Harvest for Barton Pershing et al 2013 Created 05 Jul 17:47

Stage: completed
Fetched: 05 Jul 17:47
Validated: 05 Jul 17:47
Deltas Created 05 Jul 17:47
Units Normalized: 05 Jul 17:47
Ancestry Built: 05 Jul 17:47
Nodes Matched: 05 Jul 17:47
Names Parsed: 05 Jul 17:47
New Models Stored: 05 Jul 17:47
Indexed: 05 Jul 17:47
Completed: 05 Jul 17:48
Time to Harvest: less than a minute
Harvesting Log

(155 lines)
# Logfile created on 2019-07-05 17:47:05 -0400 by logger.rb/56815
[START] [2019-07-05 17:47:05] logged process
[START] [2019-07-05 17:47:05] create_harvest_instance
[STOP] [2019-07-05 17:47:07] create_harvest_instance
[START] [2019-07-05 17:47:07] fetch_files
[STOP] [2019-07-05 17:47:07] fetch_files
[START] [2019-07-05 17:47:07] validate_each_file
[STOP] [2019-07-05 17:47:08] validate_each_file
[START] [2019-07-05 17:47:08] convert_to_csv
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_agents_13948.csv > /app/public/converted_csv/bpea2_agents_13948.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_refs_13949.csv > /app/public/converted_csv/bpea2_refs_13949.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_nodes_13950.csv > /app/public/converted_csv/bpea2_nodes_13950.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_media_13951.csv > /app/public/converted_csv/bpea2_media_13951.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_vernaculars_13952.csv > /app/public/converted_csv/bpea2_vernaculars_13952.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_occurrences_13953.csv > /app/public/converted_csv/bpea2_occurrences_13953.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_assocs_13954.csv > /app/public/converted_csv/bpea2_assocs_13954.csv_sorted
[CMD] [2019-07-05 17:47:08] /usr/bin/sort /app/public/converted_csv/bpea2_measurements_13955.csv > /app/public/converted_csv/bpea2_measurements_13955.csv_sorted
[STOP] [2019-07-05 17:47:08] convert_to_csv
[START] [2019-07-05 17:47:08] calculate_delta
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_agents_13948.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_agents_13948.csv >> /app/public/diff/bpea2_agents_13948.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_agents_13948.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_refs_13949.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_refs_13949.csv >> /app/public/diff/bpea2_refs_13949.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_refs_13949.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_nodes_13950.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_nodes_13950.csv >> /app/public/diff/bpea2_nodes_13950.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_nodes_13950.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_media_13951.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_media_13951.csv >> /app/public/diff/bpea2_media_13951.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_media_13951.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_vernaculars_13952.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_vernaculars_13952.csv >> /app/public/diff/bpea2_vernaculars_13952.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_vernaculars_13952.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_occurrences_13953.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_occurrences_13953.csv >> /app/public/diff/bpea2_occurrences_13953.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_occurrences_13953.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_assocs_13954.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_assocs_13954.csv >> /app/public/diff/bpea2_assocs_13954.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_assocs_13954.diff
[CMD] [2019-07-05 17:47:08] echo "0a" > /app/public/diff/bpea2_measurements_13955.diff
[CMD] [2019-07-05 17:47:08] tail -n +1 /app/public/converted_csv/bpea2_measurements_13955.csv >> /app/public/diff/bpea2_measurements_13955.diff
[CMD] [2019-07-05 17:47:08] echo "." >> /app/public/diff/bpea2_measurements_13955.diff
[STOP] [2019-07-05 17:47:08] calculate_delta
[START] [2019-07-05 17:47:08] parse_diff_and_store
[INFO] [2019-07-05 17:47:08] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading refs diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading media diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading assocs diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Loading measurements diff file into memory (true lines)...
[INFO] [2019-07-05 17:47:08] Storing 4 References
[INFO] [2019-07-05 17:47:08] Processing group of 4 in 1 groups of 1000
[INFO] [2019-07-05 17:47:08] Average Time: 0.0
[INFO] [2019-07-05 17:47:08] Total Time: 1s
[INFO] [2019-07-05 17:47:08] Storing 30 ScientificNames
[INFO] [2019-07-05 17:47:08] Processing group of 30 in 1 groups of 1000
[INFO] [2019-07-05 17:47:08] Average Time: 0.02
[INFO] [2019-07-05 17:47:08] Total Time: 1s
[INFO] [2019-07-05 17:47:08] Storing 30 Nodes
[INFO] [2019-07-05 17:47:08] Processing group of 30 in 1 groups of 1000
[INFO] [2019-07-05 17:47:08] Average Time: 0.01
[INFO] [2019-07-05 17:47:08] Total Time: 1s
[INFO] [2019-07-05 17:47:08] Storing 29 Occurrences
[INFO] [2019-07-05 17:47:08] Processing group of 29 in 1 groups of 1000
[INFO] [2019-07-05 17:47:08] Average Time: 0.02
[INFO] [2019-07-05 17:47:08] Total Time: 1s
[INFO] [2019-07-05 17:47:08] Storing 31 Traits
[INFO] [2019-07-05 17:47:08] Processing group of 31 in 1 groups of 1000
[INFO] [2019-07-05 17:47:08] Average Time: 0.09
[INFO] [2019-07-05 17:47:08] Total Time: 1s
[INFO] [2019-07-05 17:47:08] Storing 31 MetaTraits
[INFO] [2019-07-05 17:47:08] Processing group of 31 in 1 groups of 1000
[INFO] [2019-07-05 17:47:08] Average Time: 0.05
[INFO] [2019-07-05 17:47:08] Total Time: 1s
[STOP] [2019-07-05 17:47:08] parse_diff_and_store
[START] [2019-07-05 17:47:08] resolve_keys
[INFO] [2019-07-05 17:47:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-05 17:47:12] traits to occurrences...
[INFO] [2019-07-05 17:47:12] traits to nodes (through occurrences)...
[INFO] [2019-07-05 17:47:12] Traits to sex term...
[INFO] [2019-07-05 17:47:12] Traits to lifestage term...
[INFO] [2019-07-05 17:47:12] MetaTraits to traits...
[INFO] [2019-07-05 17:47:12] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-05 17:47:12] Assocs to occurrences...
[INFO] [2019-07-05 17:47:12] Assocs to nodes...
[INFO] [2019-07-05 17:47:12] Assoc to sex term...
[INFO] [2019-07-05 17:47:12] Assoc to lifestage term...
[STOP] [2019-07-05 17:47:12] resolve_keys
[START] [2019-07-05 17:47:12] hold_for_later_1
[STOP] [2019-07-05 17:47:12] hold_for_later_1
[START] [2019-07-05 17:47:12] hold_for_later_2
[STOP] [2019-07-05 17:47:12] hold_for_later_2
[START] [2019-07-05 17:47:12] resolve_missing_parents
[STOP] [2019-07-05 17:47:12] resolve_missing_parents
[START] [2019-07-05 17:47:12] rebuild_nodes
[START] [2019-07-05 17:47:12] Flattener#flatten
[START] [2019-07-05 17:47:12] Flattener#study_resource
[START] [2019-07-05 17:47:12] Flattener#build_ancestry
[STOP] [2019-07-05 17:47:12] Flattener#build_ancestry
[INFO] [2019-07-05 17:47:12] 30 ancestry keys
[START] [2019-07-05 17:47:12] build_node_ancestors
[INFO] [2019-07-05 17:47:12] old ancestors deleted.
[STOP] [2019-07-05 17:47:12] build_node_ancestors
[START] [2019-07-05 17:47:12] Flattener#propagate_ancestor_ids
[STOP] [2019-07-05 17:47:12] Flattener#propagate_ancestor_ids
[STOP] [2019-07-05 17:47:12] Flattener#flatten
[STOP] [2019-07-05 17:47:12] rebuild_nodes
[START] [2019-07-05 17:47:12] resolve_missing_media_owners
[STOP] [2019-07-05 17:47:12] resolve_missing_media_owners
[START] [2019-07-05 17:47:12] sanitize_media_verbatims
[STOP] [2019-07-05 17:47:12] sanitize_media_verbatims
[START] [2019-07-05 17:47:12] queue_downloads
[STOP] [2019-07-05 17:47:12] queue_downloads
[START] [2019-07-05 17:47:12] parse_names
[WARN] [2019-07-05 17:47:12] I see 30 names which still need to be parsed.
[STOP] [2019-07-05 17:47:14] parse_names
[START] [2019-07-05 17:47:14] denormalize_canonical_names_to_nodes
[STOP] [2019-07-05 17:47:14] denormalize_canonical_names_to_nodes
[START] [2019-07-05 17:47:14] match_nodes
[START] [2019-07-05 17:47:14] map_all_nodes_to_pages
[STOP] [2019-07-05 17:47:15] map_all_nodes_to_pages
[INFO] [2019-07-05 17:47:15] ZERO unmatched nodes (of 30)! Nicely done.
[START] [2019-07-05 17:47:15] update_nodes
[STOP] [2019-07-05 17:47:15] update_nodes
[STOP] [2019-07-05 17:47:15] match_nodes
[START] [2019-07-05 17:47:15] reindex_search
[STOP] [2019-07-05 17:47:15] reindex_search
[START] [2019-07-05 17:47:15] normalize_units
[STOP] [2019-07-05 17:47:15] normalize_units
[START] [2019-07-05 17:47:15] calculate_statistics
[STOP] [2019-07-05 17:47:15] calculate_statistics
[START] [2019-07-05 17:47:15] complete_harvest_instance
[START] [2019-07-05 17:47:15] overall_tsv_creation
[INFO] [2019-07-05 17:47:15] Processing group of 30 in 1 batches of 10000
[INFO] [2019-07-05 17:48:07] 31 Traits (unfiltered)...
[INFO] [2019-07-05 17:48:19] 31 Traits (filtered)...
[INFO] [2019-07-05 17:48:19] 0 Associations (filtered)...
[INFO] [2019-07-05 17:48:54] 31 metadata added.
[INFO] [2019-07-05 17:48:54] 0 metadata added.
[INFO] [2019-07-05 17:48:54] Average Time: 73.48
[INFO] [2019-07-05 17:48:54] Total Time: 1m39s
[STOP] [2019-07-05 17:48:54] overall_tsv_creation
[INFO] [2019-07-05 17:48:54] Done. Check your files:
[INFO] [2019-07-05 17:48:54] (30 lines) /app/public/data/bpea2/publish_nodes.tsv
[INFO] [2019-07-05 17:48:54] (29 lines) /app/public/data/bpea2/publish_node_ancestors.tsv
[INFO] [2019-07-05 17:48:54] (30 lines) /app/public/data/bpea2/publish_scientific_names.tsv
[INFO] [2019-07-05 17:48:54] (32 lines) /app/public/data/bpea2/publish_traits.tsv
[INFO] [2019-07-05 17:48:54] (32 lines) /app/public/data/bpea2/publish_metadata.tsv
[STOP] [2019-07-05 17:48:54] complete_harvest_instance
[START] [2019-07-05 17:48:54] completed
[STOP] [2019-07-05 17:48:54] completed
[STOP] [2019-07-05 17:48:54] logged process, took 108.92
Latest Process

05 Jul 17:47 EXITED currently processing 0