Harvest for Saint Martin Species List Created 15 Oct 16:25

Stage: completed
Fetched: 15 Oct 16:25
Validated: 15 Oct 16:25
Deltas Created 15 Oct 16:25
Units Normalized: 15 Oct 16:26
Ancestry Built: 15 Oct 16:25
Nodes Matched: 15 Oct 16:26
Names Parsed: 15 Oct 16:25
New Models Stored: 15 Oct 16:25
Indexed: 15 Oct 16:26
Completed: 15 Oct 16:28
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:25:26 -0400 by logger.rb/56815
[START] [2019-10-15 16:25:26] logged process
[START] [2019-10-15 16:25:26] create_harvest_instance
[STOP] [2019-10-15 16:25:27] create_harvest_instance
[START] [2019-10-15 16:25:27] fetch_files
[STOP] [2019-10-15 16:25:27] fetch_files
[START] [2019-10-15 16:25:27] validate_each_file
[STOP] [2019-10-15 16:25:27] validate_each_file
[START] [2019-10-15 16:25:27] convert_to_csv
[CMD] [2019-10-15 16:25:27] /usr/bin/sort /app/public/converted_csv/saint_martin_sp__refs_17053.csv > /app/public/converted_csv/saint_martin_sp__refs_17053.csv_sorted
[CMD] [2019-10-15 16:25:27] /usr/bin/sort /app/public/converted_csv/saint_martin_sp__nodes_17054.csv > /app/public/converted_csv/saint_martin_sp__nodes_17054.csv_sorted
[CMD] [2019-10-15 16:25:28] /usr/bin/sort /app/public/converted_csv/saint_martin_sp__occurrences_17055.csv > /app/public/converted_csv/saint_martin_sp__occurrences_17055.csv_sorted
[CMD] [2019-10-15 16:25:28] /usr/bin/sort /app/public/converted_csv/saint_martin_sp__measurements_17056.csv > /app/public/converted_csv/saint_martin_sp__measurements_17056.csv_sorted
[STOP] [2019-10-15 16:25:28] convert_to_csv
[START] [2019-10-15 16:25:28] calculate_delta
[CMD] [2019-10-15 16:25:28] echo "0a" > /app/public/diff/saint_martin_sp__refs_17053.diff
[CMD] [2019-10-15 16:25:29] tail -n +1 /app/public/converted_csv/saint_martin_sp__refs_17053.csv >> /app/public/diff/saint_martin_sp__refs_17053.diff
[CMD] [2019-10-15 16:25:29] echo "." >> /app/public/diff/saint_martin_sp__refs_17053.diff
[CMD] [2019-10-15 16:25:29] echo "0a" > /app/public/diff/saint_martin_sp__nodes_17054.diff
[CMD] [2019-10-15 16:25:29] tail -n +1 /app/public/converted_csv/saint_martin_sp__nodes_17054.csv >> /app/public/diff/saint_martin_sp__nodes_17054.diff
[CMD] [2019-10-15 16:25:30] echo "." >> /app/public/diff/saint_martin_sp__nodes_17054.diff
[CMD] [2019-10-15 16:25:30] echo "0a" > /app/public/diff/saint_martin_sp__occurrences_17055.diff
[CMD] [2019-10-15 16:25:30] tail -n +1 /app/public/converted_csv/saint_martin_sp__occurrences_17055.csv >> /app/public/diff/saint_martin_sp__occurrences_17055.diff
[CMD] [2019-10-15 16:25:31] echo "." >> /app/public/diff/saint_martin_sp__occurrences_17055.diff
[CMD] [2019-10-15 16:25:31] echo "0a" > /app/public/diff/saint_martin_sp__measurements_17056.diff
[CMD] [2019-10-15 16:25:31] tail -n +1 /app/public/converted_csv/saint_martin_sp__measurements_17056.csv >> /app/public/diff/saint_martin_sp__measurements_17056.diff
[CMD] [2019-10-15 16:25:31] echo "." >> /app/public/diff/saint_martin_sp__measurements_17056.diff
[STOP] [2019-10-15 16:25:32] calculate_delta
[START] [2019-10-15 16:25:32] parse_diff_and_store
[INFO] [2019-10-15 16:25:32] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:25:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:25:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:25:33] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:25:36] Storing 2 References
[INFO] [2019-10-15 16:25:36] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:25:36] Average Time: 0.0
[INFO] [2019-10-15 16:25:36] Total Time: 1s
[INFO] [2019-10-15 16:25:36] Storing 1115 ScientificNames
[INFO] [2019-10-15 16:25:36] Processing group of 1115 in 2 groups of 1000
[INFO] [2019-10-15 16:25:37] Average Time: 0.24
[INFO] [2019-10-15 16:25:37] Total Time: 1s
[INFO] [2019-10-15 16:25:37] Storing 1115 Nodes
[INFO] [2019-10-15 16:25:37] Processing group of 1115 in 2 groups of 1000
[INFO] [2019-10-15 16:25:37] Average Time: 0.16
[INFO] [2019-10-15 16:25:37] Total Time: 1s
[INFO] [2019-10-15 16:25:37] Storing 482 Occurrences
[INFO] [2019-10-15 16:25:37] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-15 16:25:37] Average Time: 0.07
[INFO] [2019-10-15 16:25:37] Total Time: 1s
[INFO] [2019-10-15 16:25:37] Storing 1030 TraitsReferences
[INFO] [2019-10-15 16:25:37] Processing group of 1030 in 2 groups of 1000
[INFO] [2019-10-15 16:25:37] Average Time: 0.075
[INFO] [2019-10-15 16:25:37] Total Time: 1s
[INFO] [2019-10-15 16:25:37] Storing 1029 Traits
[INFO] [2019-10-15 16:25:37] Processing group of 1029 in 2 groups of 1000
[INFO] [2019-10-15 16:25:38] Average Time: 0.195
[INFO] [2019-10-15 16:25:38] Total Time: 1s
[INFO] [2019-10-15 16:25:38] Storing 1030 MetaTraits
[INFO] [2019-10-15 16:25:38] Processing group of 1030 in 2 groups of 1000
[INFO] [2019-10-15 16:25:38] Average Time: 0.07
[INFO] [2019-10-15 16:25:38] Total Time: 1s
[STOP] [2019-10-15 16:25:38] parse_diff_and_store
[START] [2019-10-15 16:25:38] resolve_keys
[INFO] [2019-10-15 16:25:44] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:25:45] traits to occurrences...
[INFO] [2019-10-15 16:25:45] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:25:45] Traits to sex term...
[INFO] [2019-10-15 16:25:45] Traits to lifestage term...
[INFO] [2019-10-15 16:25:45] MetaTraits to traits...
[INFO] [2019-10-15 16:25:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:25:45] Assocs to occurrences...
[INFO] [2019-10-15 16:25:45] Assocs to nodes...
[INFO] [2019-10-15 16:25:45] Assoc to sex term...
[INFO] [2019-10-15 16:25:45] Assoc to lifestage term...
[STOP] [2019-10-15 16:25:46] resolve_keys
[START] [2019-10-15 16:25:46] hold_for_later_1
[STOP] [2019-10-15 16:25:46] hold_for_later_1
[START] [2019-10-15 16:25:46] hold_for_later_2
[STOP] [2019-10-15 16:25:46] hold_for_later_2
[START] [2019-10-15 16:25:46] resolve_missing_parents
[STOP] [2019-10-15 16:25:46] resolve_missing_parents
[START] [2019-10-15 16:25:46] rebuild_nodes
[START] [2019-10-15 16:25:46] Flattener#flatten
[START] [2019-10-15 16:25:46] Flattener#study_resource
[START] [2019-10-15 16:25:46] Flattener#build_ancestry
[STOP] [2019-10-15 16:25:46] Flattener#build_ancestry
[INFO] [2019-10-15 16:25:46] 1115 ancestry keys
[START] [2019-10-15 16:25:46] build_node_ancestors
[INFO] [2019-10-15 16:25:46] old ancestors deleted.
[STOP] [2019-10-15 16:25:46] build_node_ancestors
[START] [2019-10-15 16:25:47] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:25:47] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:25:47] Flattener#flatten
[STOP] [2019-10-15 16:25:47] rebuild_nodes
[START] [2019-10-15 16:25:47] resolve_missing_media_owners
[STOP] [2019-10-15 16:25:47] resolve_missing_media_owners
[START] [2019-10-15 16:25:47] sanitize_media_verbatims
[STOP] [2019-10-15 16:25:47] sanitize_media_verbatims
[START] [2019-10-15 16:25:47] queue_downloads
[STOP] [2019-10-15 16:25:47] queue_downloads
[START] [2019-10-15 16:25:47] parse_names
[WARN] [2019-10-15 16:25:47] I see 1115 names which still need to be parsed.
[STOP] [2019-10-15 16:25:49] parse_names
[START] [2019-10-15 16:25:49] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:25:49] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:25:49] match_nodes
[START] [2019-10-15 16:25:49] map_all_nodes_to_pages
[STOP] [2019-10-15 16:26:46] map_all_nodes_to_pages
[INFO] [2019-10-15 16:26:46] 40 Unmatched nodes (of 1115)! That's too many to output. First 10: Limnodromus (#51755184); Coerebidae (#51754870); Anas discors (#51754911); Thalaseus (#51754918); Thalaseus maximus (#51754917); Thalaseus sandvicensis (#51754993); Porphyrio martinicus (#51755863); Strumigenys eggersi (#51755629); Schwartziella bouryi (#51755696); Lindapecten (#51755820)
[START] [2019-10-15 16:26:46] update_nodes
[STOP] [2019-10-15 16:26:46] update_nodes
[STOP] [2019-10-15 16:26:46] match_nodes
[START] [2019-10-15 16:26:46] reindex_search
[STOP] [2019-10-15 16:26:49] reindex_search
[START] [2019-10-15 16:26:49] normalize_units
[STOP] [2019-10-15 16:26:49] normalize_units
[START] [2019-10-15 16:26:49] calculate_statistics
[STOP] [2019-10-15 16:26:49] calculate_statistics
[START] [2019-10-15 16:26:49] complete_harvest_instance
[START] [2019-10-15 16:26:49] overall_tsv_creation
[INFO] [2019-10-15 16:26:49] Processing group of 1115 in 1 batches of 10000
[INFO] [2019-10-15 16:27:38] 482 Traits (unfiltered)...
[INFO] [2019-10-15 16:27:52] 482 Traits (filtered)...
[INFO] [2019-10-15 16:27:52] 0 Associations (filtered)...
[INFO] [2019-10-15 16:28:31] 2410 metadata added.
[INFO] [2019-10-15 16:28:31] 0 metadata added.
[INFO] [2019-10-15 16:28:31] Average Time: 80.08
[INFO] [2019-10-15 16:28:31] Total Time: 1m42s
[STOP] [2019-10-15 16:28:31] overall_tsv_creation
[INFO] [2019-10-15 16:28:31] Done. Check your files:
[INFO] [2019-10-15 16:28:31] (1115 lines) /app/public/data/saint_martin_sp_/publish_nodes.tsv
[INFO] [2019-10-15 16:28:31] (1371 lines) /app/public/data/saint_martin_sp_/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:28:32] (1115 lines) /app/public/data/saint_martin_sp_/publish_scientific_names.tsv
[INFO] [2019-10-15 16:28:32] (483 lines) /app/public/data/saint_martin_sp_/publish_traits.tsv
[INFO] [2019-10-15 16:28:32] (2411 lines) /app/public/data/saint_martin_sp_/publish_metadata.tsv
[STOP] [2019-10-15 16:28:32] complete_harvest_instance
[START] [2019-10-15 16:28:32] completed
[STOP] [2019-10-15 16:28:32] completed
[STOP] [2019-10-15 16:28:32] logged process, took 185.9
Latest Process

15 Oct 16:25 EXITED currently processing 0