Harvest for Saunders 2002 Created 19 Jan 14:27

Stage: completed
Fetched: 19 Jan 14:27
Validated: 19 Jan 14:27
Deltas Created 19 Jan 14:27
Units Normalized: 19 Jan 14:28
Ancestry Built: 19 Jan 14:28
Nodes Matched: 19 Jan 14:28
Names Parsed: 19 Jan 14:28
New Models Stored: 19 Jan 14:27
Indexed: 19 Jan 14:28
Completed: 19 Jan 14:28
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2023-01-19 14:27:50] Created harvest instance #4258
[STOP] [2023-01-19 14:27:50] create_harvest_instance
[START] [2023-01-19 14:27:50] fetch_files
[STOP] [2023-01-19 14:27:50] fetch_files
[START] [2023-01-19 14:27:50] validate_each_file
[INFO] [2023-01-19 14:27:50] Looping over 3 formats...
[INFO] [2023-01-19 14:27:50] ...nodes (/app/public/data/saunders_saunder/taxa.txt)
[INFO] [2023-01-19 14:27:50] Valid: /app/public/data/saunders_saunder/converted_csv/saunders_saunder_nodes_30022.csv (5 lines)
[INFO] [2023-01-19 14:27:50] ...occurrences (/app/public/data/saunders_saunder/occurrences.txt)
[INFO] [2023-01-19 14:27:52] Valid: /app/public/data/saunders_saunder/converted_csv/saunders_saunder_occurrences_30023.csv (5 lines)
[INFO] [2023-01-19 14:27:52] ...measurements (/app/public/data/saunders_saunder/measurementsorfacts.txt)
[INFO] [2023-01-19 14:27:52] Valid: /app/public/data/saunders_saunder/converted_csv/saunders_saunder_measurements_30024.csv (36 lines)
[STOP] [2023-01-19 14:27:52] validate_each_file
[START] [2023-01-19 14:27:52] convert_to_csv
[INFO] [2023-01-19 14:27:52] Looping over 3 formats...
[INFO] [2023-01-19 14:27:52] ...nodes (/app/public/data/saunders_saunder/taxa.txt)
[CMD] [2023-01-19 14:27:52] /usr/bin/sort /app/public/data/saunders_saunder/converted_csv/saunders_saunder_nodes_30022.csv > /app/public/data/saunders_saunder/converted_csv/saunders_saunder_nodes_30022.csv_sorted
[INFO] [2023-01-19 14:27:52] Converted: /app/public/data/saunders_saunder/converted_csv/saunders_saunder_nodes_30022.csv (5 lines)
[INFO] [2023-01-19 14:27:52] ...occurrences (/app/public/data/saunders_saunder/occurrences.txt)
[CMD] [2023-01-19 14:27:52] /usr/bin/sort /app/public/data/saunders_saunder/converted_csv/saunders_saunder_occurrences_30023.csv > /app/public/data/saunders_saunder/converted_csv/saunders_saunder_occurrences_30023.csv_sorted
[INFO] [2023-01-19 14:27:52] Converted: /app/public/data/saunders_saunder/converted_csv/saunders_saunder_occurrences_30023.csv (5 lines)
[INFO] [2023-01-19 14:27:52] ...measurements (/app/public/data/saunders_saunder/measurementsorfacts.txt)
[CMD] [2023-01-19 14:27:52] /usr/bin/sort /app/public/data/saunders_saunder/converted_csv/saunders_saunder_measurements_30024.csv > /app/public/data/saunders_saunder/converted_csv/saunders_saunder_measurements_30024.csv_sorted
[INFO] [2023-01-19 14:27:52] Converted: /app/public/data/saunders_saunder/converted_csv/saunders_saunder_measurements_30024.csv (36 lines)
[STOP] [2023-01-19 14:27:52] convert_to_csv
[START] [2023-01-19 14:27:52] calculate_delta
[INFO] [2023-01-19 14:27:52] Looping over 3 formats...
[INFO] [2023-01-19 14:27:52] ...nodes (/app/public/data/saunders_saunder/taxa.txt)
[CMD] [2023-01-19 14:27:52] echo "0a" > /app/public/data/saunders_saunder/diff/saunders_saunder_nodes_30022.diff
[CMD] [2023-01-19 14:27:52] tail -n +1 /app/public/data/saunders_saunder/converted_csv/saunders_saunder_nodes_30022.csv >> /app/public/data/saunders_saunder/diff/saunders_saunder_nodes_30022.diff
[CMD] [2023-01-19 14:27:52] echo "." >> /app/public/data/saunders_saunder/diff/saunders_saunder_nodes_30022.diff
[INFO] [2023-01-19 14:27:52] Created diff: /app/public/data/saunders_saunder/diff/saunders_saunder_nodes_30022.diff (7 lines)
[INFO] [2023-01-19 14:27:52] ...occurrences (/app/public/data/saunders_saunder/occurrences.txt)
[CMD] [2023-01-19 14:27:52] echo "0a" > /app/public/data/saunders_saunder/diff/saunders_saunder_occurrences_30023.diff
[CMD] [2023-01-19 14:27:52] tail -n +1 /app/public/data/saunders_saunder/converted_csv/saunders_saunder_occurrences_30023.csv >> /app/public/data/saunders_saunder/diff/saunders_saunder_occurrences_30023.diff
[CMD] [2023-01-19 14:27:52] echo "." >> /app/public/data/saunders_saunder/diff/saunders_saunder_occurrences_30023.diff
[INFO] [2023-01-19 14:27:52] Created diff: /app/public/data/saunders_saunder/diff/saunders_saunder_occurrences_30023.diff (7 lines)
[INFO] [2023-01-19 14:27:52] ...measurements (/app/public/data/saunders_saunder/measurementsorfacts.txt)
[CMD] [2023-01-19 14:27:52] echo "0a" > /app/public/data/saunders_saunder/diff/saunders_saunder_measurements_30024.diff
[CMD] [2023-01-19 14:27:52] tail -n +1 /app/public/data/saunders_saunder/converted_csv/saunders_saunder_measurements_30024.csv >> /app/public/data/saunders_saunder/diff/saunders_saunder_measurements_30024.diff
[CMD] [2023-01-19 14:27:52] echo "." >> /app/public/data/saunders_saunder/diff/saunders_saunder_measurements_30024.diff
[INFO] [2023-01-19 14:27:52] Created diff: /app/public/data/saunders_saunder/diff/saunders_saunder_measurements_30024.diff (38 lines)
[STOP] [2023-01-19 14:27:52] calculate_delta
[START] [2023-01-19 14:27:52] parse_diff_and_store
[INFO] [2023-01-19 14:27:52] Handling diff: /app/public/data/saunders_saunder/diff/saunders_saunder_nodes_30022.diff (7 lines)
[INFO] [2023-01-19 14:27:52] Loading nodes diff file into memory (7 lines)...
[INFO] [2023-01-19 14:27:52] Storing 5 ScientificNames (10/5/7)
[INFO] [2023-01-19 14:27:52] Storing 5 Nodes (10/5/7)
[INFO] [2023-01-19 14:27:52] Handling diff: /app/public/data/saunders_saunder/diff/saunders_saunder_occurrences_30023.diff (7 lines)
[INFO] [2023-01-19 14:27:52] Loading occurrences diff file into memory (7 lines)...
[INFO] [2023-01-19 14:27:52] Storing 5 Occurrences (9/5/7)
[INFO] [2023-01-19 14:27:52] Storing 4 OccurrenceMetadata (9/5/7)
[INFO] [2023-01-19 14:27:52] Handling diff: /app/public/data/saunders_saunder/diff/saunders_saunder_measurements_30024.diff (38 lines)
[INFO] [2023-01-19 14:27:52] Loading measurements diff file into memory (38 lines)...
[INFO] [2023-01-19 14:27:52] Storing 36 Traits (41/36/38)
[INFO] [2023-01-19 14:27:52] Storing 5 MetaTraits (41/36/38)
[STOP] [2023-01-19 14:27:52] parse_diff_and_store
[START] [2023-01-19 14:27:52] resolve_keys
[2023-01-19 14:27:53] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 14:28:00] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 14:28:00] traits to occurrences...
[INFO] [2023-01-19 14:28:00] traits to nodes (through occurrences)...
[INFO] [2023-01-19 14:28:00] Traits to sex term...
[INFO] [2023-01-19 14:28:00] Traits to lifestage term...
[INFO] [2023-01-19 14:28:00] MetaTraits to traits...
[INFO] [2023-01-19 14:28:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 14:28:00] Assocs to occurrences...
[INFO] [2023-01-19 14:28:00] Assocs to nodes...
[INFO] [2023-01-19 14:28:00] Assoc to sex term...
[INFO] [2023-01-19 14:28:00] Assoc to lifestage term...
[INFO] [2023-01-19 14:28:00] MetaAssoc to assocs...
[STOP] [2023-01-19 14:28:00] resolve_keys
[START] [2023-01-19 14:28:00] hold_for_later_1
[STOP] [2023-01-19 14:28:00] hold_for_later_1
[START] [2023-01-19 14:28:00] hold_for_later_2
[STOP] [2023-01-19 14:28:00] hold_for_later_2
[START] [2023-01-19 14:28:00] resolve_missing_parents
[STOP] [2023-01-19 14:28:00] resolve_missing_parents
[START] [2023-01-19 14:28:00] rebuild_nodes
[START] [2023-01-19 14:28:00] Flattener#flatten
[START] [2023-01-19 14:28:00] Flattener#study_resource
[START] [2023-01-19 14:28:00] Flattener#build_ancestry
[STOP] [2023-01-19 14:28:00] Flattener#build_ancestry
[INFO] [2023-01-19 14:28:00] 5 ancestry keys
[START] [2023-01-19 14:28:00] build_node_ancestors
[INFO] [2023-01-19 14:28:00] old ancestors deleted.
[STOP] [2023-01-19 14:28:00] build_node_ancestors
[WARN] [2023-01-19 14:28:00] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-19 14:28:00] Flattener#flatten
[STOP] [2023-01-19 14:28:00] rebuild_nodes
[START] [2023-01-19 14:28:00] resolve_missing_media_owners
[STOP] [2023-01-19 14:28:00] resolve_missing_media_owners
[START] [2023-01-19 14:28:00] sanitize_media_verbatims
[STOP] [2023-01-19 14:28:00] sanitize_media_verbatims
[START] [2023-01-19 14:28:00] queue_downloads
[STOP] [2023-01-19 14:28:00] queue_downloads
[START] [2023-01-19 14:28:00] parse_names
[WARN] [2023-01-19 14:28:00] I see 5 names which still need to be parsed.
[WARN] [2023-01-19 14:28:00] Names to parse: 5 formatted: 5 learned: 5 parsed: 5
[STOP] [2023-01-19 14:28:01] parse_names
[START] [2023-01-19 14:28:01] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 14:28:01] denormalize_canonical_names_to_nodes
[START] [2023-01-19 14:28:01] match_nodes
[START] [2023-01-19 14:28:01] map_all_nodes_to_pages
[STOP] [2023-01-19 14:28:01] map_all_nodes_to_pages
[INFO] [2023-01-19 14:28:01] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2023-01-19 14:28:01] update_nodes
[STOP] [2023-01-19 14:28:01] update_nodes
[STOP] [2023-01-19 14:28:01] match_nodes
[START] [2023-01-19 14:28:01] reindex_search
[STOP] [2023-01-19 14:28:01] reindex_search
[START] [2023-01-19 14:28:01] normalize_units
[STOP] [2023-01-19 14:28:01] normalize_units
[START] [2023-01-19 14:28:01] calculate_statistics
[2023-01-19 14:28:01] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-19 14:28:01] Duplicate page_id count: 0
[STOP] [2023-01-19 14:28:01] calculate_statistics
[START] [2023-01-19 14:28:01] complete_harvest_instance
[START] [2023-01-19 14:28:01] overall_tsv_creation
[INFO] [2023-01-19 14:28:01] Exporting 5 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 14:28:01] Processing group of 5 in 1 batches of 10000
[INFO] [2023-01-19 14:28:01] 5 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 14:28:01] Building Traits map for 5 nodes (this can take a while)...
[INFO] [2023-01-19 14:28:01] Mapped 5 traits (5 meta) for 5 nodes.
[INFO] [2023-01-19 14:28:01] Building Associations map (this can take a while)...
[INFO] [2023-01-19 14:28:01] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 14:28:03] Adding 5 traits...
[INFO] [2023-01-19 14:28:03] Trait #285041693 in key 285041693 has 28 metadata... that seems high?
[INFO] [2023-01-19 14:28:03] 31 metadata added.
[INFO] [2023-01-19 14:28:03] Adding 0 assocs...
[INFO] [2023-01-19 14:28:03] 0 metadata added.
[INFO] [2023-01-19 14:28:48] Processed 5/5 nodes
[INFO] [2023-01-19 14:28:48] Average Time: 46.12
[INFO] [2023-01-19 14:28:48] Total Time: 47s
[STOP] [2023-01-19 14:28:48] overall_tsv_creation
[INFO] [2023-01-19 14:28:48] Done. Check your files:
[INFO] [2023-01-19 14:28:48] (5 lines) /app/public/data/saunders_saunder/publish_nodes.tsv
[INFO] [2023-01-19 14:28:48] (5 lines) /app/public/data/saunders_saunder/publish_scientific_names.tsv
[INFO] [2023-01-19 14:28:48] (6 lines) /app/public/data/saunders_saunder/publish_traits.tsv
[INFO] [2023-01-19 14:28:48] (32 lines) /app/public/data/saunders_saunder/publish_metadata.tsv
[STOP] [2023-01-19 14:28:48] complete_harvest_instance
[START] [2023-01-19 14:28:48] completed
[STOP] [2023-01-19 14:28:48] completed
[STOP] [2023-01-19 14:28:48] logged process, took 57.42
Latest Process

19 Jan 14:27 EXITED currently processing 0