Harvest for Chia 1966 Created 03 Aug 17:31

Harvesting Log

[INFO] [2022-08-03 17:31:27] Created harvest instance #4201
[STOP] [2022-08-03 17:31:27] create_harvest_instance
[START] [2022-08-03 17:31:27] fetch_files
[STOP] [2022-08-03 17:31:27] fetch_files
[START] [2022-08-03 17:31:27] validate_each_file
[INFO] [2022-08-03 17:31:27] Looping over 3 formats...
[INFO] [2022-08-03 17:31:27] ...nodes (/app/public/data/chia_chia_1966/taxa.txt)
[INFO] [2022-08-03 17:31:27] Valid: /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_nodes_29665.csv (1 lines)
[INFO] [2022-08-03 17:31:27] ...occurrences (/app/public/data/chia_chia_1966/occurrence.txt)
[INFO] [2022-08-03 17:31:27] Valid: /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_occurrences_29666.csv (1 lines)
[INFO] [2022-08-03 17:31:27] ...measurements (/app/public/data/chia_chia_1966/measurementOrFact.txt)
[INFO] [2022-08-03 17:31:27] Valid: /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_measurements_29667.csv (2 lines)
[STOP] [2022-08-03 17:31:27] validate_each_file
[START] [2022-08-03 17:31:27] convert_to_csv
[INFO] [2022-08-03 17:31:27] Looping over 3 formats...
[INFO] [2022-08-03 17:31:27] ...nodes (/app/public/data/chia_chia_1966/taxa.txt)
[CMD] [2022-08-03 17:31:27] /usr/bin/sort /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_nodes_29665.csv > /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_nodes_29665.csv_sorted
[INFO] [2022-08-03 17:31:27] Converted: /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_nodes_29665.csv (1 lines)
[INFO] [2022-08-03 17:31:27] ...occurrences (/app/public/data/chia_chia_1966/occurrence.txt)
[CMD] [2022-08-03 17:31:27] /usr/bin/sort /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_occurrences_29666.csv > /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_occurrences_29666.csv_sorted
[INFO] [2022-08-03 17:31:27] Converted: /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_occurrences_29666.csv (1 lines)
[INFO] [2022-08-03 17:31:27] ...measurements (/app/public/data/chia_chia_1966/measurementOrFact.txt)
[CMD] [2022-08-03 17:31:27] /usr/bin/sort /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_measurements_29667.csv > /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_measurements_29667.csv_sorted
[INFO] [2022-08-03 17:31:27] Converted: /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_measurements_29667.csv (2 lines)
[STOP] [2022-08-03 17:31:27] convert_to_csv
[START] [2022-08-03 17:31:27] calculate_delta
[INFO] [2022-08-03 17:31:27] Looping over 3 formats...
[INFO] [2022-08-03 17:31:27] ...nodes (/app/public/data/chia_chia_1966/taxa.txt)
[CMD] [2022-08-03 17:31:27] echo "0a" > /app/public/data/chia_chia_1966/diff/chia_chia_1966_nodes_29665.diff
[CMD] [2022-08-03 17:31:27] tail -n +1 /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_nodes_29665.csv >> /app/public/data/chia_chia_1966/diff/chia_chia_1966_nodes_29665.diff
[CMD] [2022-08-03 17:31:27] echo "." >> /app/public/data/chia_chia_1966/diff/chia_chia_1966_nodes_29665.diff
[INFO] [2022-08-03 17:31:27] Created diff: /app/public/data/chia_chia_1966/diff/chia_chia_1966_nodes_29665.diff (3 lines)
[INFO] [2022-08-03 17:31:27] ...occurrences (/app/public/data/chia_chia_1966/occurrence.txt)
[CMD] [2022-08-03 17:31:27] echo "0a" > /app/public/data/chia_chia_1966/diff/chia_chia_1966_occurrences_29666.diff
[CMD] [2022-08-03 17:31:27] tail -n +1 /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_occurrences_29666.csv >> /app/public/data/chia_chia_1966/diff/chia_chia_1966_occurrences_29666.diff
[CMD] [2022-08-03 17:31:27] echo "." >> /app/public/data/chia_chia_1966/diff/chia_chia_1966_occurrences_29666.diff
[INFO] [2022-08-03 17:31:27] Created diff: /app/public/data/chia_chia_1966/diff/chia_chia_1966_occurrences_29666.diff (3 lines)
[INFO] [2022-08-03 17:31:27] ...measurements (/app/public/data/chia_chia_1966/measurementOrFact.txt)
[CMD] [2022-08-03 17:31:27] echo "0a" > /app/public/data/chia_chia_1966/diff/chia_chia_1966_measurements_29667.diff
[CMD] [2022-08-03 17:31:27] tail -n +1 /app/public/data/chia_chia_1966/converted_csv/chia_chia_1966_measurements_29667.csv >> /app/public/data/chia_chia_1966/diff/chia_chia_1966_measurements_29667.diff
[CMD] [2022-08-03 17:31:27] echo "." >> /app/public/data/chia_chia_1966/diff/chia_chia_1966_measurements_29667.diff
[INFO] [2022-08-03 17:31:27] Created diff: /app/public/data/chia_chia_1966/diff/chia_chia_1966_measurements_29667.diff (4 lines)
[STOP] [2022-08-03 17:31:27] calculate_delta
[START] [2022-08-03 17:31:27] parse_diff_and_store
[INFO] [2022-08-03 17:31:27] Handling diff: /app/public/data/chia_chia_1966/diff/chia_chia_1966_nodes_29665.diff (3 lines)
[INFO] [2022-08-03 17:31:27] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 17:31:27] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 17:31:27] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 17:31:27] Handling diff: /app/public/data/chia_chia_1966/diff/chia_chia_1966_occurrences_29666.diff (3 lines)
[INFO] [2022-08-03 17:31:27] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 17:31:27] Storing 1 Occurrences (2/1/3)
[INFO] [2022-08-03 17:31:27] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2022-08-03 17:31:27] Handling diff: /app/public/data/chia_chia_1966/diff/chia_chia_1966_measurements_29667.diff (4 lines)
[INFO] [2022-08-03 17:31:27] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 17:31:27] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 17:31:27] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 17:31:27] parse_diff_and_store
[START] [2022-08-03 17:31:27] resolve_keys
[2022-08-03 17:31:27] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:31:34] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:31:34] traits to occurrences...
[INFO] [2022-08-03 17:31:34] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:31:34] Traits to sex term...
[INFO] [2022-08-03 17:31:34] Traits to lifestage term...
[INFO] [2022-08-03 17:31:34] MetaTraits to traits...
[INFO] [2022-08-03 17:31:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:31:34] Assocs to occurrences...
[INFO] [2022-08-03 17:31:34] Assocs to nodes...
[INFO] [2022-08-03 17:31:34] Assoc to sex term...
[INFO] [2022-08-03 17:31:34] Assoc to lifestage term...
[INFO] [2022-08-03 17:31:34] MetaAssoc to assocs...
[STOP] [2022-08-03 17:31:34] resolve_keys
[START] [2022-08-03 17:31:34] hold_for_later_1
[STOP] [2022-08-03 17:31:34] hold_for_later_1
[START] [2022-08-03 17:31:34] hold_for_later_2
[STOP] [2022-08-03 17:31:34] hold_for_later_2
[START] [2022-08-03 17:31:34] resolve_missing_parents
[STOP] [2022-08-03 17:31:34] resolve_missing_parents
[START] [2022-08-03 17:31:34] rebuild_nodes
[START] [2022-08-03 17:31:34] Flattener#flatten
[START] [2022-08-03 17:31:34] Flattener#study_resource
[START] [2022-08-03 17:31:34] Flattener#build_ancestry
[STOP] [2022-08-03 17:31:34] Flattener#build_ancestry
[INFO] [2022-08-03 17:31:34] 1 ancestry keys
[START] [2022-08-03 17:31:34] build_node_ancestors
[INFO] [2022-08-03 17:31:34] old ancestors deleted.
[STOP] [2022-08-03 17:31:34] build_node_ancestors
[WARN] [2022-08-03 17:31:34] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:31:34] Flattener#flatten
[STOP] [2022-08-03 17:31:34] rebuild_nodes
[START] [2022-08-03 17:31:34] resolve_missing_media_owners
[STOP] [2022-08-03 17:31:34] resolve_missing_media_owners
[START] [2022-08-03 17:31:34] sanitize_media_verbatims
[STOP] [2022-08-03 17:31:34] sanitize_media_verbatims
[START] [2022-08-03 17:31:34] queue_downloads
[STOP] [2022-08-03 17:31:34] queue_downloads
[START] [2022-08-03 17:31:34] parse_names
[WARN] [2022-08-03 17:31:34] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 17:31:34] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 17:31:35] parse_names
[START] [2022-08-03 17:31:35] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:31:35] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:31:35] match_nodes
[START] [2022-08-03 17:31:35] map_all_nodes_to_pages
[STOP] [2022-08-03 17:31:35] map_all_nodes_to_pages
[INFO] [2022-08-03 17:31:35] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 17:31:35] update_nodes
[STOP] [2022-08-03 17:31:35] update_nodes
[STOP] [2022-08-03 17:31:35] match_nodes
[START] [2022-08-03 17:31:35] reindex_search
[STOP] [2022-08-03 17:31:35] reindex_search
[START] [2022-08-03 17:31:35] normalize_units
[STOP] [2022-08-03 17:31:35] normalize_units
[START] [2022-08-03 17:31:35] calculate_statistics
[2022-08-03 17:31:36] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:31:36] Duplicate page_id count: 0
[STOP] [2022-08-03 17:31:36] calculate_statistics
[START] [2022-08-03 17:31:36] complete_harvest_instance
[START] [2022-08-03 17:31:36] overall_tsv_creation
[INFO] [2022-08-03 17:31:36] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:31:36] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 17:32:17] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:32:17] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 17:33:09] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 17:33:09] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:33:09] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:33:09] Adding 1 traits...
[INFO] [2022-08-03 17:33:09] 1 metadata added.
[INFO] [2022-08-03 17:33:09] Adding 0 assocs...
[INFO] [2022-08-03 17:33:09] 0 metadata added.
[INFO] [2022-08-03 17:33:53] Processed 1/1 nodes
[INFO] [2022-08-03 17:33:53] Average Time: 112.35
[INFO] [2022-08-03 17:33:53] Total Time: 2m18s
[STOP] [2022-08-03 17:33:53] overall_tsv_creation
[INFO] [2022-08-03 17:33:53] Done. Check your files:
[INFO] [2022-08-03 17:33:53] (1 lines) /app/public/data/chia_chia_1966/publish_nodes.tsv
[INFO] [2022-08-03 17:33:53] (1 lines) /app/public/data/chia_chia_1966/publish_scientific_names.tsv
[INFO] [2022-08-03 17:33:53] (2 lines) /app/public/data/chia_chia_1966/publish_traits.tsv
[INFO] [2022-08-03 17:33:53] (2 lines) /app/public/data/chia_chia_1966/publish_metadata.tsv
[STOP] [2022-08-03 17:33:53] complete_harvest_instance
[START] [2022-08-03 17:33:53] completed
[STOP] [2022-08-03 17:33:53] completed
[STOP] [2022-08-03 17:33:53] logged process, took 146.25

Latest Process

03 Aug 17:31 EXITED currently processing 0