Harvest for Littlewood et al 1998 Created 03 Aug 16:23

Harvesting Log

[INFO] [2022-08-03 16:23:22] Created harvest instance #4169
[STOP] [2022-08-03 16:23:22] create_harvest_instance
[START] [2022-08-03 16:23:22] fetch_files
[STOP] [2022-08-03 16:23:22] fetch_files
[START] [2022-08-03 16:23:22] validate_each_file
[INFO] [2022-08-03 16:23:22] Looping over 3 formats...
[INFO] [2022-08-03 16:23:22] ...nodes (/app/public/data/littlewood_et_al/taxa.txt)
[INFO] [2022-08-03 16:23:22] Valid: /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_nodes_29570.csv (1 lines)
[INFO] [2022-08-03 16:23:22] ...occurrences (/app/public/data/littlewood_et_al/occurrences.txt)
[INFO] [2022-08-03 16:23:22] Valid: /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_occurrences_29571.csv (1 lines)
[INFO] [2022-08-03 16:23:22] ...measurements (/app/public/data/littlewood_et_al/measurementOrFact.txt)
[INFO] [2022-08-03 16:23:22] Valid: /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_measurements_29572.csv (6 lines)
[STOP] [2022-08-03 16:23:22] validate_each_file
[START] [2022-08-03 16:23:22] convert_to_csv
[INFO] [2022-08-03 16:23:22] Looping over 3 formats...
[INFO] [2022-08-03 16:23:22] ...nodes (/app/public/data/littlewood_et_al/taxa.txt)
[CMD] [2022-08-03 16:23:22] /usr/bin/sort /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_nodes_29570.csv > /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_nodes_29570.csv_sorted
[INFO] [2022-08-03 16:23:22] Converted: /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_nodes_29570.csv (1 lines)
[INFO] [2022-08-03 16:23:22] ...occurrences (/app/public/data/littlewood_et_al/occurrences.txt)
[CMD] [2022-08-03 16:23:22] /usr/bin/sort /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_occurrences_29571.csv > /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_occurrences_29571.csv_sorted
[INFO] [2022-08-03 16:23:22] Converted: /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_occurrences_29571.csv (1 lines)
[INFO] [2022-08-03 16:23:22] ...measurements (/app/public/data/littlewood_et_al/measurementOrFact.txt)
[CMD] [2022-08-03 16:23:22] /usr/bin/sort /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_measurements_29572.csv > /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_measurements_29572.csv_sorted
[INFO] [2022-08-03 16:23:22] Converted: /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_measurements_29572.csv (6 lines)
[STOP] [2022-08-03 16:23:22] convert_to_csv
[START] [2022-08-03 16:23:22] calculate_delta
[INFO] [2022-08-03 16:23:22] Looping over 3 formats...
[INFO] [2022-08-03 16:23:22] ...nodes (/app/public/data/littlewood_et_al/taxa.txt)
[CMD] [2022-08-03 16:23:22] echo "0a" > /app/public/data/littlewood_et_al/diff/littlewood_et_al_nodes_29570.diff
[CMD] [2022-08-03 16:23:22] tail -n +1 /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_nodes_29570.csv >> /app/public/data/littlewood_et_al/diff/littlewood_et_al_nodes_29570.diff
[CMD] [2022-08-03 16:23:22] echo "." >> /app/public/data/littlewood_et_al/diff/littlewood_et_al_nodes_29570.diff
[INFO] [2022-08-03 16:23:22] Created diff: /app/public/data/littlewood_et_al/diff/littlewood_et_al_nodes_29570.diff (3 lines)
[INFO] [2022-08-03 16:23:22] ...occurrences (/app/public/data/littlewood_et_al/occurrences.txt)
[CMD] [2022-08-03 16:23:22] echo "0a" > /app/public/data/littlewood_et_al/diff/littlewood_et_al_occurrences_29571.diff
[CMD] [2022-08-03 16:23:22] tail -n +1 /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_occurrences_29571.csv >> /app/public/data/littlewood_et_al/diff/littlewood_et_al_occurrences_29571.diff
[CMD] [2022-08-03 16:23:22] echo "." >> /app/public/data/littlewood_et_al/diff/littlewood_et_al_occurrences_29571.diff
[INFO] [2022-08-03 16:23:22] Created diff: /app/public/data/littlewood_et_al/diff/littlewood_et_al_occurrences_29571.diff (3 lines)
[INFO] [2022-08-03 16:23:22] ...measurements (/app/public/data/littlewood_et_al/measurementOrFact.txt)
[CMD] [2022-08-03 16:23:22] echo "0a" > /app/public/data/littlewood_et_al/diff/littlewood_et_al_measurements_29572.diff
[CMD] [2022-08-03 16:23:22] tail -n +1 /app/public/data/littlewood_et_al/converted_csv/littlewood_et_al_measurements_29572.csv >> /app/public/data/littlewood_et_al/diff/littlewood_et_al_measurements_29572.diff
[CMD] [2022-08-03 16:23:22] echo "." >> /app/public/data/littlewood_et_al/diff/littlewood_et_al_measurements_29572.diff
[INFO] [2022-08-03 16:23:22] Created diff: /app/public/data/littlewood_et_al/diff/littlewood_et_al_measurements_29572.diff (8 lines)
[STOP] [2022-08-03 16:23:22] calculate_delta
[START] [2022-08-03 16:23:22] parse_diff_and_store
[INFO] [2022-08-03 16:23:22] Handling diff: /app/public/data/littlewood_et_al/diff/littlewood_et_al_nodes_29570.diff (3 lines)
[INFO] [2022-08-03 16:23:22] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:23:22] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:23:22] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:23:22] Handling diff: /app/public/data/littlewood_et_al/diff/littlewood_et_al_occurrences_29571.diff (3 lines)
[INFO] [2022-08-03 16:23:22] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:23:22] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:23:22] Handling diff: /app/public/data/littlewood_et_al/diff/littlewood_et_al_measurements_29572.diff (8 lines)
[INFO] [2022-08-03 16:23:22] Loading measurements diff file into memory (8 lines)...
[INFO] [2022-08-03 16:23:22] Storing 6 Traits (9/6/8)
[INFO] [2022-08-03 16:23:22] Storing 3 MetaTraits (9/6/8)
[STOP] [2022-08-03 16:23:22] parse_diff_and_store
[START] [2022-08-03 16:23:22] resolve_keys
[2022-08-03 16:23:22] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:23:29] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:23:29] traits to occurrences...
[INFO] [2022-08-03 16:23:29] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:23:29] Traits to sex term...
[INFO] [2022-08-03 16:23:29] Traits to lifestage term...
[INFO] [2022-08-03 16:23:29] MetaTraits to traits...
[INFO] [2022-08-03 16:23:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:23:29] Assocs to occurrences...
[INFO] [2022-08-03 16:23:29] Assocs to nodes...
[INFO] [2022-08-03 16:23:29] Assoc to sex term...
[INFO] [2022-08-03 16:23:29] Assoc to lifestage term...
[INFO] [2022-08-03 16:23:29] MetaAssoc to assocs...
[STOP] [2022-08-03 16:23:29] resolve_keys
[START] [2022-08-03 16:23:29] hold_for_later_1
[STOP] [2022-08-03 16:23:29] hold_for_later_1
[START] [2022-08-03 16:23:29] hold_for_later_2
[STOP] [2022-08-03 16:23:29] hold_for_later_2
[START] [2022-08-03 16:23:29] resolve_missing_parents
[STOP] [2022-08-03 16:23:29] resolve_missing_parents
[START] [2022-08-03 16:23:29] rebuild_nodes
[START] [2022-08-03 16:23:29] Flattener#flatten
[START] [2022-08-03 16:23:29] Flattener#study_resource
[START] [2022-08-03 16:23:29] Flattener#build_ancestry
[STOP] [2022-08-03 16:23:29] Flattener#build_ancestry
[INFO] [2022-08-03 16:23:29] 1 ancestry keys
[START] [2022-08-03 16:23:29] build_node_ancestors
[INFO] [2022-08-03 16:23:29] old ancestors deleted.
[STOP] [2022-08-03 16:23:29] build_node_ancestors
[WARN] [2022-08-03 16:23:29] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:23:29] Flattener#flatten
[STOP] [2022-08-03 16:23:29] rebuild_nodes
[START] [2022-08-03 16:23:29] resolve_missing_media_owners
[STOP] [2022-08-03 16:23:29] resolve_missing_media_owners
[START] [2022-08-03 16:23:29] sanitize_media_verbatims
[STOP] [2022-08-03 16:23:29] sanitize_media_verbatims
[START] [2022-08-03 16:23:29] queue_downloads
[STOP] [2022-08-03 16:23:29] queue_downloads
[START] [2022-08-03 16:23:29] parse_names
[WARN] [2022-08-03 16:23:29] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:23:29] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:23:30] parse_names
[START] [2022-08-03 16:23:30] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:23:30] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:23:30] match_nodes
[START] [2022-08-03 16:23:30] map_all_nodes_to_pages
[STOP] [2022-08-03 16:23:30] map_all_nodes_to_pages
[INFO] [2022-08-03 16:23:30] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:23:30] update_nodes
[STOP] [2022-08-03 16:23:30] update_nodes
[STOP] [2022-08-03 16:23:30] match_nodes
[START] [2022-08-03 16:23:30] reindex_search
[STOP] [2022-08-03 16:23:31] reindex_search
[START] [2022-08-03 16:23:31] normalize_units
[STOP] [2022-08-03 16:23:31] normalize_units
[START] [2022-08-03 16:23:31] calculate_statistics
[2022-08-03 16:23:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:23:31] Duplicate page_id count: 0
[STOP] [2022-08-03 16:23:31] calculate_statistics
[START] [2022-08-03 16:23:31] complete_harvest_instance
[START] [2022-08-03 16:23:31] overall_tsv_creation
[INFO] [2022-08-03 16:23:31] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:23:31] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:24:11] 3 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:24:11] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:25:03] Mapped 3 traits (3 meta) for 1 nodes.
[INFO] [2022-08-03 16:25:03] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:25:03] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:25:03] Adding 3 traits...
[INFO] [2022-08-03 16:25:03] 3 metadata added.
[INFO] [2022-08-03 16:25:03] Adding 0 assocs...
[INFO] [2022-08-03 16:25:03] 0 metadata added.
[INFO] [2022-08-03 16:25:46] Processed 1/1 nodes
[INFO] [2022-08-03 16:25:46] Average Time: 110.6
[INFO] [2022-08-03 16:25:46] Total Time: 2m16s
[STOP] [2022-08-03 16:25:46] overall_tsv_creation
[INFO] [2022-08-03 16:25:46] Done. Check your files:
[INFO] [2022-08-03 16:25:46] (1 lines) /app/public/data/littlewood_et_al/publish_nodes.tsv
[INFO] [2022-08-03 16:25:46] (1 lines) /app/public/data/littlewood_et_al/publish_scientific_names.tsv
[INFO] [2022-08-03 16:25:46] (4 lines) /app/public/data/littlewood_et_al/publish_traits.tsv
[INFO] [2022-08-03 16:25:46] (4 lines) /app/public/data/littlewood_et_al/publish_metadata.tsv
[STOP] [2022-08-03 16:25:46] complete_harvest_instance
[START] [2022-08-03 16:25:46] completed
[STOP] [2022-08-03 16:25:46] completed
[STOP] [2022-08-03 16:25:46] logged process, took 144.14

Latest Process

03 Aug 16:23 EXITED currently processing 0