Harvest for Littlewood and Bray 2000 Created 03 Aug 15:58

Stage: completed
Fetched: 03 Aug 15:58
Validated: 03 Aug 15:58
Deltas Created 03 Aug 15:58
Units Normalized: 03 Aug 15:59
Ancestry Built: 03 Aug 15:58
Nodes Matched: 03 Aug 15:59
Names Parsed: 03 Aug 15:59
New Models Stored: 03 Aug 15:58
Indexed: 03 Aug 15:59
Completed: 03 Aug 16:01
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 15:58:48] Created harvest instance #4159
[STOP] [2022-08-03 15:58:48] create_harvest_instance
[START] [2022-08-03 15:58:48] fetch_files
[STOP] [2022-08-03 15:58:48] fetch_files
[START] [2022-08-03 15:58:48] validate_each_file
[INFO] [2022-08-03 15:58:48] Looping over 3 formats...
[INFO] [2022-08-03 15:58:48] ...nodes (/app/public/data/littlewood_bray_/taxa.txt)
[INFO] [2022-08-03 15:58:48] Valid: /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__nodes_29540.csv (2 lines)
[INFO] [2022-08-03 15:58:48] ...occurrences (/app/public/data/littlewood_bray_/occurrences.txt)
[INFO] [2022-08-03 15:58:48] Valid: /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__occurrences_29541.csv (2 lines)
[INFO] [2022-08-03 15:58:48] ...measurements (/app/public/data/littlewood_bray_/measurementOrFact.txt)
[INFO] [2022-08-03 15:58:48] Valid: /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__measurements_29542.csv (6 lines)
[STOP] [2022-08-03 15:58:48] validate_each_file
[START] [2022-08-03 15:58:48] convert_to_csv
[INFO] [2022-08-03 15:58:48] Looping over 3 formats...
[INFO] [2022-08-03 15:58:48] ...nodes (/app/public/data/littlewood_bray_/taxa.txt)
[CMD] [2022-08-03 15:58:48] /usr/bin/sort /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__nodes_29540.csv > /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__nodes_29540.csv_sorted
[INFO] [2022-08-03 15:58:48] Converted: /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__nodes_29540.csv (2 lines)
[INFO] [2022-08-03 15:58:48] ...occurrences (/app/public/data/littlewood_bray_/occurrences.txt)
[CMD] [2022-08-03 15:58:48] /usr/bin/sort /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__occurrences_29541.csv > /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__occurrences_29541.csv_sorted
[INFO] [2022-08-03 15:58:48] Converted: /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__occurrences_29541.csv (2 lines)
[INFO] [2022-08-03 15:58:48] ...measurements (/app/public/data/littlewood_bray_/measurementOrFact.txt)
[CMD] [2022-08-03 15:58:48] /usr/bin/sort /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__measurements_29542.csv > /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__measurements_29542.csv_sorted
[INFO] [2022-08-03 15:58:48] Converted: /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__measurements_29542.csv (6 lines)
[STOP] [2022-08-03 15:58:48] convert_to_csv
[START] [2022-08-03 15:58:48] calculate_delta
[INFO] [2022-08-03 15:58:48] Looping over 3 formats...
[INFO] [2022-08-03 15:58:48] ...nodes (/app/public/data/littlewood_bray_/taxa.txt)
[CMD] [2022-08-03 15:58:51] echo "0a" > /app/public/data/littlewood_bray_/diff/littlewood_bray__nodes_29540.diff
[CMD] [2022-08-03 15:58:51] tail -n +1 /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__nodes_29540.csv >> /app/public/data/littlewood_bray_/diff/littlewood_bray__nodes_29540.diff
[CMD] [2022-08-03 15:58:51] echo "." >> /app/public/data/littlewood_bray_/diff/littlewood_bray__nodes_29540.diff
[INFO] [2022-08-03 15:58:51] Created diff: /app/public/data/littlewood_bray_/diff/littlewood_bray__nodes_29540.diff (4 lines)
[INFO] [2022-08-03 15:58:51] ...occurrences (/app/public/data/littlewood_bray_/occurrences.txt)
[CMD] [2022-08-03 15:58:51] echo "0a" > /app/public/data/littlewood_bray_/diff/littlewood_bray__occurrences_29541.diff
[CMD] [2022-08-03 15:58:51] tail -n +1 /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__occurrences_29541.csv >> /app/public/data/littlewood_bray_/diff/littlewood_bray__occurrences_29541.diff
[CMD] [2022-08-03 15:58:51] echo "." >> /app/public/data/littlewood_bray_/diff/littlewood_bray__occurrences_29541.diff
[INFO] [2022-08-03 15:58:51] Created diff: /app/public/data/littlewood_bray_/diff/littlewood_bray__occurrences_29541.diff (4 lines)
[INFO] [2022-08-03 15:58:51] ...measurements (/app/public/data/littlewood_bray_/measurementOrFact.txt)
[CMD] [2022-08-03 15:58:51] echo "0a" > /app/public/data/littlewood_bray_/diff/littlewood_bray__measurements_29542.diff
[CMD] [2022-08-03 15:58:51] tail -n +1 /app/public/data/littlewood_bray_/converted_csv/littlewood_bray__measurements_29542.csv >> /app/public/data/littlewood_bray_/diff/littlewood_bray__measurements_29542.diff
[CMD] [2022-08-03 15:58:51] echo "." >> /app/public/data/littlewood_bray_/diff/littlewood_bray__measurements_29542.diff
[INFO] [2022-08-03 15:58:51] Created diff: /app/public/data/littlewood_bray_/diff/littlewood_bray__measurements_29542.diff (8 lines)
[STOP] [2022-08-03 15:58:51] calculate_delta
[START] [2022-08-03 15:58:51] parse_diff_and_store
[INFO] [2022-08-03 15:58:51] Handling diff: /app/public/data/littlewood_bray_/diff/littlewood_bray__nodes_29540.diff (4 lines)
[INFO] [2022-08-03 15:58:51] Loading nodes diff file into memory (4 lines)...
[INFO] [2022-08-03 15:58:51] Storing 2 ScientificNames (4/2/4)
[INFO] [2022-08-03 15:58:51] Storing 2 Nodes (4/2/4)
[INFO] [2022-08-03 15:58:51] Handling diff: /app/public/data/littlewood_bray_/diff/littlewood_bray__occurrences_29541.diff (4 lines)
[INFO] [2022-08-03 15:58:51] Loading occurrences diff file into memory (4 lines)...
[INFO] [2022-08-03 15:58:51] Storing 2 Occurrences (2/2/4)
[INFO] [2022-08-03 15:58:51] Handling diff: /app/public/data/littlewood_bray_/diff/littlewood_bray__measurements_29542.diff (8 lines)
[INFO] [2022-08-03 15:58:51] Loading measurements diff file into memory (8 lines)...
[INFO] [2022-08-03 15:58:51] Storing 6 Traits (9/6/8)
[INFO] [2022-08-03 15:58:51] Storing 3 MetaTraits (9/6/8)
[STOP] [2022-08-03 15:58:51] parse_diff_and_store
[START] [2022-08-03 15:58:51] resolve_keys
[2022-08-03 15:58:51] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 15:58:58] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 15:58:58] traits to occurrences...
[INFO] [2022-08-03 15:58:58] traits to nodes (through occurrences)...
[INFO] [2022-08-03 15:58:58] Traits to sex term...
[INFO] [2022-08-03 15:58:58] Traits to lifestage term...
[INFO] [2022-08-03 15:58:58] MetaTraits to traits...
[INFO] [2022-08-03 15:58:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 15:58:58] Assocs to occurrences...
[INFO] [2022-08-03 15:58:58] Assocs to nodes...
[INFO] [2022-08-03 15:58:58] Assoc to sex term...
[INFO] [2022-08-03 15:58:58] Assoc to lifestage term...
[INFO] [2022-08-03 15:58:58] MetaAssoc to assocs...
[STOP] [2022-08-03 15:58:58] resolve_keys
[START] [2022-08-03 15:58:58] hold_for_later_1
[STOP] [2022-08-03 15:58:58] hold_for_later_1
[START] [2022-08-03 15:58:58] hold_for_later_2
[STOP] [2022-08-03 15:58:58] hold_for_later_2
[START] [2022-08-03 15:58:58] resolve_missing_parents
[STOP] [2022-08-03 15:58:58] resolve_missing_parents
[START] [2022-08-03 15:58:58] rebuild_nodes
[START] [2022-08-03 15:58:58] Flattener#flatten
[START] [2022-08-03 15:58:58] Flattener#study_resource
[START] [2022-08-03 15:58:58] Flattener#build_ancestry
[STOP] [2022-08-03 15:58:58] Flattener#build_ancestry
[INFO] [2022-08-03 15:58:58] 2 ancestry keys
[START] [2022-08-03 15:58:58] build_node_ancestors
[INFO] [2022-08-03 15:58:58] old ancestors deleted.
[STOP] [2022-08-03 15:58:58] build_node_ancestors
[WARN] [2022-08-03 15:58:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 15:58:58] Flattener#flatten
[STOP] [2022-08-03 15:58:58] rebuild_nodes
[START] [2022-08-03 15:58:58] resolve_missing_media_owners
[STOP] [2022-08-03 15:58:58] resolve_missing_media_owners
[START] [2022-08-03 15:58:58] sanitize_media_verbatims
[STOP] [2022-08-03 15:58:58] sanitize_media_verbatims
[START] [2022-08-03 15:58:58] queue_downloads
[STOP] [2022-08-03 15:58:58] queue_downloads
[START] [2022-08-03 15:58:59] parse_names
[WARN] [2022-08-03 15:58:59] I see 2 names which still need to be parsed.
[WARN] [2022-08-03 15:58:59] Names to parse: 2 formatted: 2 learned: 2 parsed: 2
[STOP] [2022-08-03 15:59:00] parse_names
[START] [2022-08-03 15:59:00] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 15:59:00] denormalize_canonical_names_to_nodes
[START] [2022-08-03 15:59:00] match_nodes
[START] [2022-08-03 15:59:00] map_all_nodes_to_pages
[STOP] [2022-08-03 15:59:00] map_all_nodes_to_pages
[INFO] [2022-08-03 15:59:00] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2022-08-03 15:59:00] update_nodes
[STOP] [2022-08-03 15:59:00] update_nodes
[STOP] [2022-08-03 15:59:00] match_nodes
[START] [2022-08-03 15:59:00] reindex_search
[STOP] [2022-08-03 15:59:00] reindex_search
[START] [2022-08-03 15:59:00] normalize_units
[STOP] [2022-08-03 15:59:00] normalize_units
[START] [2022-08-03 15:59:00] calculate_statistics
[2022-08-03 15:59:00] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 15:59:00] Duplicate page_id count: 0
[STOP] [2022-08-03 15:59:00] calculate_statistics
[START] [2022-08-03 15:59:00] complete_harvest_instance
[START] [2022-08-03 15:59:00] overall_tsv_creation
[INFO] [2022-08-03 15:59:00] Exporting 2 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 15:59:00] Processing group of 2 in 1 batches of 10000
[INFO] [2022-08-03 15:59:42] 3 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 15:59:42] Building Traits map for 2 nodes (this can take a while)...
[INFO] [2022-08-03 16:00:35] Mapped 3 traits (3 meta) for 2 nodes.
[INFO] [2022-08-03 16:00:35] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:00:35] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:00:37] Adding 3 traits...
[INFO] [2022-08-03 16:00:37] 3 metadata added.
[INFO] [2022-08-03 16:00:37] Adding 0 assocs...
[INFO] [2022-08-03 16:00:37] 0 metadata added.
[INFO] [2022-08-03 16:01:20] Processed 2/2 nodes
[INFO] [2022-08-03 16:01:20] Average Time: 115.05
[INFO] [2022-08-03 16:01:20] Total Time: 2m21s
[STOP] [2022-08-03 16:01:20] overall_tsv_creation
[INFO] [2022-08-03 16:01:20] Done. Check your files:
[INFO] [2022-08-03 16:01:21] (2 lines) /app/public/data/littlewood_bray_/publish_nodes.tsv
[INFO] [2022-08-03 16:01:21] (2 lines) /app/public/data/littlewood_bray_/publish_scientific_names.tsv
[INFO] [2022-08-03 16:01:21] (4 lines) /app/public/data/littlewood_bray_/publish_traits.tsv
[INFO] [2022-08-03 16:01:21] (4 lines) /app/public/data/littlewood_bray_/publish_metadata.tsv
[STOP] [2022-08-03 16:01:21] complete_harvest_instance
[START] [2022-08-03 16:01:21] completed
[STOP] [2022-08-03 16:01:21] completed
[STOP] [2022-08-03 16:01:21] logged process, took 154.11
Latest Process

03 Aug 15:55 EXITED currently processing 0