Harvest for Coral Sea Species List Created 23 Dec 00:31

Stage: completed
Fetched: 23 Dec 00:31
Validated: 23 Dec 00:31
Deltas Created 23 Dec 00:31
Units Normalized: 23 Dec 03:10
Ancestry Built: 23 Dec 00:39
Nodes Matched: 23 Dec 03:08
Names Parsed: 23 Dec 00:39
New Models Stored: 23 Dec 00:35
Indexed: 23 Dec 03:10
Completed: 23 Dec 03:21
Time to Harvest: 3 minutes
Harvesting Log

(166 lines)
# Logfile created on 2019-12-23 00:31:09 -0500 by logger.rb/56815
[START] [2019-12-23 00:31:09] logged process
[START] [2019-12-23 00:31:09] create_harvest_instance
[STOP] [2019-12-23 00:31:09] create_harvest_instance
[START] [2019-12-23 00:31:09] fetch_files
[STOP] [2019-12-23 00:31:09] fetch_files
[START] [2019-12-23 00:31:09] validate_each_file
[STOP] [2019-12-23 00:31:15] validate_each_file
[START] [2019-12-23 00:31:15] convert_to_csv
[CMD] [2019-12-23 00:31:15] /usr/bin/sort /app/public/converted_csv/coral_sea_sp_lis_refs_19194.csv > /app/public/converted_csv/coral_sea_sp_lis_refs_19194.csv_sorted
[CMD] [2019-12-23 00:31:15] /usr/bin/sort /app/public/converted_csv/coral_sea_sp_lis_nodes_19195.csv > /app/public/converted_csv/coral_sea_sp_lis_nodes_19195.csv_sorted
[CMD] [2019-12-23 00:31:16] /usr/bin/sort /app/public/converted_csv/coral_sea_sp_lis_occurrences_19196.csv > /app/public/converted_csv/coral_sea_sp_lis_occurrences_19196.csv_sorted
[CMD] [2019-12-23 00:31:17] /usr/bin/sort /app/public/converted_csv/coral_sea_sp_lis_measurements_19197.csv > /app/public/converted_csv/coral_sea_sp_lis_measurements_19197.csv_sorted
[STOP] [2019-12-23 00:31:17] convert_to_csv
[START] [2019-12-23 00:31:17] calculate_delta
[CMD] [2019-12-23 00:31:17] echo "0a" > /app/public/diff/coral_sea_sp_lis_refs_19194.diff
[CMD] [2019-12-23 00:31:18] tail -n +1 /app/public/converted_csv/coral_sea_sp_lis_refs_19194.csv >> /app/public/diff/coral_sea_sp_lis_refs_19194.diff
[CMD] [2019-12-23 00:31:19] echo "." >> /app/public/diff/coral_sea_sp_lis_refs_19194.diff
[CMD] [2019-12-23 00:31:19] echo "0a" > /app/public/diff/coral_sea_sp_lis_nodes_19195.diff
[CMD] [2019-12-23 00:31:20] tail -n +1 /app/public/converted_csv/coral_sea_sp_lis_nodes_19195.csv >> /app/public/diff/coral_sea_sp_lis_nodes_19195.diff
[CMD] [2019-12-23 00:31:21] echo "." >> /app/public/diff/coral_sea_sp_lis_nodes_19195.diff
[CMD] [2019-12-23 00:31:21] echo "0a" > /app/public/diff/coral_sea_sp_lis_occurrences_19196.diff
[CMD] [2019-12-23 00:31:22] tail -n +1 /app/public/converted_csv/coral_sea_sp_lis_occurrences_19196.csv >> /app/public/diff/coral_sea_sp_lis_occurrences_19196.diff
[CMD] [2019-12-23 00:31:23] echo "." >> /app/public/diff/coral_sea_sp_lis_occurrences_19196.diff
[CMD] [2019-12-23 00:31:23] echo "0a" > /app/public/diff/coral_sea_sp_lis_measurements_19197.diff
[CMD] [2019-12-23 00:31:24] tail -n +1 /app/public/converted_csv/coral_sea_sp_lis_measurements_19197.csv >> /app/public/diff/coral_sea_sp_lis_measurements_19197.diff
[CMD] [2019-12-23 00:31:25] echo "." >> /app/public/diff/coral_sea_sp_lis_measurements_19197.diff
[STOP] [2019-12-23 00:31:25] calculate_delta
[START] [2019-12-23 00:31:25] parse_diff_and_store
[INFO] [2019-12-23 00:31:26] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 00:31:27] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 00:31:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 00:31:47] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 00:33:58] Storing 2 References
[INFO] [2019-12-23 00:33:58] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 00:33:59] Average Time: 0.0
[INFO] [2019-12-23 00:33:59] Total Time: 1s
[INFO] [2019-12-23 00:33:59] Storing 36323 ScientificNames
[INFO] [2019-12-23 00:33:59] Processing group of 36323 in 37 groups of 1000
[INFO] [2019-12-23 00:34:13] Average Time: 0.4
[INFO] [2019-12-23 00:34:13] Total Time: 15s
[INFO] [2019-12-23 00:34:13] last 3 / first 3: 0.77
[INFO] [2019-12-23 00:34:13] Std.Dev: 0.1341640786499874; Max: 0.82
[INFO] [2019-12-23 00:34:13] Storing 36323 Nodes
[INFO] [2019-12-23 00:34:13] Processing group of 36323 in 37 groups of 1000
[INFO] [2019-12-23 00:34:25] Average Time: 0.303
[INFO] [2019-12-23 00:34:25] Total Time: 12s
[INFO] [2019-12-23 00:34:25] last 3 / first 3: 0.55
[INFO] [2019-12-23 00:34:25] Std.Dev: 0.06324555320336758; Max: 0.6
[INFO] [2019-12-23 00:34:25] Storing 25342 Occurrences
[INFO] [2019-12-23 00:34:25] Processing group of 25342 in 26 groups of 1000
[INFO] [2019-12-23 00:34:28] Average Time: 0.118
[INFO] [2019-12-23 00:34:28] Total Time: 4s
[INFO] [2019-12-23 00:34:28] last 3 / first 3: 1.71
[INFO] [2019-12-23 00:34:28] Std.Dev: 0.05477225575051661; Max: 0.37
[INFO] [2019-12-23 00:34:28] Storing 50684 TraitsReferences
[INFO] [2019-12-23 00:34:28] Processing group of 50684 in 51 groups of 1000
[INFO] [2019-12-23 00:34:34] Average Time: 0.111
[INFO] [2019-12-23 00:34:34] Total Time: 6s
[INFO] [2019-12-23 00:34:34] last 3 / first 3: 0.84
[INFO] [2019-12-23 00:34:34] Std.Dev: 0.1; Max: 0.78
[INFO] [2019-12-23 00:34:34] Storing 50684 Traits
[INFO] [2019-12-23 00:34:34] Processing group of 50684 in 51 groups of 1000
[INFO] [2019-12-23 00:34:53] Average Time: 0.367
[INFO] [2019-12-23 00:34:53] Total Time: 19s
[INFO] [2019-12-23 00:34:53] last 3 / first 3: 0.73
[INFO] [2019-12-23 00:34:53] Std.Dev: 0.2645751311064591; Max: 1.82
[INFO] [2019-12-23 00:34:53] Storing 50651 MetaTraits
[INFO] [2019-12-23 00:34:53] Processing group of 50651 in 51 groups of 1000
[INFO] [2019-12-23 00:35:00] Average Time: 0.129
[INFO] [2019-12-23 00:35:00] Total Time: 7s
[INFO] [2019-12-23 00:35:00] last 3 / first 3: 1.06
[INFO] [2019-12-23 00:35:00] Std.Dev: 0.03162277660168379; Max: 0.2
[STOP] [2019-12-23 00:35:00] parse_diff_and_store
[START] [2019-12-23 00:35:00] resolve_keys
[INFO] [2019-12-23 00:36:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 00:36:52] traits to occurrences...
[INFO] [2019-12-23 00:36:59] traits to nodes (through occurrences)...
[INFO] [2019-12-23 00:36:59] Traits to sex term...
[INFO] [2019-12-23 00:37:05] Traits to lifestage term...
[INFO] [2019-12-23 00:37:11] MetaTraits to traits...
[INFO] [2019-12-23 00:37:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 00:37:21] Assocs to occurrences...
[INFO] [2019-12-23 00:37:22] Assocs to nodes...
[INFO] [2019-12-23 00:37:22] Assoc to sex term...
[INFO] [2019-12-23 00:37:22] Assoc to lifestage term...
[STOP] [2019-12-23 00:37:22] resolve_keys
[START] [2019-12-23 00:37:22] hold_for_later_1
[STOP] [2019-12-23 00:37:22] hold_for_later_1
[START] [2019-12-23 00:37:22] hold_for_later_2
[STOP] [2019-12-23 00:37:22] hold_for_later_2
[START] [2019-12-23 00:37:22] resolve_missing_parents
[STOP] [2019-12-23 00:38:25] resolve_missing_parents
[START] [2019-12-23 00:38:25] rebuild_nodes
[START] [2019-12-23 00:38:25] Flattener#flatten
[START] [2019-12-23 00:38:25] Flattener#study_resource
[START] [2019-12-23 00:38:25] Flattener#build_ancestry
[STOP] [2019-12-23 00:38:31] Flattener#build_ancestry
[INFO] [2019-12-23 00:38:31] 36323 ancestry keys
[START] [2019-12-23 00:38:31] build_node_ancestors
[INFO] [2019-12-23 00:38:31] old ancestors deleted.
[STOP] [2019-12-23 00:38:57] build_node_ancestors
[START] [2019-12-23 00:39:05] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:39:10] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:39:10] Flattener#flatten
[STOP] [2019-12-23 00:39:10] rebuild_nodes
[START] [2019-12-23 00:39:10] resolve_missing_media_owners
[STOP] [2019-12-23 00:39:10] resolve_missing_media_owners
[START] [2019-12-23 00:39:10] sanitize_media_verbatims
[STOP] [2019-12-23 00:39:10] sanitize_media_verbatims
[START] [2019-12-23 00:39:10] queue_downloads
[STOP] [2019-12-23 00:39:10] queue_downloads
[START] [2019-12-23 00:39:10] parse_names
[WARN] [2019-12-23 00:39:10] I see 36323 names which still need to be parsed.
[STOP] [2019-12-23 00:39:41] parse_names
[START] [2019-12-23 00:39:41] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 00:39:42] denormalize_canonical_names_to_nodes
[START] [2019-12-23 00:39:42] match_nodes
[START] [2019-12-23 00:39:42] map_all_nodes_to_pages
[STOP] [2019-12-23 03:08:22] map_all_nodes_to_pages
[INFO] [2019-12-23 03:08:22] 2113 Unmatched nodes (of 36323)! That's too many to output. First 10: Procelsterna cerulea (#61831071); Limicola (#61822412); Limicola falcinellus (#61822411); Limnodromus (#61825867); Philomachus (#61838668); Philomachus pugnax (#61838667); Puffinus pacifica (#61820320); Puffinus pacificus (#61820721); Puffinus tenuirostris (#61821049); Puffinus carneipes (#61822113)
[START] [2019-12-23 03:08:22] update_nodes
[STOP] [2019-12-23 03:08:36] update_nodes
[STOP] [2019-12-23 03:08:36] match_nodes
[START] [2019-12-23 03:08:36] reindex_search
[STOP] [2019-12-23 03:10:42] reindex_search
[START] [2019-12-23 03:10:42] normalize_units
[STOP] [2019-12-23 03:10:42] normalize_units
[START] [2019-12-23 03:10:42] calculate_statistics
[STOP] [2019-12-23 03:10:42] calculate_statistics
[START] [2019-12-23 03:10:42] complete_harvest_instance
[START] [2019-12-23 03:10:42] overall_tsv_creation
[INFO] [2019-12-23 03:10:42] Processing group of 36323 in 4 batches of 10000
[INFO] [2019-12-23 03:12:17] 5903 Traits (unfiltered)...
[INFO] [2019-12-23 03:12:30] 5903 Traits (filtered)...
[INFO] [2019-12-23 03:12:30] 0 Associations (filtered)...
[INFO] [2019-12-23 03:13:19] 29509 metadata added.
[INFO] [2019-12-23 03:13:19] 0 metadata added.
[INFO] [2019-12-23 03:14:56] 6883 Traits (unfiltered)...
[INFO] [2019-12-23 03:15:10] 6883 Traits (filtered)...
[INFO] [2019-12-23 03:15:10] 0 Associations (filtered)...
[INFO] [2019-12-23 03:16:05] 34404 metadata added.
[INFO] [2019-12-23 03:16:05] 0 metadata added.
[INFO] [2019-12-23 03:17:45] 7498 Traits (unfiltered)...
[INFO] [2019-12-23 03:18:03] 7498 Traits (filtered)...
[INFO] [2019-12-23 03:18:03] 0 Associations (filtered)...
[INFO] [2019-12-23 03:19:10] 37481 metadata added.
[INFO] [2019-12-23 03:19:10] 0 metadata added.
[INFO] [2019-12-23 03:20:30] 5058 Traits (unfiltered)...
[INFO] [2019-12-23 03:20:43] 5058 Traits (filtered)...
[INFO] [2019-12-23 03:20:43] 0 Associations (filtered)...
[INFO] [2019-12-23 03:21:34] 25283 metadata added.
[INFO] [2019-12-23 03:21:34] 0 metadata added.
[INFO] [2019-12-23 03:21:34] Average Time: 133.913
[INFO] [2019-12-23 03:21:34] Total Time: 10m52s
[STOP] [2019-12-23 03:21:34] overall_tsv_creation
[INFO] [2019-12-23 03:21:34] Done. Check your files:
[INFO] [2019-12-23 03:21:35] (36323 lines) /app/public/data/coral_sea_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 03:21:36] (199251 lines) /app/public/data/coral_sea_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:21:36] (36323 lines) /app/public/data/coral_sea_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 03:21:37] (25343 lines) /app/public/data/coral_sea_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 03:21:38] (126678 lines) /app/public/data/coral_sea_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 03:21:38] complete_harvest_instance
[START] [2019-12-23 03:21:38] completed
[STOP] [2019-12-23 03:21:38] completed
[STOP] [2019-12-23 03:21:38] logged process, took 10229.05
Latest Process

23 Dec 00:31 EXITED currently processing 0