Harvest for Saint Kitts and Nevis Species List Created 15 Oct 16:17

Stage: completed
Fetched: 15 Oct 16:17
Validated: 15 Oct 16:17
Deltas Created 15 Oct 16:17
Units Normalized: 15 Oct 16:19
Ancestry Built: 15 Oct 16:18
Nodes Matched: 15 Oct 16:19
Names Parsed: 15 Oct 16:18
New Models Stored: 15 Oct 16:18
Indexed: 15 Oct 16:19
Completed: 15 Oct 16:21
Time to Harvest: less than a minute
Harvesting Log

(140 lines)
# Logfile created on 2019-10-15 16:17:50 -0400 by logger.rb/56815
[START] [2019-10-15 16:17:50] logged process
[START] [2019-10-15 16:17:50] create_harvest_instance
[STOP] [2019-10-15 16:17:50] create_harvest_instance
[START] [2019-10-15 16:17:50] fetch_files
[STOP] [2019-10-15 16:17:50] fetch_files
[START] [2019-10-15 16:17:50] validate_each_file
[STOP] [2019-10-15 16:17:50] validate_each_file
[START] [2019-10-15 16:17:50] convert_to_csv
[CMD] [2019-10-15 16:17:50] /usr/bin/sort /app/public/converted_csv/sknsl_refs_17037.csv > /app/public/converted_csv/sknsl_refs_17037.csv_sorted
[CMD] [2019-10-15 16:17:51] /usr/bin/sort /app/public/converted_csv/sknsl_nodes_17038.csv > /app/public/converted_csv/sknsl_nodes_17038.csv_sorted
[CMD] [2019-10-15 16:17:51] /usr/bin/sort /app/public/converted_csv/sknsl_occurrences_17039.csv > /app/public/converted_csv/sknsl_occurrences_17039.csv_sorted
[CMD] [2019-10-15 16:17:51] /usr/bin/sort /app/public/converted_csv/sknsl_measurements_17040.csv > /app/public/converted_csv/sknsl_measurements_17040.csv_sorted
[STOP] [2019-10-15 16:17:51] convert_to_csv
[START] [2019-10-15 16:17:51] calculate_delta
[CMD] [2019-10-15 16:17:51] echo "0a" > /app/public/diff/sknsl_refs_17037.diff
[CMD] [2019-10-15 16:17:52] tail -n +1 /app/public/converted_csv/sknsl_refs_17037.csv >> /app/public/diff/sknsl_refs_17037.diff
[CMD] [2019-10-15 16:17:52] echo "." >> /app/public/diff/sknsl_refs_17037.diff
[CMD] [2019-10-15 16:17:52] echo "0a" > /app/public/diff/sknsl_nodes_17038.diff
[CMD] [2019-10-15 16:17:53] tail -n +1 /app/public/converted_csv/sknsl_nodes_17038.csv >> /app/public/diff/sknsl_nodes_17038.diff
[CMD] [2019-10-15 16:17:53] echo "." >> /app/public/diff/sknsl_nodes_17038.diff
[CMD] [2019-10-15 16:17:53] echo "0a" > /app/public/diff/sknsl_occurrences_17039.diff
[CMD] [2019-10-15 16:17:53] tail -n +1 /app/public/converted_csv/sknsl_occurrences_17039.csv >> /app/public/diff/sknsl_occurrences_17039.diff
[CMD] [2019-10-15 16:17:54] echo "." >> /app/public/diff/sknsl_occurrences_17039.diff
[CMD] [2019-10-15 16:17:54] echo "0a" > /app/public/diff/sknsl_measurements_17040.diff
[CMD] [2019-10-15 16:17:54] tail -n +1 /app/public/converted_csv/sknsl_measurements_17040.csv >> /app/public/diff/sknsl_measurements_17040.diff
[CMD] [2019-10-15 16:17:54] echo "." >> /app/public/diff/sknsl_measurements_17040.diff
[STOP] [2019-10-15 16:17:55] calculate_delta
[START] [2019-10-15 16:17:55] parse_diff_and_store
[INFO] [2019-10-15 16:17:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:17:55] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:17:56] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:17:56] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:17:59] Storing 2 References
[INFO] [2019-10-15 16:17:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:17:59] Average Time: 0.0
[INFO] [2019-10-15 16:17:59] Total Time: 1s
[INFO] [2019-10-15 16:17:59] Storing 1150 ScientificNames
[INFO] [2019-10-15 16:17:59] Processing group of 1150 in 2 groups of 1000
[INFO] [2019-10-15 16:18:00] Average Time: 0.245
[INFO] [2019-10-15 16:18:00] Total Time: 1s
[INFO] [2019-10-15 16:18:00] Storing 1150 Nodes
[INFO] [2019-10-15 16:18:00] Processing group of 1150 in 2 groups of 1000
[INFO] [2019-10-15 16:18:00] Average Time: 0.185
[INFO] [2019-10-15 16:18:00] Total Time: 1s
[INFO] [2019-10-15 16:18:00] Storing 692 Occurrences
[INFO] [2019-10-15 16:18:00] Processing group of 692 in 1 groups of 1000
[INFO] [2019-10-15 16:18:00] Average Time: 0.11
[INFO] [2019-10-15 16:18:00] Total Time: 1s
[INFO] [2019-10-15 16:18:00] Storing 876 TraitsReferences
[INFO] [2019-10-15 16:18:00] Processing group of 876 in 1 groups of 1000
[INFO] [2019-10-15 16:18:00] Average Time: 0.15
[INFO] [2019-10-15 16:18:00] Total Time: 1s
[INFO] [2019-10-15 16:18:00] Storing 876 Traits
[INFO] [2019-10-15 16:18:00] Processing group of 876 in 1 groups of 1000
[INFO] [2019-10-15 16:18:01] Average Time: 0.4
[INFO] [2019-10-15 16:18:01] Total Time: 1s
[INFO] [2019-10-15 16:18:01] Storing 876 MetaTraits
[INFO] [2019-10-15 16:18:01] Processing group of 876 in 1 groups of 1000
[INFO] [2019-10-15 16:18:01] Average Time: 0.14
[INFO] [2019-10-15 16:18:01] Total Time: 1s
[STOP] [2019-10-15 16:18:01] parse_diff_and_store
[START] [2019-10-15 16:18:01] resolve_keys
[INFO] [2019-10-15 16:18:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:18:08] traits to occurrences...
[INFO] [2019-10-15 16:18:08] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:18:08] Traits to sex term...
[INFO] [2019-10-15 16:18:08] Traits to lifestage term...
[INFO] [2019-10-15 16:18:09] MetaTraits to traits...
[INFO] [2019-10-15 16:18:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:18:09] Assocs to occurrences...
[INFO] [2019-10-15 16:18:09] Assocs to nodes...
[INFO] [2019-10-15 16:18:09] Assoc to sex term...
[INFO] [2019-10-15 16:18:09] Assoc to lifestage term...
[STOP] [2019-10-15 16:18:09] resolve_keys
[START] [2019-10-15 16:18:09] hold_for_later_1
[STOP] [2019-10-15 16:18:09] hold_for_later_1
[START] [2019-10-15 16:18:09] hold_for_later_2
[STOP] [2019-10-15 16:18:09] hold_for_later_2
[START] [2019-10-15 16:18:09] resolve_missing_parents
[STOP] [2019-10-15 16:18:10] resolve_missing_parents
[START] [2019-10-15 16:18:10] rebuild_nodes
[START] [2019-10-15 16:18:10] Flattener#flatten
[START] [2019-10-15 16:18:10] Flattener#study_resource
[START] [2019-10-15 16:18:10] Flattener#build_ancestry
[STOP] [2019-10-15 16:18:10] Flattener#build_ancestry
[INFO] [2019-10-15 16:18:10] 1150 ancestry keys
[START] [2019-10-15 16:18:10] build_node_ancestors
[INFO] [2019-10-15 16:18:10] old ancestors deleted.
[STOP] [2019-10-15 16:18:10] build_node_ancestors
[START] [2019-10-15 16:18:11] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:18:11] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:18:11] Flattener#flatten
[STOP] [2019-10-15 16:18:11] rebuild_nodes
[START] [2019-10-15 16:18:11] resolve_missing_media_owners
[STOP] [2019-10-15 16:18:11] resolve_missing_media_owners
[START] [2019-10-15 16:18:11] sanitize_media_verbatims
[STOP] [2019-10-15 16:18:11] sanitize_media_verbatims
[START] [2019-10-15 16:18:11] queue_downloads
[STOP] [2019-10-15 16:18:11] queue_downloads
[START] [2019-10-15 16:18:11] parse_names
[WARN] [2019-10-15 16:18:11] I see 1150 names which still need to be parsed.
[WARN] [2019-10-15 16:18:13] I see 19 names which still need to be parsed.
[STOP] [2019-10-15 16:18:14] parse_names
[START] [2019-10-15 16:18:14] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:18:14] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:18:14] match_nodes
[START] [2019-10-15 16:18:14] map_all_nodes_to_pages
[STOP] [2019-10-15 16:19:54] map_all_nodes_to_pages
[INFO] [2019-10-15 16:19:54] 57 Unmatched nodes (of 1150)! That's too many to output. First 10: Coerebidae (#51752179); Escalloniales (#51753284); Nymphaeales (#51753310); Maxillopoda (#51753275); Limnodromus (#51752927); Thalaseus (#51752255); Thalaseus maximus (#51752254); Anas discors (#51752291); Ameiva erythrocephala (#51752632); Rhinesomus (#51752858)
[START] [2019-10-15 16:19:54] update_nodes
[STOP] [2019-10-15 16:19:55] update_nodes
[STOP] [2019-10-15 16:19:55] match_nodes
[START] [2019-10-15 16:19:55] reindex_search
[STOP] [2019-10-15 16:19:57] reindex_search
[START] [2019-10-15 16:19:57] normalize_units
[STOP] [2019-10-15 16:19:57] normalize_units
[START] [2019-10-15 16:19:57] calculate_statistics
[STOP] [2019-10-15 16:19:57] calculate_statistics
[START] [2019-10-15 16:19:57] complete_harvest_instance
[START] [2019-10-15 16:19:57] overall_tsv_creation
[INFO] [2019-10-15 16:19:57] Processing group of 1150 in 1 batches of 10000
[INFO] [2019-10-15 16:20:47] 437 Traits (unfiltered)...
[INFO] [2019-10-15 16:21:01] 437 Traits (filtered)...
[INFO] [2019-10-15 16:21:01] 0 Associations (filtered)...
[INFO] [2019-10-15 16:21:40] 2185 metadata added.
[INFO] [2019-10-15 16:21:40] 0 metadata added.
[INFO] [2019-10-15 16:21:40] Average Time: 80.38
[INFO] [2019-10-15 16:21:40] Total Time: 1m43s
[STOP] [2019-10-15 16:21:40] overall_tsv_creation
[INFO] [2019-10-15 16:21:40] Done. Check your files:
[INFO] [2019-10-15 16:21:40] (1150 lines) /app/public/data/sknsl/publish_nodes.tsv
[INFO] [2019-10-15 16:21:40] (5481 lines) /app/public/data/sknsl/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:21:40] (1150 lines) /app/public/data/sknsl/publish_scientific_names.tsv
[INFO] [2019-10-15 16:21:41] (438 lines) /app/public/data/sknsl/publish_traits.tsv
[INFO] [2019-10-15 16:21:41] (2186 lines) /app/public/data/sknsl/publish_metadata.tsv
[STOP] [2019-10-15 16:21:41] complete_harvest_instance
[START] [2019-10-15 16:21:41] completed
[STOP] [2019-10-15 16:21:41] completed
[STOP] [2019-10-15 16:21:41] logged process, took 231.43
Latest Process

15 Oct 16:17 EXITED currently processing 0