Harvest for Cocos Islands Species List Created 12 Oct 05:41

Stage: completed
Fetched: 12 Oct 05:41
Validated: 12 Oct 05:41
Deltas Created 12 Oct 05:41
Units Normalized: 12 Oct 05:43
Ancestry Built: 12 Oct 05:41
Nodes Matched: 12 Oct 05:43
Names Parsed: 12 Oct 05:41
New Models Stored: 12 Oct 05:41
Indexed: 12 Oct 05:43
Completed: 12 Oct 05:45
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 05:41:03 -0400 by logger.rb/56815
[START] [2019-10-12 05:41:03] logged process
[START] [2019-10-12 05:41:03] create_harvest_instance
[STOP] [2019-10-12 05:41:03] create_harvest_instance
[START] [2019-10-12 05:41:03] fetch_files
[STOP] [2019-10-12 05:41:03] fetch_files
[START] [2019-10-12 05:41:03] validate_each_file
[STOP] [2019-10-12 05:41:04] validate_each_file
[START] [2019-10-12 05:41:04] convert_to_csv
[CMD] [2019-10-12 05:41:04] /usr/bin/sort /app/public/converted_csv/cocos_islands_refs_15443.csv > /app/public/converted_csv/cocos_islands_refs_15443.csv_sorted
[CMD] [2019-10-12 05:41:04] /usr/bin/sort /app/public/converted_csv/cocos_islands_nodes_15444.csv > /app/public/converted_csv/cocos_islands_nodes_15444.csv_sorted
[CMD] [2019-10-12 05:41:04] /usr/bin/sort /app/public/converted_csv/cocos_islands_occurrences_15445.csv > /app/public/converted_csv/cocos_islands_occurrences_15445.csv_sorted
[CMD] [2019-10-12 05:41:04] /usr/bin/sort /app/public/converted_csv/cocos_islands_measurements_15446.csv > /app/public/converted_csv/cocos_islands_measurements_15446.csv_sorted
[STOP] [2019-10-12 05:41:04] convert_to_csv
[START] [2019-10-12 05:41:04] calculate_delta
[CMD] [2019-10-12 05:41:04] echo "0a" > /app/public/diff/cocos_islands_refs_15443.diff
[CMD] [2019-10-12 05:41:04] tail -n +1 /app/public/converted_csv/cocos_islands_refs_15443.csv >> /app/public/diff/cocos_islands_refs_15443.diff
[CMD] [2019-10-12 05:41:04] echo "." >> /app/public/diff/cocos_islands_refs_15443.diff
[CMD] [2019-10-12 05:41:04] echo "0a" > /app/public/diff/cocos_islands_nodes_15444.diff
[CMD] [2019-10-12 05:41:04] tail -n +1 /app/public/converted_csv/cocos_islands_nodes_15444.csv >> /app/public/diff/cocos_islands_nodes_15444.diff
[CMD] [2019-10-12 05:41:04] echo "." >> /app/public/diff/cocos_islands_nodes_15444.diff
[CMD] [2019-10-12 05:41:04] echo "0a" > /app/public/diff/cocos_islands_occurrences_15445.diff
[CMD] [2019-10-12 05:41:05] tail -n +1 /app/public/converted_csv/cocos_islands_occurrences_15445.csv >> /app/public/diff/cocos_islands_occurrences_15445.diff
[CMD] [2019-10-12 05:41:05] echo "." >> /app/public/diff/cocos_islands_occurrences_15445.diff
[CMD] [2019-10-12 05:41:05] echo "0a" > /app/public/diff/cocos_islands_measurements_15446.diff
[CMD] [2019-10-12 05:41:05] tail -n +1 /app/public/converted_csv/cocos_islands_measurements_15446.csv >> /app/public/diff/cocos_islands_measurements_15446.diff
[CMD] [2019-10-12 05:41:05] echo "." >> /app/public/diff/cocos_islands_measurements_15446.diff
[STOP] [2019-10-12 05:41:05] calculate_delta
[START] [2019-10-12 05:41:05] parse_diff_and_store
[INFO] [2019-10-12 05:41:05] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 05:41:05] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 05:41:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 05:41:06] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 05:41:14] Storing 2 References
[INFO] [2019-10-12 05:41:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 05:41:14] Average Time: 0.0
[INFO] [2019-10-12 05:41:14] Total Time: 1s
[INFO] [2019-10-12 05:41:14] Storing 2411 ScientificNames
[INFO] [2019-10-12 05:41:14] Processing group of 2411 in 3 groups of 1000
[INFO] [2019-10-12 05:41:15] Average Time: 0.32
[INFO] [2019-10-12 05:41:15] Total Time: 1s
[INFO] [2019-10-12 05:41:15] Storing 2411 Nodes
[INFO] [2019-10-12 05:41:15] Processing group of 2411 in 3 groups of 1000
[INFO] [2019-10-12 05:41:15] Average Time: 0.287
[INFO] [2019-10-12 05:41:15] Total Time: 1s
[INFO] [2019-10-12 05:41:15] Storing 964 Occurrences
[INFO] [2019-10-12 05:41:15] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-12 05:41:16] Average Time: 0.12
[INFO] [2019-10-12 05:41:16] Total Time: 1s
[INFO] [2019-10-12 05:41:16] Storing 2450 TraitsReferences
[INFO] [2019-10-12 05:41:16] Processing group of 2450 in 3 groups of 1000
[INFO] [2019-10-12 05:41:16] Average Time: 0.083
[INFO] [2019-10-12 05:41:16] Total Time: 1s
[INFO] [2019-10-12 05:41:16] Storing 2449 Traits
[INFO] [2019-10-12 05:41:16] Processing group of 2449 in 3 groups of 1000
[INFO] [2019-10-12 05:41:17] Average Time: 0.313
[INFO] [2019-10-12 05:41:17] Total Time: 1s
[INFO] [2019-10-12 05:41:17] Storing 2449 MetaTraits
[INFO] [2019-10-12 05:41:17] Processing group of 2449 in 3 groups of 1000
[INFO] [2019-10-12 05:41:17] Average Time: 0.123
[INFO] [2019-10-12 05:41:17] Total Time: 1s
[STOP] [2019-10-12 05:41:17] parse_diff_and_store
[START] [2019-10-12 05:41:17] resolve_keys
[INFO] [2019-10-12 05:41:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 05:41:29] traits to occurrences...
[INFO] [2019-10-12 05:41:30] traits to nodes (through occurrences)...
[INFO] [2019-10-12 05:41:30] Traits to sex term...
[INFO] [2019-10-12 05:41:30] Traits to lifestage term...
[INFO] [2019-10-12 05:41:30] MetaTraits to traits...
[INFO] [2019-10-12 05:41:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 05:41:31] Assocs to occurrences...
[INFO] [2019-10-12 05:41:31] Assocs to nodes...
[INFO] [2019-10-12 05:41:31] Assoc to sex term...
[INFO] [2019-10-12 05:41:31] Assoc to lifestage term...
[STOP] [2019-10-12 05:41:31] resolve_keys
[START] [2019-10-12 05:41:31] hold_for_later_1
[STOP] [2019-10-12 05:41:31] hold_for_later_1
[START] [2019-10-12 05:41:31] hold_for_later_2
[STOP] [2019-10-12 05:41:31] hold_for_later_2
[START] [2019-10-12 05:41:31] resolve_missing_parents
[STOP] [2019-10-12 05:41:35] resolve_missing_parents
[START] [2019-10-12 05:41:35] rebuild_nodes
[START] [2019-10-12 05:41:35] Flattener#flatten
[START] [2019-10-12 05:41:35] Flattener#study_resource
[START] [2019-10-12 05:41:35] Flattener#build_ancestry
[STOP] [2019-10-12 05:41:35] Flattener#build_ancestry
[INFO] [2019-10-12 05:41:35] 2411 ancestry keys
[START] [2019-10-12 05:41:35] build_node_ancestors
[INFO] [2019-10-12 05:41:35] old ancestors deleted.
[STOP] [2019-10-12 05:41:35] build_node_ancestors
[START] [2019-10-12 05:41:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 05:41:36] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 05:41:36] Flattener#flatten
[STOP] [2019-10-12 05:41:36] rebuild_nodes
[START] [2019-10-12 05:41:36] resolve_missing_media_owners
[STOP] [2019-10-12 05:41:36] resolve_missing_media_owners
[START] [2019-10-12 05:41:36] sanitize_media_verbatims
[STOP] [2019-10-12 05:41:36] sanitize_media_verbatims
[START] [2019-10-12 05:41:36] queue_downloads
[STOP] [2019-10-12 05:41:36] queue_downloads
[START] [2019-10-12 05:41:36] parse_names
[WARN] [2019-10-12 05:41:36] I see 2411 names which still need to be parsed.
[STOP] [2019-10-12 05:41:38] parse_names
[START] [2019-10-12 05:41:38] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 05:41:38] denormalize_canonical_names_to_nodes
[START] [2019-10-12 05:41:38] match_nodes
[START] [2019-10-12 05:41:38] map_all_nodes_to_pages
[STOP] [2019-10-12 05:43:19] map_all_nodes_to_pages
[INFO] [2019-10-12 05:43:19] 88 Unmatched nodes (of 2411)! That's too many to output. First 10: Egretta intermedia (#49207682); Thalaseus (#49208401); Thalaseus bengalensis (#49208400); Thalaseus bergii (#49209515); Anas strepera (#49208772); Anas querquedula (#49209865); Protellidae (#49207985); Pariambidae (#49209889); Conus chaldeus (#49208144); Maculotriton digitalis (#49208609)
[START] [2019-10-12 05:43:19] update_nodes
[STOP] [2019-10-12 05:43:20] update_nodes
[STOP] [2019-10-12 05:43:20] match_nodes
[START] [2019-10-12 05:43:20] reindex_search
[STOP] [2019-10-12 05:43:25] reindex_search
[START] [2019-10-12 05:43:25] normalize_units
[STOP] [2019-10-12 05:43:25] normalize_units
[START] [2019-10-12 05:43:25] calculate_statistics
[STOP] [2019-10-12 05:43:25] calculate_statistics
[START] [2019-10-12 05:43:25] complete_harvest_instance
[START] [2019-10-12 05:43:25] overall_tsv_creation
[INFO] [2019-10-12 05:43:25] Processing group of 2411 in 1 batches of 10000
[INFO] [2019-10-12 05:44:20] 964 Traits (unfiltered)...
[INFO] [2019-10-12 05:44:34] 964 Traits (filtered)...
[INFO] [2019-10-12 05:44:34] 0 Associations (filtered)...
[INFO] [2019-10-12 05:45:12] 4819 metadata added.
[INFO] [2019-10-12 05:45:12] 0 metadata added.
[INFO] [2019-10-12 05:45:12] Average Time: 84.94
[INFO] [2019-10-12 05:45:12] Total Time: 1m48s
[STOP] [2019-10-12 05:45:12] overall_tsv_creation
[INFO] [2019-10-12 05:45:12] Done. Check your files:
[INFO] [2019-10-12 05:45:13] (2411 lines) /app/public/data/cocos_islands/publish_nodes.tsv
[INFO] [2019-10-12 05:45:13] (5268 lines) /app/public/data/cocos_islands/publish_node_ancestors.tsv
[INFO] [2019-10-12 05:45:13] (2411 lines) /app/public/data/cocos_islands/publish_scientific_names.tsv
[INFO] [2019-10-12 05:45:13] (965 lines) /app/public/data/cocos_islands/publish_traits.tsv
[INFO] [2019-10-12 05:45:13] (4820 lines) /app/public/data/cocos_islands/publish_metadata.tsv
[STOP] [2019-10-12 05:45:13] complete_harvest_instance
[START] [2019-10-12 05:45:13] completed
[STOP] [2019-10-12 05:45:13] completed
[STOP] [2019-10-12 05:45:13] logged process, took 250.31
Latest Process

12 Oct 05:41 EXITED currently processing 0