Harvest for Yemen Species List Created 17 Oct 11:27

Stage: completed
Fetched: 17 Oct 11:27
Validated: 17 Oct 11:27
Deltas Created 17 Oct 11:27
Units Normalized: 17 Oct 11:30
Ancestry Built: 17 Oct 11:28
Nodes Matched: 17 Oct 11:30
Names Parsed: 17 Oct 11:28
New Models Stored: 17 Oct 11:27
Indexed: 17 Oct 11:30
Completed: 17 Oct 11:32
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2019-10-17 11:27:27 -0400 by logger.rb/56815
[START] [2019-10-17 11:27:27] logged process
[START] [2019-10-17 11:27:27] create_harvest_instance
[STOP] [2019-10-17 11:27:28] create_harvest_instance
[START] [2019-10-17 11:27:28] fetch_files
[STOP] [2019-10-17 11:27:28] fetch_files
[START] [2019-10-17 11:27:28] validate_each_file
[STOP] [2019-10-17 11:27:28] validate_each_file
[START] [2019-10-17 11:27:28] convert_to_csv
[CMD] [2019-10-17 11:27:28] /usr/bin/sort /app/public/converted_csv/yemen_sp_list_refs_17745.csv > /app/public/converted_csv/yemen_sp_list_refs_17745.csv_sorted
[CMD] [2019-10-17 11:27:28] /usr/bin/sort /app/public/converted_csv/yemen_sp_list_nodes_17746.csv > /app/public/converted_csv/yemen_sp_list_nodes_17746.csv_sorted
[CMD] [2019-10-17 11:27:28] /usr/bin/sort /app/public/converted_csv/yemen_sp_list_occurrences_17747.csv > /app/public/converted_csv/yemen_sp_list_occurrences_17747.csv_sorted
[CMD] [2019-10-17 11:27:28] /usr/bin/sort /app/public/converted_csv/yemen_sp_list_measurements_17748.csv > /app/public/converted_csv/yemen_sp_list_measurements_17748.csv_sorted
[STOP] [2019-10-17 11:27:29] convert_to_csv
[START] [2019-10-17 11:27:29] calculate_delta
[CMD] [2019-10-17 11:27:29] echo "0a" > /app/public/diff/yemen_sp_list_refs_17745.diff
[CMD] [2019-10-17 11:27:29] tail -n +1 /app/public/converted_csv/yemen_sp_list_refs_17745.csv >> /app/public/diff/yemen_sp_list_refs_17745.diff
[CMD] [2019-10-17 11:27:29] echo "." >> /app/public/diff/yemen_sp_list_refs_17745.diff
[CMD] [2019-10-17 11:27:29] echo "0a" > /app/public/diff/yemen_sp_list_nodes_17746.diff
[CMD] [2019-10-17 11:27:29] tail -n +1 /app/public/converted_csv/yemen_sp_list_nodes_17746.csv >> /app/public/diff/yemen_sp_list_nodes_17746.diff
[CMD] [2019-10-17 11:27:29] echo "." >> /app/public/diff/yemen_sp_list_nodes_17746.diff
[CMD] [2019-10-17 11:27:29] echo "0a" > /app/public/diff/yemen_sp_list_occurrences_17747.diff
[CMD] [2019-10-17 11:27:29] tail -n +1 /app/public/converted_csv/yemen_sp_list_occurrences_17747.csv >> /app/public/diff/yemen_sp_list_occurrences_17747.diff
[CMD] [2019-10-17 11:27:29] echo "." >> /app/public/diff/yemen_sp_list_occurrences_17747.diff
[CMD] [2019-10-17 11:27:29] echo "0a" > /app/public/diff/yemen_sp_list_measurements_17748.diff
[CMD] [2019-10-17 11:27:29] tail -n +1 /app/public/converted_csv/yemen_sp_list_measurements_17748.csv >> /app/public/diff/yemen_sp_list_measurements_17748.diff
[CMD] [2019-10-17 11:27:30] echo "." >> /app/public/diff/yemen_sp_list_measurements_17748.diff
[STOP] [2019-10-17 11:27:30] calculate_delta
[START] [2019-10-17 11:27:30] parse_diff_and_store
[INFO] [2019-10-17 11:27:30] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:27:30] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:27:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:27:32] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:27:45] Storing 2 References
[INFO] [2019-10-17 11:27:45] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:27:45] Average Time: 0.0
[INFO] [2019-10-17 11:27:45] Total Time: 1s
[INFO] [2019-10-17 11:27:45] Storing 4030 ScientificNames
[INFO] [2019-10-17 11:27:45] Processing group of 4030 in 5 groups of 1000
[INFO] [2019-10-17 11:27:46] Average Time: 0.296
[INFO] [2019-10-17 11:27:46] Total Time: 2s
[INFO] [2019-10-17 11:27:46] Storing 4030 Nodes
[INFO] [2019-10-17 11:27:46] Processing group of 4030 in 5 groups of 1000
[INFO] [2019-10-17 11:27:48] Average Time: 0.238
[INFO] [2019-10-17 11:27:48] Total Time: 2s
[INFO] [2019-10-17 11:27:48] Storing 2410 Occurrences
[INFO] [2019-10-17 11:27:48] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-17 11:27:48] Average Time: 0.08
[INFO] [2019-10-17 11:27:48] Total Time: 1s
[INFO] [2019-10-17 11:27:48] Storing 4830 TraitsReferences
[INFO] [2019-10-17 11:27:48] Processing group of 4830 in 5 groups of 1000
[INFO] [2019-10-17 11:27:48] Average Time: 0.084
[INFO] [2019-10-17 11:27:48] Total Time: 1s
[INFO] [2019-10-17 11:27:48] Storing 4829 Traits
[INFO] [2019-10-17 11:27:48] Processing group of 4829 in 5 groups of 1000
[INFO] [2019-10-17 11:27:50] Average Time: 0.29
[INFO] [2019-10-17 11:27:50] Total Time: 2s
[INFO] [2019-10-17 11:27:50] Storing 4830 MetaTraits
[INFO] [2019-10-17 11:27:50] Processing group of 4830 in 5 groups of 1000
[INFO] [2019-10-17 11:27:50] Average Time: 0.108
[INFO] [2019-10-17 11:27:50] Total Time: 1s
[STOP] [2019-10-17 11:27:50] parse_diff_and_store
[START] [2019-10-17 11:27:50] resolve_keys
[INFO] [2019-10-17 11:28:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:28:11] traits to occurrences...
[INFO] [2019-10-17 11:28:14] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:28:14] Traits to sex term...
[INFO] [2019-10-17 11:28:16] Traits to lifestage term...
[INFO] [2019-10-17 11:28:18] MetaTraits to traits...
[INFO] [2019-10-17 11:28:18] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:28:19] Assocs to occurrences...
[INFO] [2019-10-17 11:28:19] Assocs to nodes...
[INFO] [2019-10-17 11:28:19] Assoc to sex term...
[INFO] [2019-10-17 11:28:19] Assoc to lifestage term...
[STOP] [2019-10-17 11:28:19] resolve_keys
[START] [2019-10-17 11:28:19] hold_for_later_1
[STOP] [2019-10-17 11:28:19] hold_for_later_1
[START] [2019-10-17 11:28:19] hold_for_later_2
[STOP] [2019-10-17 11:28:19] hold_for_later_2
[START] [2019-10-17 11:28:19] resolve_missing_parents
[STOP] [2019-10-17 11:28:27] resolve_missing_parents
[START] [2019-10-17 11:28:27] rebuild_nodes
[START] [2019-10-17 11:28:27] Flattener#flatten
[START] [2019-10-17 11:28:27] Flattener#study_resource
[START] [2019-10-17 11:28:27] Flattener#build_ancestry
[STOP] [2019-10-17 11:28:27] Flattener#build_ancestry
[INFO] [2019-10-17 11:28:27] 4030 ancestry keys
[START] [2019-10-17 11:28:27] build_node_ancestors
[INFO] [2019-10-17 11:28:27] old ancestors deleted.
[STOP] [2019-10-17 11:28:27] build_node_ancestors
[START] [2019-10-17 11:28:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:28:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:28:28] Flattener#flatten
[STOP] [2019-10-17 11:28:28] rebuild_nodes
[START] [2019-10-17 11:28:28] resolve_missing_media_owners
[STOP] [2019-10-17 11:28:28] resolve_missing_media_owners
[START] [2019-10-17 11:28:28] sanitize_media_verbatims
[STOP] [2019-10-17 11:28:28] sanitize_media_verbatims
[START] [2019-10-17 11:28:28] queue_downloads
[STOP] [2019-10-17 11:28:28] queue_downloads
[START] [2019-10-17 11:28:28] parse_names
[WARN] [2019-10-17 11:28:28] I see 4030 names which still need to be parsed.
[STOP] [2019-10-17 11:28:33] parse_names
[START] [2019-10-17 11:28:33] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:28:33] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:28:33] match_nodes
[START] [2019-10-17 11:28:33] map_all_nodes_to_pages
[STOP] [2019-10-17 11:30:46] map_all_nodes_to_pages
[INFO] [2019-10-17 11:30:46] 254 Unmatched nodes (of 4030)! That's too many to output. First 10: Pennisetum (#52722486); Panicum compressa (#52725751); Cymbopogon jwarancusa (#52723445); Paspalidium (#52724139); Coelachyrum yemenica (#52726453); Ochthochloa (#52726423); Cistanche phelypaea (#52724767); Euphorbia longituberculosa (#52725598); Chrozophora obliqua (#52726016); Tephrosia hadramautica (#52722795)
[START] [2019-10-17 11:30:46] update_nodes
[STOP] [2019-10-17 11:30:48] update_nodes
[STOP] [2019-10-17 11:30:48] match_nodes
[START] [2019-10-17 11:30:48] reindex_search
[STOP] [2019-10-17 11:30:54] reindex_search
[START] [2019-10-17 11:30:54] normalize_units
[STOP] [2019-10-17 11:30:54] normalize_units
[START] [2019-10-17 11:30:54] calculate_statistics
[STOP] [2019-10-17 11:30:54] calculate_statistics
[START] [2019-10-17 11:30:54] complete_harvest_instance
[START] [2019-10-17 11:30:54] overall_tsv_creation
[INFO] [2019-10-17 11:30:54] Processing group of 4030 in 1 batches of 10000
[INFO] [2019-10-17 11:31:55] 2410 Traits (unfiltered)...
[INFO] [2019-10-17 11:32:08] 2410 Traits (filtered)...
[INFO] [2019-10-17 11:32:08] 0 Associations (filtered)...
[INFO] [2019-10-17 11:32:49] 12050 metadata added.
[INFO] [2019-10-17 11:32:49] 0 metadata added.
[INFO] [2019-10-17 11:32:49] Average Time: 90.13
[INFO] [2019-10-17 11:32:49] Total Time: 1m56s
[STOP] [2019-10-17 11:32:49] overall_tsv_creation
[INFO] [2019-10-17 11:32:49] Done. Check your files:
[INFO] [2019-10-17 11:32:49] (4030 lines) /app/public/data/yemen_sp_list/publish_nodes.tsv
[INFO] [2019-10-17 11:32:49] (5914 lines) /app/public/data/yemen_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:32:50] (4030 lines) /app/public/data/yemen_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-17 11:32:50] (2411 lines) /app/public/data/yemen_sp_list/publish_traits.tsv
[INFO] [2019-10-17 11:32:50] (12051 lines) /app/public/data/yemen_sp_list/publish_metadata.tsv
[STOP] [2019-10-17 11:32:50] complete_harvest_instance
[START] [2019-10-17 11:32:50] completed
[STOP] [2019-10-17 11:32:50] completed
[STOP] [2019-10-17 11:32:50] logged process, took 322.89

Latest Process