Harvest for Pettibone 1982 Created 03 Aug 16:11

Stage: completed
Fetched: 03 Aug 16:11
Validated: 03 Aug 16:11
Deltas Created 03 Aug 16:11
Units Normalized: 03 Aug 16:11
Ancestry Built: 03 Aug 16:11
Nodes Matched: 03 Aug 16:11
Names Parsed: 03 Aug 16:11
New Models Stored: 03 Aug 16:11
Indexed: 03 Aug 16:11
Completed: 03 Aug 16:13
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:11:07] Created harvest instance #4164
[STOP] [2022-08-03 16:11:07] create_harvest_instance
[START] [2022-08-03 16:11:07] fetch_files
[STOP] [2022-08-03 16:11:07] fetch_files
[START] [2022-08-03 16:11:07] validate_each_file
[INFO] [2022-08-03 16:11:07] Looping over 3 formats...
[INFO] [2022-08-03 16:11:07] ...nodes (/app/public/data/pettibone_pettib/taxa.txt)
[INFO] [2022-08-03 16:11:07] Valid: /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_nodes_29555.csv (32 lines)
[INFO] [2022-08-03 16:11:07] ...occurrences (/app/public/data/pettibone_pettib/occurrences.txt)
[INFO] [2022-08-03 16:11:07] Valid: /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_occurrences_29556.csv (32 lines)
[INFO] [2022-08-03 16:11:07] ...measurements (/app/public/data/pettibone_pettib/measurementOrFact.txt)
[INFO] [2022-08-03 16:11:07] Valid: /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_measurements_29557.csv (76 lines)
[STOP] [2022-08-03 16:11:07] validate_each_file
[START] [2022-08-03 16:11:07] convert_to_csv
[INFO] [2022-08-03 16:11:07] Looping over 3 formats...
[INFO] [2022-08-03 16:11:07] ...nodes (/app/public/data/pettibone_pettib/taxa.txt)
[CMD] [2022-08-03 16:11:07] /usr/bin/sort /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_nodes_29555.csv > /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_nodes_29555.csv_sorted
[INFO] [2022-08-03 16:11:07] Converted: /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_nodes_29555.csv (32 lines)
[INFO] [2022-08-03 16:11:07] ...occurrences (/app/public/data/pettibone_pettib/occurrences.txt)
[CMD] [2022-08-03 16:11:07] /usr/bin/sort /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_occurrences_29556.csv > /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_occurrences_29556.csv_sorted
[INFO] [2022-08-03 16:11:07] Converted: /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_occurrences_29556.csv (32 lines)
[INFO] [2022-08-03 16:11:07] ...measurements (/app/public/data/pettibone_pettib/measurementOrFact.txt)
[CMD] [2022-08-03 16:11:07] /usr/bin/sort /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_measurements_29557.csv > /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_measurements_29557.csv_sorted
[INFO] [2022-08-03 16:11:07] Converted: /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_measurements_29557.csv (76 lines)
[STOP] [2022-08-03 16:11:07] convert_to_csv
[START] [2022-08-03 16:11:07] calculate_delta
[INFO] [2022-08-03 16:11:07] Looping over 3 formats...
[INFO] [2022-08-03 16:11:07] ...nodes (/app/public/data/pettibone_pettib/taxa.txt)
[CMD] [2022-08-03 16:11:07] echo "0a" > /app/public/data/pettibone_pettib/diff/pettibone_pettib_nodes_29555.diff
[CMD] [2022-08-03 16:11:07] tail -n +1 /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_nodes_29555.csv >> /app/public/data/pettibone_pettib/diff/pettibone_pettib_nodes_29555.diff
[CMD] [2022-08-03 16:11:07] echo "." >> /app/public/data/pettibone_pettib/diff/pettibone_pettib_nodes_29555.diff
[INFO] [2022-08-03 16:11:07] Created diff: /app/public/data/pettibone_pettib/diff/pettibone_pettib_nodes_29555.diff (34 lines)
[INFO] [2022-08-03 16:11:07] ...occurrences (/app/public/data/pettibone_pettib/occurrences.txt)
[CMD] [2022-08-03 16:11:07] echo "0a" > /app/public/data/pettibone_pettib/diff/pettibone_pettib_occurrences_29556.diff
[CMD] [2022-08-03 16:11:07] tail -n +1 /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_occurrences_29556.csv >> /app/public/data/pettibone_pettib/diff/pettibone_pettib_occurrences_29556.diff
[CMD] [2022-08-03 16:11:07] echo "." >> /app/public/data/pettibone_pettib/diff/pettibone_pettib_occurrences_29556.diff
[INFO] [2022-08-03 16:11:07] Created diff: /app/public/data/pettibone_pettib/diff/pettibone_pettib_occurrences_29556.diff (34 lines)
[INFO] [2022-08-03 16:11:07] ...measurements (/app/public/data/pettibone_pettib/measurementOrFact.txt)
[CMD] [2022-08-03 16:11:07] echo "0a" > /app/public/data/pettibone_pettib/diff/pettibone_pettib_measurements_29557.diff
[CMD] [2022-08-03 16:11:07] tail -n +1 /app/public/data/pettibone_pettib/converted_csv/pettibone_pettib_measurements_29557.csv >> /app/public/data/pettibone_pettib/diff/pettibone_pettib_measurements_29557.diff
[CMD] [2022-08-03 16:11:07] echo "." >> /app/public/data/pettibone_pettib/diff/pettibone_pettib_measurements_29557.diff
[INFO] [2022-08-03 16:11:07] Created diff: /app/public/data/pettibone_pettib/diff/pettibone_pettib_measurements_29557.diff (78 lines)
[STOP] [2022-08-03 16:11:07] calculate_delta
[START] [2022-08-03 16:11:07] parse_diff_and_store
[INFO] [2022-08-03 16:11:07] Handling diff: /app/public/data/pettibone_pettib/diff/pettibone_pettib_nodes_29555.diff (34 lines)
[INFO] [2022-08-03 16:11:07] Loading nodes diff file into memory (34 lines)...
[INFO] [2022-08-03 16:11:07] Storing 32 ScientificNames (64/32/34)
[INFO] [2022-08-03 16:11:07] Storing 32 Nodes (64/32/34)
[INFO] [2022-08-03 16:11:07] Handling diff: /app/public/data/pettibone_pettib/diff/pettibone_pettib_occurrences_29556.diff (34 lines)
[INFO] [2022-08-03 16:11:07] Loading occurrences diff file into memory (34 lines)...
[INFO] [2022-08-03 16:11:07] Storing 32 Occurrences (32/32/34)
[INFO] [2022-08-03 16:11:07] Handling diff: /app/public/data/pettibone_pettib/diff/pettibone_pettib_measurements_29557.diff (78 lines)
[INFO] [2022-08-03 16:11:07] Loading measurements diff file into memory (78 lines)...
[INFO] [2022-08-03 16:11:07] Storing 76 Traits (115/76/78)
[INFO] [2022-08-03 16:11:07] Storing 39 MetaTraits (115/76/78)
[STOP] [2022-08-03 16:11:07] parse_diff_and_store
[START] [2022-08-03 16:11:07] resolve_keys
[2022-08-03 16:11:08] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:11:15] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:11:15] traits to occurrences...
[INFO] [2022-08-03 16:11:15] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:11:15] Traits to sex term...
[INFO] [2022-08-03 16:11:15] Traits to lifestage term...
[INFO] [2022-08-03 16:11:15] MetaTraits to traits...
[INFO] [2022-08-03 16:11:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:11:15] Assocs to occurrences...
[INFO] [2022-08-03 16:11:15] Assocs to nodes...
[INFO] [2022-08-03 16:11:15] Assoc to sex term...
[INFO] [2022-08-03 16:11:15] Assoc to lifestage term...
[INFO] [2022-08-03 16:11:15] MetaAssoc to assocs...
[STOP] [2022-08-03 16:11:15] resolve_keys
[START] [2022-08-03 16:11:15] hold_for_later_1
[STOP] [2022-08-03 16:11:15] hold_for_later_1
[START] [2022-08-03 16:11:15] hold_for_later_2
[STOP] [2022-08-03 16:11:15] hold_for_later_2
[START] [2022-08-03 16:11:15] resolve_missing_parents
[STOP] [2022-08-03 16:11:15] resolve_missing_parents
[START] [2022-08-03 16:11:15] rebuild_nodes
[START] [2022-08-03 16:11:15] Flattener#flatten
[START] [2022-08-03 16:11:15] Flattener#study_resource
[START] [2022-08-03 16:11:15] Flattener#build_ancestry
[STOP] [2022-08-03 16:11:15] Flattener#build_ancestry
[INFO] [2022-08-03 16:11:15] 32 ancestry keys
[START] [2022-08-03 16:11:15] build_node_ancestors
[INFO] [2022-08-03 16:11:15] old ancestors deleted.
[STOP] [2022-08-03 16:11:15] build_node_ancestors
[WARN] [2022-08-03 16:11:15] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:11:15] Flattener#flatten
[STOP] [2022-08-03 16:11:15] rebuild_nodes
[START] [2022-08-03 16:11:15] resolve_missing_media_owners
[STOP] [2022-08-03 16:11:15] resolve_missing_media_owners
[START] [2022-08-03 16:11:15] sanitize_media_verbatims
[STOP] [2022-08-03 16:11:15] sanitize_media_verbatims
[START] [2022-08-03 16:11:15] queue_downloads
[STOP] [2022-08-03 16:11:15] queue_downloads
[START] [2022-08-03 16:11:15] parse_names
[WARN] [2022-08-03 16:11:15] I see 32 names which still need to be parsed.
[WARN] [2022-08-03 16:11:15] Names to parse: 32 formatted: 32 learned: 32 parsed: 32
[STOP] [2022-08-03 16:11:16] parse_names
[START] [2022-08-03 16:11:16] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:11:16] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:11:16] match_nodes
[START] [2022-08-03 16:11:16] map_all_nodes_to_pages
[STOP] [2022-08-03 16:11:17] map_all_nodes_to_pages
[INFO] [2022-08-03 16:11:17] ZERO unmatched nodes (of 32)! Nicely done.
[START] [2022-08-03 16:11:17] update_nodes
[STOP] [2022-08-03 16:11:17] update_nodes
[STOP] [2022-08-03 16:11:17] match_nodes
[START] [2022-08-03 16:11:17] reindex_search
[STOP] [2022-08-03 16:11:18] reindex_search
[START] [2022-08-03 16:11:18] normalize_units
[STOP] [2022-08-03 16:11:18] normalize_units
[START] [2022-08-03 16:11:18] calculate_statistics
[2022-08-03 16:11:18] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:11:21] Duplicate page_id count: 0
[STOP] [2022-08-03 16:11:21] calculate_statistics
[START] [2022-08-03 16:11:21] complete_harvest_instance
[START] [2022-08-03 16:11:21] overall_tsv_creation
[INFO] [2022-08-03 16:11:21] Exporting 32 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:11:21] Processing group of 32 in 1 batches of 10000
[INFO] [2022-08-03 16:12:04] 38 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:12:04] Building Traits map for 32 nodes (this can take a while)...
[INFO] [2022-08-03 16:12:58] Mapped 38 traits (39 meta) for 32 nodes.
[INFO] [2022-08-03 16:12:58] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:12:58] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:12:58] Adding 38 traits...
[INFO] [2022-08-03 16:12:58] 38 metadata added.
[INFO] [2022-08-03 16:12:58] Adding 0 assocs...
[INFO] [2022-08-03 16:12:58] 0 metadata added.
[INFO] [2022-08-03 16:13:41] Processed 32/32 nodes
[INFO] [2022-08-03 16:13:41] Average Time: 113.68
[INFO] [2022-08-03 16:13:41] Total Time: 2m20s
[STOP] [2022-08-03 16:13:41] overall_tsv_creation
[INFO] [2022-08-03 16:13:41] Done. Check your files:
[INFO] [2022-08-03 16:13:41] (32 lines) /app/public/data/pettibone_pettib/publish_nodes.tsv
[INFO] [2022-08-03 16:13:41] (32 lines) /app/public/data/pettibone_pettib/publish_scientific_names.tsv
[INFO] [2022-08-03 16:13:41] (39 lines) /app/public/data/pettibone_pettib/publish_traits.tsv
[INFO] [2022-08-03 16:13:41] (39 lines) /app/public/data/pettibone_pettib/publish_metadata.tsv
[STOP] [2022-08-03 16:13:41] complete_harvest_instance
[START] [2022-08-03 16:13:41] completed
[STOP] [2022-08-03 16:13:41] completed
[STOP] [2022-08-03 16:13:41] logged process, took 154.32
Latest Process

03 Aug 16:11 EXITED currently processing 0