Harvest for Java Sea Species List Created 23 Dec 15:32

Stage: completed
Fetched: 23 Dec 15:32
Validated: 23 Dec 15:32
Deltas Created 23 Dec 15:32
Units Normalized: 23 Dec 15:57
Ancestry Built: 23 Dec 15:33
Nodes Matched: 23 Dec 15:57
Names Parsed: 23 Dec 15:33
New Models Stored: 23 Dec 15:32
Indexed: 23 Dec 15:57
Completed: 23 Dec 15:59
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 15:32:20 -0500 by logger.rb/56815
[START] [2019-12-23 15:32:20] logged process
[START] [2019-12-23 15:32:20] create_harvest_instance
[STOP] [2019-12-23 15:32:21] create_harvest_instance
[START] [2019-12-23 15:32:21] fetch_files
[STOP] [2019-12-23 15:32:21] fetch_files
[START] [2019-12-23 15:32:21] validate_each_file
[STOP] [2019-12-23 15:32:22] validate_each_file
[START] [2019-12-23 15:32:22] convert_to_csv
[CMD] [2019-12-23 15:32:22] /usr/bin/sort /app/public/converted_csv/java_sea_sp_list_refs_19410.csv > /app/public/converted_csv/java_sea_sp_list_refs_19410.csv_sorted
[CMD] [2019-12-23 15:32:22] /usr/bin/sort /app/public/converted_csv/java_sea_sp_list_nodes_19411.csv > /app/public/converted_csv/java_sea_sp_list_nodes_19411.csv_sorted
[CMD] [2019-12-23 15:32:23] /usr/bin/sort /app/public/converted_csv/java_sea_sp_list_occurrences_19412.csv > /app/public/converted_csv/java_sea_sp_list_occurrences_19412.csv_sorted
[CMD] [2019-12-23 15:32:24] /usr/bin/sort /app/public/converted_csv/java_sea_sp_list_measurements_19413.csv > /app/public/converted_csv/java_sea_sp_list_measurements_19413.csv_sorted
[STOP] [2019-12-23 15:32:24] convert_to_csv
[START] [2019-12-23 15:32:24] calculate_delta
[CMD] [2019-12-23 15:32:24] echo "0a" > /app/public/diff/java_sea_sp_list_refs_19410.diff
[CMD] [2019-12-23 15:32:25] tail -n +1 /app/public/converted_csv/java_sea_sp_list_refs_19410.csv >> /app/public/diff/java_sea_sp_list_refs_19410.diff
[CMD] [2019-12-23 15:32:26] echo "." >> /app/public/diff/java_sea_sp_list_refs_19410.diff
[CMD] [2019-12-23 15:32:26] echo "0a" > /app/public/diff/java_sea_sp_list_nodes_19411.diff
[CMD] [2019-12-23 15:32:27] tail -n +1 /app/public/converted_csv/java_sea_sp_list_nodes_19411.csv >> /app/public/diff/java_sea_sp_list_nodes_19411.diff
[CMD] [2019-12-23 15:32:28] echo "." >> /app/public/diff/java_sea_sp_list_nodes_19411.diff
[CMD] [2019-12-23 15:32:28] echo "0a" > /app/public/diff/java_sea_sp_list_occurrences_19412.diff
[CMD] [2019-12-23 15:32:29] tail -n +1 /app/public/converted_csv/java_sea_sp_list_occurrences_19412.csv >> /app/public/diff/java_sea_sp_list_occurrences_19412.diff
[CMD] [2019-12-23 15:32:30] echo "." >> /app/public/diff/java_sea_sp_list_occurrences_19412.diff
[CMD] [2019-12-23 15:32:30] echo "0a" > /app/public/diff/java_sea_sp_list_measurements_19413.diff
[CMD] [2019-12-23 15:32:31] tail -n +1 /app/public/converted_csv/java_sea_sp_list_measurements_19413.csv >> /app/public/diff/java_sea_sp_list_measurements_19413.diff
[CMD] [2019-12-23 15:32:32] echo "." >> /app/public/diff/java_sea_sp_list_measurements_19413.diff
[STOP] [2019-12-23 15:32:32] calculate_delta
[START] [2019-12-23 15:32:32] parse_diff_and_store
[INFO] [2019-12-23 15:32:33] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 15:32:34] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 15:32:36] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 15:32:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 15:32:46] Storing 2 References
[INFO] [2019-12-23 15:32:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 15:32:46] Average Time: 0.0
[INFO] [2019-12-23 15:32:46] Total Time: 1s
[INFO] [2019-12-23 15:32:46] Storing 3303 ScientificNames
[INFO] [2019-12-23 15:32:46] Processing group of 3303 in 4 groups of 1000
[INFO] [2019-12-23 15:32:48] Average Time: 0.368
[INFO] [2019-12-23 15:32:48] Total Time: 2s
[INFO] [2019-12-23 15:32:48] Storing 3303 Nodes
[INFO] [2019-12-23 15:32:48] Processing group of 3303 in 4 groups of 1000
[INFO] [2019-12-23 15:32:49] Average Time: 0.28
[INFO] [2019-12-23 15:32:49] Total Time: 2s
[INFO] [2019-12-23 15:32:49] Storing 1725 Occurrences
[INFO] [2019-12-23 15:32:49] Processing group of 1725 in 2 groups of 1000
[INFO] [2019-12-23 15:32:49] Average Time: 0.11
[INFO] [2019-12-23 15:32:49] Total Time: 1s
[INFO] [2019-12-23 15:32:49] Storing 3450 TraitsReferences
[INFO] [2019-12-23 15:32:49] Processing group of 3450 in 4 groups of 1000
[INFO] [2019-12-23 15:32:50] Average Time: 0.092
[INFO] [2019-12-23 15:32:50] Total Time: 1s
[INFO] [2019-12-23 15:32:50] Storing 3450 Traits
[INFO] [2019-12-23 15:32:50] Processing group of 3450 in 4 groups of 1000
[INFO] [2019-12-23 15:32:51] Average Time: 0.348
[INFO] [2019-12-23 15:32:51] Total Time: 2s
[INFO] [2019-12-23 15:32:51] Storing 3450 MetaTraits
[INFO] [2019-12-23 15:32:51] Processing group of 3450 in 4 groups of 1000
[INFO] [2019-12-23 15:32:52] Average Time: 0.123
[INFO] [2019-12-23 15:32:52] Total Time: 1s
[STOP] [2019-12-23 15:32:52] parse_diff_and_store
[START] [2019-12-23 15:32:52] resolve_keys
[INFO] [2019-12-23 15:33:07] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 15:33:08] traits to occurrences...
[INFO] [2019-12-23 15:33:09] traits to nodes (through occurrences)...
[INFO] [2019-12-23 15:33:09] Traits to sex term...
[INFO] [2019-12-23 15:33:10] Traits to lifestage term...
[INFO] [2019-12-23 15:33:10] MetaTraits to traits...
[INFO] [2019-12-23 15:33:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 15:33:11] Assocs to occurrences...
[INFO] [2019-12-23 15:33:11] Assocs to nodes...
[INFO] [2019-12-23 15:33:11] Assoc to sex term...
[INFO] [2019-12-23 15:33:11] Assoc to lifestage term...
[STOP] [2019-12-23 15:33:11] resolve_keys
[START] [2019-12-23 15:33:11] hold_for_later_1
[STOP] [2019-12-23 15:33:11] hold_for_later_1
[START] [2019-12-23 15:33:11] hold_for_later_2
[STOP] [2019-12-23 15:33:11] hold_for_later_2
[START] [2019-12-23 15:33:11] resolve_missing_parents
[STOP] [2019-12-23 15:33:17] resolve_missing_parents
[START] [2019-12-23 15:33:17] rebuild_nodes
[START] [2019-12-23 15:33:17] Flattener#flatten
[START] [2019-12-23 15:33:17] Flattener#study_resource
[START] [2019-12-23 15:33:17] Flattener#build_ancestry
[STOP] [2019-12-23 15:33:17] Flattener#build_ancestry
[INFO] [2019-12-23 15:33:17] 3303 ancestry keys
[START] [2019-12-23 15:33:17] build_node_ancestors
[INFO] [2019-12-23 15:33:17] old ancestors deleted.
[STOP] [2019-12-23 15:33:19] build_node_ancestors
[START] [2019-12-23 15:33:20] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 15:33:20] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 15:33:20] Flattener#flatten
[STOP] [2019-12-23 15:33:20] rebuild_nodes
[START] [2019-12-23 15:33:20] resolve_missing_media_owners
[STOP] [2019-12-23 15:33:20] resolve_missing_media_owners
[START] [2019-12-23 15:33:20] sanitize_media_verbatims
[STOP] [2019-12-23 15:33:20] sanitize_media_verbatims
[START] [2019-12-23 15:33:20] queue_downloads
[STOP] [2019-12-23 15:33:20] queue_downloads
[START] [2019-12-23 15:33:20] parse_names
[WARN] [2019-12-23 15:33:20] I see 3303 names which still need to be parsed.
[STOP] [2019-12-23 15:33:24] parse_names
[START] [2019-12-23 15:33:24] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 15:33:24] denormalize_canonical_names_to_nodes
[START] [2019-12-23 15:33:24] match_nodes
[START] [2019-12-23 15:33:24] map_all_nodes_to_pages
[STOP] [2019-12-23 15:57:13] map_all_nodes_to_pages
[INFO] [2019-12-23 15:57:13] 95 Unmatched nodes (of 3303)! That's too many to output. First 10: Acropora teres (#62082713); Turbinaria crater (#62081773); Pectiniidae (#62081495); Mussidae (#62081873); Symphyllia (#62082954); Egretta intermedia (#62080871); Philomachus (#62082365); Philomachus pugnax (#62082364); Megalaima (#62081153); Megalaima haemacephala (#62081152)
[START] [2019-12-23 15:57:13] update_nodes
[STOP] [2019-12-23 15:57:14] update_nodes
[STOP] [2019-12-23 15:57:14] match_nodes
[START] [2019-12-23 15:57:14] reindex_search
[STOP] [2019-12-23 15:57:32] reindex_search
[START] [2019-12-23 15:57:32] normalize_units
[STOP] [2019-12-23 15:57:32] normalize_units
[START] [2019-12-23 15:57:32] calculate_statistics
[STOP] [2019-12-23 15:57:32] calculate_statistics
[START] [2019-12-23 15:57:32] complete_harvest_instance
[START] [2019-12-23 15:57:32] overall_tsv_creation
[INFO] [2019-12-23 15:57:32] Processing group of 3303 in 1 batches of 10000
[INFO] [2019-12-23 15:58:32] 1725 Traits (unfiltered)...
[INFO] [2019-12-23 15:58:45] 1725 Traits (filtered)...
[INFO] [2019-12-23 15:58:45] 0 Associations (filtered)...
[INFO] [2019-12-23 15:59:25] 8625 metadata added.
[INFO] [2019-12-23 15:59:25] 0 metadata added.
[INFO] [2019-12-23 15:59:25] Average Time: 89.7
[INFO] [2019-12-23 15:59:25] Total Time: 1m54s
[STOP] [2019-12-23 15:59:25] overall_tsv_creation
[INFO] [2019-12-23 15:59:25] Done. Check your files:
[INFO] [2019-12-23 15:59:26] (3303 lines) /app/public/data/java_sea_sp_list/publish_nodes.tsv
[INFO] [2019-12-23 15:59:27] (16876 lines) /app/public/data/java_sea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-23 15:59:28] (3303 lines) /app/public/data/java_sea_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-23 15:59:28] (1726 lines) /app/public/data/java_sea_sp_list/publish_traits.tsv
[INFO] [2019-12-23 15:59:29] (8626 lines) /app/public/data/java_sea_sp_list/publish_metadata.tsv
[STOP] [2019-12-23 15:59:29] complete_harvest_instance
[START] [2019-12-23 15:59:29] completed
[STOP] [2019-12-23 15:59:29] completed
[STOP] [2019-12-23 15:59:29] logged process, took 1628.61
Latest Process

23 Dec 15:32 EXITED currently processing 0