Harvest for Hong Kong Species List Created 13 Oct 10:58

Stage: completed
Fetched: 13 Oct 10:58
Validated: 13 Oct 10:58
Deltas Created 13 Oct 10:58
Units Normalized: 13 Oct 11:07
Ancestry Built: 13 Oct 10:59
Nodes Matched: 13 Oct 11:06
Names Parsed: 13 Oct 10:59
New Models Stored: 13 Oct 10:58
Indexed: 13 Oct 11:07
Completed: 13 Oct 11:09
Time to Harvest: less than a minute
Harvesting Log

(154 lines)
# Logfile created on 2019-10-13 10:58:13 -0400 by logger.rb/56815
[START] [2019-10-13 10:58:13] logged process
[START] [2019-10-13 10:58:13] create_harvest_instance
[STOP] [2019-10-13 10:58:14] create_harvest_instance
[START] [2019-10-13 10:58:14] fetch_files
[STOP] [2019-10-13 10:58:14] fetch_files
[START] [2019-10-13 10:58:14] validate_each_file
[STOP] [2019-10-13 10:58:15] validate_each_file
[START] [2019-10-13 10:58:15] convert_to_csv
[CMD] [2019-10-13 10:58:15] /usr/bin/sort /app/public/converted_csv/hong_kong_sp_lis_refs_16099.csv > /app/public/converted_csv/hong_kong_sp_lis_refs_16099.csv_sorted
[CMD] [2019-10-13 10:58:15] /usr/bin/sort /app/public/converted_csv/hong_kong_sp_lis_nodes_16100.csv > /app/public/converted_csv/hong_kong_sp_lis_nodes_16100.csv_sorted
[CMD] [2019-10-13 10:58:15] /usr/bin/sort /app/public/converted_csv/hong_kong_sp_lis_occurrences_16101.csv > /app/public/converted_csv/hong_kong_sp_lis_occurrences_16101.csv_sorted
[CMD] [2019-10-13 10:58:15] /usr/bin/sort /app/public/converted_csv/hong_kong_sp_lis_measurements_16102.csv > /app/public/converted_csv/hong_kong_sp_lis_measurements_16102.csv_sorted
[STOP] [2019-10-13 10:58:15] convert_to_csv
[START] [2019-10-13 10:58:15] calculate_delta
[CMD] [2019-10-13 10:58:15] echo "0a" > /app/public/diff/hong_kong_sp_lis_refs_16099.diff
[CMD] [2019-10-13 10:58:15] tail -n +1 /app/public/converted_csv/hong_kong_sp_lis_refs_16099.csv >> /app/public/diff/hong_kong_sp_lis_refs_16099.diff
[CMD] [2019-10-13 10:58:15] echo "." >> /app/public/diff/hong_kong_sp_lis_refs_16099.diff
[CMD] [2019-10-13 10:58:15] echo "0a" > /app/public/diff/hong_kong_sp_lis_nodes_16100.diff
[CMD] [2019-10-13 10:58:15] tail -n +1 /app/public/converted_csv/hong_kong_sp_lis_nodes_16100.csv >> /app/public/diff/hong_kong_sp_lis_nodes_16100.diff
[CMD] [2019-10-13 10:58:15] echo "." >> /app/public/diff/hong_kong_sp_lis_nodes_16100.diff
[CMD] [2019-10-13 10:58:16] echo "0a" > /app/public/diff/hong_kong_sp_lis_occurrences_16101.diff
[CMD] [2019-10-13 10:58:16] tail -n +1 /app/public/converted_csv/hong_kong_sp_lis_occurrences_16101.csv >> /app/public/diff/hong_kong_sp_lis_occurrences_16101.diff
[CMD] [2019-10-13 10:58:16] echo "." >> /app/public/diff/hong_kong_sp_lis_occurrences_16101.diff
[CMD] [2019-10-13 10:58:16] echo "0a" > /app/public/diff/hong_kong_sp_lis_measurements_16102.diff
[CMD] [2019-10-13 10:58:16] tail -n +1 /app/public/converted_csv/hong_kong_sp_lis_measurements_16102.csv >> /app/public/diff/hong_kong_sp_lis_measurements_16102.diff
[CMD] [2019-10-13 10:58:16] echo "." >> /app/public/diff/hong_kong_sp_lis_measurements_16102.diff
[STOP] [2019-10-13 10:58:17] calculate_delta
[START] [2019-10-13 10:58:17] parse_diff_and_store
[INFO] [2019-10-13 10:58:17] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 10:58:17] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-13 10:58:17] Filtered Scientific Name `Macromerella  honesta` to `Macromerella honesta`
[WARN] [2019-10-13 10:58:18] Filtered Scientific Name `Huechys  sanguinea` to `Huechys sanguinea`
[WARN] [2019-10-13 10:58:18] Filtered Scientific Name `Tetroda  histeroides` to `Tetroda histeroides`
[WARN] [2019-10-13 10:58:18] Filtered Scientific Name `Pamerana  scotti` to `Pamerana scotti`
[INFO] [2019-10-13 10:58:19] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 10:58:20] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 10:58:40] Storing 2 References
[INFO] [2019-10-13 10:58:40] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 10:58:40] Average Time: 0.0
[INFO] [2019-10-13 10:58:40] Total Time: 1s
[INFO] [2019-10-13 10:58:40] Storing 6541 ScientificNames
[INFO] [2019-10-13 10:58:40] Processing group of 6541 in 7 groups of 1000
[INFO] [2019-10-13 10:58:42] Average Time: 0.379
[INFO] [2019-10-13 10:58:42] Total Time: 3s
[INFO] [2019-10-13 10:58:42] last 3 / first 3: 0.77
[INFO] [2019-10-13 10:58:42] Std.Dev: 0.11832159566199232; Max: 0.58
[INFO] [2019-10-13 10:58:42] Storing 6541 Nodes
[INFO] [2019-10-13 10:58:42] Processing group of 6541 in 7 groups of 1000
[INFO] [2019-10-13 10:58:44] Average Time: 0.283
[INFO] [2019-10-13 10:58:44] Total Time: 3s
[INFO] [2019-10-13 10:58:44] last 3 / first 3: 0.83
[INFO] [2019-10-13 10:58:44] Std.Dev: 0.05477225575051661; Max: 0.33
[INFO] [2019-10-13 10:58:44] Storing 3374 Occurrences
[INFO] [2019-10-13 10:58:44] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-13 10:58:45] Average Time: 0.093
[INFO] [2019-10-13 10:58:45] Total Time: 1s
[INFO] [2019-10-13 10:58:45] Storing 6750 TraitsReferences
[INFO] [2019-10-13 10:58:45] Processing group of 6750 in 7 groups of 1000
[INFO] [2019-10-13 10:58:45] Average Time: 0.077
[INFO] [2019-10-13 10:58:45] Total Time: 1s
[INFO] [2019-10-13 10:58:45] last 3 / first 3: 0.68
[INFO] [2019-10-13 10:58:45] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-13 10:58:45] Storing 6749 Traits
[INFO] [2019-10-13 10:58:45] Processing group of 6749 in 7 groups of 1000
[INFO] [2019-10-13 10:58:48] Average Time: 0.306
[INFO] [2019-10-13 10:58:48] Total Time: 3s
[INFO] [2019-10-13 10:58:48] last 3 / first 3: 0.79
[INFO] [2019-10-13 10:58:48] Std.Dev: 0.06324555320336758; Max: 0.43
[INFO] [2019-10-13 10:58:48] Storing 6743 MetaTraits
[INFO] [2019-10-13 10:58:48] Processing group of 6743 in 7 groups of 1000
[INFO] [2019-10-13 10:58:48] Average Time: 0.116
[INFO] [2019-10-13 10:58:48] Total Time: 1s
[INFO] [2019-10-13 10:58:48] last 3 / first 3: 0.84
[INFO] [2019-10-13 10:58:48] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-10-13 10:58:48] parse_diff_and_store
[START] [2019-10-13 10:58:48] resolve_keys
[INFO] [2019-10-13 10:59:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 10:59:16] traits to occurrences...
[INFO] [2019-10-13 10:59:18] traits to nodes (through occurrences)...
[INFO] [2019-10-13 10:59:18] Traits to sex term...
[INFO] [2019-10-13 10:59:19] Traits to lifestage term...
[INFO] [2019-10-13 10:59:21] MetaTraits to traits...
[INFO] [2019-10-13 10:59:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 10:59:22] Assocs to occurrences...
[INFO] [2019-10-13 10:59:22] Assocs to nodes...
[INFO] [2019-10-13 10:59:22] Assoc to sex term...
[INFO] [2019-10-13 10:59:22] Assoc to lifestage term...
[STOP] [2019-10-13 10:59:22] resolve_keys
[START] [2019-10-13 10:59:22] hold_for_later_1
[STOP] [2019-10-13 10:59:22] hold_for_later_1
[START] [2019-10-13 10:59:22] hold_for_later_2
[STOP] [2019-10-13 10:59:22] hold_for_later_2
[START] [2019-10-13 10:59:22] resolve_missing_parents
[STOP] [2019-10-13 10:59:35] resolve_missing_parents
[START] [2019-10-13 10:59:35] rebuild_nodes
[START] [2019-10-13 10:59:35] Flattener#flatten
[START] [2019-10-13 10:59:35] Flattener#study_resource
[START] [2019-10-13 10:59:35] Flattener#build_ancestry
[STOP] [2019-10-13 10:59:35] Flattener#build_ancestry
[INFO] [2019-10-13 10:59:35] 6541 ancestry keys
[START] [2019-10-13 10:59:35] build_node_ancestors
[INFO] [2019-10-13 10:59:35] old ancestors deleted.
[STOP] [2019-10-13 10:59:36] build_node_ancestors
[START] [2019-10-13 10:59:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:59:38] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:59:38] Flattener#flatten
[STOP] [2019-10-13 10:59:38] rebuild_nodes
[START] [2019-10-13 10:59:38] resolve_missing_media_owners
[STOP] [2019-10-13 10:59:38] resolve_missing_media_owners
[START] [2019-10-13 10:59:38] sanitize_media_verbatims
[STOP] [2019-10-13 10:59:38] sanitize_media_verbatims
[START] [2019-10-13 10:59:38] queue_downloads
[STOP] [2019-10-13 10:59:38] queue_downloads
[START] [2019-10-13 10:59:38] parse_names
[WARN] [2019-10-13 10:59:38] I see 6541 names which still need to be parsed.
[WARN] [2019-10-13 10:59:43] I see 2 names which still need to be parsed.
[STOP] [2019-10-13 10:59:45] parse_names
[START] [2019-10-13 10:59:45] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 10:59:45] denormalize_canonical_names_to_nodes
[START] [2019-10-13 10:59:45] match_nodes
[START] [2019-10-13 10:59:45] map_all_nodes_to_pages
[STOP] [2019-10-13 11:06:39] map_all_nodes_to_pages
[INFO] [2019-10-13 11:06:39] 462 Unmatched nodes (of 6541)! That's too many to output. First 10: Saxicola maura (#50074590); Luscinia sibilans (#50072776); Muscicapa latirostris (#50071908); Rhyacornis fuliginosus (#50075560); Passer rutilans (#50076537); Sturnus sericeus (#50072015); Sturnus cineraceus (#50072515); Sturnus nigricollis (#50073149); Sturnus sinensis (#50077604); Urocissa erythrorhyncha (#50071693)
[START] [2019-10-13 11:06:39] update_nodes
[STOP] [2019-10-13 11:06:41] update_nodes
[STOP] [2019-10-13 11:06:41] match_nodes
[START] [2019-10-13 11:06:41] reindex_search
[STOP] [2019-10-13 11:07:00] reindex_search
[START] [2019-10-13 11:07:00] normalize_units
[STOP] [2019-10-13 11:07:00] normalize_units
[START] [2019-10-13 11:07:00] calculate_statistics
[STOP] [2019-10-13 11:07:00] calculate_statistics
[START] [2019-10-13 11:07:00] complete_harvest_instance
[START] [2019-10-13 11:07:00] overall_tsv_creation
[INFO] [2019-10-13 11:07:00] Processing group of 6541 in 1 batches of 10000
[INFO] [2019-10-13 11:08:13] 3374 Traits (unfiltered)...
[INFO] [2019-10-13 11:08:27] 3374 Traits (filtered)...
[INFO] [2019-10-13 11:08:27] 0 Associations (filtered)...
[INFO] [2019-10-13 11:09:17] 16863 metadata added.
[INFO] [2019-10-13 11:09:17] 0 metadata added.
[INFO] [2019-10-13 11:09:17] Average Time: 111.62
[INFO] [2019-10-13 11:09:17] Total Time: 2m17s
[STOP] [2019-10-13 11:09:17] overall_tsv_creation
[INFO] [2019-10-13 11:09:17] Done. Check your files:
[INFO] [2019-10-13 11:09:17] (6541 lines) /app/public/data/hong_kong_sp_lis/publish_nodes.tsv
[INFO] [2019-10-13 11:09:17] (15178 lines) /app/public/data/hong_kong_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-13 11:09:17] (6541 lines) /app/public/data/hong_kong_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-13 11:09:17] (3375 lines) /app/public/data/hong_kong_sp_lis/publish_traits.tsv
[INFO] [2019-10-13 11:09:17] (16864 lines) /app/public/data/hong_kong_sp_lis/publish_metadata.tsv
[STOP] [2019-10-13 11:09:17] complete_harvest_instance
[START] [2019-10-13 11:09:17] completed
[STOP] [2019-10-13 11:09:17] completed
[STOP] [2019-10-13 11:09:17] logged process, took 664.35
Latest Process

13 Oct 10:58 EXITED currently processing 0