Harvest for Queiros et al 2013 Created 03 Apr 13:11

Stage: completed
Fetched: 03 Apr 13:11
Validated: 03 Apr 13:11
Deltas Created 03 Apr 13:11
Units Normalized: 03 Apr 13:11
Ancestry Built: 03 Apr 13:11
Nodes Matched: 03 Apr 13:11
Names Parsed: 03 Apr 13:11
New Models Stored: 03 Apr 13:11
Indexed: 03 Apr 13:11
Completed: 03 Apr 13:13
Time to Harvest: less than a minute
Harvesting Log

(127 lines)
# Logfile created on 2020-04-03 13:11:00 -0400 by logger.rb/56815
[START] [2020-04-03 13:11:00] logged process
[START] [2020-04-03 13:11:00] create_harvest_instance
[STOP] [2020-04-03 13:11:00] create_harvest_instance
[START] [2020-04-03 13:11:00] fetch_files
[STOP] [2020-04-03 13:11:00] fetch_files
[START] [2020-04-03 13:11:00] validate_each_file
[STOP] [2020-04-03 13:11:01] validate_each_file
[START] [2020-04-03 13:11:01] convert_to_csv
[CMD] [2020-04-03 13:11:01] /usr/bin/sort /app/public/converted_csv/qseaq2_nodes_20558.csv > /app/public/converted_csv/qseaq2_nodes_20558.csv_sorted
[CMD] [2020-04-03 13:11:01] /usr/bin/sort /app/public/converted_csv/qseaq2_occurrences_20559.csv > /app/public/converted_csv/qseaq2_occurrences_20559.csv_sorted
[CMD] [2020-04-03 13:11:01] /usr/bin/sort /app/public/converted_csv/qseaq2_measurements_20560.csv > /app/public/converted_csv/qseaq2_measurements_20560.csv_sorted
[STOP] [2020-04-03 13:11:01] convert_to_csv
[START] [2020-04-03 13:11:01] calculate_delta
[CMD] [2020-04-03 13:11:01] echo "0a" > /app/public/diff/qseaq2_nodes_20558.diff
[CMD] [2020-04-03 13:11:01] tail -n +1 /app/public/converted_csv/qseaq2_nodes_20558.csv >> /app/public/diff/qseaq2_nodes_20558.diff
[CMD] [2020-04-03 13:11:01] echo "." >> /app/public/diff/qseaq2_nodes_20558.diff
[CMD] [2020-04-03 13:11:01] echo "0a" > /app/public/diff/qseaq2_occurrences_20559.diff
[CMD] [2020-04-03 13:11:01] tail -n +1 /app/public/converted_csv/qseaq2_occurrences_20559.csv >> /app/public/diff/qseaq2_occurrences_20559.diff
[CMD] [2020-04-03 13:11:01] echo "." >> /app/public/diff/qseaq2_occurrences_20559.diff
[CMD] [2020-04-03 13:11:01] echo "0a" > /app/public/diff/qseaq2_measurements_20560.diff
[CMD] [2020-04-03 13:11:01] tail -n +1 /app/public/converted_csv/qseaq2_measurements_20560.csv >> /app/public/diff/qseaq2_measurements_20560.diff
[CMD] [2020-04-03 13:11:01] echo "." >> /app/public/diff/qseaq2_measurements_20560.diff
[STOP] [2020-04-03 13:11:01] calculate_delta
[START] [2020-04-03 13:11:01] parse_diff_and_store
[INFO] [2020-04-03 13:11:01] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-03 13:11:01] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-03 13:11:01] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-03 13:11:07] Storing 667 ScientificNames
[INFO] [2020-04-03 13:11:07] Processing group of 667 in 1 groups of 1000
[INFO] [2020-04-03 13:11:08] Average Time: 0.26
[INFO] [2020-04-03 13:11:08] Total Time: 1s
[INFO] [2020-04-03 13:11:08] Storing 667 Nodes
[INFO] [2020-04-03 13:11:08] Processing group of 667 in 1 groups of 1000
[INFO] [2020-04-03 13:11:08] Average Time: 0.17
[INFO] [2020-04-03 13:11:08] Total Time: 1s
[INFO] [2020-04-03 13:11:08] Storing 450 Occurrences
[INFO] [2020-04-03 13:11:08] Processing group of 450 in 1 groups of 1000
[INFO] [2020-04-03 13:11:08] Average Time: 0.04
[INFO] [2020-04-03 13:11:08] Total Time: 1s
[INFO] [2020-04-03 13:11:08] Storing 1195 Traits
[INFO] [2020-04-03 13:11:08] Processing group of 1195 in 2 groups of 1000
[INFO] [2020-04-03 13:11:08] Average Time: 0.18
[INFO] [2020-04-03 13:11:08] Total Time: 1s
[INFO] [2020-04-03 13:11:08] Storing 2622 MetaTraits
[INFO] [2020-04-03 13:11:08] Processing group of 2622 in 3 groups of 1000
[INFO] [2020-04-03 13:11:09] Average Time: 0.12
[INFO] [2020-04-03 13:11:09] Total Time: 1s
[STOP] [2020-04-03 13:11:09] parse_diff_and_store
[START] [2020-04-03 13:11:09] resolve_keys
[INFO] [2020-04-03 13:11:14] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-03 13:11:14] traits to occurrences...
[INFO] [2020-04-03 13:11:14] traits to nodes (through occurrences)...
[INFO] [2020-04-03 13:11:14] Traits to sex term...
[INFO] [2020-04-03 13:11:14] Traits to lifestage term...
[INFO] [2020-04-03 13:11:14] MetaTraits to traits...
[INFO] [2020-04-03 13:11:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-03 13:11:14] Assocs to occurrences...
[INFO] [2020-04-03 13:11:14] Assocs to nodes...
[INFO] [2020-04-03 13:11:14] Assoc to sex term...
[INFO] [2020-04-03 13:11:14] Assoc to lifestage term...
[STOP] [2020-04-03 13:11:14] resolve_keys
[START] [2020-04-03 13:11:14] hold_for_later_1
[STOP] [2020-04-03 13:11:14] hold_for_later_1
[START] [2020-04-03 13:11:14] hold_for_later_2
[STOP] [2020-04-03 13:11:14] hold_for_later_2
[START] [2020-04-03 13:11:14] resolve_missing_parents
[STOP] [2020-04-03 13:11:15] resolve_missing_parents
[START] [2020-04-03 13:11:15] rebuild_nodes
[START] [2020-04-03 13:11:15] Flattener#flatten
[START] [2020-04-03 13:11:15] Flattener#study_resource
[START] [2020-04-03 13:11:15] Flattener#build_ancestry
[STOP] [2020-04-03 13:11:15] Flattener#build_ancestry
[INFO] [2020-04-03 13:11:15] 667 ancestry keys
[START] [2020-04-03 13:11:15] build_node_ancestors
[INFO] [2020-04-03 13:11:15] old ancestors deleted.
[STOP] [2020-04-03 13:11:15] build_node_ancestors
[START] [2020-04-03 13:11:15] Flattener#propagate_ancestor_ids
[STOP] [2020-04-03 13:11:15] Flattener#propagate_ancestor_ids
[STOP] [2020-04-03 13:11:15] Flattener#flatten
[STOP] [2020-04-03 13:11:15] rebuild_nodes
[START] [2020-04-03 13:11:15] resolve_missing_media_owners
[STOP] [2020-04-03 13:11:15] resolve_missing_media_owners
[START] [2020-04-03 13:11:15] sanitize_media_verbatims
[STOP] [2020-04-03 13:11:15] sanitize_media_verbatims
[START] [2020-04-03 13:11:15] queue_downloads
[STOP] [2020-04-03 13:11:15] queue_downloads
[START] [2020-04-03 13:11:15] parse_names
[WARN] [2020-04-03 13:11:15] I see 667 names which still need to be parsed.
[WARN] [2020-04-03 13:11:16] I see 23 names which still need to be parsed.
[STOP] [2020-04-03 13:11:18] parse_names
[START] [2020-04-03 13:11:18] denormalize_canonical_names_to_nodes
[STOP] [2020-04-03 13:11:18] denormalize_canonical_names_to_nodes
[START] [2020-04-03 13:11:18] match_nodes
[START] [2020-04-03 13:11:18] map_all_nodes_to_pages
[STOP] [2020-04-03 13:11:42] map_all_nodes_to_pages
[INFO] [2020-04-03 13:11:42] Unmatched nodes (2 of 667): Odostomia scalaris (#68185095); Tellina nitida (#68185266)
[START] [2020-04-03 13:11:42] update_nodes
[STOP] [2020-04-03 13:11:42] update_nodes
[STOP] [2020-04-03 13:11:42] match_nodes
[START] [2020-04-03 13:11:42] reindex_search
[STOP] [2020-04-03 13:11:43] reindex_search
[START] [2020-04-03 13:11:43] normalize_units
[STOP] [2020-04-03 13:11:43] normalize_units
[START] [2020-04-03 13:11:43] calculate_statistics
[STOP] [2020-04-03 13:11:43] calculate_statistics
[START] [2020-04-03 13:11:43] complete_harvest_instance
[START] [2020-04-03 13:11:43] overall_tsv_creation
[INFO] [2020-04-03 13:11:43] Processing group of 667 in 1 batches of 10000
[INFO] [2020-04-03 13:12:36] 870 Traits (unfiltered)...
[INFO] [2020-04-03 13:12:49] 870 Traits (filtered)...
[INFO] [2020-04-03 13:12:49] 0 Associations (filtered)...
[INFO] [2020-04-03 13:13:26] 2929 metadata added.
[INFO] [2020-04-03 13:13:26] 0 metadata added.
[INFO] [2020-04-03 13:13:26] Average Time: 74.3
[INFO] [2020-04-03 13:13:26] Total Time: 1m44s
[STOP] [2020-04-03 13:13:26] overall_tsv_creation
[INFO] [2020-04-03 13:13:26] Done. Check your files:
[INFO] [2020-04-03 13:13:26] (644 lines) /app/public/data/qseaq2/publish_nodes.tsv
[INFO] [2020-04-03 13:13:26] (1551 lines) /app/public/data/qseaq2/publish_node_ancestors.tsv
[INFO] [2020-04-03 13:13:26] (667 lines) /app/public/data/qseaq2/publish_scientific_names.tsv
[INFO] [2020-04-03 13:13:26] (871 lines) /app/public/data/qseaq2/publish_traits.tsv
[INFO] [2020-04-03 13:13:26] (2930 lines) /app/public/data/qseaq2/publish_metadata.tsv
[STOP] [2020-04-03 13:13:26] complete_harvest_instance
[START] [2020-04-03 13:13:26] completed
[STOP] [2020-04-03 13:13:26] completed
[STOP] [2020-04-03 13:13:26] logged process, took 146.18
Latest Process

03 Apr 13:11 EXITED currently processing 0