_csv/gambia_sp_list_nodes_15812.csv_sorted
[CMD] [2019-10-13 01:10:43] /usr/bin/sort /app/public/converted_csv/gambia_sp_list_occurrences_15813.csv > /app/public/converted_csv/gambia_sp_list_occurrences_15813.csv_sorted
[CMD] [2019-10-13 01:10:43] /usr/bin/sort /app/public/converted_csv/gambia_sp_list_measurements_15814.csv > /app/public/converted_csv/gambia_sp_list_measurements_15814.csv_sorted
[STOP] [2019-10-13 01:10:43] convert_to_csv
[START] [2019-10-13 01:10:43] calculate_delta
[CMD] [2019-10-13 01:10:43] echo "0a" > /app/public/diff/gambia_sp_list_refs_15811.diff
[CMD] [2019-10-13 01:10:43] tail -n +1 /app/public/converted_csv/gambia_sp_list_refs_15811.csv >> /app/public/diff/gambia_sp_list_refs_15811.diff
[CMD] [2019-10-13 01:10:43] echo "." >> /app/public/diff/gambia_sp_list_refs_15811.diff
[CMD] [2019-10-13 01:10:43] echo "0a" > /app/public/diff/gambia_sp_list_nodes_15812.diff
[CMD] [2019-10-13 01:10:43] tail -n +1 /app/public/converted_csv/gambia_sp_list_nodes_15812.csv >> /app/public/diff/gambia_sp_list_nodes_15812.diff
[CMD] [2019-10-13 01:10:43] echo "." >> /app/public/diff/gambia_sp_list_nodes_15812.diff
[CMD] [2019-10-13 01:10:44] echo "0a" > /app/public/diff/gambia_sp_list_occurrences_15813.diff
[CMD] [2019-10-13 01:10:44] tail -n +1 /app/public/converted_csv/gambia_sp_list_occurrences_15813.csv >> /app/public/diff/gambia_sp_list_occurrences_15813.diff
[CMD] [2019-10-13 01:10:44] echo "." >> /app/public/diff/gambia_sp_list_occurrences_15813.diff
[CMD] [2019-10-13 01:10:44] echo "0a" > /app/public/diff/gambia_sp_list_measurements_15814.diff
[CMD] [2019-10-13 01:10:44] tail -n +1 /app/public/converted_csv/gambia_sp_list_measurements_15814.csv >> /app/public/diff/gambia_sp_list_measurements_15814.diff
[CMD] [2019-10-13 01:10:44] echo "." >> /app/public/diff/gambia_sp_list_measurements_15814.diff
[STOP] [2019-10-13 01:10:44] calculate_delta
[START] [2019-10-13 01:10:44] parse_diff_and_store
[INFO] [2019-10-13 01:10:44] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 01:10:44] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 01:10:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 01:10:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 01:10:51] Storing 2 References
[INFO] [2019-10-13 01:10:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 01:10:51] Average Time: 0.0
[INFO] [2019-10-13 01:10:51] Total Time: 1s
[INFO] [2019-10-13 01:10:51] Storing 1715 ScientificNames
[INFO] [2019-10-13 01:10:51] Processing group of 1715 in 2 groups of 1000
[INFO] [2019-10-13 01:10:52] Average Time: 0.39
[INFO] [2019-10-13 01:10:52] Total Time: 1s
[INFO] [2019-10-13 01:10:52] Storing 1715 Nodes
[INFO] [2019-10-13 01:10:52] Processing group of 1715 in 2 groups of 1000
[INFO] [2019-10-13 01:10:52] Average Time: 0.265
[INFO] [2019-10-13 01:10:52] Total Time: 1s
[INFO] [2019-10-13 01:10:52] Storing 964 Occurrences
[INFO] [2019-10-13 01:10:52] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-13 01:10:53] Average Time: 0.11
[INFO] [2019-10-13 01:10:53] Total Time: 1s
[INFO] [2019-10-13 01:10:53] Storing 1960 TraitsReferences
[INFO] [2019-10-13 01:10:53] Processing group of 1960 in 2 groups of 1000
[INFO] [2019-10-13 01:10:53] Average Time: 0.12
[INFO] [2019-10-13 01:10:53] Total Time: 1s
[INFO] [2019-10-13 01:10:53] Storing 1959 Traits
[INFO] [2019-10-13 01:10:53] Processing group of 1959 in 2 groups of 1000
[INFO] [2019-10-13 01:10:54] Average Time: 0.345
[INFO] [2019-10-13 01:10:54] Total Time: 1s
[INFO] [2019-10-13 01:10:54] Storing 1960 MetaTraits
[INFO] [2019-10-13 01:10:54] Processing group of 1960 in 2 groups of 1000
[INFO] [2019-10-13 01:10:54] Average Time: 0.13
[INFO] [2019-10-13 01:10:54] Total Time: 1s
[STOP] [2019-10-13 01:10:54] parse_diff_and_store
[START] [2019-10-13 01:10:54] resolve_keys
[INFO] [2019-10-13 01:11:03] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 01:11:04] traits to occurrences...
[INFO] [2019-10-13 01:11:04] traits to nodes (through occurrences)...
[INFO] [2019-10-13 01:11:04] Traits to sex term...
[INFO] [2019-10-13 01:11:04] Traits to lifestage term...
[INFO] [2019-10-13 01:11:05] MetaTraits to traits...
[INFO] [2019-10-13 01:11:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 01:11:05] Assocs to occurrences...
[INFO] [2019-10-13 01:11:05] Assocs to nodes...
[INFO] [2019-10-13 01:11:05] Assoc to sex term...
[INFO] [2019-10-13 01:11:05] Assoc to lifestage term...
[STOP] [2019-10-13 01:11:05] resolve_keys
[START] [2019-10-13 01:11:05] hold_for_later_1
[STOP] [2019-10-13 01:11:05] hold_for_later_1
[START] [2019-10-13 01:11:05] hold_for_later_2
[STOP] [2019-10-13 01:11:05] hold_for_later_2
[START] [2019-10-13 01:11:05] resolve_missing_parents
[STOP] [2019-10-13 01:11:07] resolve_missing_parents
[START] [2019-10-13 01:11:07] rebuild_nodes
[START] [2019-10-13 01:11:07] Flattener#flatten
[START] [2019-10-13 01:11:07] Flattener#study_resource
[START] [2019-10-13 01:11:07] Flattener#build_ancestry
[STOP] [2019-10-13 01:11:07] Flattener#build_ancestry
[INFO] [2019-10-13 01:11:07] 1715 ancestry keys
[START] [2019-10-13 01:11:07] build_node_ancestors
[INFO] [2019-10-13 01:11:07] old ancestors deleted.
[STOP] [2019-10-13 01:11:07] build_node_ancestors
[START] [2019-10-13 01:11:08] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 01:11:08] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 01:11:08] Flattener#flatten
[STOP] [2019-10-13 01:11:08] rebuild_nodes
[START] [2019-10-13 01:11:08] resolve_missing_media_owners
[STOP] [2019-10-13 01:11:08] resolve_missing_media_owners
[START] [2019-10-13 01:11:08] sanitize_media_verbatims
[STOP] [2019-10-13 01:11:08] sanitize_media_verbatims
[START] [2019-10-13 01:11:08] queue_downloads
[STOP] [2019-10-13 01:11:08] queue_downloads
[START] [2019-10-13 01:11:08] parse_names
[WARN] [2019-10-13 01:11:08] I see 1715 names which still need to be parsed.
[STOP] [2019-10-13 01:11:10] parse_names
[START] [2019-10-13 01:11:10] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 01:11:10] denormalize_canonical_names_to_nodes
[START] [2019-10-13 01:11:10] match_nodes
[START] [2019-10-13 01:11:10] map_all_nodes_to_pages
[STOP] [2019-10-13 01:12:38] map_all_nodes_to_pages
[INFO] [2019-10-13 01:12:38] 105 Unmatched nodes (of 1715)! That's too many to output. First 10: Pennisetum (#49791525); Hieraaetus pennata (#49792520); Torgos tracheliotus (#49791818); Streptopelia senegalensis (#49790844); Megaceryle maximus (#49791234); Ceyx picta (#49791124); Alcedo cristatus (#49791166); Alcedo cristata (#49792250); Andropadus virens (#49792196); Coracias abyssinica (#49791440)
[START] [2019-10-13 01:12:38] update_nodes
[STOP] [2019-10-13 01:12:39] update_nodes
[STOP] [2019-10-13 01:12:39] match_nodes
[START] [2019-10-13 01:12:39] reindex_search
[STOP] [2019-10-13 01:12:42] reindex_search
[START] [2019-10-13 01:12:42] normalize_units
[STOP] [2019-10-13 01:12:42] normalize_units
[START] [2019-10-13 01:12:42] calculate_statistics
[STOP] [2019-10-13 01:12:42] calculate_statistics
[START] [2019-10-13 01:12:42] complete_harvest_instance
[START] [2019-10-13 01:12:42] overall_tsv_creation
[INFO] [2019-10-13 01:12:42] Processing group of 1715 in 1 batches of 10000
[INFO] [2019-10-13 01:13:35] 964 Traits (unfiltered)...
[INFO] [2019-10-13 01:13:49] 964 Traits (filtered)...
[INFO] [2019-10-13 01:13:49] 0 Associations (filtered)...
[INFO] [2019-10-13 01:14:28] 4820 metadata added.
[INFO] [2019-10-13 01:14:28] 0 metadata added.
[INFO] [2019-10-13 01:14:28] Average Time: 84.92
[INFO] [2019-10-13 01:14:28] Total Time: 1m47s
[STOP] [2019-10-13 01:14:28] overall_tsv_creation
[INFO] [2019-10-13 01:14:28] Done. Check your files:
[INFO] [2019-10-13 01:14:28] (1715 lines) /app/public/data/gambia_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 01:14:28] (2122 lines) /app/public/data/gambia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 01:14:29] (1715 lines) /app/public/data/gambia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 01:14:29] (965 lines) /app/public/data/gambia_sp_list/publish_traits.tsv
[INFO] [2019-10-13 01:14:29] (4821 lines) /app/public/data/gambia_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 01:14:29] complete_harvest_instance
[START] [2019-10-13 01:14:29] completed
[STOP] [2019-10-13 01:14:29] completed
[STOP] [2019-10-13 01:14:29] logged process, took 227.06
Latest Process

13 Oct 01:10 EXITED currently processing 0