Harvest for Francis 1979 Created 03 Aug 17:02

Stage: completed
Fetched: 03 Aug 17:02
Validated: 03 Aug 17:02
Deltas Created 03 Aug 17:02
Units Normalized: 03 Aug 17:02
Ancestry Built: 03 Aug 17:02
Nodes Matched: 03 Aug 17:02
Names Parsed: 03 Aug 17:02
New Models Stored: 03 Aug 17:02
Indexed: 03 Aug 17:02
Completed: 03 Aug 17:05
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 17:02:32] Created harvest instance #4186
[STOP] [2022-08-03 17:02:32] create_harvest_instance
[START] [2022-08-03 17:02:32] fetch_files
[STOP] [2022-08-03 17:02:32] fetch_files
[START] [2022-08-03 17:02:32] validate_each_file
[INFO] [2022-08-03 17:02:32] Looping over 3 formats...
[INFO] [2022-08-03 17:02:32] ...nodes (/app/public/data/francis_francis_/taxa.txt)
[INFO] [2022-08-03 17:02:32] Valid: /app/public/data/francis_francis_/converted_csv/francis_francis__nodes_29624.csv (4 lines)
[INFO] [2022-08-03 17:02:32] ...occurrences (/app/public/data/francis_francis_/occurrences.txt)
[INFO] [2022-08-03 17:02:32] Valid: /app/public/data/francis_francis_/converted_csv/francis_francis__occurrences_29625.csv (4 lines)
[INFO] [2022-08-03 17:02:32] ...measurements (/app/public/data/francis_francis_/measurementOrFact.txt)
[INFO] [2022-08-03 17:02:32] Valid: /app/public/data/francis_francis_/converted_csv/francis_francis__measurements_29626.csv (5 lines)
[STOP] [2022-08-03 17:02:32] validate_each_file
[START] [2022-08-03 17:02:32] convert_to_csv
[INFO] [2022-08-03 17:02:32] Looping over 3 formats...
[INFO] [2022-08-03 17:02:32] ...nodes (/app/public/data/francis_francis_/taxa.txt)
[CMD] [2022-08-03 17:02:32] /usr/bin/sort /app/public/data/francis_francis_/converted_csv/francis_francis__nodes_29624.csv > /app/public/data/francis_francis_/converted_csv/francis_francis__nodes_29624.csv_sorted
[INFO] [2022-08-03 17:02:32] Converted: /app/public/data/francis_francis_/converted_csv/francis_francis__nodes_29624.csv (4 lines)
[INFO] [2022-08-03 17:02:32] ...occurrences (/app/public/data/francis_francis_/occurrences.txt)
[CMD] [2022-08-03 17:02:32] /usr/bin/sort /app/public/data/francis_francis_/converted_csv/francis_francis__occurrences_29625.csv > /app/public/data/francis_francis_/converted_csv/francis_francis__occurrences_29625.csv_sorted
[INFO] [2022-08-03 17:02:32] Converted: /app/public/data/francis_francis_/converted_csv/francis_francis__occurrences_29625.csv (4 lines)
[INFO] [2022-08-03 17:02:32] ...measurements (/app/public/data/francis_francis_/measurementOrFact.txt)
[CMD] [2022-08-03 17:02:32] /usr/bin/sort /app/public/data/francis_francis_/converted_csv/francis_francis__measurements_29626.csv > /app/public/data/francis_francis_/converted_csv/francis_francis__measurements_29626.csv_sorted
[INFO] [2022-08-03 17:02:32] Converted: /app/public/data/francis_francis_/converted_csv/francis_francis__measurements_29626.csv (5 lines)
[STOP] [2022-08-03 17:02:32] convert_to_csv
[START] [2022-08-03 17:02:32] calculate_delta
[INFO] [2022-08-03 17:02:32] Looping over 3 formats...
[INFO] [2022-08-03 17:02:32] ...nodes (/app/public/data/francis_francis_/taxa.txt)
[CMD] [2022-08-03 17:02:32] echo "0a" > /app/public/data/francis_francis_/diff/francis_francis__nodes_29624.diff
[CMD] [2022-08-03 17:02:32] tail -n +1 /app/public/data/francis_francis_/converted_csv/francis_francis__nodes_29624.csv >> /app/public/data/francis_francis_/diff/francis_francis__nodes_29624.diff
[CMD] [2022-08-03 17:02:32] echo "." >> /app/public/data/francis_francis_/diff/francis_francis__nodes_29624.diff
[INFO] [2022-08-03 17:02:32] Created diff: /app/public/data/francis_francis_/diff/francis_francis__nodes_29624.diff (6 lines)
[INFO] [2022-08-03 17:02:32] ...occurrences (/app/public/data/francis_francis_/occurrences.txt)
[CMD] [2022-08-03 17:02:32] echo "0a" > /app/public/data/francis_francis_/diff/francis_francis__occurrences_29625.diff
[CMD] [2022-08-03 17:02:32] tail -n +1 /app/public/data/francis_francis_/converted_csv/francis_francis__occurrences_29625.csv >> /app/public/data/francis_francis_/diff/francis_francis__occurrences_29625.diff
[CMD] [2022-08-03 17:02:32] echo "." >> /app/public/data/francis_francis_/diff/francis_francis__occurrences_29625.diff
[INFO] [2022-08-03 17:02:32] Created diff: /app/public/data/francis_francis_/diff/francis_francis__occurrences_29625.diff (6 lines)
[INFO] [2022-08-03 17:02:32] ...measurements (/app/public/data/francis_francis_/measurementOrFact.txt)
[CMD] [2022-08-03 17:02:32] echo "0a" > /app/public/data/francis_francis_/diff/francis_francis__measurements_29626.diff
[CMD] [2022-08-03 17:02:32] tail -n +1 /app/public/data/francis_francis_/converted_csv/francis_francis__measurements_29626.csv >> /app/public/data/francis_francis_/diff/francis_francis__measurements_29626.diff
[CMD] [2022-08-03 17:02:32] echo "." >> /app/public/data/francis_francis_/diff/francis_francis__measurements_29626.diff
[INFO] [2022-08-03 17:02:32] Created diff: /app/public/data/francis_francis_/diff/francis_francis__measurements_29626.diff (7 lines)
[STOP] [2022-08-03 17:02:32] calculate_delta
[START] [2022-08-03 17:02:32] parse_diff_and_store
[INFO] [2022-08-03 17:02:32] Handling diff: /app/public/data/francis_francis_/diff/francis_francis__nodes_29624.diff (6 lines)
[INFO] [2022-08-03 17:02:32] Loading nodes diff file into memory (6 lines)...
[INFO] [2022-08-03 17:02:32] Storing 4 ScientificNames (8/4/6)
[INFO] [2022-08-03 17:02:32] Storing 4 Nodes (8/4/6)
[INFO] [2022-08-03 17:02:32] Handling diff: /app/public/data/francis_francis_/diff/francis_francis__occurrences_29625.diff (6 lines)
[INFO] [2022-08-03 17:02:32] Loading occurrences diff file into memory (6 lines)...
[INFO] [2022-08-03 17:02:32] Storing 4 Occurrences (4/4/6)
[INFO] [2022-08-03 17:02:32] Handling diff: /app/public/data/francis_francis_/diff/francis_francis__measurements_29626.diff (7 lines)
[INFO] [2022-08-03 17:02:32] Loading measurements diff file into memory (7 lines)...
[INFO] [2022-08-03 17:02:32] Storing 5 Traits (9/5/7)
[INFO] [2022-08-03 17:02:32] Storing 4 MetaTraits (9/5/7)
[STOP] [2022-08-03 17:02:32] parse_diff_and_store
[START] [2022-08-03 17:02:32] resolve_keys
[2022-08-03 17:02:32] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:02:40] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:02:40] traits to occurrences...
[INFO] [2022-08-03 17:02:40] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:02:40] Traits to sex term...
[INFO] [2022-08-03 17:02:40] Traits to lifestage term...
[INFO] [2022-08-03 17:02:40] MetaTraits to traits...
[INFO] [2022-08-03 17:02:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:02:40] Assocs to occurrences...
[INFO] [2022-08-03 17:02:40] Assocs to nodes...
[INFO] [2022-08-03 17:02:40] Assoc to sex term...
[INFO] [2022-08-03 17:02:40] Assoc to lifestage term...
[INFO] [2022-08-03 17:02:40] MetaAssoc to assocs...
[STOP] [2022-08-03 17:02:40] resolve_keys
[START] [2022-08-03 17:02:40] hold_for_later_1
[STOP] [2022-08-03 17:02:40] hold_for_later_1
[START] [2022-08-03 17:02:40] hold_for_later_2
[STOP] [2022-08-03 17:02:40] hold_for_later_2
[START] [2022-08-03 17:02:40] resolve_missing_parents
[STOP] [2022-08-03 17:02:40] resolve_missing_parents
[START] [2022-08-03 17:02:40] rebuild_nodes
[START] [2022-08-03 17:02:40] Flattener#flatten
[START] [2022-08-03 17:02:40] Flattener#study_resource
[START] [2022-08-03 17:02:40] Flattener#build_ancestry
[STOP] [2022-08-03 17:02:40] Flattener#build_ancestry
[INFO] [2022-08-03 17:02:40] 4 ancestry keys
[START] [2022-08-03 17:02:40] build_node_ancestors
[INFO] [2022-08-03 17:02:40] old ancestors deleted.
[STOP] [2022-08-03 17:02:40] build_node_ancestors
[WARN] [2022-08-03 17:02:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:02:40] Flattener#flatten
[STOP] [2022-08-03 17:02:40] rebuild_nodes
[START] [2022-08-03 17:02:40] resolve_missing_media_owners
[STOP] [2022-08-03 17:02:40] resolve_missing_media_owners
[START] [2022-08-03 17:02:40] sanitize_media_verbatims
[STOP] [2022-08-03 17:02:40] sanitize_media_verbatims
[START] [2022-08-03 17:02:40] queue_downloads
[STOP] [2022-08-03 17:02:40] queue_downloads
[START] [2022-08-03 17:02:40] parse_names
[WARN] [2022-08-03 17:02:40] I see 4 names which still need to be parsed.
[WARN] [2022-08-03 17:02:40] Names to parse: 4 formatted: 4 learned: 4 parsed: 4
[STOP] [2022-08-03 17:02:41] parse_names
[START] [2022-08-03 17:02:41] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:02:41] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:02:41] match_nodes
[START] [2022-08-03 17:02:41] map_all_nodes_to_pages
[STOP] [2022-08-03 17:02:41] map_all_nodes_to_pages
[INFO] [2022-08-03 17:02:41] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2022-08-03 17:02:41] update_nodes
[STOP] [2022-08-03 17:02:41] update_nodes
[STOP] [2022-08-03 17:02:41] match_nodes
[START] [2022-08-03 17:02:41] reindex_search
[STOP] [2022-08-03 17:02:41] reindex_search
[START] [2022-08-03 17:02:41] normalize_units
[STOP] [2022-08-03 17:02:41] normalize_units
[START] [2022-08-03 17:02:41] calculate_statistics
[2022-08-03 17:02:41] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:02:41] Duplicate page_id count: 0
[STOP] [2022-08-03 17:02:41] calculate_statistics
[START] [2022-08-03 17:02:41] complete_harvest_instance
[START] [2022-08-03 17:02:41] overall_tsv_creation
[INFO] [2022-08-03 17:02:41] Exporting 4 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:02:41] Processing group of 4 in 1 batches of 10000
[INFO] [2022-08-03 17:03:24] 4 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:03:24] Building Traits map for 4 nodes (this can take a while)...
[INFO] [2022-08-03 17:04:18] Mapped 4 traits (4 meta) for 4 nodes.
[INFO] [2022-08-03 17:04:18] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:04:18] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:04:19] Adding 4 traits...
[INFO] [2022-08-03 17:04:19] 1 metadata added.
[INFO] [2022-08-03 17:04:19] Adding 0 assocs...
[INFO] [2022-08-03 17:04:19] 0 metadata added.
[INFO] [2022-08-03 17:05:02] Processed 4/4 nodes
[INFO] [2022-08-03 17:05:02] Average Time: 115.09
[INFO] [2022-08-03 17:05:02] Total Time: 2m21s
[STOP] [2022-08-03 17:05:02] overall_tsv_creation
[INFO] [2022-08-03 17:05:02] Done. Check your files:
[INFO] [2022-08-03 17:05:02] (4 lines) /app/public/data/francis_francis_/publish_nodes.tsv
[INFO] [2022-08-03 17:05:02] (4 lines) /app/public/data/francis_francis_/publish_scientific_names.tsv
[INFO] [2022-08-03 17:05:02] (5 lines) /app/public/data/francis_francis_/publish_traits.tsv
[INFO] [2022-08-03 17:05:02] (2 lines) /app/public/data/francis_francis_/publish_metadata.tsv
[STOP] [2022-08-03 17:05:02] complete_harvest_instance
[START] [2022-08-03 17:05:02] completed
[STOP] [2022-08-03 17:05:02] completed
[STOP] [2022-08-03 17:05:02] logged process, took 149.96
Latest Process

03 Aug 17:02 EXITED currently processing 0