Harvest for South Sudan Species List Created 16 Oct 04:48

Stage: completed
Fetched: 16 Oct 04:48
Validated: 16 Oct 04:48
Deltas Created 16 Oct 04:49
Units Normalized: 16 Oct 04:50
Ancestry Built: 16 Oct 04:49
Nodes Matched: 16 Oct 04:50
Names Parsed: 16 Oct 04:49
New Models Stored: 16 Oct 04:49
Indexed: 16 Oct 04:50
Completed: 16 Oct 04:52
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 04:48:55 -0400 by logger.rb/56815
[START] [2019-10-16 04:48:55] logged process
[START] [2019-10-16 04:48:55] create_harvest_instance
[STOP] [2019-10-16 04:48:56] create_harvest_instance
[START] [2019-10-16 04:48:56] fetch_files
[STOP] [2019-10-16 04:48:56] fetch_files
[START] [2019-10-16 04:48:56] validate_each_file
[STOP] [2019-10-16 04:48:56] validate_each_file
[START] [2019-10-16 04:48:56] convert_to_csv
[CMD] [2019-10-16 04:48:56] /usr/bin/sort /app/public/converted_csv/s_sudan_sp_list_refs_17309.csv > /app/public/converted_csv/s_sudan_sp_list_refs_17309.csv_sorted
[CMD] [2019-10-16 04:48:56] /usr/bin/sort /app/public/converted_csv/s_sudan_sp_list_nodes_17310.csv > /app/public/converted_csv/s_sudan_sp_list_nodes_17310.csv_sorted
[CMD] [2019-10-16 04:48:57] /usr/bin/sort /app/public/converted_csv/s_sudan_sp_list_occurrences_17311.csv > /app/public/converted_csv/s_sudan_sp_list_occurrences_17311.csv_sorted
[CMD] [2019-10-16 04:48:57] /usr/bin/sort /app/public/converted_csv/s_sudan_sp_list_measurements_17312.csv > /app/public/converted_csv/s_sudan_sp_list_measurements_17312.csv_sorted
[STOP] [2019-10-16 04:48:57] convert_to_csv
[START] [2019-10-16 04:48:57] calculate_delta
[CMD] [2019-10-16 04:48:57] echo "0a" > /app/public/diff/s_sudan_sp_list_refs_17309.diff
[CMD] [2019-10-16 04:48:57] tail -n +1 /app/public/converted_csv/s_sudan_sp_list_refs_17309.csv >> /app/public/diff/s_sudan_sp_list_refs_17309.diff
[CMD] [2019-10-16 04:48:58] echo "." >> /app/public/diff/s_sudan_sp_list_refs_17309.diff
[CMD] [2019-10-16 04:48:58] echo "0a" > /app/public/diff/s_sudan_sp_list_nodes_17310.diff
[CMD] [2019-10-16 04:48:58] tail -n +1 /app/public/converted_csv/s_sudan_sp_list_nodes_17310.csv >> /app/public/diff/s_sudan_sp_list_nodes_17310.diff
[CMD] [2019-10-16 04:48:59] echo "." >> /app/public/diff/s_sudan_sp_list_nodes_17310.diff
[CMD] [2019-10-16 04:48:59] echo "0a" > /app/public/diff/s_sudan_sp_list_occurrences_17311.diff
[CMD] [2019-10-16 04:48:59] tail -n +1 /app/public/converted_csv/s_sudan_sp_list_occurrences_17311.csv >> /app/public/diff/s_sudan_sp_list_occurrences_17311.diff
[CMD] [2019-10-16 04:48:59] echo "." >> /app/public/diff/s_sudan_sp_list_occurrences_17311.diff
[CMD] [2019-10-16 04:49:00] echo "0a" > /app/public/diff/s_sudan_sp_list_measurements_17312.diff
[CMD] [2019-10-16 04:49:00] tail -n +1 /app/public/converted_csv/s_sudan_sp_list_measurements_17312.csv >> /app/public/diff/s_sudan_sp_list_measurements_17312.diff
[CMD] [2019-10-16 04:49:00] echo "." >> /app/public/diff/s_sudan_sp_list_measurements_17312.diff
[STOP] [2019-10-16 04:49:01] calculate_delta
[START] [2019-10-16 04:49:01] parse_diff_and_store
[INFO] [2019-10-16 04:49:01] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 04:49:01] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 04:49:02] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 04:49:02] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 04:49:05] Storing 2 References
[INFO] [2019-10-16 04:49:05] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 04:49:06] Average Time: 0.0
[INFO] [2019-10-16 04:49:06] Total Time: 1s
[INFO] [2019-10-16 04:49:06] Storing 1111 ScientificNames
[INFO] [2019-10-16 04:49:06] Processing group of 1111 in 2 groups of 1000
[INFO] [2019-10-16 04:49:06] Average Time: 0.215
[INFO] [2019-10-16 04:49:06] Total Time: 1s
[INFO] [2019-10-16 04:49:06] Storing 1111 Nodes
[INFO] [2019-10-16 04:49:06] Processing group of 1111 in 2 groups of 1000
[INFO] [2019-10-16 04:49:06] Average Time: 0.165
[INFO] [2019-10-16 04:49:06] Total Time: 1s
[INFO] [2019-10-16 04:49:06] Storing 482 Occurrences
[INFO] [2019-10-16 04:49:06] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-16 04:49:06] Average Time: 0.07
[INFO] [2019-10-16 04:49:06] Total Time: 1s
[INFO] [2019-10-16 04:49:06] Storing 1070 TraitsReferences
[INFO] [2019-10-16 04:49:06] Processing group of 1070 in 2 groups of 1000
[INFO] [2019-10-16 04:49:07] Average Time: 0.08
[INFO] [2019-10-16 04:49:07] Total Time: 1s
[INFO] [2019-10-16 04:49:07] Storing 1069 Traits
[INFO] [2019-10-16 04:49:07] Processing group of 1069 in 2 groups of 1000
[INFO] [2019-10-16 04:49:07] Average Time: 0.3
[INFO] [2019-10-16 04:49:07] Total Time: 1s
[INFO] [2019-10-16 04:49:07] Storing 1070 MetaTraits
[INFO] [2019-10-16 04:49:07] Processing group of 1070 in 2 groups of 1000
[INFO] [2019-10-16 04:49:07] Average Time: 0.075
[INFO] [2019-10-16 04:49:07] Total Time: 1s
[STOP] [2019-10-16 04:49:07] parse_diff_and_store
[START] [2019-10-16 04:49:07] resolve_keys
[INFO] [2019-10-16 04:49:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 04:49:14] traits to occurrences...
[INFO] [2019-10-16 04:49:15] traits to nodes (through occurrences)...
[INFO] [2019-10-16 04:49:15] Traits to sex term...
[INFO] [2019-10-16 04:49:15] Traits to lifestage term...
[INFO] [2019-10-16 04:49:15] MetaTraits to traits...
[INFO] [2019-10-16 04:49:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 04:49:16] Assocs to occurrences...
[INFO] [2019-10-16 04:49:16] Assocs to nodes...
[INFO] [2019-10-16 04:49:16] Assoc to sex term...
[INFO] [2019-10-16 04:49:16] Assoc to lifestage term...
[STOP] [2019-10-16 04:49:16] resolve_keys
[START] [2019-10-16 04:49:16] hold_for_later_1
[STOP] [2019-10-16 04:49:16] hold_for_later_1
[START] [2019-10-16 04:49:16] hold_for_later_2
[STOP] [2019-10-16 04:49:16] hold_for_later_2
[START] [2019-10-16 04:49:16] resolve_missing_parents
[STOP] [2019-10-16 04:49:17] resolve_missing_parents
[START] [2019-10-16 04:49:17] rebuild_nodes
[START] [2019-10-16 04:49:17] Flattener#flatten
[START] [2019-10-16 04:49:17] Flattener#study_resource
[START] [2019-10-16 04:49:17] Flattener#build_ancestry
[STOP] [2019-10-16 04:49:17] Flattener#build_ancestry
[INFO] [2019-10-16 04:49:17] 1111 ancestry keys
[START] [2019-10-16 04:49:17] build_node_ancestors
[INFO] [2019-10-16 04:49:17] old ancestors deleted.
[STOP] [2019-10-16 04:49:17] build_node_ancestors
[START] [2019-10-16 04:49:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 04:49:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 04:49:17] Flattener#flatten
[STOP] [2019-10-16 04:49:17] rebuild_nodes
[START] [2019-10-16 04:49:17] resolve_missing_media_owners
[STOP] [2019-10-16 04:49:17] resolve_missing_media_owners
[START] [2019-10-16 04:49:17] sanitize_media_verbatims
[STOP] [2019-10-16 04:49:17] sanitize_media_verbatims
[START] [2019-10-16 04:49:17] queue_downloads
[STOP] [2019-10-16 04:49:17] queue_downloads
[START] [2019-10-16 04:49:17] parse_names
[WARN] [2019-10-16 04:49:17] I see 1111 names which still need to be parsed.
[STOP] [2019-10-16 04:49:19] parse_names
[START] [2019-10-16 04:49:19] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 04:49:19] denormalize_canonical_names_to_nodes
[START] [2019-10-16 04:49:19] match_nodes
[START] [2019-10-16 04:49:19] map_all_nodes_to_pages
[STOP] [2019-10-16 04:50:21] map_all_nodes_to_pages
[INFO] [2019-10-16 04:50:21] 39 Unmatched nodes (of 1111)! That's too many to output. First 10: Pennisetum glauca (#52122308); Dasypeltis typus (#52122118); Lanius excubitorius (#52121828); Cinnyris venusta (#52122790); Nectarinia venusta (#52122142); Crithagra mozambicus (#52121869); Prionopidae (#52121890); Spermestes (#52121997); Spermestes cucullata (#52121996); Spermestes cucullatus (#52122229)
[START] [2019-10-16 04:50:21] update_nodes
[STOP] [2019-10-16 04:50:21] update_nodes
[STOP] [2019-10-16 04:50:21] match_nodes
[START] [2019-10-16 04:50:21] reindex_search
[STOP] [2019-10-16 04:50:24] reindex_search
[START] [2019-10-16 04:50:24] normalize_units
[STOP] [2019-10-16 04:50:24] normalize_units
[START] [2019-10-16 04:50:24] calculate_statistics
[STOP] [2019-10-16 04:50:24] calculate_statistics
[START] [2019-10-16 04:50:24] complete_harvest_instance
[START] [2019-10-16 04:50:24] overall_tsv_creation
[INFO] [2019-10-16 04:50:24] Processing group of 1111 in 1 batches of 10000
[INFO] [2019-10-16 04:51:13] 482 Traits (unfiltered)...
[INFO] [2019-10-16 04:51:27] 482 Traits (filtered)...
[INFO] [2019-10-16 04:51:27] 0 Associations (filtered)...
[INFO] [2019-10-16 04:52:05] 2410 metadata added.
[INFO] [2019-10-16 04:52:05] 0 metadata added.
[INFO] [2019-10-16 04:52:05] Average Time: 79.51
[INFO] [2019-10-16 04:52:05] Total Time: 1m42s
[STOP] [2019-10-16 04:52:05] overall_tsv_creation
[INFO] [2019-10-16 04:52:05] Done. Check your files:
[INFO] [2019-10-16 04:52:05] (1111 lines) /app/public/data/s_sudan_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 04:52:05] (1913 lines) /app/public/data/s_sudan_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 04:52:06] (1111 lines) /app/public/data/s_sudan_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 04:52:06] (483 lines) /app/public/data/s_sudan_sp_list/publish_traits.tsv
[INFO] [2019-10-16 04:52:06] (2411 lines) /app/public/data/s_sudan_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 04:52:06] complete_harvest_instance
[START] [2019-10-16 04:52:06] completed
[STOP] [2019-10-16 04:52:06] completed
[STOP] [2019-10-16 04:52:06] logged process, took 190.97
Latest Process

16 Oct 04:48 EXITED currently processing 0