Harvest for Uzbekistan Species List Created 17 Oct 11:12

Stage: completed
Fetched: 17 Oct 11:12
Validated: 17 Oct 11:12
Deltas Created 17 Oct 11:12
Units Normalized: 17 Oct 11:14
Ancestry Built: 17 Oct 11:13
Nodes Matched: 17 Oct 11:14
Names Parsed: 17 Oct 11:13
New Models Stored: 17 Oct 11:12
Indexed: 17 Oct 11:14
Completed: 17 Oct 11:16
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-17 11:12:42 -0400 by logger.rb/56815
[START] [2019-10-17 11:12:42] logged process
[START] [2019-10-17 11:12:42] create_harvest_instance
[STOP] [2019-10-17 11:12:43] create_harvest_instance
[START] [2019-10-17 11:12:43] fetch_files
[STOP] [2019-10-17 11:12:43] fetch_files
[START] [2019-10-17 11:12:43] validate_each_file
[STOP] [2019-10-17 11:12:43] validate_each_file
[START] [2019-10-17 11:12:43] convert_to_csv
[CMD] [2019-10-17 11:12:43] /usr/bin/sort /app/public/converted_csv/uzbekistan_sp_li_refs_17721.csv > /app/public/converted_csv/uzbekistan_sp_li_refs_17721.csv_sorted
[CMD] [2019-10-17 11:12:43] /usr/bin/sort /app/public/converted_csv/uzbekistan_sp_li_nodes_17722.csv > /app/public/converted_csv/uzbekistan_sp_li_nodes_17722.csv_sorted
[CMD] [2019-10-17 11:12:43] /usr/bin/sort /app/public/converted_csv/uzbekistan_sp_li_occurrences_17723.csv > /app/public/converted_csv/uzbekistan_sp_li_occurrences_17723.csv_sorted
[CMD] [2019-10-17 11:12:43] /usr/bin/sort /app/public/converted_csv/uzbekistan_sp_li_measurements_17724.csv > /app/public/converted_csv/uzbekistan_sp_li_measurements_17724.csv_sorted
[STOP] [2019-10-17 11:12:43] convert_to_csv
[START] [2019-10-17 11:12:43] calculate_delta
[CMD] [2019-10-17 11:12:43] echo "0a" > /app/public/diff/uzbekistan_sp_li_refs_17721.diff
[CMD] [2019-10-17 11:12:43] tail -n +1 /app/public/converted_csv/uzbekistan_sp_li_refs_17721.csv >> /app/public/diff/uzbekistan_sp_li_refs_17721.diff
[CMD] [2019-10-17 11:12:43] echo "." >> /app/public/diff/uzbekistan_sp_li_refs_17721.diff
[CMD] [2019-10-17 11:12:44] echo "0a" > /app/public/diff/uzbekistan_sp_li_nodes_17722.diff
[CMD] [2019-10-17 11:12:44] tail -n +1 /app/public/converted_csv/uzbekistan_sp_li_nodes_17722.csv >> /app/public/diff/uzbekistan_sp_li_nodes_17722.diff
[CMD] [2019-10-17 11:12:44] echo "." >> /app/public/diff/uzbekistan_sp_li_nodes_17722.diff
[CMD] [2019-10-17 11:12:44] echo "0a" > /app/public/diff/uzbekistan_sp_li_occurrences_17723.diff
[CMD] [2019-10-17 11:12:44] tail -n +1 /app/public/converted_csv/uzbekistan_sp_li_occurrences_17723.csv >> /app/public/diff/uzbekistan_sp_li_occurrences_17723.diff
[CMD] [2019-10-17 11:12:44] echo "." >> /app/public/diff/uzbekistan_sp_li_occurrences_17723.diff
[CMD] [2019-10-17 11:12:44] echo "0a" > /app/public/diff/uzbekistan_sp_li_measurements_17724.diff
[CMD] [2019-10-17 11:12:44] tail -n +1 /app/public/converted_csv/uzbekistan_sp_li_measurements_17724.csv >> /app/public/diff/uzbekistan_sp_li_measurements_17724.diff
[CMD] [2019-10-17 11:12:44] echo "." >> /app/public/diff/uzbekistan_sp_li_measurements_17724.diff
[STOP] [2019-10-17 11:12:44] calculate_delta
[START] [2019-10-17 11:12:44] parse_diff_and_store
[INFO] [2019-10-17 11:12:44] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:12:45] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:12:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:12:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:12:52] Storing 2 References
[INFO] [2019-10-17 11:12:52] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:12:53] Average Time: 0.0
[INFO] [2019-10-17 11:12:53] Total Time: 1s
[INFO] [2019-10-17 11:12:53] Storing 2400 ScientificNames
[INFO] [2019-10-17 11:12:53] Processing group of 2400 in 3 groups of 1000
[INFO] [2019-10-17 11:12:53] Average Time: 0.297
[INFO] [2019-10-17 11:12:53] Total Time: 1s
[INFO] [2019-10-17 11:12:53] Storing 2400 Nodes
[INFO] [2019-10-17 11:12:53] Processing group of 2400 in 3 groups of 1000
[INFO] [2019-10-17 11:12:54] Average Time: 0.23
[INFO] [2019-10-17 11:12:54] Total Time: 1s
[INFO] [2019-10-17 11:12:54] Storing 964 Occurrences
[INFO] [2019-10-17 11:12:54] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-17 11:12:54] Average Time: 0.13
[INFO] [2019-10-17 11:12:54] Total Time: 1s
[INFO] [2019-10-17 11:12:54] Storing 2460 TraitsReferences
[INFO] [2019-10-17 11:12:54] Processing group of 2460 in 3 groups of 1000
[INFO] [2019-10-17 11:12:55] Average Time: 0.103
[INFO] [2019-10-17 11:12:55] Total Time: 1s
[INFO] [2019-10-17 11:12:55] Storing 2459 Traits
[INFO] [2019-10-17 11:12:55] Processing group of 2459 in 3 groups of 1000
[INFO] [2019-10-17 11:12:56] Average Time: 0.31
[INFO] [2019-10-17 11:12:56] Total Time: 1s
[INFO] [2019-10-17 11:12:56] Storing 2459 MetaTraits
[INFO] [2019-10-17 11:12:56] Processing group of 2459 in 3 groups of 1000
[INFO] [2019-10-17 11:12:56] Average Time: 0.107
[INFO] [2019-10-17 11:12:56] Total Time: 1s
[STOP] [2019-10-17 11:12:56] parse_diff_and_store
[START] [2019-10-17 11:12:56] resolve_keys
[INFO] [2019-10-17 11:13:07] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:13:08] traits to occurrences...
[INFO] [2019-10-17 11:13:09] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:13:09] Traits to sex term...
[INFO] [2019-10-17 11:13:10] Traits to lifestage term...
[INFO] [2019-10-17 11:13:11] MetaTraits to traits...
[INFO] [2019-10-17 11:13:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:13:11] Assocs to occurrences...
[INFO] [2019-10-17 11:13:11] Assocs to nodes...
[INFO] [2019-10-17 11:13:11] Assoc to sex term...
[INFO] [2019-10-17 11:13:11] Assoc to lifestage term...
[STOP] [2019-10-17 11:13:11] resolve_keys
[START] [2019-10-17 11:13:11] hold_for_later_1
[STOP] [2019-10-17 11:13:11] hold_for_later_1
[START] [2019-10-17 11:13:11] hold_for_later_2
[STOP] [2019-10-17 11:13:11] hold_for_later_2
[START] [2019-10-17 11:13:11] resolve_missing_parents
[STOP] [2019-10-17 11:13:15] resolve_missing_parents
[START] [2019-10-17 11:13:15] rebuild_nodes
[START] [2019-10-17 11:13:15] Flattener#flatten
[START] [2019-10-17 11:13:15] Flattener#study_resource
[START] [2019-10-17 11:13:15] Flattener#build_ancestry
[STOP] [2019-10-17 11:13:15] Flattener#build_ancestry
[INFO] [2019-10-17 11:13:15] 2400 ancestry keys
[START] [2019-10-17 11:13:15] build_node_ancestors
[INFO] [2019-10-17 11:13:15] old ancestors deleted.
[STOP] [2019-10-17 11:13:15] build_node_ancestors
[START] [2019-10-17 11:13:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:13:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:13:16] Flattener#flatten
[STOP] [2019-10-17 11:13:16] rebuild_nodes
[START] [2019-10-17 11:13:16] resolve_missing_media_owners
[STOP] [2019-10-17 11:13:16] resolve_missing_media_owners
[START] [2019-10-17 11:13:16] sanitize_media_verbatims
[STOP] [2019-10-17 11:13:16] sanitize_media_verbatims
[START] [2019-10-17 11:13:16] queue_downloads
[STOP] [2019-10-17 11:13:16] queue_downloads
[START] [2019-10-17 11:13:16] parse_names
[WARN] [2019-10-17 11:13:16] I see 2400 names which still need to be parsed.
[STOP] [2019-10-17 11:13:19] parse_names
[START] [2019-10-17 11:13:19] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:13:19] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:13:19] match_nodes
[START] [2019-10-17 11:13:19] map_all_nodes_to_pages
[STOP] [2019-10-17 11:14:40] map_all_nodes_to_pages
[INFO] [2019-10-17 11:14:40] 228 Unmatched nodes (of 2400)! That's too many to output. First 10: Sorghum halepensis (#52716186); Allium kaufmanni (#52717077); Xanthorrhoeaceae (#52715279); Iris parvula (#52716957); Gobiatidae (#52717117); Gobiates (#52717116); Eoscapherpeton (#52716111); Eoscapherpeton surgayi (#52716110); Magnoliopsida (#52714959); Astragalus stipulosa (#52716574)
[START] [2019-10-17 11:14:40] update_nodes
[STOP] [2019-10-17 11:14:40] update_nodes
[STOP] [2019-10-17 11:14:40] match_nodes
[START] [2019-10-17 11:14:40] reindex_search
[STOP] [2019-10-17 11:14:44] reindex_search
[START] [2019-10-17 11:14:44] normalize_units
[STOP] [2019-10-17 11:14:44] normalize_units
[START] [2019-10-17 11:14:44] calculate_statistics
[STOP] [2019-10-17 11:14:44] calculate_statistics
[START] [2019-10-17 11:14:44] complete_harvest_instance
[START] [2019-10-17 11:14:44] overall_tsv_creation
[INFO] [2019-10-17 11:14:44] Processing group of 2400 in 1 batches of 10000
[INFO] [2019-10-17 11:15:37] 964 Traits (unfiltered)...
[INFO] [2019-10-17 11:15:50] 964 Traits (filtered)...
[INFO] [2019-10-17 11:15:50] 0 Associations (filtered)...
[INFO] [2019-10-17 11:16:28] 4819 metadata added.
[INFO] [2019-10-17 11:16:28] 0 metadata added.
[INFO] [2019-10-17 11:16:28] Average Time: 81.01
[INFO] [2019-10-17 11:16:28] Total Time: 1m44s
[STOP] [2019-10-17 11:16:28] overall_tsv_creation
[INFO] [2019-10-17 11:16:28] Done. Check your files:
[INFO] [2019-10-17 11:16:28] (2400 lines) /app/public/data/uzbekistan_sp_li/publish_nodes.tsv
[INFO] [2019-10-17 11:16:28] (6750 lines) /app/public/data/uzbekistan_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:16:28] (2400 lines) /app/public/data/uzbekistan_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-17 11:16:28] (965 lines) /app/public/data/uzbekistan_sp_li/publish_traits.tsv
[INFO] [2019-10-17 11:16:28] (4820 lines) /app/public/data/uzbekistan_sp_li/publish_metadata.tsv
[STOP] [2019-10-17 11:16:28] complete_harvest_instance
[START] [2019-10-17 11:16:28] completed
[STOP] [2019-10-17 11:16:28] completed
[STOP] [2019-10-17 11:16:28] logged process, took 226.15
Latest Process

17 Oct 11:12 EXITED currently processing 0