Harvest for Young 1997 Created 14 Oct 08:26

Harvesting Log

[INFO] [2023-10-14 08:26:22] Created harvest instance #4467
[STOP] [2023-10-14 08:26:22] create_harvest_instance
[START] [2023-10-14 08:26:22] fetch_files
[STOP] [2023-10-14 08:26:22] fetch_files
[START] [2023-10-14 08:26:22] validate_each_file
[INFO] [2023-10-14 08:26:22] Looping over 4 formats...
[INFO] [2023-10-14 08:26:22] ...refs (/app/public/data/young_young_1997/references.txt)
[INFO] [2023-10-14 08:26:22] Valid: /app/public/data/young_young_1997/converted_csv/young_young_1997_refs_30876.csv (5 lines)
[INFO] [2023-10-14 08:26:22] ...nodes (/app/public/data/young_young_1997/taxa.txt)
[INFO] [2023-10-14 08:26:22] Valid: /app/public/data/young_young_1997/converted_csv/young_young_1997_nodes_30873.csv (1 lines)
[INFO] [2023-10-14 08:26:22] ...occurrences (/app/public/data/young_young_1997/occurrences.txt)
[INFO] [2023-10-14 08:26:22] Valid: /app/public/data/young_young_1997/converted_csv/young_young_1997_occurrences_30874.csv (1 lines)
[INFO] [2023-10-14 08:26:22] ...measurements (/app/public/data/young_young_1997/measurementsorfacts.txt)
[INFO] [2023-10-14 08:26:22] Valid: /app/public/data/young_young_1997/converted_csv/young_young_1997_measurements_30875.csv (6 lines)
[STOP] [2023-10-14 08:26:22] validate_each_file
[START] [2023-10-14 08:26:22] convert_to_csv
[INFO] [2023-10-14 08:26:22] Looping over 4 formats...
[INFO] [2023-10-14 08:26:22] ...refs (/app/public/data/young_young_1997/references.txt)
[CMD] [2023-10-14 08:26:22] /usr/bin/sort /app/public/data/young_young_1997/converted_csv/young_young_1997_refs_30876.csv > /app/public/data/young_young_1997/converted_csv/young_young_1997_refs_30876.csv_sorted
[INFO] [2023-10-14 08:26:22] Converted: /app/public/data/young_young_1997/converted_csv/young_young_1997_refs_30876.csv (5 lines)
[INFO] [2023-10-14 08:26:22] ...nodes (/app/public/data/young_young_1997/taxa.txt)
[CMD] [2023-10-14 08:26:22] /usr/bin/sort /app/public/data/young_young_1997/converted_csv/young_young_1997_nodes_30873.csv > /app/public/data/young_young_1997/converted_csv/young_young_1997_nodes_30873.csv_sorted
[INFO] [2023-10-14 08:26:22] Converted: /app/public/data/young_young_1997/converted_csv/young_young_1997_nodes_30873.csv (1 lines)
[INFO] [2023-10-14 08:26:22] ...occurrences (/app/public/data/young_young_1997/occurrences.txt)
[CMD] [2023-10-14 08:26:22] /usr/bin/sort /app/public/data/young_young_1997/converted_csv/young_young_1997_occurrences_30874.csv > /app/public/data/young_young_1997/converted_csv/young_young_1997_occurrences_30874.csv_sorted
[INFO] [2023-10-14 08:26:22] Converted: /app/public/data/young_young_1997/converted_csv/young_young_1997_occurrences_30874.csv (1 lines)
[INFO] [2023-10-14 08:26:22] ...measurements (/app/public/data/young_young_1997/measurementsorfacts.txt)
[CMD] [2023-10-14 08:26:22] /usr/bin/sort /app/public/data/young_young_1997/converted_csv/young_young_1997_measurements_30875.csv > /app/public/data/young_young_1997/converted_csv/young_young_1997_measurements_30875.csv_sorted
[INFO] [2023-10-14 08:26:22] Converted: /app/public/data/young_young_1997/converted_csv/young_young_1997_measurements_30875.csv (6 lines)
[STOP] [2023-10-14 08:26:22] convert_to_csv
[START] [2023-10-14 08:26:22] calculate_delta
[INFO] [2023-10-14 08:26:22] Looping over 4 formats...
[INFO] [2023-10-14 08:26:22] ...refs (/app/public/data/young_young_1997/references.txt)
[CMD] [2023-10-14 08:26:22] echo "0a" > /app/public/data/young_young_1997/diff/young_young_1997_refs_30876.diff
[CMD] [2023-10-14 08:26:22] tail -n +1 /app/public/data/young_young_1997/converted_csv/young_young_1997_refs_30876.csv >> /app/public/data/young_young_1997/diff/young_young_1997_refs_30876.diff
[CMD] [2023-10-14 08:26:22] echo "." >> /app/public/data/young_young_1997/diff/young_young_1997_refs_30876.diff
[INFO] [2023-10-14 08:26:22] Created diff: /app/public/data/young_young_1997/diff/young_young_1997_refs_30876.diff (7 lines)
[INFO] [2023-10-14 08:26:22] ...nodes (/app/public/data/young_young_1997/taxa.txt)
[CMD] [2023-10-14 08:26:22] echo "0a" > /app/public/data/young_young_1997/diff/young_young_1997_nodes_30873.diff
[CMD] [2023-10-14 08:26:22] tail -n +1 /app/public/data/young_young_1997/converted_csv/young_young_1997_nodes_30873.csv >> /app/public/data/young_young_1997/diff/young_young_1997_nodes_30873.diff
[CMD] [2023-10-14 08:26:22] echo "." >> /app/public/data/young_young_1997/diff/young_young_1997_nodes_30873.diff
[INFO] [2023-10-14 08:26:22] Created diff: /app/public/data/young_young_1997/diff/young_young_1997_nodes_30873.diff (3 lines)
[INFO] [2023-10-14 08:26:22] ...occurrences (/app/public/data/young_young_1997/occurrences.txt)
[CMD] [2023-10-14 08:26:22] echo "0a" > /app/public/data/young_young_1997/diff/young_young_1997_occurrences_30874.diff
[CMD] [2023-10-14 08:26:22] tail -n +1 /app/public/data/young_young_1997/converted_csv/young_young_1997_occurrences_30874.csv >> /app/public/data/young_young_1997/diff/young_young_1997_occurrences_30874.diff
[CMD] [2023-10-14 08:26:22] echo "." >> /app/public/data/young_young_1997/diff/young_young_1997_occurrences_30874.diff
[INFO] [2023-10-14 08:26:23] Created diff: /app/public/data/young_young_1997/diff/young_young_1997_occurrences_30874.diff (3 lines)
[INFO] [2023-10-14 08:26:23] ...measurements (/app/public/data/young_young_1997/measurementsorfacts.txt)
[CMD] [2023-10-14 08:26:23] echo "0a" > /app/public/data/young_young_1997/diff/young_young_1997_measurements_30875.diff
[CMD] [2023-10-14 08:26:23] tail -n +1 /app/public/data/young_young_1997/converted_csv/young_young_1997_measurements_30875.csv >> /app/public/data/young_young_1997/diff/young_young_1997_measurements_30875.diff
[CMD] [2023-10-14 08:26:23] echo "." >> /app/public/data/young_young_1997/diff/young_young_1997_measurements_30875.diff
[INFO] [2023-10-14 08:26:23] Created diff: /app/public/data/young_young_1997/diff/young_young_1997_measurements_30875.diff (8 lines)
[STOP] [2023-10-14 08:26:23] calculate_delta
[START] [2023-10-14 08:26:23] parse_diff_and_store
[INFO] [2023-10-14 08:26:23] Handling diff: /app/public/data/young_young_1997/diff/young_young_1997_refs_30876.diff (7 lines)
[INFO] [2023-10-14 08:26:23] Loading refs diff file into memory (7 lines)...
[INFO] [2023-10-14 08:26:23] Storing 5 References (5/5/7)
[INFO] [2023-10-14 08:26:23] Handling diff: /app/public/data/young_young_1997/diff/young_young_1997_nodes_30873.diff (3 lines)
[INFO] [2023-10-14 08:26:23] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-14 08:26:23] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-14 08:26:23] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-14 08:26:23] Handling diff: /app/public/data/young_young_1997/diff/young_young_1997_occurrences_30874.diff (3 lines)
[INFO] [2023-10-14 08:26:23] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-14 08:26:23] Storing 1 Occurrences (1/1/3)
[INFO] [2023-10-14 08:26:23] Handling diff: /app/public/data/young_young_1997/diff/young_young_1997_measurements_30875.diff (8 lines)
[INFO] [2023-10-14 08:26:23] Loading measurements diff file into memory (8 lines)...
[INFO] [2023-10-14 08:26:23] Storing 15 TraitsReferences (29/6/8)
[INFO] [2023-10-14 08:26:23] Storing 6 Traits (29/6/8)
[INFO] [2023-10-14 08:26:23] Storing 8 MetaTraits (29/6/8)
[STOP] [2023-10-14 08:26:23] parse_diff_and_store
[START] [2023-10-14 08:26:23] resolve_keys
[2023-10-14 08:26:23] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:26:31] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:26:31] traits to occurrences...
[INFO] [2023-10-14 08:26:31] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:26:31] Traits to sex term...
[INFO] [2023-10-14 08:26:31] Traits to lifestage term...
[INFO] [2023-10-14 08:26:31] MetaTraits to traits...
[INFO] [2023-10-14 08:26:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:26:31] Assocs to occurrences...
[INFO] [2023-10-14 08:26:31] Assocs to nodes...
[INFO] [2023-10-14 08:26:31] Assoc to sex term...
[INFO] [2023-10-14 08:26:31] Assoc to lifestage term...
[INFO] [2023-10-14 08:26:31] MetaAssoc to assocs...
[STOP] [2023-10-14 08:26:31] resolve_keys
[START] [2023-10-14 08:26:31] hold_for_later_1
[STOP] [2023-10-14 08:26:31] hold_for_later_1
[START] [2023-10-14 08:26:31] hold_for_later_2
[STOP] [2023-10-14 08:26:31] hold_for_later_2
[START] [2023-10-14 08:26:31] resolve_missing_parents
[STOP] [2023-10-14 08:26:31] resolve_missing_parents
[START] [2023-10-14 08:26:31] rebuild_nodes
[START] [2023-10-14 08:26:31] Flattener#flatten
[START] [2023-10-14 08:26:31] Flattener#study_resource
[START] [2023-10-14 08:26:31] Flattener#build_ancestry
[STOP] [2023-10-14 08:26:31] Flattener#build_ancestry
[INFO] [2023-10-14 08:26:31] 1 ancestry keys
[START] [2023-10-14 08:26:31] build_node_ancestors
[INFO] [2023-10-14 08:26:31] old ancestors deleted.
[STOP] [2023-10-14 08:26:31] build_node_ancestors
[WARN] [2023-10-14 08:26:31] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:26:31] Flattener#flatten
[STOP] [2023-10-14 08:26:31] rebuild_nodes
[START] [2023-10-14 08:26:31] resolve_missing_media_owners
[STOP] [2023-10-14 08:26:31] resolve_missing_media_owners
[START] [2023-10-14 08:26:31] sanitize_media_verbatims
[STOP] [2023-10-14 08:26:31] sanitize_media_verbatims
[START] [2023-10-14 08:26:31] queue_downloads
[STOP] [2023-10-14 08:26:31] queue_downloads
[START] [2023-10-14 08:26:31] parse_names
[WARN] [2023-10-14 08:26:31] I see 1 names which still need to be parsed.
[WARN] [2023-10-14 08:26:31] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-14 08:26:32] parse_names
[START] [2023-10-14 08:26:32] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:26:32] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:26:32] match_nodes
[START] [2023-10-14 08:26:32] map_all_nodes_to_pages
[STOP] [2023-10-14 08:26:32] map_all_nodes_to_pages
[INFO] [2023-10-14 08:26:32] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-14 08:26:32] update_nodes
[STOP] [2023-10-14 08:26:32] update_nodes
[STOP] [2023-10-14 08:26:32] match_nodes
[START] [2023-10-14 08:26:32] reindex_search
[STOP] [2023-10-14 08:26:32] reindex_search
[START] [2023-10-14 08:26:32] normalize_units
[STOP] [2023-10-14 08:26:32] normalize_units
[START] [2023-10-14 08:26:32] calculate_statistics
[2023-10-14 08:26:32] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:26:32] Duplicate page_id count: 0
[STOP] [2023-10-14 08:26:32] calculate_statistics
[START] [2023-10-14 08:26:32] complete_harvest_instance
[START] [2023-10-14 08:26:32] overall_tsv_creation
[INFO] [2023-10-14 08:26:32] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:26:32] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-14 08:26:32] 3 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:26:32] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-14 08:26:32] Mapped 3 traits (8 meta) for 1 nodes.
[INFO] [2023-10-14 08:26:32] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:26:32] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:26:32] Adding 3 traits...
[INFO] [2023-10-14 08:26:32] 18 metadata added.
[INFO] [2023-10-14 08:26:32] Adding 0 assocs...
[INFO] [2023-10-14 08:26:32] 0 metadata added.
[INFO] [2023-10-14 08:27:16] Processed 1/1 nodes
[INFO] [2023-10-14 08:27:16] Average Time: 43.96
[INFO] [2023-10-14 08:27:16] Total Time: 44s
[STOP] [2023-10-14 08:27:16] overall_tsv_creation
[INFO] [2023-10-14 08:27:16] Done. Check your files:
[INFO] [2023-10-14 08:27:16] (1 lines) /app/public/data/young_young_1997/publish_nodes.tsv
[INFO] [2023-10-14 08:27:16] (1 lines) /app/public/data/young_young_1997/publish_scientific_names.tsv
[INFO] [2023-10-14 08:27:16] (4 lines) /app/public/data/young_young_1997/publish_traits.tsv
[INFO] [2023-10-14 08:27:16] (19 lines) /app/public/data/young_young_1997/publish_metadata.tsv
[STOP] [2023-10-14 08:27:17] complete_harvest_instance
[START] [2023-10-14 08:27:17] completed
[STOP] [2023-10-14 08:27:17] completed
[STOP] [2023-10-14 08:27:17] logged process, took 55.12

Latest Process

14 Oct 08:26 EXITED currently processing 0