Harvest for CreatureCast Created 03 Jul 17:18

Stage: completed
Fetched: 03 Jul 17:18
Validated: 03 Jul 17:18
Deltas Created 03 Jul 17:18
Units Normalized: 03 Jul 17:18
Ancestry Built: 03 Jul 17:18
Nodes Matched: 03 Jul 17:18
Names Parsed: 03 Jul 17:18
New Models Stored: 03 Jul 17:18
Indexed: 03 Jul 17:18
Completed: 03 Jul 17:19
Time to Harvest: less than a minute
Harvesting Log

(119 lines)
# Logfile created on 2019-07-03 17:18:24 -0400 by logger.rb/56815
[START] [2019-07-03 17:18:24] logged process
[START] [2019-07-03 17:18:24] create_harvest_instance
[STOP] [2019-07-03 17:18:24] create_harvest_instance
[START] [2019-07-03 17:18:24] fetch_files
[STOP] [2019-07-03 17:18:24] fetch_files
[START] [2019-07-03 17:18:24] validate_each_file
[STOP] [2019-07-03 17:18:24] validate_each_file
[START] [2019-07-03 17:18:24] convert_to_csv
[CMD] [2019-07-03 17:18:24] /usr/bin/sort /app/public/converted_csv/creature_cast_agents_13937.csv > /app/public/converted_csv/creature_cast_agents_13937.csv_sorted
[CMD] [2019-07-03 17:18:24] /usr/bin/sort /app/public/converted_csv/creature_cast_nodes_13938.csv > /app/public/converted_csv/creature_cast_nodes_13938.csv_sorted
[CMD] [2019-07-03 17:18:24] /usr/bin/sort /app/public/converted_csv/creature_cast_media_13939.csv > /app/public/converted_csv/creature_cast_media_13939.csv_sorted
[STOP] [2019-07-03 17:18:24] convert_to_csv
[START] [2019-07-03 17:18:24] calculate_delta
[CMD] [2019-07-03 17:18:24] echo "0a" > /app/public/diff/creature_cast_agents_13937.diff
[CMD] [2019-07-03 17:18:24] tail -n +1 /app/public/converted_csv/creature_cast_agents_13937.csv >> /app/public/diff/creature_cast_agents_13937.diff
[CMD] [2019-07-03 17:18:24] echo "." >> /app/public/diff/creature_cast_agents_13937.diff
[CMD] [2019-07-03 17:18:24] echo "0a" > /app/public/diff/creature_cast_nodes_13938.diff
[CMD] [2019-07-03 17:18:24] tail -n +1 /app/public/converted_csv/creature_cast_nodes_13938.csv >> /app/public/diff/creature_cast_nodes_13938.diff
[CMD] [2019-07-03 17:18:24] echo "." >> /app/public/diff/creature_cast_nodes_13938.diff
[CMD] [2019-07-03 17:18:24] echo "0a" > /app/public/diff/creature_cast_media_13939.diff
[CMD] [2019-07-03 17:18:24] tail -n +1 /app/public/converted_csv/creature_cast_media_13939.csv >> /app/public/diff/creature_cast_media_13939.diff
[CMD] [2019-07-03 17:18:24] echo "." >> /app/public/diff/creature_cast_media_13939.diff
[STOP] [2019-07-03 17:18:24] calculate_delta
[START] [2019-07-03 17:18:24] parse_diff_and_store
[INFO] [2019-07-03 17:18:24] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-03 17:18:24] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-03 17:18:24] Loading media diff file into memory (true lines)...
[INFO] [2019-07-03 17:18:24] Storing 1 Attributions
[INFO] [2019-07-03 17:18:24] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-03 17:18:24] Average Time: 0.0
[INFO] [2019-07-03 17:18:24] Total Time: 1s
[INFO] [2019-07-03 17:18:24] Storing 36 ScientificNames
[INFO] [2019-07-03 17:18:24] Processing group of 36 in 1 groups of 1000
[INFO] [2019-07-03 17:18:24] Average Time: 0.02
[INFO] [2019-07-03 17:18:24] Total Time: 1s
[INFO] [2019-07-03 17:18:24] Storing 36 Nodes
[INFO] [2019-07-03 17:18:24] Processing group of 36 in 1 groups of 1000
[INFO] [2019-07-03 17:18:24] Average Time: 0.02
[INFO] [2019-07-03 17:18:24] Total Time: 1s
[INFO] [2019-07-03 17:18:24] Storing 41 ContentAttributions
[INFO] [2019-07-03 17:18:24] Processing group of 41 in 1 groups of 1000
[INFO] [2019-07-03 17:18:24] Average Time: 0.02
[INFO] [2019-07-03 17:18:24] Total Time: 1s
[INFO] [2019-07-03 17:18:24] Storing 41 Media
[INFO] [2019-07-03 17:18:24] Processing group of 41 in 1 groups of 1000
[INFO] [2019-07-03 17:18:25] Average Time: 0.03
[INFO] [2019-07-03 17:18:25] Total Time: 1s
[STOP] [2019-07-03 17:18:25] parse_diff_and_store
[START] [2019-07-03 17:18:25] resolve_keys
[INFO] [2019-07-03 17:18:28] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-03 17:18:28] traits to occurrences...
[INFO] [2019-07-03 17:18:28] traits to nodes (through occurrences)...
[INFO] [2019-07-03 17:18:28] Traits to sex term...
[INFO] [2019-07-03 17:18:28] Traits to lifestage term...
[INFO] [2019-07-03 17:18:28] MetaTraits to traits...
[INFO] [2019-07-03 17:18:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-03 17:18:28] Assocs to occurrences...
[INFO] [2019-07-03 17:18:28] Assocs to nodes...
[INFO] [2019-07-03 17:18:28] Assoc to sex term...
[INFO] [2019-07-03 17:18:28] Assoc to lifestage term...
[STOP] [2019-07-03 17:18:28] resolve_keys
[START] [2019-07-03 17:18:28] hold_for_later_1
[STOP] [2019-07-03 17:18:28] hold_for_later_1
[START] [2019-07-03 17:18:28] hold_for_later_2
[STOP] [2019-07-03 17:18:28] hold_for_later_2
[START] [2019-07-03 17:18:28] resolve_missing_parents
[STOP] [2019-07-03 17:18:28] resolve_missing_parents
[START] [2019-07-03 17:18:28] rebuild_nodes
[START] [2019-07-03 17:18:28] Flattener#flatten
[START] [2019-07-03 17:18:28] Flattener#study_resource
[START] [2019-07-03 17:18:28] Flattener#build_ancestry
[STOP] [2019-07-03 17:18:28] Flattener#build_ancestry
[INFO] [2019-07-03 17:18:28] 36 ancestry keys
[START] [2019-07-03 17:18:28] build_node_ancestors
[INFO] [2019-07-03 17:18:28] old ancestors deleted.
[STOP] [2019-07-03 17:18:28] build_node_ancestors
[WARN] [2019-07-03 17:18:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2019-07-03 17:18:28] Flattener#flatten
[STOP] [2019-07-03 17:18:28] rebuild_nodes
[START] [2019-07-03 17:18:28] resolve_missing_media_owners
[STOP] [2019-07-03 17:18:28] resolve_missing_media_owners
[START] [2019-07-03 17:18:28] sanitize_media_verbatims
[STOP] [2019-07-03 17:18:28] sanitize_media_verbatims
[START] [2019-07-03 17:18:28] queue_downloads
[STOP] [2019-07-03 17:18:28] queue_downloads
[START] [2019-07-03 17:18:28] parse_names
[WARN] [2019-07-03 17:18:28] I see 36 names which still need to be parsed.
[STOP] [2019-07-03 17:18:29] parse_names
[START] [2019-07-03 17:18:29] denormalize_canonical_names_to_nodes
[STOP] [2019-07-03 17:18:29] denormalize_canonical_names_to_nodes
[START] [2019-07-03 17:18:29] match_nodes
[START] [2019-07-03 17:18:29] map_all_nodes_to_pages
[STOP] [2019-07-03 17:18:30] map_all_nodes_to_pages
[INFO] [2019-07-03 17:18:30] Unmatched nodes (6 of 36): Teuthida (#44044476); Appendicularia (#44044482); Ctenophora (#44044483); Biota (#44044500); Turbellaria (#44044501); Copepoda (#44044503)
[START] [2019-07-03 17:18:30] update_nodes
[STOP] [2019-07-03 17:18:30] update_nodes
[STOP] [2019-07-03 17:18:30] match_nodes
[START] [2019-07-03 17:18:30] reindex_search
[STOP] [2019-07-03 17:18:30] reindex_search
[START] [2019-07-03 17:18:30] normalize_units
[STOP] [2019-07-03 17:18:30] normalize_units
[START] [2019-07-03 17:18:30] calculate_statistics
[STOP] [2019-07-03 17:18:30] calculate_statistics
[START] [2019-07-03 17:18:30] complete_harvest_instance
[START] [2019-07-03 17:18:30] overall_tsv_creation
[INFO] [2019-07-03 17:18:30] Processing group of 36 in 1 batches of 10000
[INFO] [2019-07-03 17:19:01] Average Time: 10.96
[INFO] [2019-07-03 17:19:01] Total Time: 32s
[STOP] [2019-07-03 17:19:01] overall_tsv_creation
[INFO] [2019-07-03 17:19:01] Done. Check your files:
[INFO] [2019-07-03 17:19:01] (36 lines) /app/public/data/creature_cast/publish_nodes.tsv
[INFO] [2019-07-03 17:19:01] (36 lines) /app/public/data/creature_cast/publish_scientific_names.tsv
[INFO] [2019-07-03 17:19:01] (41 lines) /app/public/data/creature_cast/publish_media.tsv
[INFO] [2019-07-03 17:19:01] (41 lines) /app/public/data/creature_cast/publish_attributions.tsv
[STOP] [2019-07-03 17:19:01] complete_harvest_instance
[START] [2019-07-03 17:19:01] completed
[STOP] [2019-07-03 17:19:01] completed
[STOP] [2019-07-03 17:19:01] logged process, took 37.87
Latest Process

03 Jul 17:18 EXITED currently processing 0