Harvest for Irish Sea Species List Created 23 Dec 14:27

Stage: completed
Fetched: 23 Dec 14:27
Validated: 23 Dec 14:27
Deltas Created 23 Dec 14:27
Units Normalized: 23 Dec 15:29
Ancestry Built: 23 Dec 14:28
Nodes Matched: 23 Dec 15:28
Names Parsed: 23 Dec 14:29
New Models Stored: 23 Dec 14:27
Indexed: 23 Dec 15:29
Completed: 23 Dec 15:32
Time to Harvest: 1 minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-23 14:27:00 -0500 by logger.rb/56815
[START] [2019-12-23 14:27:00] logged process
[START] [2019-12-23 14:27:00] create_harvest_instance
[STOP] [2019-12-23 14:27:00] create_harvest_instance
[START] [2019-12-23 14:27:00] fetch_files
[STOP] [2019-12-23 14:27:00] fetch_files
[START] [2019-12-23 14:27:00] validate_each_file
[STOP] [2019-12-23 14:27:01] validate_each_file
[START] [2019-12-23 14:27:01] convert_to_csv
[CMD] [2019-12-23 14:27:01] /usr/bin/sort /app/public/converted_csv/irish_sea_sp_lis_refs_19402.csv > /app/public/converted_csv/irish_sea_sp_lis_refs_19402.csv_sorted
[CMD] [2019-12-23 14:27:02] /usr/bin/sort /app/public/converted_csv/irish_sea_sp_lis_nodes_19403.csv > /app/public/converted_csv/irish_sea_sp_lis_nodes_19403.csv_sorted
[CMD] [2019-12-23 14:27:02] /usr/bin/sort /app/public/converted_csv/irish_sea_sp_lis_occurrences_19404.csv > /app/public/converted_csv/irish_sea_sp_lis_occurrences_19404.csv_sorted
[CMD] [2019-12-23 14:27:03] /usr/bin/sort /app/public/converted_csv/irish_sea_sp_lis_measurements_19405.csv > /app/public/converted_csv/irish_sea_sp_lis_measurements_19405.csv_sorted
[STOP] [2019-12-23 14:27:04] convert_to_csv
[START] [2019-12-23 14:27:04] calculate_delta
[CMD] [2019-12-23 14:27:04] echo "0a" > /app/public/diff/irish_sea_sp_lis_refs_19402.diff
[CMD] [2019-12-23 14:27:04] tail -n +1 /app/public/converted_csv/irish_sea_sp_lis_refs_19402.csv >> /app/public/diff/irish_sea_sp_lis_refs_19402.diff
[CMD] [2019-12-23 14:27:05] echo "." >> /app/public/diff/irish_sea_sp_lis_refs_19402.diff
[CMD] [2019-12-23 14:27:06] echo "0a" > /app/public/diff/irish_sea_sp_lis_nodes_19403.diff
[CMD] [2019-12-23 14:27:06] tail -n +1 /app/public/converted_csv/irish_sea_sp_lis_nodes_19403.csv >> /app/public/diff/irish_sea_sp_lis_nodes_19403.diff
[CMD] [2019-12-23 14:27:07] echo "." >> /app/public/diff/irish_sea_sp_lis_nodes_19403.diff
[CMD] [2019-12-23 14:27:08] echo "0a" > /app/public/diff/irish_sea_sp_lis_occurrences_19404.diff
[CMD] [2019-12-23 14:27:08] tail -n +1 /app/public/converted_csv/irish_sea_sp_lis_occurrences_19404.csv >> /app/public/diff/irish_sea_sp_lis_occurrences_19404.diff
[CMD] [2019-12-23 14:27:09] echo "." >> /app/public/diff/irish_sea_sp_lis_occurrences_19404.diff
[CMD] [2019-12-23 14:27:10] echo "0a" > /app/public/diff/irish_sea_sp_lis_measurements_19405.diff
[CMD] [2019-12-23 14:27:10] tail -n +1 /app/public/converted_csv/irish_sea_sp_lis_measurements_19405.csv >> /app/public/diff/irish_sea_sp_lis_measurements_19405.diff
[CMD] [2019-12-23 14:27:11] echo "." >> /app/public/diff/irish_sea_sp_lis_measurements_19405.diff
[STOP] [2019-12-23 14:27:12] calculate_delta
[START] [2019-12-23 14:27:12] parse_diff_and_store
[INFO] [2019-12-23 14:27:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 14:27:13] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 14:27:17] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 14:27:18] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 14:27:41] Storing 2 References
[INFO] [2019-12-23 14:27:41] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 14:27:41] Average Time: 0.0
[INFO] [2019-12-23 14:27:41] Total Time: 1s
[INFO] [2019-12-23 14:27:41] Storing 7846 ScientificNames
[INFO] [2019-12-23 14:27:41] Processing group of 7846 in 8 groups of 1000
[INFO] [2019-12-23 14:27:45] Average Time: 0.416
[INFO] [2019-12-23 14:27:45] Total Time: 4s
[INFO] [2019-12-23 14:27:45] last 3 / first 3: 1.01
[INFO] [2019-12-23 14:27:45] Std.Dev: 0.03162277660168379; Max: 0.48
[INFO] [2019-12-23 14:27:45] Storing 7846 Nodes
[INFO] [2019-12-23 14:27:45] Processing group of 7846 in 8 groups of 1000
[INFO] [2019-12-23 14:27:47] Average Time: 0.319
[INFO] [2019-12-23 14:27:47] Total Time: 3s
[INFO] [2019-12-23 14:27:47] last 3 / first 3: 0.95
[INFO] [2019-12-23 14:27:47] Std.Dev: 0.03162277660168379; Max: 0.37
[INFO] [2019-12-23 14:27:47] Storing 3968 Occurrences
[INFO] [2019-12-23 14:27:47] Processing group of 3968 in 4 groups of 1000
[INFO] [2019-12-23 14:27:48] Average Time: 0.125
[INFO] [2019-12-23 14:27:48] Total Time: 1s
[INFO] [2019-12-23 14:27:48] Storing 7936 TraitsReferences
[INFO] [2019-12-23 14:27:48] Processing group of 7936 in 8 groups of 1000
[INFO] [2019-12-23 14:27:49] Average Time: 0.088
[INFO] [2019-12-23 14:27:49] Total Time: 1s
[INFO] [2019-12-23 14:27:49] last 3 / first 3: 0.77
[INFO] [2019-12-23 14:27:49] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-12-23 14:27:49] Storing 7936 Traits
[INFO] [2019-12-23 14:27:49] Processing group of 7936 in 8 groups of 1000
[INFO] [2019-12-23 14:27:51] Average Time: 0.345
[INFO] [2019-12-23 14:27:51] Total Time: 3s
[INFO] [2019-12-23 14:27:51] last 3 / first 3: 0.96
[INFO] [2019-12-23 14:27:51] Std.Dev: 0.044721359549995794; Max: 0.41
[INFO] [2019-12-23 14:27:51] Storing 7935 MetaTraits
[INFO] [2019-12-23 14:27:51] Processing group of 7935 in 8 groups of 1000
[INFO] [2019-12-23 14:27:53] Average Time: 0.154
[INFO] [2019-12-23 14:27:53] Total Time: 2s
[INFO] [2019-12-23 14:27:53] last 3 / first 3: 0.96
[INFO] [2019-12-23 14:27:53] Std.Dev: 0.0; Max: 0.18
[STOP] [2019-12-23 14:27:53] parse_diff_and_store
[START] [2019-12-23 14:27:53] resolve_keys
[INFO] [2019-12-23 14:28:25] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 14:28:28] traits to occurrences...
[INFO] [2019-12-23 14:28:29] traits to nodes (through occurrences)...
[INFO] [2019-12-23 14:28:29] Traits to sex term...
[INFO] [2019-12-23 14:28:31] Traits to lifestage term...
[INFO] [2019-12-23 14:28:33] MetaTraits to traits...
[INFO] [2019-12-23 14:28:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 14:28:35] Assocs to occurrences...
[INFO] [2019-12-23 14:28:35] Assocs to nodes...
[INFO] [2019-12-23 14:28:35] Assoc to sex term...
[INFO] [2019-12-23 14:28:35] Assoc to lifestage term...
[STOP] [2019-12-23 14:28:35] resolve_keys
[START] [2019-12-23 14:28:35] hold_for_later_1
[STOP] [2019-12-23 14:28:35] hold_for_later_1
[START] [2019-12-23 14:28:35] hold_for_later_2
[STOP] [2019-12-23 14:28:35] hold_for_later_2
[START] [2019-12-23 14:28:35] resolve_missing_parents
[STOP] [2019-12-23 14:28:50] resolve_missing_parents
[START] [2019-12-23 14:28:50] rebuild_nodes
[START] [2019-12-23 14:28:50] Flattener#flatten
[START] [2019-12-23 14:28:50] Flattener#study_resource
[START] [2019-12-23 14:28:50] Flattener#build_ancestry
[STOP] [2019-12-23 14:28:50] Flattener#build_ancestry
[INFO] [2019-12-23 14:28:50] 7846 ancestry keys
[START] [2019-12-23 14:28:50] build_node_ancestors
[INFO] [2019-12-23 14:28:50] old ancestors deleted.
[STOP] [2019-12-23 14:28:53] build_node_ancestors
[START] [2019-12-23 14:28:57] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 14:28:58] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 14:28:58] Flattener#flatten
[STOP] [2019-12-23 14:28:58] rebuild_nodes
[START] [2019-12-23 14:28:58] resolve_missing_media_owners
[STOP] [2019-12-23 14:28:58] resolve_missing_media_owners
[START] [2019-12-23 14:28:58] sanitize_media_verbatims
[STOP] [2019-12-23 14:28:58] sanitize_media_verbatims
[START] [2019-12-23 14:28:58] queue_downloads
[STOP] [2019-12-23 14:28:58] queue_downloads
[START] [2019-12-23 14:28:58] parse_names
[WARN] [2019-12-23 14:28:58] I see 7846 names which still need to be parsed.
[STOP] [2019-12-23 14:29:05] parse_names
[START] [2019-12-23 14:29:05] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 14:29:05] denormalize_canonical_names_to_nodes
[START] [2019-12-23 14:29:05] match_nodes
[START] [2019-12-23 14:29:05] map_all_nodes_to_pages
[STOP] [2019-12-23 15:28:49] map_all_nodes_to_pages
[INFO] [2019-12-23 15:28:49] 468 Unmatched nodes (of 7846)! That's too many to output. First 10: Puffinus griseus (#62076160); Larus melanocephalus (#62075193); Larus ichthyaetus (#62079554); Arenaria serpyllifolia (#62073777); Philomachus (#62075927); Philomachus pugnax (#62075926); Anas penelope (#62073862); Anas clypeata (#62074445); Anas strepera (#62074952); Anas querquedula (#62077105)
[START] [2019-12-23 15:28:49] update_nodes
[STOP] [2019-12-23 15:28:52] update_nodes
[STOP] [2019-12-23 15:28:52] match_nodes
[START] [2019-12-23 15:28:52] reindex_search
[STOP] [2019-12-23 15:29:39] reindex_search
[START] [2019-12-23 15:29:39] normalize_units
[STOP] [2019-12-23 15:29:39] normalize_units
[START] [2019-12-23 15:29:39] calculate_statistics
[STOP] [2019-12-23 15:29:40] calculate_statistics
[START] [2019-12-23 15:29:40] complete_harvest_instance
[START] [2019-12-23 15:29:40] overall_tsv_creation
[INFO] [2019-12-23 15:29:40] Processing group of 7846 in 1 batches of 10000
[INFO] [2019-12-23 15:31:02] 3968 Traits (unfiltered)...
[INFO] [2019-12-23 15:31:15] 3968 Traits (filtered)...
[INFO] [2019-12-23 15:31:15] 0 Associations (filtered)...
[INFO] [2019-12-23 15:32:01] 19839 metadata added.
[INFO] [2019-12-23 15:32:01] 0 metadata added.
[INFO] [2019-12-23 15:32:01] Average Time: 113.61
[INFO] [2019-12-23 15:32:01] Total Time: 2m22s
[STOP] [2019-12-23 15:32:01] overall_tsv_creation
[INFO] [2019-12-23 15:32:01] Done. Check your files:
[INFO] [2019-12-23 15:32:02] (7846 lines) /app/public/data/irish_sea_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 15:32:02] (39140 lines) /app/public/data/irish_sea_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 15:32:03] (7846 lines) /app/public/data/irish_sea_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 15:32:04] (3969 lines) /app/public/data/irish_sea_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 15:32:04] (19840 lines) /app/public/data/irish_sea_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 15:32:05] complete_harvest_instance
[START] [2019-12-23 15:32:05] completed
[STOP] [2019-12-23 15:32:05] completed
[STOP] [2019-12-23 15:32:05] logged process, took 3905.01
Latest Process

23 Dec 14:27 EXITED currently processing 0