Harvest for Fairbairn 2013 Created 08 May 13:50

Stage: completed
Fetched: 08 May 13:50
Validated: 08 May 13:50
Deltas Created 08 May 13:50
Units Normalized: 08 May 13:50
Ancestry Built: 08 May 13:50
Nodes Matched: 08 May 13:50
Names Parsed: 08 May 13:50
New Models Stored: 08 May 13:50
Indexed: 08 May 13:50
Completed: 08 May 13:52
Time to Harvest: less than a minute

Harvesting Log

(156 lines)
# Logfile created on 2020-05-08 13:50:18 -0400 by logger.rb/v1.4.2
[INFO] [2020-05-08 13:50:18] ## HARVEST: type = -harvest
[START] [2020-05-08 13:50:23] logged process
[START] [2020-05-08 13:50:23] create_harvest_instance
[STOP] [2020-05-08 13:50:30] create_harvest_instance
[START] [2020-05-08 13:50:30] fetch_files
[STOP] [2020-05-08 13:50:30] fetch_files
[START] [2020-05-08 13:50:30] validate_each_file
[STOP] [2020-05-08 13:50:30] validate_each_file
[START] [2020-05-08 13:50:30] convert_to_csv
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_agents_20925.csv > /app/public/converted_csv/fairbairn_fairb2_agents_20925.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_refs_20926.csv > /app/public/converted_csv/fairbairn_fairb2_refs_20926.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_nodes_20927.csv > /app/public/converted_csv/fairbairn_fairb2_nodes_20927.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_media_20928.csv > /app/public/converted_csv/fairbairn_fairb2_media_20928.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_vernaculars_20929.csv > /app/public/converted_csv/fairbairn_fairb2_vernaculars_20929.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_occurrences_20930.csv > /app/public/converted_csv/fairbairn_fairb2_occurrences_20930.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_assocs_20931.csv > /app/public/converted_csv/fairbairn_fairb2_assocs_20931.csv_sorted
[CMD] [2020-05-08 13:50:30] /usr/bin/sort /app/public/converted_csv/fairbairn_fairb2_measurements_20932.csv > /app/public/converted_csv/fairbairn_fairb2_measurements_20932.csv_sorted
[STOP] [2020-05-08 13:50:30] convert_to_csv
[START] [2020-05-08 13:50:30] calculate_delta
[CMD] [2020-05-08 13:50:30] echo "0a" > /app/public/diff/fairbairn_fairb2_agents_20925.diff
[CMD] [2020-05-08 13:50:30] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_agents_20925.csv >> /app/public/diff/fairbairn_fairb2_agents_20925.diff
[CMD] [2020-05-08 13:50:30] echo "." >> /app/public/diff/fairbairn_fairb2_agents_20925.diff
[CMD] [2020-05-08 13:50:30] echo "0a" > /app/public/diff/fairbairn_fairb2_refs_20926.diff
[CMD] [2020-05-08 13:50:30] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_refs_20926.csv >> /app/public/diff/fairbairn_fairb2_refs_20926.diff
[CMD] [2020-05-08 13:50:30] echo "." >> /app/public/diff/fairbairn_fairb2_refs_20926.diff
[CMD] [2020-05-08 13:50:30] echo "0a" > /app/public/diff/fairbairn_fairb2_nodes_20927.diff
[CMD] [2020-05-08 13:50:30] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_nodes_20927.csv >> /app/public/diff/fairbairn_fairb2_nodes_20927.diff
[CMD] [2020-05-08 13:50:30] echo "." >> /app/public/diff/fairbairn_fairb2_nodes_20927.diff
[CMD] [2020-05-08 13:50:31] echo "0a" > /app/public/diff/fairbairn_fairb2_media_20928.diff
[CMD] [2020-05-08 13:50:31] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_media_20928.csv >> /app/public/diff/fairbairn_fairb2_media_20928.diff
[CMD] [2020-05-08 13:50:31] echo "." >> /app/public/diff/fairbairn_fairb2_media_20928.diff
[CMD] [2020-05-08 13:50:31] echo "0a" > /app/public/diff/fairbairn_fairb2_vernaculars_20929.diff
[CMD] [2020-05-08 13:50:31] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_vernaculars_20929.csv >> /app/public/diff/fairbairn_fairb2_vernaculars_20929.diff
[CMD] [2020-05-08 13:50:31] echo "." >> /app/public/diff/fairbairn_fairb2_vernaculars_20929.diff
[CMD] [2020-05-08 13:50:31] echo "0a" > /app/public/diff/fairbairn_fairb2_occurrences_20930.diff
[CMD] [2020-05-08 13:50:31] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_occurrences_20930.csv >> /app/public/diff/fairbairn_fairb2_occurrences_20930.diff
[CMD] [2020-05-08 13:50:31] echo "." >> /app/public/diff/fairbairn_fairb2_occurrences_20930.diff
[CMD] [2020-05-08 13:50:31] echo "0a" > /app/public/diff/fairbairn_fairb2_assocs_20931.diff
[CMD] [2020-05-08 13:50:31] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_assocs_20931.csv >> /app/public/diff/fairbairn_fairb2_assocs_20931.diff
[CMD] [2020-05-08 13:50:31] echo "." >> /app/public/diff/fairbairn_fairb2_assocs_20931.diff
[CMD] [2020-05-08 13:50:31] echo "0a" > /app/public/diff/fairbairn_fairb2_measurements_20932.diff
[CMD] [2020-05-08 13:50:31] tail -n +1 /app/public/converted_csv/fairbairn_fairb2_measurements_20932.csv >> /app/public/diff/fairbairn_fairb2_measurements_20932.diff
[CMD] [2020-05-08 13:50:31] echo "." >> /app/public/diff/fairbairn_fairb2_measurements_20932.diff
[STOP] [2020-05-08 13:50:31] calculate_delta
[START] [2020-05-08 13:50:31] parse_diff_and_store
[INFO] [2020-05-08 13:50:31] Loading agents diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading refs diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading nodes diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading media diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading vernaculars diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading assocs diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:31] Loading measurements diff file into memory (true lines)...
[INFO] [2020-05-08 13:50:32] Storing 79 References
[INFO] [2020-05-08 13:50:32] Processing group of 79 in 1 groups of 1000
[INFO] [2020-05-08 13:50:32] Average Time: 0.03
[INFO] [2020-05-08 13:50:32] Total Time: 1s
[INFO] [2020-05-08 13:50:32] Storing 86 ScientificNames
[INFO] [2020-05-08 13:50:32] Processing group of 86 in 1 groups of 1000
[INFO] [2020-05-08 13:50:32] Average Time: 0.12
[INFO] [2020-05-08 13:50:32] Total Time: 1s
[INFO] [2020-05-08 13:50:32] Storing 86 Nodes
[INFO] [2020-05-08 13:50:32] Processing group of 86 in 1 groups of 1000
[INFO] [2020-05-08 13:50:33] Average Time: 0.09
[INFO] [2020-05-08 13:50:33] Total Time: 1s
[INFO] [2020-05-08 13:50:33] Storing 84 Occurrences
[INFO] [2020-05-08 13:50:33] Processing group of 84 in 1 groups of 1000
[INFO] [2020-05-08 13:50:33] Average Time: 0.12
[INFO] [2020-05-08 13:50:33] Total Time: 1s
[INFO] [2020-05-08 13:50:33] Storing 257 Traits
[INFO] [2020-05-08 13:50:33] Processing group of 257 in 1 groups of 1000
[INFO] [2020-05-08 13:50:33] Average Time: 0.3
[INFO] [2020-05-08 13:50:33] Total Time: 1s
[INFO] [2020-05-08 13:50:33] Storing 382 MetaTraits
[INFO] [2020-05-08 13:50:33] Processing group of 382 in 1 groups of 1000
[INFO] [2020-05-08 13:50:33] Average Time: 0.12
[INFO] [2020-05-08 13:50:33] Total Time: 1s
[STOP] [2020-05-08 13:50:33] parse_diff_and_store
[START] [2020-05-08 13:50:33] resolve_keys
[INFO] [2020-05-08 13:50:41] Occurrences to nodes (through scientific_names)...
[INFO] [2020-05-08 13:50:41] traits to occurrences...
[INFO] [2020-05-08 13:50:41] traits to nodes (through occurrences)...
[INFO] [2020-05-08 13:50:41] Traits to sex term...
[INFO] [2020-05-08 13:50:41] Traits to lifestage term...
[INFO] [2020-05-08 13:50:41] MetaTraits to traits...
[INFO] [2020-05-08 13:50:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-05-08 13:50:41] Assocs to occurrences...
[INFO] [2020-05-08 13:50:41] Assocs to nodes...
[INFO] [2020-05-08 13:50:41] Assoc to sex term...
[INFO] [2020-05-08 13:50:41] Assoc to lifestage term...
[STOP] [2020-05-08 13:50:41] resolve_keys
[START] [2020-05-08 13:50:41] hold_for_later_1
[STOP] [2020-05-08 13:50:41] hold_for_later_1
[START] [2020-05-08 13:50:41] hold_for_later_2
[STOP] [2020-05-08 13:50:41] hold_for_later_2
[START] [2020-05-08 13:50:41] resolve_missing_parents
[STOP] [2020-05-08 13:50:41] resolve_missing_parents
[START] [2020-05-08 13:50:41] rebuild_nodes
[START] [2020-05-08 13:50:41] Flattener#flatten
[START] [2020-05-08 13:50:41] Flattener#study_resource
[START] [2020-05-08 13:50:41] Flattener#build_ancestry
[STOP] [2020-05-08 13:50:41] Flattener#build_ancestry
[INFO] [2020-05-08 13:50:41] 86 ancestry keys
[START] [2020-05-08 13:50:41] build_node_ancestors
[INFO] [2020-05-08 13:50:41] old ancestors deleted.
[STOP] [2020-05-08 13:50:41] build_node_ancestors
[START] [2020-05-08 13:50:41] Flattener#propagate_ancestor_ids
[STOP] [2020-05-08 13:50:41] Flattener#propagate_ancestor_ids
[STOP] [2020-05-08 13:50:41] Flattener#flatten
[STOP] [2020-05-08 13:50:41] rebuild_nodes
[START] [2020-05-08 13:50:41] resolve_missing_media_owners
[STOP] [2020-05-08 13:50:41] resolve_missing_media_owners
[START] [2020-05-08 13:50:41] sanitize_media_verbatims
[STOP] [2020-05-08 13:50:41] sanitize_media_verbatims
[START] [2020-05-08 13:50:41] queue_downloads
[STOP] [2020-05-08 13:50:41] queue_downloads
[START] [2020-05-08 13:50:41] parse_names
[WARN] [2020-05-08 13:50:41] I see 86 names which still need to be parsed.
[STOP] [2020-05-08 13:50:42] parse_names
[START] [2020-05-08 13:50:42] denormalize_canonical_names_to_nodes
[STOP] [2020-05-08 13:50:42] denormalize_canonical_names_to_nodes
[START] [2020-05-08 13:50:42] match_nodes
[START] [2020-05-08 13:50:42] map_all_nodes_to_pages
[STOP] [2020-05-08 13:50:43] map_all_nodes_to_pages
[INFO] [2020-05-08 13:50:43] ZERO unmatched nodes (of 86)! Nicely done.
[START] [2020-05-08 13:50:43] update_nodes
[STOP] [2020-05-08 13:50:43] update_nodes
[STOP] [2020-05-08 13:50:43] match_nodes
[START] [2020-05-08 13:50:43] reindex_search
[STOP] [2020-05-08 13:50:43] reindex_search
[START] [2020-05-08 13:50:43] normalize_units
[STOP] [2020-05-08 13:50:43] normalize_units
[START] [2020-05-08 13:50:43] calculate_statistics
[STOP] [2020-05-08 13:50:43] calculate_statistics
[START] [2020-05-08 13:50:43] complete_harvest_instance
[START] [2020-05-08 13:50:43] overall_tsv_creation
[INFO] [2020-05-08 13:50:43] Processing group of 86 in 1 batches of 10000
[INFO] [2020-05-08 13:51:39] 156 Traits (unfiltered)...
[INFO] [2020-05-08 13:51:53] 156 Traits (filtered)...
[INFO] [2020-05-08 13:51:53] 0 Associations (filtered)...
[INFO] [2020-05-08 13:52:32] 483 metadata added.
[INFO] [2020-05-08 13:52:32] 0 metadata added.
[INFO] [2020-05-08 13:52:32] Average Time: 77.54
[INFO] [2020-05-08 13:52:32] Total Time: 1m50s
[STOP] [2020-05-08 13:52:32] overall_tsv_creation
[INFO] [2020-05-08 13:52:32] Done. Check your files:
[INFO] [2020-05-08 13:52:32] (86 lines) /app/public/data/fairbairn_fairb2/publish_nodes.tsv
[INFO] [2020-05-08 13:52:32] (3 lines) /app/public/data/fairbairn_fairb2/publish_node_ancestors.tsv
[INFO] [2020-05-08 13:52:32] (86 lines) /app/public/data/fairbairn_fairb2/publish_scientific_names.tsv
[INFO] [2020-05-08 13:52:32] (157 lines) /app/public/data/fairbairn_fairb2/publish_traits.tsv
[INFO] [2020-05-08 13:52:32] (484 lines) /app/public/data/fairbairn_fairb2/publish_metadata.tsv
[STOP] [2020-05-08 13:52:32] complete_harvest_instance
[START] [2020-05-08 13:52:32] completed
[STOP] [2020-05-08 13:52:32] completed
[STOP] [2020-05-08 13:52:32] logged process, took 129.17

Latest Process