Harvest for Caribbean Sea Species List Created 22 Dec 23:17

Stage: completed
Fetched: 22 Dec 23:17
Validated: 22 Dec 23:17
Deltas Created 22 Dec 23:17
Units Normalized: 23 Dec 00:24
Ancestry Built: 22 Dec 23:21
Nodes Matched: 23 Dec 00:23
Names Parsed: 22 Dec 23:21
New Models Stored: 22 Dec 23:19
Indexed: 23 Dec 00:24
Completed: 23 Dec 00:30
Time to Harvest: 1 minute
Harvesting Log

(156 lines)
# Logfile created on 2019-12-22 23:17:12 -0500 by logger.rb/56815
[START] [2019-12-22 23:17:12] logged process
[START] [2019-12-22 23:17:12] create_harvest_instance
[STOP] [2019-12-22 23:17:12] create_harvest_instance
[START] [2019-12-22 23:17:12] fetch_files
[STOP] [2019-12-22 23:17:12] fetch_files
[START] [2019-12-22 23:17:12] validate_each_file
[STOP] [2019-12-22 23:17:15] validate_each_file
[START] [2019-12-22 23:17:15] convert_to_csv
[CMD] [2019-12-22 23:17:15] /usr/bin/sort /app/public/converted_csv/caribbean_sea_sp_refs_19162.csv > /app/public/converted_csv/caribbean_sea_sp_refs_19162.csv_sorted
[CMD] [2019-12-22 23:17:15] /usr/bin/sort /app/public/converted_csv/caribbean_sea_sp_nodes_19163.csv > /app/public/converted_csv/caribbean_sea_sp_nodes_19163.csv_sorted
[CMD] [2019-12-22 23:17:16] /usr/bin/sort /app/public/converted_csv/caribbean_sea_sp_occurrences_19164.csv > /app/public/converted_csv/caribbean_sea_sp_occurrences_19164.csv_sorted
[CMD] [2019-12-22 23:17:17] /usr/bin/sort /app/public/converted_csv/caribbean_sea_sp_measurements_19165.csv > /app/public/converted_csv/caribbean_sea_sp_measurements_19165.csv_sorted
[STOP] [2019-12-22 23:17:17] convert_to_csv
[START] [2019-12-22 23:17:17] calculate_delta
[CMD] [2019-12-22 23:17:17] echo "0a" > /app/public/diff/caribbean_sea_sp_refs_19162.diff
[CMD] [2019-12-22 23:17:18] tail -n +1 /app/public/converted_csv/caribbean_sea_sp_refs_19162.csv >> /app/public/diff/caribbean_sea_sp_refs_19162.diff
[CMD] [2019-12-22 23:17:18] echo "." >> /app/public/diff/caribbean_sea_sp_refs_19162.diff
[CMD] [2019-12-22 23:17:19] echo "0a" > /app/public/diff/caribbean_sea_sp_nodes_19163.diff
[CMD] [2019-12-22 23:17:20] tail -n +1 /app/public/converted_csv/caribbean_sea_sp_nodes_19163.csv >> /app/public/diff/caribbean_sea_sp_nodes_19163.diff
[CMD] [2019-12-22 23:17:20] echo "." >> /app/public/diff/caribbean_sea_sp_nodes_19163.diff
[CMD] [2019-12-22 23:17:21] echo "0a" > /app/public/diff/caribbean_sea_sp_occurrences_19164.diff
[CMD] [2019-12-22 23:17:22] tail -n +1 /app/public/converted_csv/caribbean_sea_sp_occurrences_19164.csv >> /app/public/diff/caribbean_sea_sp_occurrences_19164.diff
[CMD] [2019-12-22 23:17:22] echo "." >> /app/public/diff/caribbean_sea_sp_occurrences_19164.diff
[CMD] [2019-12-22 23:17:23] echo "0a" > /app/public/diff/caribbean_sea_sp_measurements_19165.diff
[CMD] [2019-12-22 23:17:23] tail -n +1 /app/public/converted_csv/caribbean_sea_sp_measurements_19165.csv >> /app/public/diff/caribbean_sea_sp_measurements_19165.diff
[CMD] [2019-12-22 23:17:24] echo "." >> /app/public/diff/caribbean_sea_sp_measurements_19165.diff
[STOP] [2019-12-22 23:17:25] calculate_delta
[START] [2019-12-22 23:17:25] parse_diff_and_store
[INFO] [2019-12-22 23:17:25] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 23:17:26] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 23:17:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 23:17:35] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 23:18:37] Storing 2 References
[INFO] [2019-12-22 23:18:37] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 23:18:37] Average Time: 0.01
[INFO] [2019-12-22 23:18:37] Total Time: 1s
[INFO] [2019-12-22 23:18:37] Storing 18872 ScientificNames
[INFO] [2019-12-22 23:18:37] Processing group of 18872 in 19 groups of 1000
[INFO] [2019-12-22 23:18:45] Average Time: 0.431
[INFO] [2019-12-22 23:18:45] Total Time: 9s
[INFO] [2019-12-22 23:18:45] last 3 / first 3: 1.01
[INFO] [2019-12-22 23:18:45] Std.Dev: 0.14832396974191325; Max: 1.02
[INFO] [2019-12-22 23:18:45] Storing 18872 Nodes
[INFO] [2019-12-22 23:18:45] Processing group of 18872 in 19 groups of 1000
[INFO] [2019-12-22 23:18:51] Average Time: 0.317
[INFO] [2019-12-22 23:18:51] Total Time: 7s
[INFO] [2019-12-22 23:18:51] last 3 / first 3: 0.94
[INFO] [2019-12-22 23:18:51] Std.Dev: 0.03162277660168379; Max: 0.39
[INFO] [2019-12-22 23:18:51] Storing 11569 Occurrences
[INFO] [2019-12-22 23:18:51] Processing group of 11569 in 12 groups of 1000
[INFO] [2019-12-22 23:18:52] Average Time: 0.11
[INFO] [2019-12-22 23:18:52] Total Time: 2s
[INFO] [2019-12-22 23:18:52] last 3 / first 3: 0.81
[INFO] [2019-12-22 23:18:52] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-12-22 23:18:52] Storing 23138 TraitsReferences
[INFO] [2019-12-22 23:18:52] Processing group of 23138 in 24 groups of 1000
[INFO] [2019-12-22 23:18:54] Average Time: 0.076
[INFO] [2019-12-22 23:18:54] Total Time: 2s
[INFO] [2019-12-22 23:18:54] last 3 / first 3: 0.6
[INFO] [2019-12-22 23:18:54] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-12-22 23:18:54] Storing 23138 Traits
[INFO] [2019-12-22 23:18:54] Processing group of 23138 in 24 groups of 1000
[INFO] [2019-12-22 23:19:04] Average Time: 0.408
[INFO] [2019-12-22 23:19:04] Total Time: 10s
[INFO] [2019-12-22 23:19:04] last 3 / first 3: 0.69
[INFO] [2019-12-22 23:19:04] Std.Dev: 0.2569046515733026; Max: 1.26
[INFO] [2019-12-22 23:19:04] Storing 23132 MetaTraits
[INFO] [2019-12-22 23:19:04] Processing group of 23132 in 24 groups of 1000
[INFO] [2019-12-22 23:19:08] Average Time: 0.137
[INFO] [2019-12-22 23:19:08] Total Time: 4s
[INFO] [2019-12-22 23:19:08] last 3 / first 3: 0.66
[INFO] [2019-12-22 23:19:08] Std.Dev: 0.03162277660168379; Max: 0.19
[STOP] [2019-12-22 23:19:08] parse_diff_and_store
[START] [2019-12-22 23:19:08] resolve_keys
[INFO] [2019-12-22 23:20:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 23:20:15] traits to occurrences...
[INFO] [2019-12-22 23:20:19] traits to nodes (through occurrences)...
[INFO] [2019-12-22 23:20:19] Traits to sex term...
[INFO] [2019-12-22 23:20:23] Traits to lifestage term...
[INFO] [2019-12-22 23:20:27] MetaTraits to traits...
[INFO] [2019-12-22 23:20:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 23:20:32] Assocs to occurrences...
[INFO] [2019-12-22 23:20:32] Assocs to nodes...
[INFO] [2019-12-22 23:20:32] Assoc to sex term...
[INFO] [2019-12-22 23:20:32] Assoc to lifestage term...
[STOP] [2019-12-22 23:20:32] resolve_keys
[START] [2019-12-22 23:20:32] hold_for_later_1
[STOP] [2019-12-22 23:20:32] hold_for_later_1
[START] [2019-12-22 23:20:32] hold_for_later_2
[STOP] [2019-12-22 23:20:32] hold_for_later_2
[START] [2019-12-22 23:20:32] resolve_missing_parents
[STOP] [2019-12-22 23:21:14] resolve_missing_parents
[START] [2019-12-22 23:21:14] rebuild_nodes
[START] [2019-12-22 23:21:14] Flattener#flatten
[START] [2019-12-22 23:21:14] Flattener#study_resource
[START] [2019-12-22 23:21:14] Flattener#build_ancestry
[STOP] [2019-12-22 23:21:16] Flattener#build_ancestry
[INFO] [2019-12-22 23:21:16] 18872 ancestry keys
[START] [2019-12-22 23:21:16] build_node_ancestors
[INFO] [2019-12-22 23:21:16] old ancestors deleted.
[STOP] [2019-12-22 23:21:32] build_node_ancestors
[START] [2019-12-22 23:21:32] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:21:35] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:21:35] Flattener#flatten
[STOP] [2019-12-22 23:21:35] rebuild_nodes
[START] [2019-12-22 23:21:35] resolve_missing_media_owners
[STOP] [2019-12-22 23:21:35] resolve_missing_media_owners
[START] [2019-12-22 23:21:35] sanitize_media_verbatims
[STOP] [2019-12-22 23:21:35] sanitize_media_verbatims
[START] [2019-12-22 23:21:35] queue_downloads
[STOP] [2019-12-22 23:21:35] queue_downloads
[START] [2019-12-22 23:21:35] parse_names
[WARN] [2019-12-22 23:21:35] I see 18872 names which still need to be parsed.
[STOP] [2019-12-22 23:21:51] parse_names
[START] [2019-12-22 23:21:51] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 23:21:51] denormalize_canonical_names_to_nodes
[START] [2019-12-22 23:21:51] match_nodes
[START] [2019-12-22 23:21:51] map_all_nodes_to_pages
[STOP] [2019-12-23 00:23:32] map_all_nodes_to_pages
[INFO] [2019-12-23 00:23:32] 853 Unmatched nodes (of 18872)! That's too many to output. First 10: Tringa semipalmatus (#61792755); Limnodromus (#61788628); Philomachus (#61795045); Philomachus pugnax (#61795044); Thalasseus maxima (#61791354); Anas discors (#61788548); Anas clypeata (#61788715); Anas americana (#61788858); Anas cyanoptera (#61790988); Anas strepera (#61792057)
[START] [2019-12-23 00:23:32] update_nodes
[STOP] [2019-12-23 00:23:40] update_nodes
[STOP] [2019-12-23 00:23:40] match_nodes
[START] [2019-12-23 00:23:40] reindex_search
[STOP] [2019-12-23 00:24:35] reindex_search
[START] [2019-12-23 00:24:35] normalize_units
[STOP] [2019-12-23 00:24:36] normalize_units
[START] [2019-12-23 00:24:36] calculate_statistics
[STOP] [2019-12-23 00:24:36] calculate_statistics
[START] [2019-12-23 00:24:36] complete_harvest_instance
[START] [2019-12-23 00:24:36] overall_tsv_creation
[INFO] [2019-12-23 00:24:36] Processing group of 18872 in 2 batches of 10000
[INFO] [2019-12-23 00:26:09] 5593 Traits (unfiltered)...
[INFO] [2019-12-23 00:26:24] 5593 Traits (filtered)...
[INFO] [2019-12-23 00:26:24] 0 Associations (filtered)...
[INFO] [2019-12-23 00:27:17] 27963 metadata added.
[INFO] [2019-12-23 00:27:17] 0 metadata added.
[INFO] [2019-12-23 00:28:52] 5976 Traits (unfiltered)...
[INFO] [2019-12-23 00:29:06] 5976 Traits (filtered)...
[INFO] [2019-12-23 00:29:06] 0 Associations (filtered)...
[INFO] [2019-12-23 00:29:59] 29876 metadata added.
[INFO] [2019-12-23 00:29:59] 0 metadata added.
[INFO] [2019-12-23 00:29:59] Average Time: 128.975
[INFO] [2019-12-23 00:29:59] Total Time: 5m24s
[STOP] [2019-12-23 00:29:59] overall_tsv_creation
[INFO] [2019-12-23 00:29:59] Done. Check your files:
[INFO] [2019-12-23 00:30:00] (18872 lines) /app/public/data/caribbean_sea_sp/publish_nodes.tsv
[INFO] [2019-12-23 00:30:01] (100861 lines) /app/public/data/caribbean_sea_sp/publish_node_ancestors.tsv
[INFO] [2019-12-23 00:30:01] (18872 lines) /app/public/data/caribbean_sea_sp/publish_scientific_names.tsv
[INFO] [2019-12-23 00:30:02] (11570 lines) /app/public/data/caribbean_sea_sp/publish_traits.tsv
[INFO] [2019-12-23 00:30:03] (57840 lines) /app/public/data/caribbean_sea_sp/publish_metadata.tsv
[STOP] [2019-12-23 00:30:03] complete_harvest_instance
[START] [2019-12-23 00:30:03] completed
[STOP] [2019-12-23 00:30:03] completed
[STOP] [2019-12-23 00:30:03] logged process, took 4371.19
Latest Process

22 Dec 23:17 EXITED currently processing 0