Harvest for Tunisia Species List Created 16 Oct 18:28

Stage: completed
Fetched: 16 Oct 18:28
Validated: 16 Oct 18:28
Deltas Created 16 Oct 18:28
Units Normalized: 16 Oct 18:36
Ancestry Built: 16 Oct 18:29
Nodes Matched: 16 Oct 18:36
Names Parsed: 16 Oct 18:29
New Models Stored: 16 Oct 18:28
Indexed: 16 Oct 18:36
Completed: 16 Oct 18:38
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 18:28:20 -0400 by logger.rb/56815
[START] [2019-10-16 18:28:20] logged process
[START] [2019-10-16 18:28:20] create_harvest_instance
[STOP] [2019-10-16 18:28:21] create_harvest_instance
[START] [2019-10-16 18:28:21] fetch_files
[STOP] [2019-10-16 18:28:21] fetch_files
[START] [2019-10-16 18:28:21] validate_each_file
[STOP] [2019-10-16 18:28:22] validate_each_file
[START] [2019-10-16 18:28:22] convert_to_csv
[CMD] [2019-10-16 18:28:22] /usr/bin/sort /app/public/converted_csv/tunisia_sp_list_refs_17537.csv > /app/public/converted_csv/tunisia_sp_list_refs_17537.csv_sorted
[CMD] [2019-10-16 18:28:22] /usr/bin/sort /app/public/converted_csv/tunisia_sp_list_nodes_17538.csv > /app/public/converted_csv/tunisia_sp_list_nodes_17538.csv_sorted
[CMD] [2019-10-16 18:28:22] /usr/bin/sort /app/public/converted_csv/tunisia_sp_list_occurrences_17539.csv > /app/public/converted_csv/tunisia_sp_list_occurrences_17539.csv_sorted
[CMD] [2019-10-16 18:28:22] /usr/bin/sort /app/public/converted_csv/tunisia_sp_list_measurements_17540.csv > /app/public/converted_csv/tunisia_sp_list_measurements_17540.csv_sorted
[STOP] [2019-10-16 18:28:22] convert_to_csv
[START] [2019-10-16 18:28:22] calculate_delta
[CMD] [2019-10-16 18:28:22] echo "0a" > /app/public/diff/tunisia_sp_list_refs_17537.diff
[CMD] [2019-10-16 18:28:22] tail -n +1 /app/public/converted_csv/tunisia_sp_list_refs_17537.csv >> /app/public/diff/tunisia_sp_list_refs_17537.diff
[CMD] [2019-10-16 18:28:22] echo "." >> /app/public/diff/tunisia_sp_list_refs_17537.diff
[CMD] [2019-10-16 18:28:22] echo "0a" > /app/public/diff/tunisia_sp_list_nodes_17538.diff
[CMD] [2019-10-16 18:28:22] tail -n +1 /app/public/converted_csv/tunisia_sp_list_nodes_17538.csv >> /app/public/diff/tunisia_sp_list_nodes_17538.diff
[CMD] [2019-10-16 18:28:22] echo "." >> /app/public/diff/tunisia_sp_list_nodes_17538.diff
[CMD] [2019-10-16 18:28:22] echo "0a" > /app/public/diff/tunisia_sp_list_occurrences_17539.diff
[CMD] [2019-10-16 18:28:22] tail -n +1 /app/public/converted_csv/tunisia_sp_list_occurrences_17539.csv >> /app/public/diff/tunisia_sp_list_occurrences_17539.diff
[CMD] [2019-10-16 18:28:22] echo "." >> /app/public/diff/tunisia_sp_list_occurrences_17539.diff
[CMD] [2019-10-16 18:28:22] echo "0a" > /app/public/diff/tunisia_sp_list_measurements_17540.diff
[CMD] [2019-10-16 18:28:22] tail -n +1 /app/public/converted_csv/tunisia_sp_list_measurements_17540.csv >> /app/public/diff/tunisia_sp_list_measurements_17540.diff
[CMD] [2019-10-16 18:28:22] echo "." >> /app/public/diff/tunisia_sp_list_measurements_17540.diff
[STOP] [2019-10-16 18:28:22] calculate_delta
[START] [2019-10-16 18:28:22] parse_diff_and_store
[INFO] [2019-10-16 18:28:22] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 18:28:23] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 18:28:24] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 18:28:25] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 18:28:41] Storing 2 References
[INFO] [2019-10-16 18:28:41] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 18:28:41] Average Time: 0.0
[INFO] [2019-10-16 18:28:41] Total Time: 1s
[INFO] [2019-10-16 18:28:41] Storing 5389 ScientificNames
[INFO] [2019-10-16 18:28:41] Processing group of 5389 in 6 groups of 1000
[INFO] [2019-10-16 18:28:43] Average Time: 0.318
[INFO] [2019-10-16 18:28:43] Total Time: 2s
[INFO] [2019-10-16 18:28:43] Storing 5389 Nodes
[INFO] [2019-10-16 18:28:43] Processing group of 5389 in 6 groups of 1000
[INFO] [2019-10-16 18:28:45] Average Time: 0.258
[INFO] [2019-10-16 18:28:45] Total Time: 2s
[INFO] [2019-10-16 18:28:45] Storing 2892 Occurrences
[INFO] [2019-10-16 18:28:45] Processing group of 2892 in 3 groups of 1000
[INFO] [2019-10-16 18:28:45] Average Time: 0.093
[INFO] [2019-10-16 18:28:45] Total Time: 1s
[INFO] [2019-10-16 18:28:45] Storing 5940 TraitsReferences
[INFO] [2019-10-16 18:28:45] Processing group of 5940 in 6 groups of 1000
[INFO] [2019-10-16 18:28:46] Average Time: 0.07
[INFO] [2019-10-16 18:28:46] Total Time: 1s
[INFO] [2019-10-16 18:28:46] Storing 5939 Traits
[INFO] [2019-10-16 18:28:46] Processing group of 5939 in 6 groups of 1000
[INFO] [2019-10-16 18:28:47] Average Time: 0.303
[INFO] [2019-10-16 18:28:47] Total Time: 2s
[INFO] [2019-10-16 18:28:47] Storing 5936 MetaTraits
[INFO] [2019-10-16 18:28:47] Processing group of 5936 in 6 groups of 1000
[INFO] [2019-10-16 18:28:48] Average Time: 0.105
[INFO] [2019-10-16 18:28:48] Total Time: 1s
[STOP] [2019-10-16 18:28:48] parse_diff_and_store
[START] [2019-10-16 18:28:48] resolve_keys
[INFO] [2019-10-16 18:29:11] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 18:29:14] traits to occurrences...
[INFO] [2019-10-16 18:29:17] traits to nodes (through occurrences)...
[INFO] [2019-10-16 18:29:17] Traits to sex term...
[INFO] [2019-10-16 18:29:19] Traits to lifestage term...
[INFO] [2019-10-16 18:29:22] MetaTraits to traits...
[INFO] [2019-10-16 18:29:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 18:29:23] Assocs to occurrences...
[INFO] [2019-10-16 18:29:23] Assocs to nodes...
[INFO] [2019-10-16 18:29:23] Assoc to sex term...
[INFO] [2019-10-16 18:29:23] Assoc to lifestage term...
[STOP] [2019-10-16 18:29:23] resolve_keys
[START] [2019-10-16 18:29:23] hold_for_later_1
[STOP] [2019-10-16 18:29:23] hold_for_later_1
[START] [2019-10-16 18:29:23] hold_for_later_2
[STOP] [2019-10-16 18:29:23] hold_for_later_2
[START] [2019-10-16 18:29:23] resolve_missing_parents
[STOP] [2019-10-16 18:29:34] resolve_missing_parents
[START] [2019-10-16 18:29:34] rebuild_nodes
[START] [2019-10-16 18:29:34] Flattener#flatten
[START] [2019-10-16 18:29:34] Flattener#study_resource
[START] [2019-10-16 18:29:35] Flattener#build_ancestry
[STOP] [2019-10-16 18:29:35] Flattener#build_ancestry
[INFO] [2019-10-16 18:29:35] 5389 ancestry keys
[START] [2019-10-16 18:29:35] build_node_ancestors
[INFO] [2019-10-16 18:29:35] old ancestors deleted.
[STOP] [2019-10-16 18:29:36] build_node_ancestors
[START] [2019-10-16 18:29:36] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:29:37] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 18:29:37] Flattener#flatten
[STOP] [2019-10-16 18:29:37] rebuild_nodes
[START] [2019-10-16 18:29:37] resolve_missing_media_owners
[STOP] [2019-10-16 18:29:37] resolve_missing_media_owners
[START] [2019-10-16 18:29:37] sanitize_media_verbatims
[STOP] [2019-10-16 18:29:37] sanitize_media_verbatims
[START] [2019-10-16 18:29:37] queue_downloads
[STOP] [2019-10-16 18:29:37] queue_downloads
[START] [2019-10-16 18:29:37] parse_names
[WARN] [2019-10-16 18:29:37] I see 5389 names which still need to be parsed.
[STOP] [2019-10-16 18:29:41] parse_names
[START] [2019-10-16 18:29:41] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 18:29:41] denormalize_canonical_names_to_nodes
[START] [2019-10-16 18:29:41] match_nodes
[START] [2019-10-16 18:29:41] map_all_nodes_to_pages
[STOP] [2019-10-16 18:36:12] map_all_nodes_to_pages
[INFO] [2019-10-16 18:36:12] 686 Unmatched nodes (of 5389)! That's too many to output. First 10: Stipa retorta (#52505321); Stipa parviflora (#52505427); Cenchrus ciliare (#52506556); Oryzopsis miliaceum (#52505603); Brachypodium distachya (#52505676); Pennisetum (#52505823); Bromus mollis (#52507881); Arrhenatherum alba (#52506373); Aira tenorii (#52506919); Catapodium rigida (#52506646)
[START] [2019-10-16 18:36:12] update_nodes
[STOP] [2019-10-16 18:36:14] update_nodes
[STOP] [2019-10-16 18:36:14] match_nodes
[START] [2019-10-16 18:36:14] reindex_search
[STOP] [2019-10-16 18:36:29] reindex_search
[START] [2019-10-16 18:36:29] normalize_units
[STOP] [2019-10-16 18:36:29] normalize_units
[START] [2019-10-16 18:36:29] calculate_statistics
[STOP] [2019-10-16 18:36:29] calculate_statistics
[START] [2019-10-16 18:36:29] complete_harvest_instance
[START] [2019-10-16 18:36:29] overall_tsv_creation
[INFO] [2019-10-16 18:36:29] Processing group of 5389 in 1 batches of 10000
[INFO] [2019-10-16 18:37:35] 2892 Traits (unfiltered)...
[INFO] [2019-10-16 18:37:48] 2892 Traits (filtered)...
[INFO] [2019-10-16 18:37:48] 0 Associations (filtered)...
[INFO] [2019-10-16 18:38:31] 14456 metadata added.
[INFO] [2019-10-16 18:38:31] 0 metadata added.
[INFO] [2019-10-16 18:38:31] Average Time: 97.21
[INFO] [2019-10-16 18:38:31] Total Time: 2m2s
[STOP] [2019-10-16 18:38:31] overall_tsv_creation
[INFO] [2019-10-16 18:38:31] Done. Check your files:
[INFO] [2019-10-16 18:38:31] (5389 lines) /app/public/data/tunisia_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 18:38:31] (11869 lines) /app/public/data/tunisia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 18:38:31] (5389 lines) /app/public/data/tunisia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 18:38:31] (2893 lines) /app/public/data/tunisia_sp_list/publish_traits.tsv
[INFO] [2019-10-16 18:38:31] (14457 lines) /app/public/data/tunisia_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 18:38:31] complete_harvest_instance
[START] [2019-10-16 18:38:31] completed
[STOP] [2019-10-16 18:38:31] completed
[STOP] [2019-10-16 18:38:31] logged process, took 610.79
Latest Process

16 Oct 18:28 EXITED currently processing 0