Harvest for Elofsson and Hessler 1990 Created 13 Oct 13:44

Harvesting Log

[INFO] [2023-10-13 13:44:50] Created harvest instance #4454
[STOP] [2023-10-13 13:44:50] create_harvest_instance
[START] [2023-10-13 13:44:50] fetch_files
[STOP] [2023-10-13 13:44:50] fetch_files
[START] [2023-10-13 13:44:50] validate_each_file
[INFO] [2023-10-13 13:44:50] Looping over 4 formats...
[INFO] [2023-10-13 13:44:50] ...refs (/app/public/data/elofsson_hessler/references.tsv)
[INFO] [2023-10-13 13:44:50] Valid: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_refs_30823.csv (1 lines)
[INFO] [2023-10-13 13:44:50] ...nodes (/app/public/data/elofsson_hessler/taxa.txt)
[INFO] [2023-10-13 13:44:50] Valid: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_nodes_30820.csv (1 lines)
[INFO] [2023-10-13 13:44:50] ...occurrences (/app/public/data/elofsson_hessler/occurrences.txt)
[INFO] [2023-10-13 13:44:50] Valid: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_occurrences_30821.csv (1 lines)
[INFO] [2023-10-13 13:44:50] ...measurements (/app/public/data/elofsson_hessler/measurementsorfacts.txt)
[INFO] [2023-10-13 13:44:50] Valid: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_measurements_30822.csv (2 lines)
[STOP] [2023-10-13 13:44:50] validate_each_file
[START] [2023-10-13 13:44:50] convert_to_csv
[INFO] [2023-10-13 13:44:50] Looping over 4 formats...
[INFO] [2023-10-13 13:44:50] ...refs (/app/public/data/elofsson_hessler/references.tsv)
[CMD] [2023-10-13 13:44:50] /usr/bin/sort /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_refs_30823.csv > /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_refs_30823.csv_sorted
[INFO] [2023-10-13 13:44:50] Converted: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_refs_30823.csv (1 lines)
[INFO] [2023-10-13 13:44:50] ...nodes (/app/public/data/elofsson_hessler/taxa.txt)
[CMD] [2023-10-13 13:44:50] /usr/bin/sort /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_nodes_30820.csv > /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_nodes_30820.csv_sorted
[INFO] [2023-10-13 13:44:50] Converted: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_nodes_30820.csv (1 lines)
[INFO] [2023-10-13 13:44:50] ...occurrences (/app/public/data/elofsson_hessler/occurrences.txt)
[CMD] [2023-10-13 13:44:50] /usr/bin/sort /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_occurrences_30821.csv > /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_occurrences_30821.csv_sorted
[INFO] [2023-10-13 13:44:50] Converted: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_occurrences_30821.csv (1 lines)
[INFO] [2023-10-13 13:44:50] ...measurements (/app/public/data/elofsson_hessler/measurementsorfacts.txt)
[CMD] [2023-10-13 13:44:50] /usr/bin/sort /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_measurements_30822.csv > /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_measurements_30822.csv_sorted
[INFO] [2023-10-13 13:44:50] Converted: /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_measurements_30822.csv (2 lines)
[STOP] [2023-10-13 13:44:50] convert_to_csv
[START] [2023-10-13 13:44:50] calculate_delta
[INFO] [2023-10-13 13:44:50] Looping over 4 formats...
[INFO] [2023-10-13 13:44:50] ...refs (/app/public/data/elofsson_hessler/references.tsv)
[CMD] [2023-10-13 13:44:50] echo "0a" > /app/public/data/elofsson_hessler/diff/elofsson_hessler_refs_30823.diff
[CMD] [2023-10-13 13:44:50] tail -n +1 /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_refs_30823.csv >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_refs_30823.diff
[CMD] [2023-10-13 13:44:50] echo "." >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_refs_30823.diff
[INFO] [2023-10-13 13:44:50] Created diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_refs_30823.diff (3 lines)
[INFO] [2023-10-13 13:44:50] ...nodes (/app/public/data/elofsson_hessler/taxa.txt)
[CMD] [2023-10-13 13:44:50] echo "0a" > /app/public/data/elofsson_hessler/diff/elofsson_hessler_nodes_30820.diff
[CMD] [2023-10-13 13:44:50] tail -n +1 /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_nodes_30820.csv >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_nodes_30820.diff
[CMD] [2023-10-13 13:44:50] echo "." >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_nodes_30820.diff
[INFO] [2023-10-13 13:44:50] Created diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_nodes_30820.diff (3 lines)
[INFO] [2023-10-13 13:44:50] ...occurrences (/app/public/data/elofsson_hessler/occurrences.txt)
[CMD] [2023-10-13 13:44:50] echo "0a" > /app/public/data/elofsson_hessler/diff/elofsson_hessler_occurrences_30821.diff
[CMD] [2023-10-13 13:44:51] tail -n +1 /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_occurrences_30821.csv >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_occurrences_30821.diff
[CMD] [2023-10-13 13:44:51] echo "." >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_occurrences_30821.diff
[INFO] [2023-10-13 13:44:51] Created diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_occurrences_30821.diff (3 lines)
[INFO] [2023-10-13 13:44:51] ...measurements (/app/public/data/elofsson_hessler/measurementsorfacts.txt)
[CMD] [2023-10-13 13:44:51] echo "0a" > /app/public/data/elofsson_hessler/diff/elofsson_hessler_measurements_30822.diff
[CMD] [2023-10-13 13:44:51] tail -n +1 /app/public/data/elofsson_hessler/converted_csv/elofsson_hessler_measurements_30822.csv >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_measurements_30822.diff
[CMD] [2023-10-13 13:44:51] echo "." >> /app/public/data/elofsson_hessler/diff/elofsson_hessler_measurements_30822.diff
[INFO] [2023-10-13 13:44:51] Created diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_measurements_30822.diff (4 lines)
[STOP] [2023-10-13 13:44:51] calculate_delta
[START] [2023-10-13 13:44:51] parse_diff_and_store
[INFO] [2023-10-13 13:44:51] Handling diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_refs_30823.diff (3 lines)
[INFO] [2023-10-13 13:44:51] Loading refs diff file into memory (3 lines)...
[INFO] [2023-10-13 13:44:51] Storing 1 References (1/1/3)
[INFO] [2023-10-13 13:44:51] Handling diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_nodes_30820.diff (3 lines)
[INFO] [2023-10-13 13:44:51] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-13 13:44:51] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-13 13:44:51] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-13 13:44:51] Handling diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_occurrences_30821.diff (3 lines)
[INFO] [2023-10-13 13:44:51] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-13 13:44:51] Storing 1 Occurrences (1/1/3)
[INFO] [2023-10-13 13:44:51] Handling diff: /app/public/data/elofsson_hessler/diff/elofsson_hessler_measurements_30822.diff (4 lines)
[INFO] [2023-10-13 13:44:51] Loading measurements diff file into memory (4 lines)...
[INFO] [2023-10-13 13:44:51] Storing 1 TraitsReferences (4/2/4)
[INFO] [2023-10-13 13:44:51] Storing 2 Traits (4/2/4)
[INFO] [2023-10-13 13:44:51] Storing 1 MetaTraits (4/2/4)
[STOP] [2023-10-13 13:44:51] parse_diff_and_store
[START] [2023-10-13 13:44:51] resolve_keys
[2023-10-13 13:44:51] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:44:59] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:44:59] traits to occurrences...
[INFO] [2023-10-13 13:44:59] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:44:59] Traits to sex term...
[INFO] [2023-10-13 13:44:59] Traits to lifestage term...
[INFO] [2023-10-13 13:44:59] MetaTraits to traits...
[INFO] [2023-10-13 13:44:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:44:59] Assocs to occurrences...
[INFO] [2023-10-13 13:44:59] Assocs to nodes...
[INFO] [2023-10-13 13:44:59] Assoc to sex term...
[INFO] [2023-10-13 13:44:59] Assoc to lifestage term...
[INFO] [2023-10-13 13:44:59] MetaAssoc to assocs...
[STOP] [2023-10-13 13:44:59] resolve_keys
[START] [2023-10-13 13:44:59] hold_for_later_1
[STOP] [2023-10-13 13:44:59] hold_for_later_1
[START] [2023-10-13 13:44:59] hold_for_later_2
[STOP] [2023-10-13 13:44:59] hold_for_later_2
[START] [2023-10-13 13:44:59] resolve_missing_parents
[STOP] [2023-10-13 13:44:59] resolve_missing_parents
[START] [2023-10-13 13:44:59] rebuild_nodes
[START] [2023-10-13 13:44:59] Flattener#flatten
[START] [2023-10-13 13:44:59] Flattener#study_resource
[START] [2023-10-13 13:44:59] Flattener#build_ancestry
[STOP] [2023-10-13 13:44:59] Flattener#build_ancestry
[INFO] [2023-10-13 13:44:59] 1 ancestry keys
[START] [2023-10-13 13:44:59] build_node_ancestors
[INFO] [2023-10-13 13:44:59] old ancestors deleted.
[STOP] [2023-10-13 13:44:59] build_node_ancestors
[WARN] [2023-10-13 13:44:59] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:44:59] Flattener#flatten
[STOP] [2023-10-13 13:44:59] rebuild_nodes
[START] [2023-10-13 13:44:59] resolve_missing_media_owners
[STOP] [2023-10-13 13:44:59] resolve_missing_media_owners
[START] [2023-10-13 13:44:59] sanitize_media_verbatims
[STOP] [2023-10-13 13:44:59] sanitize_media_verbatims
[START] [2023-10-13 13:44:59] queue_downloads
[STOP] [2023-10-13 13:44:59] queue_downloads
[START] [2023-10-13 13:44:59] parse_names
[WARN] [2023-10-13 13:44:59] I see 1 names which still need to be parsed.
[WARN] [2023-10-13 13:44:59] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-13 13:45:00] parse_names
[START] [2023-10-13 13:45:00] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:45:00] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:45:00] match_nodes
[START] [2023-10-13 13:45:00] map_all_nodes_to_pages
[STOP] [2023-10-13 13:45:00] map_all_nodes_to_pages
[INFO] [2023-10-13 13:45:00] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-13 13:45:00] update_nodes
[STOP] [2023-10-13 13:45:00] update_nodes
[STOP] [2023-10-13 13:45:00] match_nodes
[START] [2023-10-13 13:45:00] reindex_search
[STOP] [2023-10-13 13:45:00] reindex_search
[START] [2023-10-13 13:45:00] normalize_units
[STOP] [2023-10-13 13:45:00] normalize_units
[START] [2023-10-13 13:45:00] calculate_statistics
[2023-10-13 13:45:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:45:00] Duplicate page_id count: 0
[STOP] [2023-10-13 13:45:00] calculate_statistics
[START] [2023-10-13 13:45:00] complete_harvest_instance
[START] [2023-10-13 13:45:00] overall_tsv_creation
[INFO] [2023-10-13 13:45:00] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:45:00] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-13 13:45:00] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:45:00] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-13 13:45:00] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2023-10-13 13:45:00] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:45:00] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:45:00] Adding 1 traits...
[INFO] [2023-10-13 13:45:00] 2 metadata added.
[INFO] [2023-10-13 13:45:00] Adding 0 assocs...
[INFO] [2023-10-13 13:45:00] 0 metadata added.
[INFO] [2023-10-13 13:45:44] Processed 1/1 nodes
[INFO] [2023-10-13 13:45:44] Average Time: 43.85
[INFO] [2023-10-13 13:45:44] Total Time: 44s
[STOP] [2023-10-13 13:45:44] overall_tsv_creation
[INFO] [2023-10-13 13:45:44] Done. Check your files:
[INFO] [2023-10-13 13:45:44] (1 lines) /app/public/data/elofsson_hessler/publish_nodes.tsv
[INFO] [2023-10-13 13:45:44] (1 lines) /app/public/data/elofsson_hessler/publish_scientific_names.tsv
[INFO] [2023-10-13 13:45:44] (2 lines) /app/public/data/elofsson_hessler/publish_traits.tsv
[INFO] [2023-10-13 13:45:45] (3 lines) /app/public/data/elofsson_hessler/publish_metadata.tsv
[STOP] [2023-10-13 13:45:45] complete_harvest_instance
[START] [2023-10-13 13:45:45] completed
[STOP] [2023-10-13 13:45:45] completed
[STOP] [2023-10-13 13:45:45] logged process, took 55.16

Latest Process

13 Oct 13:44 EXITED currently processing 0