Harvest for Berking 2007 Created 03 Aug 17:28

Stage: completed
Fetched: 03 Aug 17:28
Validated: 03 Aug 17:28
Deltas Created 03 Aug 17:28
Units Normalized: 03 Aug 17:28
Ancestry Built: 03 Aug 17:28
Nodes Matched: 03 Aug 17:28
Names Parsed: 03 Aug 17:28
New Models Stored: 03 Aug 17:28
Indexed: 03 Aug 17:28
Completed: 03 Aug 17:30
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 17:28:07] Created harvest instance #4199
[STOP] [2022-08-03 17:28:07] create_harvest_instance
[START] [2022-08-03 17:28:07] fetch_files
[STOP] [2022-08-03 17:28:07] fetch_files
[START] [2022-08-03 17:28:07] validate_each_file
[INFO] [2022-08-03 17:28:07] Looping over 3 formats...
[INFO] [2022-08-03 17:28:07] ...nodes (/app/public/data/berking_berking_/taxa.txt)
[INFO] [2022-08-03 17:28:08] Valid: /app/public/data/berking_berking_/converted_csv/berking_berking__nodes_29659.csv (1 lines)
[INFO] [2022-08-03 17:28:08] ...occurrences (/app/public/data/berking_berking_/occurrences.txt)
[INFO] [2022-08-03 17:28:08] Valid: /app/public/data/berking_berking_/converted_csv/berking_berking__occurrences_29660.csv (1 lines)
[INFO] [2022-08-03 17:28:08] ...measurements (/app/public/data/berking_berking_/measurementOrFact.txt)
[INFO] [2022-08-03 17:28:08] Valid: /app/public/data/berking_berking_/converted_csv/berking_berking__measurements_29661.csv (2 lines)
[STOP] [2022-08-03 17:28:08] validate_each_file
[START] [2022-08-03 17:28:08] convert_to_csv
[INFO] [2022-08-03 17:28:08] Looping over 3 formats...
[INFO] [2022-08-03 17:28:08] ...nodes (/app/public/data/berking_berking_/taxa.txt)
[CMD] [2022-08-03 17:28:08] /usr/bin/sort /app/public/data/berking_berking_/converted_csv/berking_berking__nodes_29659.csv > /app/public/data/berking_berking_/converted_csv/berking_berking__nodes_29659.csv_sorted
[INFO] [2022-08-03 17:28:08] Converted: /app/public/data/berking_berking_/converted_csv/berking_berking__nodes_29659.csv (1 lines)
[INFO] [2022-08-03 17:28:08] ...occurrences (/app/public/data/berking_berking_/occurrences.txt)
[CMD] [2022-08-03 17:28:08] /usr/bin/sort /app/public/data/berking_berking_/converted_csv/berking_berking__occurrences_29660.csv > /app/public/data/berking_berking_/converted_csv/berking_berking__occurrences_29660.csv_sorted
[INFO] [2022-08-03 17:28:08] Converted: /app/public/data/berking_berking_/converted_csv/berking_berking__occurrences_29660.csv (1 lines)
[INFO] [2022-08-03 17:28:08] ...measurements (/app/public/data/berking_berking_/measurementOrFact.txt)
[CMD] [2022-08-03 17:28:08] /usr/bin/sort /app/public/data/berking_berking_/converted_csv/berking_berking__measurements_29661.csv > /app/public/data/berking_berking_/converted_csv/berking_berking__measurements_29661.csv_sorted
[INFO] [2022-08-03 17:28:08] Converted: /app/public/data/berking_berking_/converted_csv/berking_berking__measurements_29661.csv (2 lines)
[STOP] [2022-08-03 17:28:08] convert_to_csv
[START] [2022-08-03 17:28:08] calculate_delta
[INFO] [2022-08-03 17:28:08] Looping over 3 formats...
[INFO] [2022-08-03 17:28:08] ...nodes (/app/public/data/berking_berking_/taxa.txt)
[CMD] [2022-08-03 17:28:08] echo "0a" > /app/public/data/berking_berking_/diff/berking_berking__nodes_29659.diff
[CMD] [2022-08-03 17:28:08] tail -n +1 /app/public/data/berking_berking_/converted_csv/berking_berking__nodes_29659.csv >> /app/public/data/berking_berking_/diff/berking_berking__nodes_29659.diff
[CMD] [2022-08-03 17:28:08] echo "." >> /app/public/data/berking_berking_/diff/berking_berking__nodes_29659.diff
[INFO] [2022-08-03 17:28:08] Created diff: /app/public/data/berking_berking_/diff/berking_berking__nodes_29659.diff (3 lines)
[INFO] [2022-08-03 17:28:08] ...occurrences (/app/public/data/berking_berking_/occurrences.txt)
[CMD] [2022-08-03 17:28:08] echo "0a" > /app/public/data/berking_berking_/diff/berking_berking__occurrences_29660.diff
[CMD] [2022-08-03 17:28:08] tail -n +1 /app/public/data/berking_berking_/converted_csv/berking_berking__occurrences_29660.csv >> /app/public/data/berking_berking_/diff/berking_berking__occurrences_29660.diff
[CMD] [2022-08-03 17:28:08] echo "." >> /app/public/data/berking_berking_/diff/berking_berking__occurrences_29660.diff
[INFO] [2022-08-03 17:28:08] Created diff: /app/public/data/berking_berking_/diff/berking_berking__occurrences_29660.diff (3 lines)
[INFO] [2022-08-03 17:28:08] ...measurements (/app/public/data/berking_berking_/measurementOrFact.txt)
[CMD] [2022-08-03 17:28:08] echo "0a" > /app/public/data/berking_berking_/diff/berking_berking__measurements_29661.diff
[CMD] [2022-08-03 17:28:08] tail -n +1 /app/public/data/berking_berking_/converted_csv/berking_berking__measurements_29661.csv >> /app/public/data/berking_berking_/diff/berking_berking__measurements_29661.diff
[CMD] [2022-08-03 17:28:08] echo "." >> /app/public/data/berking_berking_/diff/berking_berking__measurements_29661.diff
[INFO] [2022-08-03 17:28:08] Created diff: /app/public/data/berking_berking_/diff/berking_berking__measurements_29661.diff (4 lines)
[STOP] [2022-08-03 17:28:08] calculate_delta
[START] [2022-08-03 17:28:08] parse_diff_and_store
[INFO] [2022-08-03 17:28:08] Handling diff: /app/public/data/berking_berking_/diff/berking_berking__nodes_29659.diff (3 lines)
[INFO] [2022-08-03 17:28:08] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 17:28:08] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 17:28:08] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 17:28:08] Handling diff: /app/public/data/berking_berking_/diff/berking_berking__occurrences_29660.diff (3 lines)
[INFO] [2022-08-03 17:28:08] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 17:28:08] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 17:28:08] Handling diff: /app/public/data/berking_berking_/diff/berking_berking__measurements_29661.diff (4 lines)
[INFO] [2022-08-03 17:28:08] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 17:28:08] Storing 2 Traits (4/2/4)
[INFO] [2022-08-03 17:28:08] Storing 2 MetaTraits (4/2/4)
[STOP] [2022-08-03 17:28:08] parse_diff_and_store
[START] [2022-08-03 17:28:08] resolve_keys
[2022-08-03 17:28:08] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:28:16] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:28:16] traits to occurrences...
[INFO] [2022-08-03 17:28:16] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:28:16] Traits to sex term...
[INFO] [2022-08-03 17:28:16] Traits to lifestage term...
[INFO] [2022-08-03 17:28:16] MetaTraits to traits...
[INFO] [2022-08-03 17:28:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:28:16] Assocs to occurrences...
[INFO] [2022-08-03 17:28:16] Assocs to nodes...
[INFO] [2022-08-03 17:28:16] Assoc to sex term...
[INFO] [2022-08-03 17:28:16] Assoc to lifestage term...
[INFO] [2022-08-03 17:28:16] MetaAssoc to assocs...
[STOP] [2022-08-03 17:28:16] resolve_keys
[START] [2022-08-03 17:28:16] hold_for_later_1
[STOP] [2022-08-03 17:28:16] hold_for_later_1
[START] [2022-08-03 17:28:16] hold_for_later_2
[STOP] [2022-08-03 17:28:16] hold_for_later_2
[START] [2022-08-03 17:28:16] resolve_missing_parents
[STOP] [2022-08-03 17:28:16] resolve_missing_parents
[START] [2022-08-03 17:28:16] rebuild_nodes
[START] [2022-08-03 17:28:16] Flattener#flatten
[START] [2022-08-03 17:28:16] Flattener#study_resource
[START] [2022-08-03 17:28:16] Flattener#build_ancestry
[STOP] [2022-08-03 17:28:16] Flattener#build_ancestry
[INFO] [2022-08-03 17:28:16] 1 ancestry keys
[START] [2022-08-03 17:28:16] build_node_ancestors
[INFO] [2022-08-03 17:28:16] old ancestors deleted.
[STOP] [2022-08-03 17:28:16] build_node_ancestors
[WARN] [2022-08-03 17:28:16] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:28:16] Flattener#flatten
[STOP] [2022-08-03 17:28:16] rebuild_nodes
[START] [2022-08-03 17:28:16] resolve_missing_media_owners
[STOP] [2022-08-03 17:28:16] resolve_missing_media_owners
[START] [2022-08-03 17:28:16] sanitize_media_verbatims
[STOP] [2022-08-03 17:28:16] sanitize_media_verbatims
[START] [2022-08-03 17:28:16] queue_downloads
[STOP] [2022-08-03 17:28:16] queue_downloads
[START] [2022-08-03 17:28:16] parse_names
[WARN] [2022-08-03 17:28:16] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 17:28:16] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 17:28:17] parse_names
[START] [2022-08-03 17:28:17] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:28:17] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:28:17] match_nodes
[START] [2022-08-03 17:28:17] map_all_nodes_to_pages
[STOP] [2022-08-03 17:28:17] map_all_nodes_to_pages
[INFO] [2022-08-03 17:28:17] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 17:28:17] update_nodes
[STOP] [2022-08-03 17:28:17] update_nodes
[STOP] [2022-08-03 17:28:17] match_nodes
[START] [2022-08-03 17:28:17] reindex_search
[STOP] [2022-08-03 17:28:17] reindex_search
[START] [2022-08-03 17:28:17] normalize_units
[STOP] [2022-08-03 17:28:17] normalize_units
[START] [2022-08-03 17:28:17] calculate_statistics
[2022-08-03 17:28:17] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:28:17] Duplicate page_id count: 0
[STOP] [2022-08-03 17:28:17] calculate_statistics
[START] [2022-08-03 17:28:17] complete_harvest_instance
[START] [2022-08-03 17:28:17] overall_tsv_creation
[INFO] [2022-08-03 17:28:17] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:28:17] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 17:28:59] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:28:59] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 17:29:53] Mapped 1 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 17:29:53] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:29:53] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:29:53] Adding 1 traits...
[INFO] [2022-08-03 17:29:53] 1 metadata added.
[INFO] [2022-08-03 17:29:53] Adding 0 assocs...
[INFO] [2022-08-03 17:29:53] 0 metadata added.
[INFO] [2022-08-03 17:30:35] Processed 1/1 nodes
[INFO] [2022-08-03 17:30:35] Average Time: 112.27
[INFO] [2022-08-03 17:30:35] Total Time: 2m18s
[STOP] [2022-08-03 17:30:35] overall_tsv_creation
[INFO] [2022-08-03 17:30:35] Done. Check your files:
[INFO] [2022-08-03 17:30:35] (1 lines) /app/public/data/berking_berking_/publish_nodes.tsv
[INFO] [2022-08-03 17:30:35] (1 lines) /app/public/data/berking_berking_/publish_scientific_names.tsv
[INFO] [2022-08-03 17:30:35] (2 lines) /app/public/data/berking_berking_/publish_traits.tsv
[INFO] [2022-08-03 17:30:35] (2 lines) /app/public/data/berking_berking_/publish_metadata.tsv
[STOP] [2022-08-03 17:30:35] complete_harvest_instance
[START] [2022-08-03 17:30:35] completed
[STOP] [2022-08-03 17:30:35] completed
[STOP] [2022-08-03 17:30:35] logged process, took 147.53
Latest Process

03 Aug 17:28 EXITED currently processing 0