Harvest for Smirnov 2014 Created 03 Aug 17:18

Harvesting Log

[INFO] [2022-08-03 17:18:13] Created harvest instance #4195
[STOP] [2022-08-03 17:18:13] create_harvest_instance
[START] [2022-08-03 17:18:13] fetch_files
[STOP] [2022-08-03 17:18:13] fetch_files
[START] [2022-08-03 17:18:13] validate_each_file
[INFO] [2022-08-03 17:18:13] Looping over 3 formats...
[INFO] [2022-08-03 17:18:13] ...nodes (/app/public/data/smirnov_smirnov_/taxa.txt)
[INFO] [2022-08-03 17:18:13] Valid: /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__nodes_29647.csv (1 lines)
[INFO] [2022-08-03 17:18:13] ...occurrences (/app/public/data/smirnov_smirnov_/occurrences.txt)
[INFO] [2022-08-03 17:18:13] Valid: /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__occurrences_29648.csv (1 lines)
[INFO] [2022-08-03 17:18:13] ...measurements (/app/public/data/smirnov_smirnov_/measurementOrFact.txt)
[INFO] [2022-08-03 17:18:13] Valid: /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__measurements_29649.csv (2 lines)
[STOP] [2022-08-03 17:18:13] validate_each_file
[START] [2022-08-03 17:18:13] convert_to_csv
[INFO] [2022-08-03 17:18:13] Looping over 3 formats...
[INFO] [2022-08-03 17:18:13] ...nodes (/app/public/data/smirnov_smirnov_/taxa.txt)
[CMD] [2022-08-03 17:18:13] /usr/bin/sort /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__nodes_29647.csv > /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__nodes_29647.csv_sorted
[INFO] [2022-08-03 17:18:13] Converted: /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__nodes_29647.csv (1 lines)
[INFO] [2022-08-03 17:18:13] ...occurrences (/app/public/data/smirnov_smirnov_/occurrences.txt)
[CMD] [2022-08-03 17:18:13] /usr/bin/sort /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__occurrences_29648.csv > /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__occurrences_29648.csv_sorted
[INFO] [2022-08-03 17:18:13] Converted: /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__occurrences_29648.csv (1 lines)
[INFO] [2022-08-03 17:18:13] ...measurements (/app/public/data/smirnov_smirnov_/measurementOrFact.txt)
[CMD] [2022-08-03 17:18:13] /usr/bin/sort /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__measurements_29649.csv > /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__measurements_29649.csv_sorted
[INFO] [2022-08-03 17:18:13] Converted: /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__measurements_29649.csv (2 lines)
[STOP] [2022-08-03 17:18:13] convert_to_csv
[START] [2022-08-03 17:18:13] calculate_delta
[INFO] [2022-08-03 17:18:13] Looping over 3 formats...
[INFO] [2022-08-03 17:18:13] ...nodes (/app/public/data/smirnov_smirnov_/taxa.txt)
[CMD] [2022-08-03 17:18:13] echo "0a" > /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__nodes_29647.diff
[CMD] [2022-08-03 17:18:13] tail -n +1 /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__nodes_29647.csv >> /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__nodes_29647.diff
[CMD] [2022-08-03 17:18:13] echo "." >> /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__nodes_29647.diff
[INFO] [2022-08-03 17:18:13] Created diff: /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__nodes_29647.diff (3 lines)
[INFO] [2022-08-03 17:18:13] ...occurrences (/app/public/data/smirnov_smirnov_/occurrences.txt)
[CMD] [2022-08-03 17:18:13] echo "0a" > /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__occurrences_29648.diff
[CMD] [2022-08-03 17:18:13] tail -n +1 /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__occurrences_29648.csv >> /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__occurrences_29648.diff
[CMD] [2022-08-03 17:18:13] echo "." >> /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__occurrences_29648.diff
[INFO] [2022-08-03 17:18:13] Created diff: /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__occurrences_29648.diff (3 lines)
[INFO] [2022-08-03 17:18:13] ...measurements (/app/public/data/smirnov_smirnov_/measurementOrFact.txt)
[CMD] [2022-08-03 17:18:13] echo "0a" > /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__measurements_29649.diff
[CMD] [2022-08-03 17:18:13] tail -n +1 /app/public/data/smirnov_smirnov_/converted_csv/smirnov_smirnov__measurements_29649.csv >> /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__measurements_29649.diff
[CMD] [2022-08-03 17:18:13] echo "." >> /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__measurements_29649.diff
[INFO] [2022-08-03 17:18:13] Created diff: /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__measurements_29649.diff (4 lines)
[STOP] [2022-08-03 17:18:13] calculate_delta
[START] [2022-08-03 17:18:13] parse_diff_and_store
[INFO] [2022-08-03 17:18:13] Handling diff: /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__nodes_29647.diff (3 lines)
[INFO] [2022-08-03 17:18:13] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 17:18:13] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 17:18:13] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 17:18:13] Handling diff: /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__occurrences_29648.diff (3 lines)
[INFO] [2022-08-03 17:18:13] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 17:18:13] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 17:18:13] Handling diff: /app/public/data/smirnov_smirnov_/diff/smirnov_smirnov__measurements_29649.diff (4 lines)
[INFO] [2022-08-03 17:18:13] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 17:18:13] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 17:18:13] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 17:18:13] parse_diff_and_store
[START] [2022-08-03 17:18:13] resolve_keys
[2022-08-03 17:18:13] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:18:21] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:18:21] traits to occurrences...
[INFO] [2022-08-03 17:18:21] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:18:21] Traits to sex term...
[INFO] [2022-08-03 17:18:21] Traits to lifestage term...
[INFO] [2022-08-03 17:18:21] MetaTraits to traits...
[INFO] [2022-08-03 17:18:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:18:21] Assocs to occurrences...
[INFO] [2022-08-03 17:18:21] Assocs to nodes...
[INFO] [2022-08-03 17:18:21] Assoc to sex term...
[INFO] [2022-08-03 17:18:21] Assoc to lifestage term...
[INFO] [2022-08-03 17:18:21] MetaAssoc to assocs...
[STOP] [2022-08-03 17:18:21] resolve_keys
[START] [2022-08-03 17:18:21] hold_for_later_1
[STOP] [2022-08-03 17:18:21] hold_for_later_1
[START] [2022-08-03 17:18:21] hold_for_later_2
[STOP] [2022-08-03 17:18:21] hold_for_later_2
[START] [2022-08-03 17:18:21] resolve_missing_parents
[STOP] [2022-08-03 17:18:21] resolve_missing_parents
[START] [2022-08-03 17:18:21] rebuild_nodes
[START] [2022-08-03 17:18:21] Flattener#flatten
[START] [2022-08-03 17:18:21] Flattener#study_resource
[START] [2022-08-03 17:18:21] Flattener#build_ancestry
[STOP] [2022-08-03 17:18:21] Flattener#build_ancestry
[INFO] [2022-08-03 17:18:21] 1 ancestry keys
[START] [2022-08-03 17:18:21] build_node_ancestors
[INFO] [2022-08-03 17:18:21] old ancestors deleted.
[STOP] [2022-08-03 17:18:21] build_node_ancestors
[WARN] [2022-08-03 17:18:21] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:18:21] Flattener#flatten
[STOP] [2022-08-03 17:18:21] rebuild_nodes
[START] [2022-08-03 17:18:21] resolve_missing_media_owners
[STOP] [2022-08-03 17:18:21] resolve_missing_media_owners
[START] [2022-08-03 17:18:21] sanitize_media_verbatims
[STOP] [2022-08-03 17:18:21] sanitize_media_verbatims
[START] [2022-08-03 17:18:21] queue_downloads
[STOP] [2022-08-03 17:18:21] queue_downloads
[START] [2022-08-03 17:18:21] parse_names
[WARN] [2022-08-03 17:18:21] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 17:18:21] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 17:18:22] parse_names
[START] [2022-08-03 17:18:22] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:18:22] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:18:22] match_nodes
[START] [2022-08-03 17:18:22] map_all_nodes_to_pages
[STOP] [2022-08-03 17:18:22] map_all_nodes_to_pages
[INFO] [2022-08-03 17:18:22] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 17:18:22] update_nodes
[STOP] [2022-08-03 17:18:22] update_nodes
[STOP] [2022-08-03 17:18:22] match_nodes
[START] [2022-08-03 17:18:22] reindex_search
[STOP] [2022-08-03 17:18:22] reindex_search
[START] [2022-08-03 17:18:22] normalize_units
[STOP] [2022-08-03 17:18:22] normalize_units
[START] [2022-08-03 17:18:22] calculate_statistics
[2022-08-03 17:18:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:18:22] Duplicate page_id count: 0
[STOP] [2022-08-03 17:18:22] calculate_statistics
[START] [2022-08-03 17:18:22] complete_harvest_instance
[START] [2022-08-03 17:18:22] overall_tsv_creation
[INFO] [2022-08-03 17:18:22] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:18:22] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 17:19:03] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:19:03] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 17:19:55] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 17:19:55] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:19:55] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:19:55] Adding 1 traits...
[INFO] [2022-08-03 17:19:55] 1 metadata added.
[INFO] [2022-08-03 17:19:55] Adding 0 assocs...
[INFO] [2022-08-03 17:19:55] 0 metadata added.
[INFO] [2022-08-03 17:20:37] Processed 1/1 nodes
[INFO] [2022-08-03 17:20:37] Average Time: 110.9
[INFO] [2022-08-03 17:20:37] Total Time: 2m16s
[STOP] [2022-08-03 17:20:37] overall_tsv_creation
[INFO] [2022-08-03 17:20:37] Done. Check your files:
[INFO] [2022-08-03 17:20:37] (1 lines) /app/public/data/smirnov_smirnov_/publish_nodes.tsv
[INFO] [2022-08-03 17:20:37] (1 lines) /app/public/data/smirnov_smirnov_/publish_scientific_names.tsv
[INFO] [2022-08-03 17:20:37] (2 lines) /app/public/data/smirnov_smirnov_/publish_traits.tsv
[INFO] [2022-08-03 17:20:37] (2 lines) /app/public/data/smirnov_smirnov_/publish_metadata.tsv
[STOP] [2022-08-03 17:20:37] complete_harvest_instance
[START] [2022-08-03 17:20:38] completed
[STOP] [2022-08-03 17:20:38] completed
[STOP] [2022-08-03 17:20:38] logged process, took 144.43

Latest Process

03 Aug 17:18 EXITED currently processing 0