Harvest for NEWMAN AND CANNON, 1997 Created 31 Jan 12:31

Harvesting Log

[INFO] [2023-01-31 12:31:27] Created harvest instance #4291
[STOP] [2023-01-31 12:31:27] create_harvest_instance
[START] [2023-01-31 12:31:27] fetch_files
[STOP] [2023-01-31 12:31:27] fetch_files
[START] [2023-01-31 12:31:27] validate_each_file
[INFO] [2023-01-31 12:31:27] Looping over 3 formats...
[INFO] [2023-01-31 12:31:27] ...nodes (/app/public/data/newman_and_canno/taxa.tsv)
[INFO] [2023-01-31 12:31:27] Valid: /app/public/data/newman_and_canno/converted_csv/newman_and_canno_nodes_30176.csv (1 lines)
[INFO] [2023-01-31 12:31:27] ...occurrences (/app/public/data/newman_and_canno/occurrences.tsv)
[INFO] [2023-01-31 12:31:27] Valid: /app/public/data/newman_and_canno/converted_csv/newman_and_canno_occurrences_30177.csv (1 lines)
[INFO] [2023-01-31 12:31:27] ...measurements (/app/public/data/newman_and_canno/measurementOrFact.tsv)
[INFO] [2023-01-31 12:31:27] Valid: /app/public/data/newman_and_canno/converted_csv/newman_and_canno_measurements_30178.csv (1 lines)
[STOP] [2023-01-31 12:31:27] validate_each_file
[START] [2023-01-31 12:31:27] convert_to_csv
[INFO] [2023-01-31 12:31:27] Looping over 3 formats...
[INFO] [2023-01-31 12:31:27] ...nodes (/app/public/data/newman_and_canno/taxa.tsv)
[CMD] [2023-01-31 12:31:27] /usr/bin/sort /app/public/data/newman_and_canno/converted_csv/newman_and_canno_nodes_30176.csv > /app/public/data/newman_and_canno/converted_csv/newman_and_canno_nodes_30176.csv_sorted
[INFO] [2023-01-31 12:31:27] Converted: /app/public/data/newman_and_canno/converted_csv/newman_and_canno_nodes_30176.csv (1 lines)
[INFO] [2023-01-31 12:31:27] ...occurrences (/app/public/data/newman_and_canno/occurrences.tsv)
[CMD] [2023-01-31 12:31:27] /usr/bin/sort /app/public/data/newman_and_canno/converted_csv/newman_and_canno_occurrences_30177.csv > /app/public/data/newman_and_canno/converted_csv/newman_and_canno_occurrences_30177.csv_sorted
[INFO] [2023-01-31 12:31:27] Converted: /app/public/data/newman_and_canno/converted_csv/newman_and_canno_occurrences_30177.csv (1 lines)
[INFO] [2023-01-31 12:31:27] ...measurements (/app/public/data/newman_and_canno/measurementOrFact.tsv)
[CMD] [2023-01-31 12:31:27] /usr/bin/sort /app/public/data/newman_and_canno/converted_csv/newman_and_canno_measurements_30178.csv > /app/public/data/newman_and_canno/converted_csv/newman_and_canno_measurements_30178.csv_sorted
[INFO] [2023-01-31 12:31:27] Converted: /app/public/data/newman_and_canno/converted_csv/newman_and_canno_measurements_30178.csv (1 lines)
[STOP] [2023-01-31 12:31:27] convert_to_csv
[START] [2023-01-31 12:31:27] calculate_delta
[INFO] [2023-01-31 12:31:27] Looping over 3 formats...
[INFO] [2023-01-31 12:31:27] ...nodes (/app/public/data/newman_and_canno/taxa.tsv)
[CMD] [2023-01-31 12:31:27] echo "0a" > /app/public/data/newman_and_canno/diff/newman_and_canno_nodes_30176.diff
[CMD] [2023-01-31 12:31:27] tail -n +1 /app/public/data/newman_and_canno/converted_csv/newman_and_canno_nodes_30176.csv >> /app/public/data/newman_and_canno/diff/newman_and_canno_nodes_30176.diff
[CMD] [2023-01-31 12:31:27] echo "." >> /app/public/data/newman_and_canno/diff/newman_and_canno_nodes_30176.diff
[INFO] [2023-01-31 12:31:27] Created diff: /app/public/data/newman_and_canno/diff/newman_and_canno_nodes_30176.diff (3 lines)
[INFO] [2023-01-31 12:31:27] ...occurrences (/app/public/data/newman_and_canno/occurrences.tsv)
[CMD] [2023-01-31 12:31:27] echo "0a" > /app/public/data/newman_and_canno/diff/newman_and_canno_occurrences_30177.diff
[CMD] [2023-01-31 12:31:27] tail -n +1 /app/public/data/newman_and_canno/converted_csv/newman_and_canno_occurrences_30177.csv >> /app/public/data/newman_and_canno/diff/newman_and_canno_occurrences_30177.diff
[CMD] [2023-01-31 12:31:27] echo "." >> /app/public/data/newman_and_canno/diff/newman_and_canno_occurrences_30177.diff
[INFO] [2023-01-31 12:31:27] Created diff: /app/public/data/newman_and_canno/diff/newman_and_canno_occurrences_30177.diff (3 lines)
[INFO] [2023-01-31 12:31:27] ...measurements (/app/public/data/newman_and_canno/measurementOrFact.tsv)
[CMD] [2023-01-31 12:31:27] echo "0a" > /app/public/data/newman_and_canno/diff/newman_and_canno_measurements_30178.diff
[CMD] [2023-01-31 12:31:27] tail -n +1 /app/public/data/newman_and_canno/converted_csv/newman_and_canno_measurements_30178.csv >> /app/public/data/newman_and_canno/diff/newman_and_canno_measurements_30178.diff
[CMD] [2023-01-31 12:31:27] echo "." >> /app/public/data/newman_and_canno/diff/newman_and_canno_measurements_30178.diff
[INFO] [2023-01-31 12:31:27] Created diff: /app/public/data/newman_and_canno/diff/newman_and_canno_measurements_30178.diff (3 lines)
[STOP] [2023-01-31 12:31:27] calculate_delta
[START] [2023-01-31 12:31:27] parse_diff_and_store
[INFO] [2023-01-31 12:31:27] Handling diff: /app/public/data/newman_and_canno/diff/newman_and_canno_nodes_30176.diff (3 lines)
[INFO] [2023-01-31 12:31:27] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-01-31 12:31:27] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-01-31 12:31:27] Storing 1 Nodes (2/1/3)
[INFO] [2023-01-31 12:31:27] Handling diff: /app/public/data/newman_and_canno/diff/newman_and_canno_occurrences_30177.diff (3 lines)
[INFO] [2023-01-31 12:31:27] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-01-31 12:31:27] Storing 1 Occurrences (1/1/3)
[INFO] [2023-01-31 12:31:27] Handling diff: /app/public/data/newman_and_canno/diff/newman_and_canno_measurements_30178.diff (3 lines)
[INFO] [2023-01-31 12:31:27] Loading measurements diff file into memory (3 lines)...
[INFO] [2023-01-31 12:31:27] Storing 1 Traits (2/1/3)
[INFO] [2023-01-31 12:31:27] Storing 1 MetaTraits (2/1/3)
[STOP] [2023-01-31 12:31:27] parse_diff_and_store
[START] [2023-01-31 12:31:27] resolve_keys
[2023-01-31 12:31:27] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 12:31:35] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 12:31:35] traits to occurrences...
[INFO] [2023-01-31 12:31:35] traits to nodes (through occurrences)...
[INFO] [2023-01-31 12:31:35] Traits to sex term...
[INFO] [2023-01-31 12:31:35] Traits to lifestage term...
[INFO] [2023-01-31 12:31:35] MetaTraits to traits...
[INFO] [2023-01-31 12:31:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 12:31:35] Assocs to occurrences...
[INFO] [2023-01-31 12:31:35] Assocs to nodes...
[INFO] [2023-01-31 12:31:35] Assoc to sex term...
[INFO] [2023-01-31 12:31:35] Assoc to lifestage term...
[INFO] [2023-01-31 12:31:35] MetaAssoc to assocs...
[STOP] [2023-01-31 12:31:35] resolve_keys
[START] [2023-01-31 12:31:35] hold_for_later_1
[STOP] [2023-01-31 12:31:35] hold_for_later_1
[START] [2023-01-31 12:31:35] hold_for_later_2
[STOP] [2023-01-31 12:31:35] hold_for_later_2
[START] [2023-01-31 12:31:35] resolve_missing_parents
[STOP] [2023-01-31 12:31:35] resolve_missing_parents
[START] [2023-01-31 12:31:35] rebuild_nodes
[START] [2023-01-31 12:31:35] Flattener#flatten
[START] [2023-01-31 12:31:35] Flattener#study_resource
[START] [2023-01-31 12:31:35] Flattener#build_ancestry
[STOP] [2023-01-31 12:31:35] Flattener#build_ancestry
[INFO] [2023-01-31 12:31:35] 1 ancestry keys
[START] [2023-01-31 12:31:35] build_node_ancestors
[INFO] [2023-01-31 12:31:35] old ancestors deleted.
[STOP] [2023-01-31 12:31:35] build_node_ancestors
[WARN] [2023-01-31 12:31:35] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-31 12:31:35] Flattener#flatten
[STOP] [2023-01-31 12:31:35] rebuild_nodes
[START] [2023-01-31 12:31:35] resolve_missing_media_owners
[STOP] [2023-01-31 12:31:35] resolve_missing_media_owners
[START] [2023-01-31 12:31:35] sanitize_media_verbatims
[STOP] [2023-01-31 12:31:35] sanitize_media_verbatims
[START] [2023-01-31 12:31:35] queue_downloads
[STOP] [2023-01-31 12:31:35] queue_downloads
[START] [2023-01-31 12:31:35] parse_names
[WARN] [2023-01-31 12:31:35] I see 1 names which still need to be parsed.
[WARN] [2023-01-31 12:31:35] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-01-31 12:31:36] parse_names
[START] [2023-01-31 12:31:36] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 12:31:36] denormalize_canonical_names_to_nodes
[START] [2023-01-31 12:31:36] match_nodes
[START] [2023-01-31 12:31:36] map_all_nodes_to_pages
[STOP] [2023-01-31 12:31:36] map_all_nodes_to_pages
[INFO] [2023-01-31 12:31:36] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-01-31 12:31:36] update_nodes
[STOP] [2023-01-31 12:31:36] update_nodes
[STOP] [2023-01-31 12:31:36] match_nodes
[START] [2023-01-31 12:31:36] reindex_search
[STOP] [2023-01-31 12:31:36] reindex_search
[START] [2023-01-31 12:31:36] normalize_units
[STOP] [2023-01-31 12:31:36] normalize_units
[START] [2023-01-31 12:31:36] calculate_statistics
[2023-01-31 12:31:36] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-31 12:31:36] Duplicate page_id count: 0
[STOP] [2023-01-31 12:31:36] calculate_statistics
[START] [2023-01-31 12:31:36] complete_harvest_instance
[START] [2023-01-31 12:31:36] overall_tsv_creation
[INFO] [2023-01-31 12:31:36] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 12:31:36] Processing group of 1 in 1 batches of 10000
[INFO] [2023-01-31 12:31:36] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 12:31:36] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-01-31 12:31:36] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2023-01-31 12:31:36] Building Associations map (this can take a while)...
[INFO] [2023-01-31 12:31:36] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 12:31:36] Adding 1 traits...
[INFO] [2023-01-31 12:31:36] 0 metadata added.
[INFO] [2023-01-31 12:31:36] Adding 0 assocs...
[INFO] [2023-01-31 12:31:36] 0 metadata added.
[INFO] [2023-01-31 12:32:21] Processed 1/1 nodes
[INFO] [2023-01-31 12:32:21] Average Time: 44.94
[INFO] [2023-01-31 12:32:21] Total Time: 45s
[STOP] [2023-01-31 12:32:21] overall_tsv_creation
[INFO] [2023-01-31 12:32:21] Done. Check your files:
[INFO] [2023-01-31 12:32:21] (1 lines) /app/public/data/newman_and_canno/publish_nodes.tsv
[INFO] [2023-01-31 12:32:21] (1 lines) /app/public/data/newman_and_canno/publish_scientific_names.tsv
[INFO] [2023-01-31 12:32:21] (2 lines) /app/public/data/newman_and_canno/publish_traits.tsv
[INFO] [2023-01-31 12:32:21] (1 lines) /app/public/data/newman_and_canno/publish_metadata.tsv
[STOP] [2023-01-31 12:32:21] complete_harvest_instance
[START] [2023-01-31 12:32:21] completed
[STOP] [2023-01-31 12:32:21] completed
[STOP] [2023-01-31 12:32:21] logged process, took 54.47

Latest Process

31 Jan 12:29 EXITED currently processing 0