Harvest for Price et al 2005 Created 13 Oct 13:58

Harvesting Log

[INFO] [2023-10-13 13:58:39] Created harvest instance #4465
[STOP] [2023-10-13 13:58:39] create_harvest_instance
[START] [2023-10-13 13:58:39] fetch_files
[STOP] [2023-10-13 13:58:39] fetch_files
[START] [2023-10-13 13:58:39] validate_each_file
[INFO] [2023-10-13 13:58:39] Looping over 4 formats...
[INFO] [2023-10-13 13:58:39] ...refs (/app/public/data/price_et_al_pric/references.txt)
[INFO] [2023-10-13 13:58:39] Valid: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_refs_30868.csv (7 lines)
[INFO] [2023-10-13 13:58:39] ...nodes (/app/public/data/price_et_al_pric/taxa.txt)
[INFO] [2023-10-13 13:58:39] Valid: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_nodes_30865.csv (6 lines)
[INFO] [2023-10-13 13:58:39] ...occurrences (/app/public/data/price_et_al_pric/occurrences.txt)
[INFO] [2023-10-13 13:58:39] Valid: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_occurrences_30866.csv (6 lines)
[INFO] [2023-10-13 13:58:39] ...measurements (/app/public/data/price_et_al_pric/measurementsorfacts.txt)
[INFO] [2023-10-13 13:58:39] Valid: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_measurements_30867.csv (17 lines)
[STOP] [2023-10-13 13:58:39] validate_each_file
[START] [2023-10-13 13:58:39] convert_to_csv
[INFO] [2023-10-13 13:58:39] Looping over 4 formats...
[INFO] [2023-10-13 13:58:39] ...refs (/app/public/data/price_et_al_pric/references.txt)
[CMD] [2023-10-13 13:58:39] /usr/bin/sort /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_refs_30868.csv > /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_refs_30868.csv_sorted
[INFO] [2023-10-13 13:58:40] Converted: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_refs_30868.csv (7 lines)
[INFO] [2023-10-13 13:58:40] ...nodes (/app/public/data/price_et_al_pric/taxa.txt)
[CMD] [2023-10-13 13:58:40] /usr/bin/sort /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_nodes_30865.csv > /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_nodes_30865.csv_sorted
[INFO] [2023-10-13 13:58:40] Converted: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_nodes_30865.csv (6 lines)
[INFO] [2023-10-13 13:58:40] ...occurrences (/app/public/data/price_et_al_pric/occurrences.txt)
[CMD] [2023-10-13 13:58:40] /usr/bin/sort /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_occurrences_30866.csv > /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_occurrences_30866.csv_sorted
[INFO] [2023-10-13 13:58:40] Converted: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_occurrences_30866.csv (6 lines)
[INFO] [2023-10-13 13:58:40] ...measurements (/app/public/data/price_et_al_pric/measurementsorfacts.txt)
[CMD] [2023-10-13 13:58:40] /usr/bin/sort /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_measurements_30867.csv > /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_measurements_30867.csv_sorted
[INFO] [2023-10-13 13:58:40] Converted: /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_measurements_30867.csv (17 lines)
[STOP] [2023-10-13 13:58:40] convert_to_csv
[START] [2023-10-13 13:58:40] calculate_delta
[INFO] [2023-10-13 13:58:40] Looping over 4 formats...
[INFO] [2023-10-13 13:58:40] ...refs (/app/public/data/price_et_al_pric/references.txt)
[CMD] [2023-10-13 13:58:40] echo "0a" > /app/public/data/price_et_al_pric/diff/price_et_al_pric_refs_30868.diff
[CMD] [2023-10-13 13:58:40] tail -n +1 /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_refs_30868.csv >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_refs_30868.diff
[CMD] [2023-10-13 13:58:40] echo "." >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_refs_30868.diff
[INFO] [2023-10-13 13:58:40] Created diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_refs_30868.diff (9 lines)
[INFO] [2023-10-13 13:58:40] ...nodes (/app/public/data/price_et_al_pric/taxa.txt)
[CMD] [2023-10-13 13:58:40] echo "0a" > /app/public/data/price_et_al_pric/diff/price_et_al_pric_nodes_30865.diff
[CMD] [2023-10-13 13:58:40] tail -n +1 /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_nodes_30865.csv >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_nodes_30865.diff
[CMD] [2023-10-13 13:58:40] echo "." >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_nodes_30865.diff
[INFO] [2023-10-13 13:58:40] Created diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_nodes_30865.diff (8 lines)
[INFO] [2023-10-13 13:58:40] ...occurrences (/app/public/data/price_et_al_pric/occurrences.txt)
[CMD] [2023-10-13 13:58:40] echo "0a" > /app/public/data/price_et_al_pric/diff/price_et_al_pric_occurrences_30866.diff
[CMD] [2023-10-13 13:58:40] tail -n +1 /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_occurrences_30866.csv >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_occurrences_30866.diff
[CMD] [2023-10-13 13:58:40] echo "." >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_occurrences_30866.diff
[INFO] [2023-10-13 13:58:40] Created diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_occurrences_30866.diff (8 lines)
[INFO] [2023-10-13 13:58:40] ...measurements (/app/public/data/price_et_al_pric/measurementsorfacts.txt)
[CMD] [2023-10-13 13:58:40] echo "0a" > /app/public/data/price_et_al_pric/diff/price_et_al_pric_measurements_30867.diff
[CMD] [2023-10-13 13:58:41] tail -n +1 /app/public/data/price_et_al_pric/converted_csv/price_et_al_pric_measurements_30867.csv >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_measurements_30867.diff
[CMD] [2023-10-13 13:58:41] echo "." >> /app/public/data/price_et_al_pric/diff/price_et_al_pric_measurements_30867.diff
[INFO] [2023-10-13 13:58:41] Created diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_measurements_30867.diff (19 lines)
[STOP] [2023-10-13 13:58:41] calculate_delta
[START] [2023-10-13 13:58:41] parse_diff_and_store
[INFO] [2023-10-13 13:58:41] Handling diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_refs_30868.diff (9 lines)
[INFO] [2023-10-13 13:58:41] Loading refs diff file into memory (9 lines)...
[INFO] [2023-10-13 13:58:41] Storing 7 References (7/7/9)
[INFO] [2023-10-13 13:58:41] Handling diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_nodes_30865.diff (8 lines)
[INFO] [2023-10-13 13:58:41] Loading nodes diff file into memory (8 lines)...
[INFO] [2023-10-13 13:58:41] Storing 6 ScientificNames (12/6/8)
[INFO] [2023-10-13 13:58:41] Storing 6 Nodes (12/6/8)
[INFO] [2023-10-13 13:58:41] Handling diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_occurrences_30866.diff (8 lines)
[INFO] [2023-10-13 13:58:41] Loading occurrences diff file into memory (8 lines)...
[INFO] [2023-10-13 13:58:41] Storing 6 Occurrences (6/6/8)
[INFO] [2023-10-13 13:58:41] Handling diff: /app/public/data/price_et_al_pric/diff/price_et_al_pric_measurements_30867.diff (19 lines)
[INFO] [2023-10-13 13:58:41] Loading measurements diff file into memory (19 lines)...
[INFO] [2023-10-13 13:58:41] Storing 8 TraitsReferences (38/17/19)
[INFO] [2023-10-13 13:58:41] Storing 17 Traits (38/17/19)
[INFO] [2023-10-13 13:58:41] Storing 13 MetaTraits (38/17/19)
[STOP] [2023-10-13 13:58:41] parse_diff_and_store
[START] [2023-10-13 13:58:41] resolve_keys
[2023-10-13 13:58:41] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:58:49] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:58:49] traits to occurrences...
[INFO] [2023-10-13 13:58:49] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:58:49] Traits to sex term...
[INFO] [2023-10-13 13:58:49] Traits to lifestage term...
[INFO] [2023-10-13 13:58:49] MetaTraits to traits...
[INFO] [2023-10-13 13:58:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:58:49] Assocs to occurrences...
[INFO] [2023-10-13 13:58:49] Assocs to nodes...
[INFO] [2023-10-13 13:58:49] Assoc to sex term...
[INFO] [2023-10-13 13:58:49] Assoc to lifestage term...
[INFO] [2023-10-13 13:58:49] MetaAssoc to assocs...
[STOP] [2023-10-13 13:58:49] resolve_keys
[START] [2023-10-13 13:58:49] hold_for_later_1
[STOP] [2023-10-13 13:58:49] hold_for_later_1
[START] [2023-10-13 13:58:49] hold_for_later_2
[STOP] [2023-10-13 13:58:49] hold_for_later_2
[START] [2023-10-13 13:58:49] resolve_missing_parents
[STOP] [2023-10-13 13:58:49] resolve_missing_parents
[START] [2023-10-13 13:58:49] rebuild_nodes
[START] [2023-10-13 13:58:49] Flattener#flatten
[START] [2023-10-13 13:58:49] Flattener#study_resource
[START] [2023-10-13 13:58:49] Flattener#build_ancestry
[STOP] [2023-10-13 13:58:49] Flattener#build_ancestry
[INFO] [2023-10-13 13:58:49] 6 ancestry keys
[START] [2023-10-13 13:58:49] build_node_ancestors
[INFO] [2023-10-13 13:58:49] old ancestors deleted.
[STOP] [2023-10-13 13:58:49] build_node_ancestors
[WARN] [2023-10-13 13:58:49] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:58:49] Flattener#flatten
[STOP] [2023-10-13 13:58:49] rebuild_nodes
[START] [2023-10-13 13:58:49] resolve_missing_media_owners
[STOP] [2023-10-13 13:58:49] resolve_missing_media_owners
[START] [2023-10-13 13:58:49] sanitize_media_verbatims
[STOP] [2023-10-13 13:58:49] sanitize_media_verbatims
[START] [2023-10-13 13:58:49] queue_downloads
[STOP] [2023-10-13 13:58:49] queue_downloads
[START] [2023-10-13 13:58:49] parse_names
[WARN] [2023-10-13 13:58:49] I see 6 names which still need to be parsed.
[WARN] [2023-10-13 13:58:49] Names to parse: 6 formatted: 6 learned: 6 parsed: 6
[STOP] [2023-10-13 13:58:50] parse_names
[START] [2023-10-13 13:58:50] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:58:50] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:58:50] match_nodes
[START] [2023-10-13 13:58:50] map_all_nodes_to_pages
[STOP] [2023-10-13 13:58:50] map_all_nodes_to_pages
[INFO] [2023-10-13 13:58:50] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2023-10-13 13:58:50] update_nodes
[STOP] [2023-10-13 13:58:50] update_nodes
[STOP] [2023-10-13 13:58:50] match_nodes
[START] [2023-10-13 13:58:50] reindex_search
[STOP] [2023-10-13 13:58:50] reindex_search
[START] [2023-10-13 13:58:50] normalize_units
[STOP] [2023-10-13 13:58:50] normalize_units
[START] [2023-10-13 13:58:50] calculate_statistics
[2023-10-13 13:58:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:58:50] Duplicate page_id count: 0
[STOP] [2023-10-13 13:58:50] calculate_statistics
[START] [2023-10-13 13:58:50] complete_harvest_instance
[START] [2023-10-13 13:58:50] overall_tsv_creation
[INFO] [2023-10-13 13:58:50] Exporting 6 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:58:50] Processing group of 6 in 1 batches of 10000
[INFO] [2023-10-13 13:58:50] 9 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:58:50] Building Traits map for 6 nodes (this can take a while)...
[INFO] [2023-10-13 13:58:50] Mapped 9 traits (13 meta) for 6 nodes.
[INFO] [2023-10-13 13:58:50] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:58:50] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:58:50] Adding 9 traits...
[INFO] [2023-10-13 13:58:50] 16 metadata added.
[INFO] [2023-10-13 13:58:50] Adding 0 assocs...
[INFO] [2023-10-13 13:58:50] 0 metadata added.
[INFO] [2023-10-13 13:59:34] Processed 6/6 nodes
[INFO] [2023-10-13 13:59:34] Average Time: 44.04
[INFO] [2023-10-13 13:59:34] Total Time: 45s
[STOP] [2023-10-13 13:59:34] overall_tsv_creation
[INFO] [2023-10-13 13:59:34] Done. Check your files:
[INFO] [2023-10-13 13:59:34] (6 lines) /app/public/data/price_et_al_pric/publish_nodes.tsv
[INFO] [2023-10-13 13:59:34] (6 lines) /app/public/data/price_et_al_pric/publish_scientific_names.tsv
[INFO] [2023-10-13 13:59:35] (10 lines) /app/public/data/price_et_al_pric/publish_traits.tsv
[INFO] [2023-10-13 13:59:35] (17 lines) /app/public/data/price_et_al_pric/publish_metadata.tsv
[STOP] [2023-10-13 13:59:35] complete_harvest_instance
[START] [2023-10-13 13:59:35] completed
[STOP] [2023-10-13 13:59:35] completed
[STOP] [2023-10-13 13:59:35] logged process, took 55.46

Latest Process

13 Oct 13:58 EXITED currently processing 0