Harvest for Lapshin and Vorontsov 2009 Created 13 Oct 13:56

Stage: completed
Fetched: 13 Oct 13:56
Validated: 13 Oct 13:56
Deltas Created 13 Oct 13:56
Units Normalized: 13 Oct 13:56
Ancestry Built: 13 Oct 13:56
Nodes Matched: 13 Oct 13:56
Names Parsed: 13 Oct 13:56
New Models Stored: 13 Oct 13:56
Indexed: 13 Oct 13:56
Completed: 13 Oct 13:57
Time to Harvest: less than a minute
Harvesting Log

(157 lines)
[INFO] [2023-10-13 13:56:37] Created harvest instance #4463
[STOP] [2023-10-13 13:56:37] create_harvest_instance
[START] [2023-10-13 13:56:37] fetch_files
[STOP] [2023-10-13 13:56:37] fetch_files
[START] [2023-10-13 13:56:37] validate_each_file
[INFO] [2023-10-13 13:56:37] Looping over 4 formats...
[INFO] [2023-10-13 13:56:37] ...refs (/app/public/data/lapshin_vorontso/references.txt)
[INFO] [2023-10-13 13:56:37] Valid: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_refs_30860.csv (3 lines)
[INFO] [2023-10-13 13:56:37] ...nodes (/app/public/data/lapshin_vorontso/taxa.txt)
[INFO] [2023-10-13 13:56:37] Valid: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_nodes_30857.csv (1 lines)
[INFO] [2023-10-13 13:56:37] ...occurrences (/app/public/data/lapshin_vorontso/occurrences.txt)
[INFO] [2023-10-13 13:56:37] Valid: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_occurrences_30858.csv (1 lines)
[INFO] [2023-10-13 13:56:37] ...measurements (/app/public/data/lapshin_vorontso/measurementsorfacts.txt)
[INFO] [2023-10-13 13:56:37] Valid: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_measurements_30859.csv (2 lines)
[STOP] [2023-10-13 13:56:37] validate_each_file
[START] [2023-10-13 13:56:37] convert_to_csv
[INFO] [2023-10-13 13:56:37] Looping over 4 formats...
[INFO] [2023-10-13 13:56:37] ...refs (/app/public/data/lapshin_vorontso/references.txt)
[CMD] [2023-10-13 13:56:37] /usr/bin/sort /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_refs_30860.csv > /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_refs_30860.csv_sorted
[INFO] [2023-10-13 13:56:37] Converted: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_refs_30860.csv (3 lines)
[INFO] [2023-10-13 13:56:37] ...nodes (/app/public/data/lapshin_vorontso/taxa.txt)
[CMD] [2023-10-13 13:56:37] /usr/bin/sort /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_nodes_30857.csv > /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_nodes_30857.csv_sorted
[INFO] [2023-10-13 13:56:37] Converted: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_nodes_30857.csv (1 lines)
[INFO] [2023-10-13 13:56:37] ...occurrences (/app/public/data/lapshin_vorontso/occurrences.txt)
[CMD] [2023-10-13 13:56:37] /usr/bin/sort /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_occurrences_30858.csv > /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_occurrences_30858.csv_sorted
[INFO] [2023-10-13 13:56:37] Converted: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_occurrences_30858.csv (1 lines)
[INFO] [2023-10-13 13:56:37] ...measurements (/app/public/data/lapshin_vorontso/measurementsorfacts.txt)
[CMD] [2023-10-13 13:56:37] /usr/bin/sort /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_measurements_30859.csv > /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_measurements_30859.csv_sorted
[INFO] [2023-10-13 13:56:37] Converted: /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_measurements_30859.csv (2 lines)
[STOP] [2023-10-13 13:56:37] convert_to_csv
[START] [2023-10-13 13:56:37] calculate_delta
[INFO] [2023-10-13 13:56:37] Looping over 4 formats...
[INFO] [2023-10-13 13:56:37] ...refs (/app/public/data/lapshin_vorontso/references.txt)
[CMD] [2023-10-13 13:56:37] echo "0a" > /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_refs_30860.diff
[CMD] [2023-10-13 13:56:37] tail -n +1 /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_refs_30860.csv >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_refs_30860.diff
[CMD] [2023-10-13 13:56:37] echo "." >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_refs_30860.diff
[INFO] [2023-10-13 13:56:38] Created diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_refs_30860.diff (5 lines)
[INFO] [2023-10-13 13:56:38] ...nodes (/app/public/data/lapshin_vorontso/taxa.txt)
[CMD] [2023-10-13 13:56:38] echo "0a" > /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_nodes_30857.diff
[CMD] [2023-10-13 13:56:38] tail -n +1 /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_nodes_30857.csv >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_nodes_30857.diff
[CMD] [2023-10-13 13:56:38] echo "." >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_nodes_30857.diff
[INFO] [2023-10-13 13:56:38] Created diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_nodes_30857.diff (3 lines)
[INFO] [2023-10-13 13:56:38] ...occurrences (/app/public/data/lapshin_vorontso/occurrences.txt)
[CMD] [2023-10-13 13:56:38] echo "0a" > /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_occurrences_30858.diff
[CMD] [2023-10-13 13:56:38] tail -n +1 /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_occurrences_30858.csv >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_occurrences_30858.diff
[CMD] [2023-10-13 13:56:38] echo "." >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_occurrences_30858.diff
[INFO] [2023-10-13 13:56:38] Created diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_occurrences_30858.diff (3 lines)
[INFO] [2023-10-13 13:56:38] ...measurements (/app/public/data/lapshin_vorontso/measurementsorfacts.txt)
[CMD] [2023-10-13 13:56:38] echo "0a" > /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_measurements_30859.diff
[CMD] [2023-10-13 13:56:38] tail -n +1 /app/public/data/lapshin_vorontso/converted_csv/lapshin_vorontso_measurements_30859.csv >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_measurements_30859.diff
[CMD] [2023-10-13 13:56:38] echo "." >> /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_measurements_30859.diff
[INFO] [2023-10-13 13:56:38] Created diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_measurements_30859.diff (4 lines)
[STOP] [2023-10-13 13:56:38] calculate_delta
[START] [2023-10-13 13:56:38] parse_diff_and_store
[INFO] [2023-10-13 13:56:38] Handling diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_refs_30860.diff (5 lines)
[INFO] [2023-10-13 13:56:39] Loading refs diff file into memory (5 lines)...
[INFO] [2023-10-13 13:56:39] Storing 3 References (3/3/5)
[INFO] [2023-10-13 13:56:39] Handling diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_nodes_30857.diff (3 lines)
[INFO] [2023-10-13 13:56:40] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-13 13:56:40] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-13 13:56:40] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-13 13:56:40] Handling diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_occurrences_30858.diff (3 lines)
[INFO] [2023-10-13 13:56:40] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-13 13:56:40] Storing 1 Occurrences (2/1/3)
[INFO] [2023-10-13 13:56:40] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2023-10-13 13:56:40] Handling diff: /app/public/data/lapshin_vorontso/diff/lapshin_vorontso_measurements_30859.diff (4 lines)
[INFO] [2023-10-13 13:56:41] Loading measurements diff file into memory (4 lines)...
[INFO] [2023-10-13 13:56:41] Storing 3 TraitsReferences (8/2/4)
[INFO] [2023-10-13 13:56:41] Storing 2 Traits (8/2/4)
[INFO] [2023-10-13 13:56:41] Storing 3 MetaTraits (8/2/4)
[STOP] [2023-10-13 13:56:41] parse_diff_and_store
[START] [2023-10-13 13:56:41] resolve_keys
[2023-10-13 13:56:41] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:56:48] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:56:48] traits to occurrences...
[INFO] [2023-10-13 13:56:48] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:56:48] Traits to sex term...
[INFO] [2023-10-13 13:56:48] Traits to lifestage term...
[INFO] [2023-10-13 13:56:48] MetaTraits to traits...
[INFO] [2023-10-13 13:56:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:56:48] Assocs to occurrences...
[INFO] [2023-10-13 13:56:48] Assocs to nodes...
[INFO] [2023-10-13 13:56:48] Assoc to sex term...
[INFO] [2023-10-13 13:56:48] Assoc to lifestage term...
[INFO] [2023-10-13 13:56:48] MetaAssoc to assocs...
[STOP] [2023-10-13 13:56:48] resolve_keys
[START] [2023-10-13 13:56:48] hold_for_later_1
[STOP] [2023-10-13 13:56:48] hold_for_later_1
[START] [2023-10-13 13:56:48] hold_for_later_2
[STOP] [2023-10-13 13:56:48] hold_for_later_2
[START] [2023-10-13 13:56:48] resolve_missing_parents
[STOP] [2023-10-13 13:56:48] resolve_missing_parents
[START] [2023-10-13 13:56:48] rebuild_nodes
[START] [2023-10-13 13:56:48] Flattener#flatten
[START] [2023-10-13 13:56:48] Flattener#study_resource
[START] [2023-10-13 13:56:48] Flattener#build_ancestry
[STOP] [2023-10-13 13:56:48] Flattener#build_ancestry
[INFO] [2023-10-13 13:56:48] 1 ancestry keys
[START] [2023-10-13 13:56:48] build_node_ancestors
[INFO] [2023-10-13 13:56:48] old ancestors deleted.
[STOP] [2023-10-13 13:56:48] build_node_ancestors
[WARN] [2023-10-13 13:56:48] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:56:48] Flattener#flatten
[STOP] [2023-10-13 13:56:48] rebuild_nodes
[START] [2023-10-13 13:56:48] resolve_missing_media_owners
[STOP] [2023-10-13 13:56:48] resolve_missing_media_owners
[START] [2023-10-13 13:56:48] sanitize_media_verbatims
[STOP] [2023-10-13 13:56:48] sanitize_media_verbatims
[START] [2023-10-13 13:56:48] queue_downloads
[STOP] [2023-10-13 13:56:48] queue_downloads
[START] [2023-10-13 13:56:48] parse_names
[WARN] [2023-10-13 13:56:49] I see 1 names which still need to be parsed.
[WARN] [2023-10-13 13:56:49] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-13 13:56:50] parse_names
[START] [2023-10-13 13:56:50] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:56:50] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:56:50] match_nodes
[START] [2023-10-13 13:56:50] map_all_nodes_to_pages
[STOP] [2023-10-13 13:56:50] map_all_nodes_to_pages
[INFO] [2023-10-13 13:56:50] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-13 13:56:50] update_nodes
[STOP] [2023-10-13 13:56:50] update_nodes
[STOP] [2023-10-13 13:56:50] match_nodes
[START] [2023-10-13 13:56:50] reindex_search
[STOP] [2023-10-13 13:56:50] reindex_search
[START] [2023-10-13 13:56:50] normalize_units
[STOP] [2023-10-13 13:56:50] normalize_units
[START] [2023-10-13 13:56:50] calculate_statistics
[2023-10-13 13:56:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:56:50] Duplicate page_id count: 0
[STOP] [2023-10-13 13:56:50] calculate_statistics
[START] [2023-10-13 13:56:50] complete_harvest_instance
[START] [2023-10-13 13:56:50] overall_tsv_creation
[INFO] [2023-10-13 13:56:50] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:56:50] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-13 13:56:50] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:56:50] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-13 13:56:50] Mapped 1 traits (3 meta) for 1 nodes.
[INFO] [2023-10-13 13:56:50] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:56:50] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:56:50] Adding 1 traits...
[INFO] [2023-10-13 13:56:50] 4 metadata added.
[INFO] [2023-10-13 13:56:50] Adding 0 assocs...
[INFO] [2023-10-13 13:56:50] 0 metadata added.
[INFO] [2023-10-13 13:57:34] Processed 1/1 nodes
[INFO] [2023-10-13 13:57:34] Average Time: 43.99
[INFO] [2023-10-13 13:57:34] Total Time: 45s
[STOP] [2023-10-13 13:57:34] overall_tsv_creation
[INFO] [2023-10-13 13:57:34] Done. Check your files:
[INFO] [2023-10-13 13:57:34] (1 lines) /app/public/data/lapshin_vorontso/publish_nodes.tsv
[INFO] [2023-10-13 13:57:34] (1 lines) /app/public/data/lapshin_vorontso/publish_scientific_names.tsv
[INFO] [2023-10-13 13:57:34] (2 lines) /app/public/data/lapshin_vorontso/publish_traits.tsv
[INFO] [2023-10-13 13:57:34] (5 lines) /app/public/data/lapshin_vorontso/publish_metadata.tsv
[STOP] [2023-10-13 13:57:34] complete_harvest_instance
[START] [2023-10-13 13:57:34] completed
[STOP] [2023-10-13 13:57:34] completed
[STOP] [2023-10-13 13:57:34] logged process, took 57.26
Latest Process

13 Oct 13:56 EXITED currently processing 0