Harvest for Oman Species List Created 15 Oct 05:44

Stage: completed
Fetched: 15 Oct 05:44
Validated: 15 Oct 05:44
Deltas Created 15 Oct 05:45
Units Normalized: 15 Oct 05:50
Ancestry Built: 15 Oct 05:46
Nodes Matched: 15 Oct 05:50
Names Parsed: 15 Oct 05:46
New Models Stored: 15 Oct 05:45
Indexed: 15 Oct 05:50
Completed: 15 Oct 05:52
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 05:44:56 -0400 by logger.rb/56815
[START] [2019-10-15 05:44:56] logged process
[START] [2019-10-15 05:44:56] create_harvest_instance
[STOP] [2019-10-15 05:44:56] create_harvest_instance
[START] [2019-10-15 05:44:56] fetch_files
[STOP] [2019-10-15 05:44:56] fetch_files
[START] [2019-10-15 05:44:56] validate_each_file
[STOP] [2019-10-15 05:44:57] validate_each_file
[START] [2019-10-15 05:44:57] convert_to_csv
[CMD] [2019-10-15 05:44:57] /usr/bin/sort /app/public/converted_csv/oman_sp_list_refs_16837.csv > /app/public/converted_csv/oman_sp_list_refs_16837.csv_sorted
[CMD] [2019-10-15 05:44:57] /usr/bin/sort /app/public/converted_csv/oman_sp_list_nodes_16838.csv > /app/public/converted_csv/oman_sp_list_nodes_16838.csv_sorted
[CMD] [2019-10-15 05:44:57] /usr/bin/sort /app/public/converted_csv/oman_sp_list_occurrences_16839.csv > /app/public/converted_csv/oman_sp_list_occurrences_16839.csv_sorted
[CMD] [2019-10-15 05:44:58] /usr/bin/sort /app/public/converted_csv/oman_sp_list_measurements_16840.csv > /app/public/converted_csv/oman_sp_list_measurements_16840.csv_sorted
[STOP] [2019-10-15 05:44:58] convert_to_csv
[START] [2019-10-15 05:44:58] calculate_delta
[CMD] [2019-10-15 05:44:58] echo "0a" > /app/public/diff/oman_sp_list_refs_16837.diff
[CMD] [2019-10-15 05:44:58] tail -n +1 /app/public/converted_csv/oman_sp_list_refs_16837.csv >> /app/public/diff/oman_sp_list_refs_16837.diff
[CMD] [2019-10-15 05:44:59] echo "." >> /app/public/diff/oman_sp_list_refs_16837.diff
[CMD] [2019-10-15 05:44:59] echo "0a" > /app/public/diff/oman_sp_list_nodes_16838.diff
[CMD] [2019-10-15 05:44:59] tail -n +1 /app/public/converted_csv/oman_sp_list_nodes_16838.csv >> /app/public/diff/oman_sp_list_nodes_16838.diff
[CMD] [2019-10-15 05:44:59] echo "." >> /app/public/diff/oman_sp_list_nodes_16838.diff
[CMD] [2019-10-15 05:45:00] echo "0a" > /app/public/diff/oman_sp_list_occurrences_16839.diff
[CMD] [2019-10-15 05:45:00] tail -n +1 /app/public/converted_csv/oman_sp_list_occurrences_16839.csv >> /app/public/diff/oman_sp_list_occurrences_16839.diff
[CMD] [2019-10-15 05:45:00] echo "." >> /app/public/diff/oman_sp_list_occurrences_16839.diff
[CMD] [2019-10-15 05:45:00] echo "0a" > /app/public/diff/oman_sp_list_measurements_16840.diff
[CMD] [2019-10-15 05:45:01] tail -n +1 /app/public/converted_csv/oman_sp_list_measurements_16840.csv >> /app/public/diff/oman_sp_list_measurements_16840.diff
[CMD] [2019-10-15 05:45:01] echo "." >> /app/public/diff/oman_sp_list_measurements_16840.diff
[STOP] [2019-10-15 05:45:01] calculate_delta
[START] [2019-10-15 05:45:01] parse_diff_and_store
[INFO] [2019-10-15 05:45:02] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 05:45:02] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 05:45:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 05:45:05] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 05:45:20] Storing 2 References
[INFO] [2019-10-15 05:45:20] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 05:45:20] Average Time: 0.0
[INFO] [2019-10-15 05:45:20] Total Time: 1s
[INFO] [2019-10-15 05:45:20] Storing 4713 ScientificNames
[INFO] [2019-10-15 05:45:20] Processing group of 4713 in 5 groups of 1000
[INFO] [2019-10-15 05:45:22] Average Time: 0.356
[INFO] [2019-10-15 05:45:22] Total Time: 3s
[INFO] [2019-10-15 05:45:22] Storing 4713 Nodes
[INFO] [2019-10-15 05:45:22] Processing group of 4713 in 5 groups of 1000
[INFO] [2019-10-15 05:45:23] Average Time: 0.284
[INFO] [2019-10-15 05:45:23] Total Time: 2s
[INFO] [2019-10-15 05:45:23] Storing 2410 Occurrences
[INFO] [2019-10-15 05:45:23] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-15 05:45:23] Average Time: 0.097
[INFO] [2019-10-15 05:45:23] Total Time: 1s
[INFO] [2019-10-15 05:45:23] Storing 5240 TraitsReferences
[INFO] [2019-10-15 05:45:23] Processing group of 5240 in 6 groups of 1000
[INFO] [2019-10-15 05:45:24] Average Time: 0.075
[INFO] [2019-10-15 05:45:24] Total Time: 1s
[INFO] [2019-10-15 05:45:24] Storing 5239 Traits
[INFO] [2019-10-15 05:45:24] Processing group of 5239 in 6 groups of 1000
[INFO] [2019-10-15 05:45:26] Average Time: 0.283
[INFO] [2019-10-15 05:45:26] Total Time: 2s
[INFO] [2019-10-15 05:45:26] Storing 5239 MetaTraits
[INFO] [2019-10-15 05:45:26] Processing group of 5239 in 6 groups of 1000
[INFO] [2019-10-15 05:45:26] Average Time: 0.125
[INFO] [2019-10-15 05:45:26] Total Time: 1s
[STOP] [2019-10-15 05:45:26] parse_diff_and_store
[START] [2019-10-15 05:45:26] resolve_keys
[INFO] [2019-10-15 05:45:47] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 05:45:49] traits to occurrences...
[INFO] [2019-10-15 05:45:51] traits to nodes (through occurrences)...
[INFO] [2019-10-15 05:45:51] Traits to sex term...
[INFO] [2019-10-15 05:45:53] Traits to lifestage term...
[INFO] [2019-10-15 05:45:55] MetaTraits to traits...
[INFO] [2019-10-15 05:45:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 05:45:56] Assocs to occurrences...
[INFO] [2019-10-15 05:45:56] Assocs to nodes...
[INFO] [2019-10-15 05:45:56] Assoc to sex term...
[INFO] [2019-10-15 05:45:56] Assoc to lifestage term...
[STOP] [2019-10-15 05:45:56] resolve_keys
[START] [2019-10-15 05:45:56] hold_for_later_1
[STOP] [2019-10-15 05:45:56] hold_for_later_1
[START] [2019-10-15 05:45:56] hold_for_later_2
[STOP] [2019-10-15 05:45:56] hold_for_later_2
[START] [2019-10-15 05:45:56] resolve_missing_parents
[STOP] [2019-10-15 05:46:05] resolve_missing_parents
[START] [2019-10-15 05:46:05] rebuild_nodes
[START] [2019-10-15 05:46:05] Flattener#flatten
[START] [2019-10-15 05:46:05] Flattener#study_resource
[START] [2019-10-15 05:46:05] Flattener#build_ancestry
[STOP] [2019-10-15 05:46:05] Flattener#build_ancestry
[INFO] [2019-10-15 05:46:05] 4713 ancestry keys
[START] [2019-10-15 05:46:05] build_node_ancestors
[INFO] [2019-10-15 05:46:05] old ancestors deleted.
[STOP] [2019-10-15 05:46:06] build_node_ancestors
[START] [2019-10-15 05:46:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 05:46:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 05:46:07] Flattener#flatten
[STOP] [2019-10-15 05:46:07] rebuild_nodes
[START] [2019-10-15 05:46:07] resolve_missing_media_owners
[STOP] [2019-10-15 05:46:07] resolve_missing_media_owners
[START] [2019-10-15 05:46:07] sanitize_media_verbatims
[STOP] [2019-10-15 05:46:07] sanitize_media_verbatims
[START] [2019-10-15 05:46:07] queue_downloads
[STOP] [2019-10-15 05:46:07] queue_downloads
[START] [2019-10-15 05:46:07] parse_names
[WARN] [2019-10-15 05:46:07] I see 4713 names which still need to be parsed.
[STOP] [2019-10-15 05:46:12] parse_names
[START] [2019-10-15 05:46:12] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 05:46:12] denormalize_canonical_names_to_nodes
[START] [2019-10-15 05:46:12] match_nodes
[START] [2019-10-15 05:46:12] map_all_nodes_to_pages
[STOP] [2019-10-15 05:50:25] map_all_nodes_to_pages
[INFO] [2019-10-15 05:50:25] 479 Unmatched nodes (of 4713)! That's too many to output. First 10: Streptopelia senegalensis (#51395764); Philomachus pugnax (#51396040); Larus hemprichii (#51396464); Thalaseus (#51396037); Thalaseus bergii (#51396036); Thalaseus bengalensis (#51396125); Thalaseus sandvicensis (#51396136); Oenanthe alboniger (#51398574); Cercomela (#51396018); Cercomela melanura (#51396017)
[START] [2019-10-15 05:50:25] update_nodes
[STOP] [2019-10-15 05:50:27] update_nodes
[STOP] [2019-10-15 05:50:27] match_nodes
[START] [2019-10-15 05:50:27] reindex_search
[STOP] [2019-10-15 05:50:37] reindex_search
[START] [2019-10-15 05:50:37] normalize_units
[STOP] [2019-10-15 05:50:37] normalize_units
[START] [2019-10-15 05:50:37] calculate_statistics
[STOP] [2019-10-15 05:50:37] calculate_statistics
[START] [2019-10-15 05:50:37] complete_harvest_instance
[START] [2019-10-15 05:50:37] overall_tsv_creation
[INFO] [2019-10-15 05:50:37] Processing group of 4713 in 1 batches of 10000
[INFO] [2019-10-15 05:51:43] 2410 Traits (unfiltered)...
[INFO] [2019-10-15 05:51:57] 2410 Traits (filtered)...
[INFO] [2019-10-15 05:51:57] 0 Associations (filtered)...
[INFO] [2019-10-15 05:52:39] 12049 metadata added.
[INFO] [2019-10-15 05:52:39] 0 metadata added.
[INFO] [2019-10-15 05:52:39] Average Time: 97.89
[INFO] [2019-10-15 05:52:39] Total Time: 2m3s
[STOP] [2019-10-15 05:52:39] overall_tsv_creation
[INFO] [2019-10-15 05:52:39] Done. Check your files:
[INFO] [2019-10-15 05:52:40] (4713 lines) /app/public/data/oman_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 05:52:40] (9501 lines) /app/public/data/oman_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 05:52:40] (4713 lines) /app/public/data/oman_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 05:52:40] (2411 lines) /app/public/data/oman_sp_list/publish_traits.tsv
[INFO] [2019-10-15 05:52:41] (12050 lines) /app/public/data/oman_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 05:52:41] complete_harvest_instance
[START] [2019-10-15 05:52:41] completed
[STOP] [2019-10-15 05:52:41] completed
[STOP] [2019-10-15 05:52:41] logged process, took 465.23
Latest Process

15 Oct 05:44 EXITED currently processing 0