Harvest for Bogo and Mantle 2000 Created 10 Sep 08:10

Stage: completed
Fetched: 10 Sep 08:10
Validated: 10 Sep 08:10
Deltas Created 10 Sep 08:10
Units Normalized: 10 Sep 08:10
Ancestry Built: 10 Sep 08:10
Nodes Matched: 10 Sep 08:10
Names Parsed: 10 Sep 08:10
New Models Stored: 10 Sep 08:10
Indexed: 10 Sep 08:10
Completed: 10 Sep 08:14
Time to Harvest: less than a minute
Harvesting Log

(151 lines)
[INFO] [2021-09-10 08:10:17] Created harvest instance #4052
[STOP] [2021-09-10 08:10:17] create_harvest_instance
[START] [2021-09-10 08:10:17] fetch_files
[STOP] [2021-09-10 08:10:17] fetch_files
[START] [2021-09-10 08:10:17] validate_each_file
[INFO] [2021-09-10 08:10:17] Created new folder: /app/public/converted_csv
[INFO] [2021-09-10 08:10:17] Looping over 3 formats...
[INFO] [2021-09-10 08:10:17] ...nodes (/app/public/data/bogo_mantle_bogo/taxa.txt)
[INFO] [2021-09-10 08:10:17] Valid: /app/public/converted_csv/bogo_mantle_bogo_nodes_4052.csv (4 lines)
[INFO] [2021-09-10 08:10:17] ...occurrences (/app/public/data/bogo_mantle_bogo/occurrences.txt)
[INFO] [2021-09-10 08:10:17] Valid: /app/public/converted_csv/bogo_mantle_bogo_occurrences_4052.csv (1 lines)
[INFO] [2021-09-10 08:10:17] ...measurements (/app/public/data/bogo_mantle_bogo/measurementsorfacts.txt)
[INFO] [2021-09-10 08:10:17] Valid: /app/public/converted_csv/bogo_mantle_bogo_measurements_4052.csv (2 lines)
[STOP] [2021-09-10 08:10:17] validate_each_file
[START] [2021-09-10 08:10:17] convert_to_csv
[INFO] [2021-09-10 08:10:17] Looping over 3 formats...
[INFO] [2021-09-10 08:10:17] ...nodes (/app/public/data/bogo_mantle_bogo/taxa.txt)
[CMD] [2021-09-10 08:10:17] /usr/bin/sort /app/public/converted_csv/bogo_mantle_bogo_nodes_4052.csv > /app/public/converted_csv/bogo_mantle_bogo_nodes_4052.csv_sorted
[INFO] [2021-09-10 08:10:17] Converted: /app/public/converted_csv/bogo_mantle_bogo_nodes_4052.csv (4 lines)
[INFO] [2021-09-10 08:10:17] ...occurrences (/app/public/data/bogo_mantle_bogo/occurrences.txt)
[CMD] [2021-09-10 08:10:17] /usr/bin/sort /app/public/converted_csv/bogo_mantle_bogo_occurrences_4052.csv > /app/public/converted_csv/bogo_mantle_bogo_occurrences_4052.csv_sorted
[INFO] [2021-09-10 08:10:17] Converted: /app/public/converted_csv/bogo_mantle_bogo_occurrences_4052.csv (1 lines)
[INFO] [2021-09-10 08:10:17] ...measurements (/app/public/data/bogo_mantle_bogo/measurementsorfacts.txt)
[CMD] [2021-09-10 08:10:17] /usr/bin/sort /app/public/converted_csv/bogo_mantle_bogo_measurements_4052.csv > /app/public/converted_csv/bogo_mantle_bogo_measurements_4052.csv_sorted
[INFO] [2021-09-10 08:10:17] Converted: /app/public/converted_csv/bogo_mantle_bogo_measurements_4052.csv (2 lines)
[STOP] [2021-09-10 08:10:17] convert_to_csv
[START] [2021-09-10 08:10:17] calculate_delta
[INFO] [2021-09-10 08:10:17] Created diff dir: /app/public/diff
[INFO] [2021-09-10 08:10:17] Looping over 3 formats...
[INFO] [2021-09-10 08:10:17] ...nodes (/app/public/data/bogo_mantle_bogo/taxa.txt)
[CMD] [2021-09-10 08:10:17] echo "0a" > /app/public/diff/bogo_mantle_bogo_nodes_4052.diff
[CMD] [2021-09-10 08:10:17] tail -n +1 /app/public/converted_csv/bogo_mantle_bogo_nodes_4052.csv >> /app/public/diff/bogo_mantle_bogo_nodes_4052.diff
[CMD] [2021-09-10 08:10:17] echo "." >> /app/public/diff/bogo_mantle_bogo_nodes_4052.diff
[INFO] [2021-09-10 08:10:17] Created diff: /app/public/diff/bogo_mantle_bogo_nodes_4052.diff (6 lines)
[INFO] [2021-09-10 08:10:17] ...occurrences (/app/public/data/bogo_mantle_bogo/occurrences.txt)
[CMD] [2021-09-10 08:10:17] echo "0a" > /app/public/diff/bogo_mantle_bogo_occurrences_4052.diff
[CMD] [2021-09-10 08:10:17] tail -n +1 /app/public/converted_csv/bogo_mantle_bogo_occurrences_4052.csv >> /app/public/diff/bogo_mantle_bogo_occurrences_4052.diff
[CMD] [2021-09-10 08:10:17] echo "." >> /app/public/diff/bogo_mantle_bogo_occurrences_4052.diff
[INFO] [2021-09-10 08:10:17] Created diff: /app/public/diff/bogo_mantle_bogo_occurrences_4052.diff (3 lines)
[INFO] [2021-09-10 08:10:17] ...measurements (/app/public/data/bogo_mantle_bogo/measurementsorfacts.txt)
[CMD] [2021-09-10 08:10:17] echo "0a" > /app/public/diff/bogo_mantle_bogo_measurements_4052.diff
[CMD] [2021-09-10 08:10:17] tail -n +1 /app/public/converted_csv/bogo_mantle_bogo_measurements_4052.csv >> /app/public/diff/bogo_mantle_bogo_measurements_4052.diff
[CMD] [2021-09-10 08:10:17] echo "." >> /app/public/diff/bogo_mantle_bogo_measurements_4052.diff
[INFO] [2021-09-10 08:10:17] Created diff: /app/public/diff/bogo_mantle_bogo_measurements_4052.diff (4 lines)
[STOP] [2021-09-10 08:10:17] calculate_delta
[START] [2021-09-10 08:10:17] parse_diff_and_store
[INFO] [2021-09-10 08:10:17] Handling diff: /app/public/diff/bogo_mantle_bogo_nodes_4052.diff (6 lines)
[INFO] [2021-09-10 08:10:17] Loading nodes diff file into memory (6 /app/public/diff/bogo_mantle_bogo_nodes_4052.diff lines)...
[INFO] [2021-09-10 08:10:17] Handling diff: /app/public/diff/bogo_mantle_bogo_occurrences_4052.diff (3 lines)
[INFO] [2021-09-10 08:10:17] Loading occurrences diff file into memory (3 /app/public/diff/bogo_mantle_bogo_occurrences_4052.diff lines)...
[INFO] [2021-09-10 08:10:17] Handling diff: /app/public/diff/bogo_mantle_bogo_measurements_4052.diff (4 lines)
[INFO] [2021-09-10 08:10:17] Loading measurements diff file into memory (4 /app/public/diff/bogo_mantle_bogo_measurements_4052.diff lines)...
[INFO] [2021-09-10 08:10:18] Storing 4 ScientificNames
[INFO] [2021-09-10 08:10:18] Processing group of 4 in 1 groups of 1000
[INFO] [2021-09-10 08:10:18] Average Time: 0.0
[INFO] [2021-09-10 08:10:18] Total Time: 1s
[INFO] [2021-09-10 08:10:18] Storing 4 Nodes
[INFO] [2021-09-10 08:10:18] Processing group of 4 in 1 groups of 1000
[INFO] [2021-09-10 08:10:18] Average Time: 0.0
[INFO] [2021-09-10 08:10:18] Total Time: 1s
[INFO] [2021-09-10 08:10:18] Storing 1 Occurrences
[INFO] [2021-09-10 08:10:18] Processing group of 1 in 1 groups of 1000
[INFO] [2021-09-10 08:10:18] Average Time: 0.0
[INFO] [2021-09-10 08:10:18] Total Time: 1s
[INFO] [2021-09-10 08:10:18] Storing 2 Traits
[INFO] [2021-09-10 08:10:18] Processing group of 2 in 1 groups of 1000
[INFO] [2021-09-10 08:10:18] Average Time: 0.0
[INFO] [2021-09-10 08:10:18] Total Time: 1s
[INFO] [2021-09-10 08:10:18] Storing 2 MetaTraits
[INFO] [2021-09-10 08:10:18] Processing group of 2 in 1 groups of 1000
[INFO] [2021-09-10 08:10:18] Average Time: 0.04
[INFO] [2021-09-10 08:10:18] Total Time: 1s
[STOP] [2021-09-10 08:10:18] parse_diff_and_store
[START] [2021-09-10 08:10:18] resolve_keys
[INFO] [2021-09-10 08:10:27] Occurrences to nodes (through scientific_names)...
[INFO] [2021-09-10 08:10:27] traits to occurrences...
[INFO] [2021-09-10 08:10:27] traits to nodes (through occurrences)...
[INFO] [2021-09-10 08:10:27] Traits to sex term...
[INFO] [2021-09-10 08:10:27] Traits to lifestage term...
[INFO] [2021-09-10 08:10:27] MetaTraits to traits...
[INFO] [2021-09-10 08:10:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-09-10 08:10:27] Assocs to occurrences...
[INFO] [2021-09-10 08:10:27] Assocs to nodes...
[INFO] [2021-09-10 08:10:27] Assoc to sex term...
[INFO] [2021-09-10 08:10:27] Assoc to lifestage term...
[INFO] [2021-09-10 08:10:27] MetaAssoc to assocs...
[STOP] [2021-09-10 08:10:27] resolve_keys
[START] [2021-09-10 08:10:27] hold_for_later_1
[STOP] [2021-09-10 08:10:27] hold_for_later_1
[START] [2021-09-10 08:10:27] hold_for_later_2
[STOP] [2021-09-10 08:10:27] hold_for_later_2
[START] [2021-09-10 08:10:27] resolve_missing_parents
[STOP] [2021-09-10 08:10:27] resolve_missing_parents
[START] [2021-09-10 08:10:27] rebuild_nodes
[START] [2021-09-10 08:10:27] Flattener#flatten
[START] [2021-09-10 08:10:27] Flattener#study_resource
[START] [2021-09-10 08:10:27] Flattener#build_ancestry
[STOP] [2021-09-10 08:10:27] Flattener#build_ancestry
[INFO] [2021-09-10 08:10:27] 4 ancestry keys
[START] [2021-09-10 08:10:27] build_node_ancestors
[INFO] [2021-09-10 08:10:27] old ancestors deleted.
[STOP] [2021-09-10 08:10:27] build_node_ancestors
[START] [2021-09-10 08:10:27] Flattener#propagate_ancestor_ids
[STOP] [2021-09-10 08:10:27] Flattener#propagate_ancestor_ids
[STOP] [2021-09-10 08:10:27] Flattener#flatten
[STOP] [2021-09-10 08:10:27] rebuild_nodes
[START] [2021-09-10 08:10:27] resolve_missing_media_owners
[STOP] [2021-09-10 08:10:27] resolve_missing_media_owners
[START] [2021-09-10 08:10:27] sanitize_media_verbatims
[STOP] [2021-09-10 08:10:27] sanitize_media_verbatims
[START] [2021-09-10 08:10:27] queue_downloads
[STOP] [2021-09-10 08:10:27] queue_downloads
[START] [2021-09-10 08:10:27] parse_names
[WARN] [2021-09-10 08:10:27] I see 4 names which still need to be parsed.
[STOP] [2021-09-10 08:10:28] parse_names
[START] [2021-09-10 08:10:28] denormalize_canonical_names_to_nodes
[STOP] [2021-09-10 08:10:28] denormalize_canonical_names_to_nodes
[START] [2021-09-10 08:10:28] match_nodes
[START] [2021-09-10 08:10:28] map_all_nodes_to_pages
[STOP] [2021-09-10 08:10:32] map_all_nodes_to_pages
[INFO] [2021-09-10 08:10:32] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2021-09-10 08:10:32] update_nodes
[STOP] [2021-09-10 08:10:32] update_nodes
[STOP] [2021-09-10 08:10:32] match_nodes
[START] [2021-09-10 08:10:32] reindex_search
[STOP] [2021-09-10 08:10:32] reindex_search
[START] [2021-09-10 08:10:32] normalize_units
[STOP] [2021-09-10 08:10:32] normalize_units
[START] [2021-09-10 08:10:32] calculate_statistics
[STOP] [2021-09-10 08:10:32] calculate_statistics
[START] [2021-09-10 08:10:33] complete_harvest_instance
[START] [2021-09-10 08:10:33] overall_tsv_creation
[INFO] [2021-09-10 08:10:33] Processing group of 4 in 1 batches of 10000
[INFO] [2021-09-10 08:13:06] 1 Traits (unfiltered)...
[INFO] [2021-09-10 08:13:52] 1 Traits (filtered)...
[INFO] [2021-09-10 08:13:52] 0 Associations (filtered)...
[INFO] [2021-09-10 08:13:52] 1 metadata added.
[INFO] [2021-09-10 08:13:52] 0 metadata added.
[INFO] [2021-09-10 08:14:24] Average Time: 95.65
[INFO] [2021-09-10 08:14:24] Total Time: 3m52s
[STOP] [2021-09-10 08:14:24] overall_tsv_creation
[INFO] [2021-09-10 08:14:24] Done. Check your files:
[INFO] [2021-09-10 08:14:24] (4 lines) /app/public/data/bogo_mantle_bogo/publish_nodes.tsv
[INFO] [2021-09-10 08:14:24] (6 lines) /app/public/data/bogo_mantle_bogo/publish_node_ancestors.tsv
[INFO] [2021-09-10 08:14:24] (4 lines) /app/public/data/bogo_mantle_bogo/publish_scientific_names.tsv
[INFO] [2021-09-10 08:14:24] (2 lines) /app/public/data/bogo_mantle_bogo/publish_traits.tsv
[INFO] [2021-09-10 08:14:24] (2 lines) /app/public/data/bogo_mantle_bogo/publish_metadata.tsv
[STOP] [2021-09-10 08:14:24] complete_harvest_instance
[START] [2021-09-10 08:14:24] completed
[STOP] [2021-09-10 08:14:24] completed
[STOP] [2021-09-10 08:14:24] logged process, took 248.25
Latest Process

10 Sep 08:10 EXITED currently processing 0