Harvest for Kanneby 2016 Created 03 Aug 16:25

Harvesting Log

[INFO] [2022-08-03 16:25:46] Created harvest instance #4170
[STOP] [2022-08-03 16:25:46] create_harvest_instance
[START] [2022-08-03 16:25:46] fetch_files
[STOP] [2022-08-03 16:25:46] fetch_files
[START] [2022-08-03 16:25:46] validate_each_file
[INFO] [2022-08-03 16:25:46] Looping over 3 formats...
[INFO] [2022-08-03 16:25:46] ...nodes (/app/public/data/kanneby_kanneby_/taxa.txt)
[INFO] [2022-08-03 16:25:46] Valid: /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__nodes_29573.csv (1 lines)
[INFO] [2022-08-03 16:25:46] ...occurrences (/app/public/data/kanneby_kanneby_/occurrences.txt)
[INFO] [2022-08-03 16:25:46] Valid: /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__occurrences_29574.csv (1 lines)
[INFO] [2022-08-03 16:25:46] ...measurements (/app/public/data/kanneby_kanneby_/measurementOrFact.txt)
[INFO] [2022-08-03 16:25:46] Valid: /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__measurements_29575.csv (2 lines)
[STOP] [2022-08-03 16:25:46] validate_each_file
[START] [2022-08-03 16:25:46] convert_to_csv
[INFO] [2022-08-03 16:25:46] Looping over 3 formats...
[INFO] [2022-08-03 16:25:46] ...nodes (/app/public/data/kanneby_kanneby_/taxa.txt)
[CMD] [2022-08-03 16:25:46] /usr/bin/sort /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__nodes_29573.csv > /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__nodes_29573.csv_sorted
[INFO] [2022-08-03 16:25:46] Converted: /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__nodes_29573.csv (1 lines)
[INFO] [2022-08-03 16:25:46] ...occurrences (/app/public/data/kanneby_kanneby_/occurrences.txt)
[CMD] [2022-08-03 16:25:46] /usr/bin/sort /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__occurrences_29574.csv > /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__occurrences_29574.csv_sorted
[INFO] [2022-08-03 16:25:46] Converted: /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__occurrences_29574.csv (1 lines)
[INFO] [2022-08-03 16:25:46] ...measurements (/app/public/data/kanneby_kanneby_/measurementOrFact.txt)
[CMD] [2022-08-03 16:25:46] /usr/bin/sort /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__measurements_29575.csv > /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__measurements_29575.csv_sorted
[INFO] [2022-08-03 16:25:46] Converted: /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__measurements_29575.csv (2 lines)
[STOP] [2022-08-03 16:25:46] convert_to_csv
[START] [2022-08-03 16:25:46] calculate_delta
[INFO] [2022-08-03 16:25:46] Looping over 3 formats...
[INFO] [2022-08-03 16:25:46] ...nodes (/app/public/data/kanneby_kanneby_/taxa.txt)
[CMD] [2022-08-03 16:25:46] echo "0a" > /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__nodes_29573.diff
[CMD] [2022-08-03 16:25:46] tail -n +1 /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__nodes_29573.csv >> /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__nodes_29573.diff
[CMD] [2022-08-03 16:25:46] echo "." >> /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__nodes_29573.diff
[INFO] [2022-08-03 16:25:46] Created diff: /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__nodes_29573.diff (3 lines)
[INFO] [2022-08-03 16:25:46] ...occurrences (/app/public/data/kanneby_kanneby_/occurrences.txt)
[CMD] [2022-08-03 16:25:46] echo "0a" > /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__occurrences_29574.diff
[CMD] [2022-08-03 16:25:46] tail -n +1 /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__occurrences_29574.csv >> /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__occurrences_29574.diff
[CMD] [2022-08-03 16:25:46] echo "." >> /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__occurrences_29574.diff
[INFO] [2022-08-03 16:25:46] Created diff: /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__occurrences_29574.diff (3 lines)
[INFO] [2022-08-03 16:25:46] ...measurements (/app/public/data/kanneby_kanneby_/measurementOrFact.txt)
[CMD] [2022-08-03 16:25:46] echo "0a" > /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__measurements_29575.diff
[CMD] [2022-08-03 16:25:46] tail -n +1 /app/public/data/kanneby_kanneby_/converted_csv/kanneby_kanneby__measurements_29575.csv >> /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__measurements_29575.diff
[CMD] [2022-08-03 16:25:46] echo "." >> /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__measurements_29575.diff
[INFO] [2022-08-03 16:25:46] Created diff: /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__measurements_29575.diff (4 lines)
[STOP] [2022-08-03 16:25:46] calculate_delta
[START] [2022-08-03 16:25:46] parse_diff_and_store
[INFO] [2022-08-03 16:25:46] Handling diff: /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__nodes_29573.diff (3 lines)
[INFO] [2022-08-03 16:25:46] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:25:46] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:25:46] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:25:46] Handling diff: /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__occurrences_29574.diff (3 lines)
[INFO] [2022-08-03 16:25:46] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:25:46] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:25:46] Handling diff: /app/public/data/kanneby_kanneby_/diff/kanneby_kanneby__measurements_29575.diff (4 lines)
[INFO] [2022-08-03 16:25:46] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:25:46] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:25:46] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:25:46] parse_diff_and_store
[START] [2022-08-03 16:25:46] resolve_keys
[2022-08-03 16:25:46] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:25:53] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:25:53] traits to occurrences...
[INFO] [2022-08-03 16:25:53] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:25:53] Traits to sex term...
[INFO] [2022-08-03 16:25:53] Traits to lifestage term...
[INFO] [2022-08-03 16:25:53] MetaTraits to traits...
[INFO] [2022-08-03 16:25:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:25:53] Assocs to occurrences...
[INFO] [2022-08-03 16:25:54] Assocs to nodes...
[INFO] [2022-08-03 16:25:54] Assoc to sex term...
[INFO] [2022-08-03 16:25:54] Assoc to lifestage term...
[INFO] [2022-08-03 16:25:54] MetaAssoc to assocs...
[STOP] [2022-08-03 16:25:54] resolve_keys
[START] [2022-08-03 16:25:54] hold_for_later_1
[STOP] [2022-08-03 16:25:54] hold_for_later_1
[START] [2022-08-03 16:25:54] hold_for_later_2
[STOP] [2022-08-03 16:25:54] hold_for_later_2
[START] [2022-08-03 16:25:54] resolve_missing_parents
[STOP] [2022-08-03 16:25:54] resolve_missing_parents
[START] [2022-08-03 16:25:54] rebuild_nodes
[START] [2022-08-03 16:25:54] Flattener#flatten
[START] [2022-08-03 16:25:54] Flattener#study_resource
[START] [2022-08-03 16:25:54] Flattener#build_ancestry
[STOP] [2022-08-03 16:25:54] Flattener#build_ancestry
[INFO] [2022-08-03 16:25:54] 1 ancestry keys
[START] [2022-08-03 16:25:54] build_node_ancestors
[INFO] [2022-08-03 16:25:54] old ancestors deleted.
[STOP] [2022-08-03 16:25:54] build_node_ancestors
[WARN] [2022-08-03 16:25:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:25:54] Flattener#flatten
[STOP] [2022-08-03 16:25:54] rebuild_nodes
[START] [2022-08-03 16:25:54] resolve_missing_media_owners
[STOP] [2022-08-03 16:25:54] resolve_missing_media_owners
[START] [2022-08-03 16:25:54] sanitize_media_verbatims
[STOP] [2022-08-03 16:25:54] sanitize_media_verbatims
[START] [2022-08-03 16:25:54] queue_downloads
[STOP] [2022-08-03 16:25:54] queue_downloads
[START] [2022-08-03 16:25:54] parse_names
[WARN] [2022-08-03 16:25:54] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:25:54] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:25:55] parse_names
[START] [2022-08-03 16:25:55] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:25:55] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:25:55] match_nodes
[START] [2022-08-03 16:25:55] map_all_nodes_to_pages
[STOP] [2022-08-03 16:25:55] map_all_nodes_to_pages
[INFO] [2022-08-03 16:25:55] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:25:55] update_nodes
[STOP] [2022-08-03 16:25:55] update_nodes
[STOP] [2022-08-03 16:25:55] match_nodes
[START] [2022-08-03 16:25:55] reindex_search
[STOP] [2022-08-03 16:25:55] reindex_search
[START] [2022-08-03 16:25:55] normalize_units
[STOP] [2022-08-03 16:25:55] normalize_units
[START] [2022-08-03 16:25:55] calculate_statistics
[2022-08-03 16:25:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:25:55] Duplicate page_id count: 0
[STOP] [2022-08-03 16:25:55] calculate_statistics
[START] [2022-08-03 16:25:55] complete_harvest_instance
[START] [2022-08-03 16:25:55] overall_tsv_creation
[INFO] [2022-08-03 16:25:55] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:25:55] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:26:37] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:26:37] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:27:28] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:27:28] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:27:28] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:27:28] Adding 1 traits...
[INFO] [2022-08-03 16:27:28] 1 metadata added.
[INFO] [2022-08-03 16:27:28] Adding 0 assocs...
[INFO] [2022-08-03 16:27:28] 0 metadata added.
[INFO] [2022-08-03 16:28:09] Processed 1/1 nodes
[INFO] [2022-08-03 16:28:09] Average Time: 109.12
[INFO] [2022-08-03 16:28:09] Total Time: 2m15s
[STOP] [2022-08-03 16:28:09] overall_tsv_creation
[INFO] [2022-08-03 16:28:09] Done. Check your files:
[INFO] [2022-08-03 16:28:09] (1 lines) /app/public/data/kanneby_kanneby_/publish_nodes.tsv
[INFO] [2022-08-03 16:28:09] (1 lines) /app/public/data/kanneby_kanneby_/publish_scientific_names.tsv
[INFO] [2022-08-03 16:28:09] (2 lines) /app/public/data/kanneby_kanneby_/publish_traits.tsv
[INFO] [2022-08-03 16:28:09] (2 lines) /app/public/data/kanneby_kanneby_/publish_metadata.tsv
[STOP] [2022-08-03 16:28:09] complete_harvest_instance
[START] [2022-08-03 16:28:09] completed
[STOP] [2022-08-03 16:28:09] completed
[STOP] [2022-08-03 16:28:09] logged process, took 143.49

Latest Process

03 Aug 16:25 EXITED currently processing 0