Harvest for Turkmenistan Species List Created 16 Oct 19:04

Stage: completed
Fetched: 16 Oct 19:04
Validated: 16 Oct 19:04
Deltas Created 16 Oct 19:04
Units Normalized: 16 Oct 19:09
Ancestry Built: 16 Oct 19:05
Nodes Matched: 16 Oct 19:08
Names Parsed: 16 Oct 19:05
New Models Stored: 16 Oct 19:04
Indexed: 16 Oct 19:09
Completed: 16 Oct 19:10
Time to Harvest: less than a minute
Harvesting Log

(140 lines)
# Logfile created on 2019-10-16 19:04:40 -0400 by logger.rb/56815
[START] [2019-10-16 19:04:40] logged process
[START] [2019-10-16 19:04:40] create_harvest_instance
[STOP] [2019-10-16 19:04:40] create_harvest_instance
[START] [2019-10-16 19:04:40] fetch_files
[STOP] [2019-10-16 19:04:40] fetch_files
[START] [2019-10-16 19:04:40] validate_each_file
[STOP] [2019-10-16 19:04:41] validate_each_file
[START] [2019-10-16 19:04:41] convert_to_csv
[CMD] [2019-10-16 19:04:41] /usr/bin/sort /app/public/converted_csv/Turkmenistan_refs_17553.csv > /app/public/converted_csv/Turkmenistan_refs_17553.csv_sorted
[CMD] [2019-10-16 19:04:41] /usr/bin/sort /app/public/converted_csv/Turkmenistan_nodes_17554.csv > /app/public/converted_csv/Turkmenistan_nodes_17554.csv_sorted
[CMD] [2019-10-16 19:04:41] /usr/bin/sort /app/public/converted_csv/Turkmenistan_occurrences_17555.csv > /app/public/converted_csv/Turkmenistan_occurrences_17555.csv_sorted
[CMD] [2019-10-16 19:04:41] /usr/bin/sort /app/public/converted_csv/Turkmenistan_measurements_17556.csv > /app/public/converted_csv/Turkmenistan_measurements_17556.csv_sorted
[STOP] [2019-10-16 19:04:41] convert_to_csv
[START] [2019-10-16 19:04:41] calculate_delta
[CMD] [2019-10-16 19:04:41] echo "0a" > /app/public/diff/Turkmenistan_refs_17553.diff
[CMD] [2019-10-16 19:04:41] tail -n +1 /app/public/converted_csv/Turkmenistan_refs_17553.csv >> /app/public/diff/Turkmenistan_refs_17553.diff
[CMD] [2019-10-16 19:04:41] echo "." >> /app/public/diff/Turkmenistan_refs_17553.diff
[CMD] [2019-10-16 19:04:41] echo "0a" > /app/public/diff/Turkmenistan_nodes_17554.diff
[CMD] [2019-10-16 19:04:41] tail -n +1 /app/public/converted_csv/Turkmenistan_nodes_17554.csv >> /app/public/diff/Turkmenistan_nodes_17554.diff
[CMD] [2019-10-16 19:04:41] echo "." >> /app/public/diff/Turkmenistan_nodes_17554.diff
[CMD] [2019-10-16 19:04:42] echo "0a" > /app/public/diff/Turkmenistan_occurrences_17555.diff
[CMD] [2019-10-16 19:04:42] tail -n +1 /app/public/converted_csv/Turkmenistan_occurrences_17555.csv >> /app/public/diff/Turkmenistan_occurrences_17555.diff
[CMD] [2019-10-16 19:04:42] echo "." >> /app/public/diff/Turkmenistan_occurrences_17555.diff
[CMD] [2019-10-16 19:04:42] echo "0a" > /app/public/diff/Turkmenistan_measurements_17556.diff
[CMD] [2019-10-16 19:04:42] tail -n +1 /app/public/converted_csv/Turkmenistan_measurements_17556.csv >> /app/public/diff/Turkmenistan_measurements_17556.diff
[CMD] [2019-10-16 19:04:42] echo "." >> /app/public/diff/Turkmenistan_measurements_17556.diff
[STOP] [2019-10-16 19:04:42] calculate_delta
[START] [2019-10-16 19:04:42] parse_diff_and_store
[INFO] [2019-10-16 19:04:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 19:04:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 19:04:43] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 19:04:43] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 19:04:51] Storing 2 References
[INFO] [2019-10-16 19:04:51] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 19:04:51] Average Time: 0.0
[INFO] [2019-10-16 19:04:51] Total Time: 1s
[INFO] [2019-10-16 19:04:51] Storing 2195 ScientificNames
[INFO] [2019-10-16 19:04:51] Processing group of 2195 in 3 groups of 1000
[INFO] [2019-10-16 19:04:51] Average Time: 0.263
[INFO] [2019-10-16 19:04:51] Total Time: 1s
[INFO] [2019-10-16 19:04:51] Storing 2195 Nodes
[INFO] [2019-10-16 19:04:51] Processing group of 2195 in 3 groups of 1000
[INFO] [2019-10-16 19:04:52] Average Time: 0.19
[INFO] [2019-10-16 19:04:52] Total Time: 1s
[INFO] [2019-10-16 19:04:52] Storing 1249 Occurrences
[INFO] [2019-10-16 19:04:52] Processing group of 1249 in 2 groups of 1000
[INFO] [2019-10-16 19:04:52] Average Time: 0.075
[INFO] [2019-10-16 19:04:52] Total Time: 1s
[INFO] [2019-10-16 19:04:52] Storing 2214 TraitsReferences
[INFO] [2019-10-16 19:04:52] Processing group of 2214 in 3 groups of 1000
[INFO] [2019-10-16 19:04:52] Average Time: 0.083
[INFO] [2019-10-16 19:04:52] Total Time: 1s
[INFO] [2019-10-16 19:04:52] Storing 2214 Traits
[INFO] [2019-10-16 19:04:52] Processing group of 2214 in 3 groups of 1000
[INFO] [2019-10-16 19:04:53] Average Time: 0.253
[INFO] [2019-10-16 19:04:53] Total Time: 1s
[INFO] [2019-10-16 19:04:53] Storing 2214 MetaTraits
[INFO] [2019-10-16 19:04:53] Processing group of 2214 in 3 groups of 1000
[INFO] [2019-10-16 19:04:53] Average Time: 0.083
[INFO] [2019-10-16 19:04:53] Total Time: 1s
[STOP] [2019-10-16 19:04:53] parse_diff_and_store
[START] [2019-10-16 19:04:53] resolve_keys
[INFO] [2019-10-16 19:05:04] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 19:05:05] traits to occurrences...
[INFO] [2019-10-16 19:05:06] traits to nodes (through occurrences)...
[INFO] [2019-10-16 19:05:07] Traits to sex term...
[INFO] [2019-10-16 19:05:07] Traits to lifestage term...
[INFO] [2019-10-16 19:05:08] MetaTraits to traits...
[INFO] [2019-10-16 19:05:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 19:05:09] Assocs to occurrences...
[INFO] [2019-10-16 19:05:09] Assocs to nodes...
[INFO] [2019-10-16 19:05:09] Assoc to sex term...
[INFO] [2019-10-16 19:05:09] Assoc to lifestage term...
[STOP] [2019-10-16 19:05:09] resolve_keys
[START] [2019-10-16 19:05:09] hold_for_later_1
[STOP] [2019-10-16 19:05:09] hold_for_later_1
[START] [2019-10-16 19:05:09] hold_for_later_2
[STOP] [2019-10-16 19:05:09] hold_for_later_2
[START] [2019-10-16 19:05:09] resolve_missing_parents
[STOP] [2019-10-16 19:05:12] resolve_missing_parents
[START] [2019-10-16 19:05:12] rebuild_nodes
[START] [2019-10-16 19:05:12] Flattener#flatten
[START] [2019-10-16 19:05:12] Flattener#study_resource
[START] [2019-10-16 19:05:12] Flattener#build_ancestry
[STOP] [2019-10-16 19:05:12] Flattener#build_ancestry
[INFO] [2019-10-16 19:05:12] 2195 ancestry keys
[START] [2019-10-16 19:05:12] build_node_ancestors
[INFO] [2019-10-16 19:05:12] old ancestors deleted.
[STOP] [2019-10-16 19:05:13] build_node_ancestors
[START] [2019-10-16 19:05:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 19:05:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 19:05:14] Flattener#flatten
[STOP] [2019-10-16 19:05:14] rebuild_nodes
[START] [2019-10-16 19:05:14] resolve_missing_media_owners
[STOP] [2019-10-16 19:05:14] resolve_missing_media_owners
[START] [2019-10-16 19:05:14] sanitize_media_verbatims
[STOP] [2019-10-16 19:05:14] sanitize_media_verbatims
[START] [2019-10-16 19:05:14] queue_downloads
[STOP] [2019-10-16 19:05:14] queue_downloads
[START] [2019-10-16 19:05:14] parse_names
[WARN] [2019-10-16 19:05:14] I see 2195 names which still need to be parsed.
[WARN] [2019-10-16 19:05:17] I see 13 names which still need to be parsed.
[STOP] [2019-10-16 19:05:18] parse_names
[START] [2019-10-16 19:05:18] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 19:05:18] denormalize_canonical_names_to_nodes
[START] [2019-10-16 19:05:18] match_nodes
[START] [2019-10-16 19:05:18] map_all_nodes_to_pages
[STOP] [2019-10-16 19:08:57] map_all_nodes_to_pages
[INFO] [2019-10-16 19:08:57] 161 Unmatched nodes (of 2195)! That's too many to output. First 10: Pseudepidalea oblongus (#52524994); Gnetopsida (#52527023); Lycopodiopsida (#52527027); Polypodiopsida (#52527015); Gnetophyta (#52527024); Equisetophyta (#52527063); Equisetopsida (#52527039); Chlorophyta (#52527073); Trebouxiophyceae (#52527072); Ulvophyceae (#52527078)
[START] [2019-10-16 19:08:57] update_nodes
[STOP] [2019-10-16 19:08:58] update_nodes
[STOP] [2019-10-16 19:08:58] match_nodes
[START] [2019-10-16 19:08:58] reindex_search
[STOP] [2019-10-16 19:09:03] reindex_search
[START] [2019-10-16 19:09:03] normalize_units
[STOP] [2019-10-16 19:09:03] normalize_units
[START] [2019-10-16 19:09:03] calculate_statistics
[STOP] [2019-10-16 19:09:03] calculate_statistics
[START] [2019-10-16 19:09:03] complete_harvest_instance
[START] [2019-10-16 19:09:03] overall_tsv_creation
[INFO] [2019-10-16 19:09:03] Processing group of 2195 in 1 batches of 10000
[INFO] [2019-10-16 19:09:56] 1103 Traits (unfiltered)...
[INFO] [2019-10-16 19:10:09] 1103 Traits (filtered)...
[INFO] [2019-10-16 19:10:09] 0 Associations (filtered)...
[INFO] [2019-10-16 19:10:48] 5515 metadata added.
[INFO] [2019-10-16 19:10:48] 0 metadata added.
[INFO] [2019-10-16 19:10:48] Average Time: 82.19
[INFO] [2019-10-16 19:10:48] Total Time: 1m46s
[STOP] [2019-10-16 19:10:48] overall_tsv_creation
[INFO] [2019-10-16 19:10:48] Done. Check your files:
[INFO] [2019-10-16 19:10:48] (2195 lines) /app/public/data/Turkmenistan/publish_nodes.tsv
[INFO] [2019-10-16 19:10:48] (11330 lines) /app/public/data/Turkmenistan/publish_node_ancestors.tsv
[INFO] [2019-10-16 19:10:48] (2195 lines) /app/public/data/Turkmenistan/publish_scientific_names.tsv
[INFO] [2019-10-16 19:10:48] (1104 lines) /app/public/data/Turkmenistan/publish_traits.tsv
[INFO] [2019-10-16 19:10:48] (5516 lines) /app/public/data/Turkmenistan/publish_metadata.tsv
[STOP] [2019-10-16 19:10:48] complete_harvest_instance
[START] [2019-10-16 19:10:48] completed
[STOP] [2019-10-16 19:10:48] completed
[STOP] [2019-10-16 19:10:48] logged process, took 368.0
Latest Process

16 Oct 19:04 EXITED currently processing 0