Harvest for Taiwan Species List Created 16 Oct 10:26

Harvesting Log

# Logfile created on 2019-10-16 10:26:08 -0400 by logger.rb/56815
[START] [2019-10-16 10:26:08] logged process
[START] [2019-10-16 10:26:08] create_harvest_instance
[STOP] [2019-10-16 10:26:08] create_harvest_instance
[START] [2019-10-16 10:26:08] fetch_files
[STOP] [2019-10-16 10:26:08] fetch_files
[START] [2019-10-16 10:26:08] validate_each_file
[STOP] [2019-10-16 10:26:12] validate_each_file
[START] [2019-10-16 10:26:12] convert_to_csv
[CMD] [2019-10-16 10:26:12] /usr/bin/sort /app/public/converted_csv/taiwan_sp_list_refs_17385.csv > /app/public/converted_csv/taiwan_sp_list_refs_17385.csv_sorted
[CMD] [2019-10-16 10:26:12] /usr/bin/sort /app/public/converted_csv/taiwan_sp_list_nodes_17386.csv > /app/public/converted_csv/taiwan_sp_list_nodes_17386.csv_sorted
[CMD] [2019-10-16 10:26:13] /usr/bin/sort /app/public/converted_csv/taiwan_sp_list_occurrences_17387.csv > /app/public/converted_csv/taiwan_sp_list_occurrences_17387.csv_sorted
[CMD] [2019-10-16 10:26:13] /usr/bin/sort /app/public/converted_csv/taiwan_sp_list_measurements_17388.csv > /app/public/converted_csv/taiwan_sp_list_measurements_17388.csv_sorted
[STOP] [2019-10-16 10:26:13] convert_to_csv
[START] [2019-10-16 10:26:13] calculate_delta
[CMD] [2019-10-16 10:26:13] echo "0a" > /app/public/diff/taiwan_sp_list_refs_17385.diff
[CMD] [2019-10-16 10:26:13] tail -n +1 /app/public/converted_csv/taiwan_sp_list_refs_17385.csv >> /app/public/diff/taiwan_sp_list_refs_17385.diff
[CMD] [2019-10-16 10:26:14] echo "." >> /app/public/diff/taiwan_sp_list_refs_17385.diff
[CMD] [2019-10-16 10:26:14] echo "0a" > /app/public/diff/taiwan_sp_list_nodes_17386.diff
[CMD] [2019-10-16 10:26:14] tail -n +1 /app/public/converted_csv/taiwan_sp_list_nodes_17386.csv >> /app/public/diff/taiwan_sp_list_nodes_17386.diff
[CMD] [2019-10-16 10:26:15] echo "." >> /app/public/diff/taiwan_sp_list_nodes_17386.diff
[CMD] [2019-10-16 10:26:15] echo "0a" > /app/public/diff/taiwan_sp_list_occurrences_17387.diff
[CMD] [2019-10-16 10:26:15] tail -n +1 /app/public/converted_csv/taiwan_sp_list_occurrences_17387.csv >> /app/public/diff/taiwan_sp_list_occurrences_17387.diff
[CMD] [2019-10-16 10:26:15] echo "." >> /app/public/diff/taiwan_sp_list_occurrences_17387.diff
[CMD] [2019-10-16 10:26:16] echo "0a" > /app/public/diff/taiwan_sp_list_measurements_17388.diff
[CMD] [2019-10-16 10:26:16] tail -n +1 /app/public/converted_csv/taiwan_sp_list_measurements_17388.csv >> /app/public/diff/taiwan_sp_list_measurements_17388.diff
[CMD] [2019-10-16 10:26:16] echo "." >> /app/public/diff/taiwan_sp_list_measurements_17388.diff
[STOP] [2019-10-16 10:26:17] calculate_delta
[START] [2019-10-16 10:26:17] parse_diff_and_store
[INFO] [2019-10-16 10:26:17] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 10:26:17] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-16 10:26:25] Filtered Scientific Name `Huechys  sanguinea` to `Huechys sanguinea`
[INFO] [2019-10-16 10:26:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 10:26:32] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 10:28:28] Storing 2 References
[INFO] [2019-10-16 10:28:28] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 10:28:28] Average Time: 0.0
[INFO] [2019-10-16 10:28:28] Total Time: 1s
[INFO] [2019-10-16 10:28:28] Storing 28605 ScientificNames
[INFO] [2019-10-16 10:28:28] Processing group of 28605 in 29 groups of 1000
[INFO] [2019-10-16 10:28:40] Average Time: 0.394
[INFO] [2019-10-16 10:28:40] Total Time: 12s
[INFO] [2019-10-16 10:28:40] last 3 / first 3: 0.79
[INFO] [2019-10-16 10:28:40] Std.Dev: 0.1341640786499874; Max: 0.88
[INFO] [2019-10-16 10:28:40] Storing 28605 Nodes
[INFO] [2019-10-16 10:28:40] Processing group of 28605 in 29 groups of 1000
[INFO] [2019-10-16 10:28:50] Average Time: 0.34
[INFO] [2019-10-16 10:28:50] Total Time: 10s
[INFO] [2019-10-16 10:28:50] last 3 / first 3: 1.95
[INFO] [2019-10-16 10:28:50] Std.Dev: 0.1; Max: 0.65
[INFO] [2019-10-16 10:28:50] Storing 19762 Occurrences
[INFO] [2019-10-16 10:28:50] Processing group of 19762 in 20 groups of 1000
[INFO] [2019-10-16 10:28:52] Average Time: 0.108
[INFO] [2019-10-16 10:28:52] Total Time: 3s
[INFO] [2019-10-16 10:28:52] last 3 / first 3: 0.61
[INFO] [2019-10-16 10:28:52] Std.Dev: 0.03162277660168379; Max: 0.24
[INFO] [2019-10-16 10:28:52] Storing 39930 TraitsReferences
[INFO] [2019-10-16 10:28:52] Processing group of 39930 in 40 groups of 1000
[INFO] [2019-10-16 10:28:55] Average Time: 0.074
[INFO] [2019-10-16 10:28:55] Total Time: 4s
[INFO] [2019-10-16 10:28:55] last 3 / first 3: 0.76
[INFO] [2019-10-16 10:28:55] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-16 10:28:55] Storing 39929 Traits
[INFO] [2019-10-16 10:28:55] Processing group of 39929 in 40 groups of 1000
[INFO] [2019-10-16 10:29:08] Average Time: 0.331
[INFO] [2019-10-16 10:29:08] Total Time: 14s
[INFO] [2019-10-16 10:29:08] last 3 / first 3: 0.8
[INFO] [2019-10-16 10:29:08] Std.Dev: 0.10488088481701516; Max: 0.68
[INFO] [2019-10-16 10:29:08] Storing 39882 MetaTraits
[INFO] [2019-10-16 10:29:08] Processing group of 39882 in 40 groups of 1000
[INFO] [2019-10-16 10:29:13] Average Time: 0.109
[INFO] [2019-10-16 10:29:13] Total Time: 5s
[INFO] [2019-10-16 10:29:13] last 3 / first 3: 0.67
[INFO] [2019-10-16 10:29:13] Std.Dev: 0.03162277660168379; Max: 0.21
[STOP] [2019-10-16 10:29:13] parse_diff_and_store
[START] [2019-10-16 10:29:13] resolve_keys
[INFO] [2019-10-16 10:30:37] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 10:30:44] traits to occurrences...
[INFO] [2019-10-16 10:30:53] traits to nodes (through occurrences)...
[INFO] [2019-10-16 10:30:54] Traits to sex term...
[INFO] [2019-10-16 10:31:02] Traits to lifestage term...
[INFO] [2019-10-16 10:31:10] MetaTraits to traits...
[INFO] [2019-10-16 10:31:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 10:31:18] Assocs to occurrences...
[INFO] [2019-10-16 10:31:18] Assocs to nodes...
[INFO] [2019-10-16 10:31:18] Assoc to sex term...
[INFO] [2019-10-16 10:31:18] Assoc to lifestage term...
[STOP] [2019-10-16 10:31:18] resolve_keys
[START] [2019-10-16 10:31:18] hold_for_later_1
[STOP] [2019-10-16 10:31:18] hold_for_later_1
[START] [2019-10-16 10:31:18] hold_for_later_2
[STOP] [2019-10-16 10:31:18] hold_for_later_2
[START] [2019-10-16 10:31:18] resolve_missing_parents
[STOP] [2019-10-16 10:32:05] resolve_missing_parents
[START] [2019-10-16 10:32:05] rebuild_nodes
[START] [2019-10-16 10:32:05] Flattener#flatten
[START] [2019-10-16 10:32:05] Flattener#study_resource
[START] [2019-10-16 10:32:05] Flattener#build_ancestry
[STOP] [2019-10-16 10:32:09] Flattener#build_ancestry
[INFO] [2019-10-16 10:32:09] 28605 ancestry keys
[START] [2019-10-16 10:32:09] build_node_ancestors
[INFO] [2019-10-16 10:32:09] old ancestors deleted.
[STOP] [2019-10-16 10:32:26] build_node_ancestors
[START] [2019-10-16 10:32:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 10:32:32] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 10:32:32] Flattener#flatten
[STOP] [2019-10-16 10:32:32] rebuild_nodes
[START] [2019-10-16 10:32:32] resolve_missing_media_owners
[STOP] [2019-10-16 10:32:32] resolve_missing_media_owners
[START] [2019-10-16 10:32:32] sanitize_media_verbatims
[STOP] [2019-10-16 10:32:32] sanitize_media_verbatims
[START] [2019-10-16 10:32:32] queue_downloads
[STOP] [2019-10-16 10:32:32] queue_downloads
[START] [2019-10-16 10:32:32] parse_names
[WARN] [2019-10-16 10:32:32] I see 28605 names which still need to be parsed.
[WARN] [2019-10-16 10:32:54] I see 2 names which still need to be parsed.
[STOP] [2019-10-16 10:32:55] parse_names
[START] [2019-10-16 10:32:55] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 10:32:56] denormalize_canonical_names_to_nodes
[START] [2019-10-16 10:32:56] match_nodes
[START] [2019-10-16 10:32:56] map_all_nodes_to_pages
[STOP] [2019-10-16 11:05:39] map_all_nodes_to_pages
[INFO] [2019-10-16 11:05:39] 1762 Unmatched nodes (of 28605)! That's too many to output. First 10: Ourapteryx yerburii (#52314525); Ourapteryx horishana (#52319145); Ourapteryx formosana (#52334219); Krananda latimarginaria (#52324989); Sarcinodes mongaku (#52319465); Sarcinodes yaeyamana (#52327463); Alcis taiwanovariegata (#52311415); Alcis tayulina (#52321656); Alcis subochrearia (#52334159); Psilalcis pulveraria (#52320823)
[START] [2019-10-16 11:05:39] update_nodes
[STOP] [2019-10-16 11:05:48] update_nodes
[STOP] [2019-10-16 11:05:48] match_nodes
[START] [2019-10-16 11:05:48] reindex_search
[STOP] [2019-10-16 11:07:15] reindex_search
[START] [2019-10-16 11:07:15] normalize_units
[STOP] [2019-10-16 11:07:15] normalize_units
[START] [2019-10-16 11:07:15] calculate_statistics
[STOP] [2019-10-16 11:07:15] calculate_statistics
[START] [2019-10-16 11:07:15] complete_harvest_instance
[START] [2019-10-16 11:07:15] overall_tsv_creation
[INFO] [2019-10-16 11:07:15] Processing group of 28605 in 3 batches of 10000
[INFO] [2019-10-16 11:08:44] 6485 Traits (unfiltered)...
[INFO] [2019-10-16 11:08:57] 6485 Traits (filtered)...
[INFO] [2019-10-16 11:08:57] 0 Associations (filtered)...
[INFO] [2019-10-16 11:09:48] 32409 metadata added.
[INFO] [2019-10-16 11:09:48] 0 metadata added.
[INFO] [2019-10-16 11:11:22] 7261 Traits (unfiltered)...
[INFO] [2019-10-16 11:11:35] 7261 Traits (filtered)...
[INFO] [2019-10-16 11:11:35] 0 Associations (filtered)...
[INFO] [2019-10-16 11:12:30] 36289 metadata added.
[INFO] [2019-10-16 11:12:30] 0 metadata added.
[INFO] [2019-10-16 11:13:59] 6016 Traits (unfiltered)...
[INFO] [2019-10-16 11:14:12] 6016 Traits (filtered)...
[INFO] [2019-10-16 11:14:12] 0 Associations (filtered)...
[INFO] [2019-10-16 11:15:05] 30064 metadata added.
[INFO] [2019-10-16 11:15:05] 0 metadata added.
[INFO] [2019-10-16 11:15:06] Average Time: 129.773
[INFO] [2019-10-16 11:15:06] Total Time: 7m51s
[STOP] [2019-10-16 11:15:06] overall_tsv_creation
[INFO] [2019-10-16 11:15:06] Done. Check your files:
[INFO] [2019-10-16 11:15:06] (28605 lines) /app/public/data/taiwan_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 11:15:06] (131046 lines) /app/public/data/taiwan_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 11:15:06] (28605 lines) /app/public/data/taiwan_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 11:15:07] (19763 lines) /app/public/data/taiwan_sp_list/publish_traits.tsv
[INFO] [2019-10-16 11:15:07] (98763 lines) /app/public/data/taiwan_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 11:15:07] complete_harvest_instance
[START] [2019-10-16 11:15:07] completed
[STOP] [2019-10-16 11:15:07] completed
[STOP] [2019-10-16 11:15:07] logged process, took 2939.26

Latest Process

16 Oct 10:26 EXITED currently processing 0