Harvest for Vietnam Species List Created 17 Oct 00:07

Stage: completed
Fetched: 17 Oct 00:07
Validated: 17 Oct 00:07
Deltas Created 17 Oct 00:07
Units Normalized: 17 Oct 00:20
Ancestry Built: 17 Oct 00:11
Nodes Matched: 17 Oct 00:20
Names Parsed: 17 Oct 00:11
New Models Stored: 17 Oct 00:09
Indexed: 17 Oct 00:20
Completed: 17 Oct 00:25
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-17 00:07:40 -0400 by logger.rb/56815
[START] [2019-10-17 00:07:40] logged process
[START] [2019-10-17 00:07:40] create_harvest_instance
[STOP] [2019-10-17 00:07:41] create_harvest_instance
[START] [2019-10-17 00:07:41] fetch_files
[STOP] [2019-10-17 00:07:41] fetch_files
[START] [2019-10-17 00:07:41] validate_each_file
[STOP] [2019-10-17 00:07:44] validate_each_file
[START] [2019-10-17 00:07:44] convert_to_csv
[CMD] [2019-10-17 00:07:44] /usr/bin/sort /app/public/converted_csv/vietnam_sp_list_refs_17641.csv > /app/public/converted_csv/vietnam_sp_list_refs_17641.csv_sorted
[CMD] [2019-10-17 00:07:44] /usr/bin/sort /app/public/converted_csv/vietnam_sp_list_nodes_17642.csv > /app/public/converted_csv/vietnam_sp_list_nodes_17642.csv_sorted
[CMD] [2019-10-17 00:07:45] /usr/bin/sort /app/public/converted_csv/vietnam_sp_list_occurrences_17643.csv > /app/public/converted_csv/vietnam_sp_list_occurrences_17643.csv_sorted
[CMD] [2019-10-17 00:07:45] /usr/bin/sort /app/public/converted_csv/vietnam_sp_list_measurements_17644.csv > /app/public/converted_csv/vietnam_sp_list_measurements_17644.csv_sorted
[STOP] [2019-10-17 00:07:45] convert_to_csv
[START] [2019-10-17 00:07:45] calculate_delta
[CMD] [2019-10-17 00:07:45] echo "0a" > /app/public/diff/vietnam_sp_list_refs_17641.diff
[CMD] [2019-10-17 00:07:45] tail -n +1 /app/public/converted_csv/vietnam_sp_list_refs_17641.csv >> /app/public/diff/vietnam_sp_list_refs_17641.diff
[CMD] [2019-10-17 00:07:45] echo "." >> /app/public/diff/vietnam_sp_list_refs_17641.diff
[CMD] [2019-10-17 00:07:45] echo "0a" > /app/public/diff/vietnam_sp_list_nodes_17642.diff
[CMD] [2019-10-17 00:07:45] tail -n +1 /app/public/converted_csv/vietnam_sp_list_nodes_17642.csv >> /app/public/diff/vietnam_sp_list_nodes_17642.diff
[CMD] [2019-10-17 00:07:45] echo "." >> /app/public/diff/vietnam_sp_list_nodes_17642.diff
[CMD] [2019-10-17 00:07:45] echo "0a" > /app/public/diff/vietnam_sp_list_occurrences_17643.diff
[CMD] [2019-10-17 00:07:45] tail -n +1 /app/public/converted_csv/vietnam_sp_list_occurrences_17643.csv >> /app/public/diff/vietnam_sp_list_occurrences_17643.diff
[CMD] [2019-10-17 00:07:45] echo "." >> /app/public/diff/vietnam_sp_list_occurrences_17643.diff
[CMD] [2019-10-17 00:07:46] echo "0a" > /app/public/diff/vietnam_sp_list_measurements_17644.diff
[CMD] [2019-10-17 00:07:46] tail -n +1 /app/public/converted_csv/vietnam_sp_list_measurements_17644.csv >> /app/public/diff/vietnam_sp_list_measurements_17644.diff
[CMD] [2019-10-17 00:07:46] echo "." >> /app/public/diff/vietnam_sp_list_measurements_17644.diff
[STOP] [2019-10-17 00:07:46] calculate_delta
[START] [2019-10-17 00:07:46] parse_diff_and_store
[INFO] [2019-10-17 00:07:46] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 00:07:46] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 00:07:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 00:07:53] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 00:08:51] Storing 2 References
[INFO] [2019-10-17 00:08:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 00:08:51] Average Time: 0.0
[INFO] [2019-10-17 00:08:51] Total Time: 1s
[INFO] [2019-10-17 00:08:51] Storing 15691 ScientificNames
[INFO] [2019-10-17 00:08:51] Processing group of 15691 in 16 groups of 1000
[INFO] [2019-10-17 00:08:57] Average Time: 0.329
[INFO] [2019-10-17 00:08:57] Total Time: 6s
[INFO] [2019-10-17 00:08:57] last 3 / first 3: 0.82
[INFO] [2019-10-17 00:08:57] Std.Dev: 0.03162277660168379; Max: 0.41
[INFO] [2019-10-17 00:08:57] Storing 15691 Nodes
[INFO] [2019-10-17 00:08:57] Processing group of 15691 in 16 groups of 1000
[INFO] [2019-10-17 00:09:01] Average Time: 0.282
[INFO] [2019-10-17 00:09:01] Total Time: 5s
[INFO] [2019-10-17 00:09:01] last 3 / first 3: 0.93
[INFO] [2019-10-17 00:09:01] Std.Dev: 0.0; Max: 0.3
[INFO] [2019-10-17 00:09:01] Storing 10604 Occurrences
[INFO] [2019-10-17 00:09:01] Processing group of 10604 in 11 groups of 1000
[INFO] [2019-10-17 00:09:03] Average Time: 0.148
[INFO] [2019-10-17 00:09:03] Total Time: 2s
[INFO] [2019-10-17 00:09:03] last 3 / first 3: 0.55
[INFO] [2019-10-17 00:09:03] Std.Dev: 0.08366600265340755; Max: 0.32
[INFO] [2019-10-17 00:09:03] Storing 21280 TraitsReferences
[INFO] [2019-10-17 00:09:03] Processing group of 21280 in 22 groups of 1000
[INFO] [2019-10-17 00:09:05] Average Time: 0.066
[INFO] [2019-10-17 00:09:05] Total Time: 2s
[INFO] [2019-10-17 00:09:05] last 3 / first 3: 0.48
[INFO] [2019-10-17 00:09:05] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-17 00:09:05] Storing 21279 Traits
[INFO] [2019-10-17 00:09:05] Processing group of 21279 in 22 groups of 1000
[INFO] [2019-10-17 00:09:11] Average Time: 0.271
[INFO] [2019-10-17 00:09:11] Total Time: 7s
[INFO] [2019-10-17 00:09:11] last 3 / first 3: 0.65
[INFO] [2019-10-17 00:09:11] Std.Dev: 0.05477225575051661; Max: 0.39
[INFO] [2019-10-17 00:09:11] Storing 21258 MetaTraits
[INFO] [2019-10-17 00:09:11] Processing group of 21258 in 22 groups of 1000
[INFO] [2019-10-17 00:09:13] Average Time: 0.105
[INFO] [2019-10-17 00:09:13] Total Time: 3s
[INFO] [2019-10-17 00:09:13] last 3 / first 3: 0.85
[INFO] [2019-10-17 00:09:13] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-17 00:09:13] parse_diff_and_store
[START] [2019-10-17 00:09:13] resolve_keys
[INFO] [2019-10-17 00:10:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 00:10:15] traits to occurrences...
[INFO] [2019-10-17 00:10:21] traits to nodes (through occurrences)...
[INFO] [2019-10-17 00:10:22] Traits to sex term...
[INFO] [2019-10-17 00:10:27] Traits to lifestage term...
[INFO] [2019-10-17 00:10:33] MetaTraits to traits...
[INFO] [2019-10-17 00:10:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 00:10:38] Assocs to occurrences...
[INFO] [2019-10-17 00:10:38] Assocs to nodes...
[INFO] [2019-10-17 00:10:38] Assoc to sex term...
[INFO] [2019-10-17 00:10:38] Assoc to lifestage term...
[STOP] [2019-10-17 00:10:38] resolve_keys
[START] [2019-10-17 00:10:38] hold_for_later_1
[STOP] [2019-10-17 00:10:38] hold_for_later_1
[START] [2019-10-17 00:10:38] hold_for_later_2
[STOP] [2019-10-17 00:10:38] hold_for_later_2
[START] [2019-10-17 00:10:38] resolve_missing_parents
[STOP] [2019-10-17 00:11:09] resolve_missing_parents
[START] [2019-10-17 00:11:09] rebuild_nodes
[START] [2019-10-17 00:11:09] Flattener#flatten
[START] [2019-10-17 00:11:09] Flattener#study_resource
[START] [2019-10-17 00:11:09] Flattener#build_ancestry
[STOP] [2019-10-17 00:11:10] Flattener#build_ancestry
[INFO] [2019-10-17 00:11:10] 15691 ancestry keys
[START] [2019-10-17 00:11:10] build_node_ancestors
[INFO] [2019-10-17 00:11:10] old ancestors deleted.
[STOP] [2019-10-17 00:11:13] build_node_ancestors
[START] [2019-10-17 00:11:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 00:11:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 00:11:17] Flattener#flatten
[STOP] [2019-10-17 00:11:17] rebuild_nodes
[START] [2019-10-17 00:11:17] resolve_missing_media_owners
[STOP] [2019-10-17 00:11:17] resolve_missing_media_owners
[START] [2019-10-17 00:11:17] sanitize_media_verbatims
[STOP] [2019-10-17 00:11:17] sanitize_media_verbatims
[START] [2019-10-17 00:11:17] queue_downloads
[STOP] [2019-10-17 00:11:17] queue_downloads
[START] [2019-10-17 00:11:17] parse_names
[WARN] [2019-10-17 00:11:17] I see 15691 names which still need to be parsed.
[STOP] [2019-10-17 00:11:29] parse_names
[START] [2019-10-17 00:11:29] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 00:11:29] denormalize_canonical_names_to_nodes
[START] [2019-10-17 00:11:29] match_nodes
[START] [2019-10-17 00:11:29] map_all_nodes_to_pages
[STOP] [2019-10-17 00:20:26] map_all_nodes_to_pages
[INFO] [2019-10-17 00:20:26] 1048 Unmatched nodes (of 15691)! That's too many to output. First 10: Passer rutilans (#52680792); Hypsipetes mcclellandii (#52671439); Muscicapa latirostris (#52665900); Saxicola ferrea (#52675164); Saxicola maura (#52679661); Brachypteryx leucophrys (#52667528); Myiomela leucurum (#52666555); Luscinia cyane (#52666728); Luscinia sibilans (#52666909); Cinclidium leucurum (#52667226)
[START] [2019-10-17 00:20:26] update_nodes
[STOP] [2019-10-17 00:20:31] update_nodes
[STOP] [2019-10-17 00:20:31] match_nodes
[START] [2019-10-17 00:20:31] reindex_search
[STOP] [2019-10-17 00:20:57] reindex_search
[START] [2019-10-17 00:20:57] normalize_units
[STOP] [2019-10-17 00:20:57] normalize_units
[START] [2019-10-17 00:20:57] calculate_statistics
[STOP] [2019-10-17 00:20:57] calculate_statistics
[START] [2019-10-17 00:20:57] complete_harvest_instance
[START] [2019-10-17 00:20:57] overall_tsv_creation
[INFO] [2019-10-17 00:20:57] Processing group of 15691 in 2 batches of 10000
[INFO] [2019-10-17 00:22:25] 6286 Traits (unfiltered)...
[INFO] [2019-10-17 00:22:38] 6286 Traits (filtered)...
[INFO] [2019-10-17 00:22:38] 0 Associations (filtered)...
[INFO] [2019-10-17 00:23:26] 31418 metadata added.
[INFO] [2019-10-17 00:23:26] 0 metadata added.
[INFO] [2019-10-17 00:24:34] 4318 Traits (unfiltered)...
[INFO] [2019-10-17 00:24:47] 4318 Traits (filtered)...
[INFO] [2019-10-17 00:24:47] 0 Associations (filtered)...
[INFO] [2019-10-17 00:25:32] 21580 metadata added.
[INFO] [2019-10-17 00:25:32] 0 metadata added.
[INFO] [2019-10-17 00:25:32] Average Time: 111.045
[INFO] [2019-10-17 00:25:32] Total Time: 4m35s
[STOP] [2019-10-17 00:25:32] overall_tsv_creation
[INFO] [2019-10-17 00:25:32] Done. Check your files:
[INFO] [2019-10-17 00:25:32] (15691 lines) /app/public/data/vietnam_sp_list/publish_nodes.tsv
[INFO] [2019-10-17 00:25:32] (39584 lines) /app/public/data/vietnam_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-17 00:25:32] (15691 lines) /app/public/data/vietnam_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-17 00:25:32] (10605 lines) /app/public/data/vietnam_sp_list/publish_traits.tsv
[INFO] [2019-10-17 00:25:32] (52999 lines) /app/public/data/vietnam_sp_list/publish_metadata.tsv
[STOP] [2019-10-17 00:25:33] complete_harvest_instance
[START] [2019-10-17 00:25:33] completed
[STOP] [2019-10-17 00:25:33] completed
[STOP] [2019-10-17 00:25:33] logged process, took 1072.56
Latest Process

17 Oct 00:07 EXITED currently processing 0