Harvest for Young 1997 Created 31 May 19:42

Stage: completed
Fetched: 31 May 19:42
Validated: 31 May 19:42
Deltas Created 31 May 19:42
Units Normalized: 31 May 19:42
Ancestry Built: 31 May 19:42
Nodes Matched: 31 May 19:42
Names Parsed: 31 May 19:42
New Models Stored: 31 May 19:42
Indexed: 31 May 19:42
Completed: 31 May 19:43
Time to Harvest: less than a minute

Harvesting Log

(168 lines)
[INFO] [2021-05-31 19:42:13] Created harvest instance #3958
[STOP] [2021-05-31 19:42:13] create_harvest_instance
[START] [2021-05-31 19:42:13] fetch_files
[STOP] [2021-05-31 19:42:13] fetch_files
[START] [2021-05-31 19:42:13] validate_each_file
[INFO] [2021-05-31 19:42:13] Looping over 4 formats...
[INFO] [2021-05-31 19:42:13] ...refs (/app/public/data/young_young_1997/references.txt)
[INFO] [2021-05-31 19:42:13] Valid: /app/public/converted_csv/young_young_1997_refs_3958.csv (5 lines)
[INFO] [2021-05-31 19:42:13] ...nodes (/app/public/data/young_young_1997/taxa.txt)
[INFO] [2021-05-31 19:42:13] Valid: /app/public/converted_csv/young_young_1997_nodes_3958.csv (1 lines)
[INFO] [2021-05-31 19:42:13] ...occurrences (/app/public/data/young_young_1997/occurrences.txt)
[INFO] [2021-05-31 19:42:13] Valid: /app/public/converted_csv/young_young_1997_occurrences_3958.csv (1 lines)
[INFO] [2021-05-31 19:42:13] ...measurements (/app/public/data/young_young_1997/measurementsorfacts.txt)
[INFO] [2021-05-31 19:42:13] Valid: /app/public/converted_csv/young_young_1997_measurements_3958.csv (6 lines)
[STOP] [2021-05-31 19:42:13] validate_each_file
[START] [2021-05-31 19:42:13] convert_to_csv
[INFO] [2021-05-31 19:42:13] Looping over 4 formats...
[INFO] [2021-05-31 19:42:13] ...refs (/app/public/data/young_young_1997/references.txt)
[CMD] [2021-05-31 19:42:13] /usr/bin/sort /app/public/converted_csv/young_young_1997_refs_3958.csv > /app/public/converted_csv/young_young_1997_refs_3958.csv_sorted
[INFO] [2021-05-31 19:42:13] Converted: /app/public/converted_csv/young_young_1997_refs_3958.csv (5 lines)
[INFO] [2021-05-31 19:42:13] ...nodes (/app/public/data/young_young_1997/taxa.txt)
[CMD] [2021-05-31 19:42:13] /usr/bin/sort /app/public/converted_csv/young_young_1997_nodes_3958.csv > /app/public/converted_csv/young_young_1997_nodes_3958.csv_sorted
[INFO] [2021-05-31 19:42:14] Converted: /app/public/converted_csv/young_young_1997_nodes_3958.csv (1 lines)
[INFO] [2021-05-31 19:42:14] ...occurrences (/app/public/data/young_young_1997/occurrences.txt)
[CMD] [2021-05-31 19:42:14] /usr/bin/sort /app/public/converted_csv/young_young_1997_occurrences_3958.csv > /app/public/converted_csv/young_young_1997_occurrences_3958.csv_sorted
[INFO] [2021-05-31 19:42:14] Converted: /app/public/converted_csv/young_young_1997_occurrences_3958.csv (1 lines)
[INFO] [2021-05-31 19:42:14] ...measurements (/app/public/data/young_young_1997/measurementsorfacts.txt)
[CMD] [2021-05-31 19:42:14] /usr/bin/sort /app/public/converted_csv/young_young_1997_measurements_3958.csv > /app/public/converted_csv/young_young_1997_measurements_3958.csv_sorted
[INFO] [2021-05-31 19:42:14] Converted: /app/public/converted_csv/young_young_1997_measurements_3958.csv (6 lines)
[STOP] [2021-05-31 19:42:14] convert_to_csv
[START] [2021-05-31 19:42:14] calculate_delta
[INFO] [2021-05-31 19:42:14] Looping over 4 formats...
[INFO] [2021-05-31 19:42:14] ...refs (/app/public/data/young_young_1997/references.txt)
[CMD] [2021-05-31 19:42:14] echo "0a" > /app/public/diff/young_young_1997_refs_3958.diff
[CMD] [2021-05-31 19:42:15] tail -n +1 /app/public/converted_csv/young_young_1997_refs_3958.csv >> /app/public/diff/young_young_1997_refs_3958.diff
[CMD] [2021-05-31 19:42:15] echo "." >> /app/public/diff/young_young_1997_refs_3958.diff
[INFO] [2021-05-31 19:42:16] Created diff: /app/public/diff/young_young_1997_refs_3958.diff (7 lines)
[INFO] [2021-05-31 19:42:16] ...nodes (/app/public/data/young_young_1997/taxa.txt)
[CMD] [2021-05-31 19:42:16] echo "0a" > /app/public/diff/young_young_1997_nodes_3958.diff
[CMD] [2021-05-31 19:42:16] tail -n +1 /app/public/converted_csv/young_young_1997_nodes_3958.csv >> /app/public/diff/young_young_1997_nodes_3958.diff
[CMD] [2021-05-31 19:42:16] echo "." >> /app/public/diff/young_young_1997_nodes_3958.diff
[INFO] [2021-05-31 19:42:17] Created diff: /app/public/diff/young_young_1997_nodes_3958.diff (3 lines)
[INFO] [2021-05-31 19:42:17] ...occurrences (/app/public/data/young_young_1997/occurrences.txt)
[CMD] [2021-05-31 19:42:17] echo "0a" > /app/public/diff/young_young_1997_occurrences_3958.diff
[CMD] [2021-05-31 19:42:17] tail -n +1 /app/public/converted_csv/young_young_1997_occurrences_3958.csv >> /app/public/diff/young_young_1997_occurrences_3958.diff
[CMD] [2021-05-31 19:42:18] echo "." >> /app/public/diff/young_young_1997_occurrences_3958.diff
[INFO] [2021-05-31 19:42:18] Created diff: /app/public/diff/young_young_1997_occurrences_3958.diff (3 lines)
[INFO] [2021-05-31 19:42:18] ...measurements (/app/public/data/young_young_1997/measurementsorfacts.txt)
[CMD] [2021-05-31 19:42:18] echo "0a" > /app/public/diff/young_young_1997_measurements_3958.diff
[CMD] [2021-05-31 19:42:18] tail -n +1 /app/public/converted_csv/young_young_1997_measurements_3958.csv >> /app/public/diff/young_young_1997_measurements_3958.diff
[CMD] [2021-05-31 19:42:19] echo "." >> /app/public/diff/young_young_1997_measurements_3958.diff
[INFO] [2021-05-31 19:42:19] Created diff: /app/public/diff/young_young_1997_measurements_3958.diff (8 lines)
[STOP] [2021-05-31 19:42:19] calculate_delta
[START] [2021-05-31 19:42:19] parse_diff_and_store
[INFO] [2021-05-31 19:42:19] Handling diff: /app/public/diff/young_young_1997_refs_3958.diff (7 lines)
[INFO] [2021-05-31 19:42:19] Loading refs diff file into memory (7 /app/public/diff/young_young_1997_refs_3958.diff lines)...
[INFO] [2021-05-31 19:42:20] Handling diff: /app/public/diff/young_young_1997_nodes_3958.diff (3 lines)
[INFO] [2021-05-31 19:42:20] Loading nodes diff file into memory (3 /app/public/diff/young_young_1997_nodes_3958.diff lines)...
[INFO] [2021-05-31 19:42:21] Handling diff: /app/public/diff/young_young_1997_occurrences_3958.diff (3 lines)
[INFO] [2021-05-31 19:42:21] Loading occurrences diff file into memory (3 /app/public/diff/young_young_1997_occurrences_3958.diff lines)...
[INFO] [2021-05-31 19:42:21] Handling diff: /app/public/diff/young_young_1997_measurements_3958.diff (8 lines)
[INFO] [2021-05-31 19:42:22] Loading measurements diff file into memory (8 /app/public/diff/young_young_1997_measurements_3958.diff lines)...
[INFO] [2021-05-31 19:42:22] Storing 5 References
[INFO] [2021-05-31 19:42:22] Processing group of 5 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[INFO] [2021-05-31 19:42:22] Storing 1 ScientificNames
[INFO] [2021-05-31 19:42:22] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[INFO] [2021-05-31 19:42:22] Storing 1 Nodes
[INFO] [2021-05-31 19:42:22] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[INFO] [2021-05-31 19:42:22] Storing 1 Occurrences
[INFO] [2021-05-31 19:42:22] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[INFO] [2021-05-31 19:42:22] Storing 15 TraitsReferences
[INFO] [2021-05-31 19:42:22] Processing group of 15 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[INFO] [2021-05-31 19:42:22] Storing 6 Traits
[INFO] [2021-05-31 19:42:22] Processing group of 6 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[INFO] [2021-05-31 19:42:22] Storing 8 MetaTraits
[INFO] [2021-05-31 19:42:22] Processing group of 8 in 1 groups of 1000
[INFO] [2021-05-31 19:42:22] Average Time: 0.0
[INFO] [2021-05-31 19:42:22] Total Time: 1s
[STOP] [2021-05-31 19:42:22] parse_diff_and_store
[START] [2021-05-31 19:42:22] resolve_keys
[INFO] [2021-05-31 19:42:28] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:42:28] traits to occurrences...
[INFO] [2021-05-31 19:42:28] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:42:28] Traits to sex term...
[INFO] [2021-05-31 19:42:28] Traits to lifestage term...
[INFO] [2021-05-31 19:42:28] MetaTraits to traits...
[INFO] [2021-05-31 19:42:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:42:28] Assocs to occurrences...
[INFO] [2021-05-31 19:42:28] Assocs to nodes...
[INFO] [2021-05-31 19:42:28] Assoc to sex term...
[INFO] [2021-05-31 19:42:28] Assoc to lifestage term...
[INFO] [2021-05-31 19:42:28] MetaAssoc to assocs...
[STOP] [2021-05-31 19:42:28] resolve_keys
[START] [2021-05-31 19:42:28] hold_for_later_1
[STOP] [2021-05-31 19:42:28] hold_for_later_1
[START] [2021-05-31 19:42:28] hold_for_later_2
[STOP] [2021-05-31 19:42:28] hold_for_later_2
[START] [2021-05-31 19:42:28] resolve_missing_parents
[STOP] [2021-05-31 19:42:28] resolve_missing_parents
[START] [2021-05-31 19:42:28] rebuild_nodes
[START] [2021-05-31 19:42:28] Flattener#flatten
[START] [2021-05-31 19:42:28] Flattener#study_resource
[START] [2021-05-31 19:42:28] Flattener#build_ancestry
[STOP] [2021-05-31 19:42:28] Flattener#build_ancestry
[INFO] [2021-05-31 19:42:28] 1 ancestry keys
[START] [2021-05-31 19:42:28] build_node_ancestors
[INFO] [2021-05-31 19:42:28] old ancestors deleted.
[STOP] [2021-05-31 19:42:28] build_node_ancestors
[WARN] [2021-05-31 19:42:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:42:28] Flattener#flatten
[STOP] [2021-05-31 19:42:28] rebuild_nodes
[START] [2021-05-31 19:42:28] resolve_missing_media_owners
[STOP] [2021-05-31 19:42:28] resolve_missing_media_owners
[START] [2021-05-31 19:42:28] sanitize_media_verbatims
[STOP] [2021-05-31 19:42:28] sanitize_media_verbatims
[START] [2021-05-31 19:42:28] queue_downloads
[STOP] [2021-05-31 19:42:28] queue_downloads
[START] [2021-05-31 19:42:28] parse_names
[WARN] [2021-05-31 19:42:28] I see 1 names which still need to be parsed.
[STOP] [2021-05-31 19:42:29] parse_names
[START] [2021-05-31 19:42:29] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:42:29] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:42:29] match_nodes
[START] [2021-05-31 19:42:29] map_all_nodes_to_pages
[STOP] [2021-05-31 19:42:29] map_all_nodes_to_pages
[INFO] [2021-05-31 19:42:29] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-05-31 19:42:29] update_nodes
[STOP] [2021-05-31 19:42:29] update_nodes
[STOP] [2021-05-31 19:42:29] match_nodes
[START] [2021-05-31 19:42:29] reindex_search
[STOP] [2021-05-31 19:42:29] reindex_search
[START] [2021-05-31 19:42:29] normalize_units
[STOP] [2021-05-31 19:42:29] normalize_units
[START] [2021-05-31 19:42:29] calculate_statistics
[2021-05-31 19:42:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:42:29] calculate_statistics
[START] [2021-05-31 19:42:29] complete_harvest_instance
[START] [2021-05-31 19:42:29] overall_tsv_creation
[INFO] [2021-05-31 19:42:29] Processing group of 1 in 1 batches of 10000
[INFO] [2021-05-31 19:43:01] 3 Traits (unfiltered)...
[INFO] [2021-05-31 19:43:27] 3 Traits (filtered)...
[INFO] [2021-05-31 19:43:27] 0 Associations (filtered)...
[INFO] [2021-05-31 19:43:27] 18 metadata added.
[INFO] [2021-05-31 19:43:27] 0 metadata added.
[INFO] [2021-05-31 19:43:50] Average Time: 59.11
[INFO] [2021-05-31 19:43:50] Total Time: 1m21s
[STOP] [2021-05-31 19:43:50] overall_tsv_creation
[INFO] [2021-05-31 19:43:50] Done. Check your files:
[INFO] [2021-05-31 19:43:51] (1 lines) /app/public/data/young_young_1997/publish_nodes.tsv
[INFO] [2021-05-31 19:43:51] (1 lines) /app/public/data/young_young_1997/publish_scientific_names.tsv
[INFO] [2021-05-31 19:43:52] (4 lines) /app/public/data/young_young_1997/publish_traits.tsv
[INFO] [2021-05-31 19:43:52] (19 lines) /app/public/data/young_young_1997/publish_metadata.tsv
[STOP] [2021-05-31 19:43:52] complete_harvest_instance
[START] [2021-05-31 19:43:52] completed
[STOP] [2021-05-31 19:43:52] completed
[STOP] [2021-05-31 19:43:52] logged process, took 99.66

Latest Process