Harvest for Womack et al 2017 Created 31 May 19:21

Harvesting Log

[INFO] [2021-05-31 19:21:55] Created harvest instance #3949
[STOP] [2021-05-31 19:21:55] create_harvest_instance
[START] [2021-05-31 19:21:55] fetch_files
[STOP] [2021-05-31 19:21:55] fetch_files
[START] [2021-05-31 19:21:55] validate_each_file
[INFO] [2021-05-31 19:21:55] Looping over 4 formats...
[INFO] [2021-05-31 19:21:55] ...refs (/app/public/data/womack_et_al_wom/references.txt)
[INFO] [2021-05-31 19:21:55] Valid: /app/public/converted_csv/womack_et_al_wom_refs_3949.csv (0 lines)
[INFO] [2021-05-31 19:21:55] ...nodes (/app/public/data/womack_et_al_wom/taxa.txt)
[INFO] [2021-05-31 19:21:55] Valid: /app/public/converted_csv/womack_et_al_wom_nodes_3949.csv (4 lines)
[INFO] [2021-05-31 19:21:55] ...occurrences (/app/public/data/womack_et_al_wom/occurrences.txt)
[INFO] [2021-05-31 19:21:55] Valid: /app/public/converted_csv/womack_et_al_wom_occurrences_3949.csv (4 lines)
[INFO] [2021-05-31 19:21:55] ...measurements (/app/public/data/womack_et_al_wom/measurementsorfacts.txt)
[INFO] [2021-05-31 19:21:55] Valid: /app/public/converted_csv/womack_et_al_wom_measurements_3949.csv (16 lines)
[STOP] [2021-05-31 19:21:55] validate_each_file
[START] [2021-05-31 19:21:55] convert_to_csv
[INFO] [2021-05-31 19:21:55] Looping over 4 formats...
[INFO] [2021-05-31 19:21:55] ...refs (/app/public/data/womack_et_al_wom/references.txt)
[CMD] [2021-05-31 19:21:55] /usr/bin/sort /app/public/converted_csv/womack_et_al_wom_refs_3949.csv > /app/public/converted_csv/womack_et_al_wom_refs_3949.csv_sorted
[INFO] [2021-05-31 19:21:56] Converted: /app/public/converted_csv/womack_et_al_wom_refs_3949.csv (0 lines)
[INFO] [2021-05-31 19:21:56] ...nodes (/app/public/data/womack_et_al_wom/taxa.txt)
[CMD] [2021-05-31 19:21:56] /usr/bin/sort /app/public/converted_csv/womack_et_al_wom_nodes_3949.csv > /app/public/converted_csv/womack_et_al_wom_nodes_3949.csv_sorted
[INFO] [2021-05-31 19:21:56] Converted: /app/public/converted_csv/womack_et_al_wom_nodes_3949.csv (4 lines)
[INFO] [2021-05-31 19:21:56] ...occurrences (/app/public/data/womack_et_al_wom/occurrences.txt)
[CMD] [2021-05-31 19:21:56] /usr/bin/sort /app/public/converted_csv/womack_et_al_wom_occurrences_3949.csv > /app/public/converted_csv/womack_et_al_wom_occurrences_3949.csv_sorted
[INFO] [2021-05-31 19:21:56] Converted: /app/public/converted_csv/womack_et_al_wom_occurrences_3949.csv (4 lines)
[INFO] [2021-05-31 19:21:56] ...measurements (/app/public/data/womack_et_al_wom/measurementsorfacts.txt)
[CMD] [2021-05-31 19:21:56] /usr/bin/sort /app/public/converted_csv/womack_et_al_wom_measurements_3949.csv > /app/public/converted_csv/womack_et_al_wom_measurements_3949.csv_sorted
[INFO] [2021-05-31 19:21:57] Converted: /app/public/converted_csv/womack_et_al_wom_measurements_3949.csv (16 lines)
[STOP] [2021-05-31 19:21:57] convert_to_csv
[START] [2021-05-31 19:21:57] calculate_delta
[INFO] [2021-05-31 19:21:57] Looping over 4 formats...
[INFO] [2021-05-31 19:21:57] ...refs (/app/public/data/womack_et_al_wom/references.txt)
[CMD] [2021-05-31 19:21:57] echo "0a" > /app/public/diff/womack_et_al_wom_refs_3949.diff
[CMD] [2021-05-31 19:21:57] tail -n +1 /app/public/converted_csv/womack_et_al_wom_refs_3949.csv >> /app/public/diff/womack_et_al_wom_refs_3949.diff
[CMD] [2021-05-31 19:21:57] echo "." >> /app/public/diff/womack_et_al_wom_refs_3949.diff
[INFO] [2021-05-31 19:21:58] Created diff: /app/public/diff/womack_et_al_wom_refs_3949.diff (2 lines)
[INFO] [2021-05-31 19:21:58] ...nodes (/app/public/data/womack_et_al_wom/taxa.txt)
[CMD] [2021-05-31 19:21:58] echo "0a" > /app/public/diff/womack_et_al_wom_nodes_3949.diff
[CMD] [2021-05-31 19:21:58] tail -n +1 /app/public/converted_csv/womack_et_al_wom_nodes_3949.csv >> /app/public/diff/womack_et_al_wom_nodes_3949.diff
[CMD] [2021-05-31 19:21:59] echo "." >> /app/public/diff/womack_et_al_wom_nodes_3949.diff
[INFO] [2021-05-31 19:21:59] Created diff: /app/public/diff/womack_et_al_wom_nodes_3949.diff (6 lines)
[INFO] [2021-05-31 19:21:59] ...occurrences (/app/public/data/womack_et_al_wom/occurrences.txt)
[CMD] [2021-05-31 19:21:59] echo "0a" > /app/public/diff/womack_et_al_wom_occurrences_3949.diff
[CMD] [2021-05-31 19:21:59] tail -n +1 /app/public/converted_csv/womack_et_al_wom_occurrences_3949.csv >> /app/public/diff/womack_et_al_wom_occurrences_3949.diff
[CMD] [2021-05-31 19:22:00] echo "." >> /app/public/diff/womack_et_al_wom_occurrences_3949.diff
[INFO] [2021-05-31 19:22:00] Created diff: /app/public/diff/womack_et_al_wom_occurrences_3949.diff (6 lines)
[INFO] [2021-05-31 19:22:00] ...measurements (/app/public/data/womack_et_al_wom/measurementsorfacts.txt)
[CMD] [2021-05-31 19:22:00] echo "0a" > /app/public/diff/womack_et_al_wom_measurements_3949.diff
[CMD] [2021-05-31 19:22:00] tail -n +1 /app/public/converted_csv/womack_et_al_wom_measurements_3949.csv >> /app/public/diff/womack_et_al_wom_measurements_3949.diff
[CMD] [2021-05-31 19:22:01] echo "." >> /app/public/diff/womack_et_al_wom_measurements_3949.diff
[INFO] [2021-05-31 19:22:01] Created diff: /app/public/diff/womack_et_al_wom_measurements_3949.diff (18 lines)
[STOP] [2021-05-31 19:22:01] calculate_delta
[START] [2021-05-31 19:22:01] parse_diff_and_store
[INFO] [2021-05-31 19:22:01] Handling diff: /app/public/diff/womack_et_al_wom_refs_3949.diff (2 lines)
[INFO] [2021-05-31 19:22:01] Loading refs diff file into memory (2 /app/public/diff/womack_et_al_wom_refs_3949.diff lines)...
[INFO] [2021-05-31 19:22:02] Handling diff: /app/public/diff/womack_et_al_wom_nodes_3949.diff (6 lines)
[INFO] [2021-05-31 19:22:02] Loading nodes diff file into memory (6 /app/public/diff/womack_et_al_wom_nodes_3949.diff lines)...
[INFO] [2021-05-31 19:22:03] Handling diff: /app/public/diff/womack_et_al_wom_occurrences_3949.diff (6 lines)
[INFO] [2021-05-31 19:22:03] Loading occurrences diff file into memory (6 /app/public/diff/womack_et_al_wom_occurrences_3949.diff lines)...
[INFO] [2021-05-31 19:22:03] Handling diff: /app/public/diff/womack_et_al_wom_measurements_3949.diff (18 lines)
[INFO] [2021-05-31 19:22:04] Loading measurements diff file into memory (18 /app/public/diff/womack_et_al_wom_measurements_3949.diff lines)...
[INFO] [2021-05-31 19:22:04] Storing 4 ScientificNames
[INFO] [2021-05-31 19:22:04] Processing group of 4 in 1 groups of 1000
[INFO] [2021-05-31 19:22:04] Average Time: 0.0
[INFO] [2021-05-31 19:22:04] Total Time: 1s
[INFO] [2021-05-31 19:22:04] Storing 4 Nodes
[INFO] [2021-05-31 19:22:04] Processing group of 4 in 1 groups of 1000
[INFO] [2021-05-31 19:22:04] Average Time: 0.0
[INFO] [2021-05-31 19:22:04] Total Time: 1s
[INFO] [2021-05-31 19:22:04] Storing 4 Occurrences
[INFO] [2021-05-31 19:22:04] Processing group of 4 in 1 groups of 1000
[INFO] [2021-05-31 19:22:04] Average Time: 0.0
[INFO] [2021-05-31 19:22:04] Total Time: 1s
[INFO] [2021-05-31 19:22:04] Storing 4 OccurrenceMetadata
[INFO] [2021-05-31 19:22:04] Processing group of 4 in 1 groups of 1000
[INFO] [2021-05-31 19:22:04] Average Time: 0.0
[INFO] [2021-05-31 19:22:04] Total Time: 1s
[INFO] [2021-05-31 19:22:04] Storing 16 Traits
[INFO] [2021-05-31 19:22:04] Processing group of 16 in 1 groups of 1000
[INFO] [2021-05-31 19:22:04] Average Time: 0.01
[INFO] [2021-05-31 19:22:04] Total Time: 1s
[INFO] [2021-05-31 19:22:04] Storing 16 MetaTraits
[INFO] [2021-05-31 19:22:04] Processing group of 16 in 1 groups of 1000
[INFO] [2021-05-31 19:22:04] Average Time: 0.0
[INFO] [2021-05-31 19:22:04] Total Time: 1s
[STOP] [2021-05-31 19:22:04] parse_diff_and_store
[START] [2021-05-31 19:22:04] resolve_keys
[INFO] [2021-05-31 19:22:10] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:22:10] traits to occurrences...
[INFO] [2021-05-31 19:22:10] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:22:10] Traits to sex term...
[INFO] [2021-05-31 19:22:10] Traits to lifestage term...
[INFO] [2021-05-31 19:22:10] MetaTraits to traits...
[INFO] [2021-05-31 19:22:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:22:10] Assocs to occurrences...
[INFO] [2021-05-31 19:22:10] Assocs to nodes...
[INFO] [2021-05-31 19:22:10] Assoc to sex term...
[INFO] [2021-05-31 19:22:10] Assoc to lifestage term...
[INFO] [2021-05-31 19:22:10] MetaAssoc to assocs...
[STOP] [2021-05-31 19:22:10] resolve_keys
[START] [2021-05-31 19:22:10] hold_for_later_1
[STOP] [2021-05-31 19:22:10] hold_for_later_1
[START] [2021-05-31 19:22:10] hold_for_later_2
[STOP] [2021-05-31 19:22:10] hold_for_later_2
[START] [2021-05-31 19:22:10] resolve_missing_parents
[STOP] [2021-05-31 19:22:10] resolve_missing_parents
[START] [2021-05-31 19:22:10] rebuild_nodes
[START] [2021-05-31 19:22:10] Flattener#flatten
[START] [2021-05-31 19:22:10] Flattener#study_resource
[START] [2021-05-31 19:22:10] Flattener#build_ancestry
[STOP] [2021-05-31 19:22:10] Flattener#build_ancestry
[INFO] [2021-05-31 19:22:10] 4 ancestry keys
[START] [2021-05-31 19:22:10] build_node_ancestors
[INFO] [2021-05-31 19:22:10] old ancestors deleted.
[STOP] [2021-05-31 19:22:10] build_node_ancestors
[WARN] [2021-05-31 19:22:10] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:22:10] Flattener#flatten
[STOP] [2021-05-31 19:22:10] rebuild_nodes
[START] [2021-05-31 19:22:10] resolve_missing_media_owners
[STOP] [2021-05-31 19:22:10] resolve_missing_media_owners
[START] [2021-05-31 19:22:10] sanitize_media_verbatims
[STOP] [2021-05-31 19:22:10] sanitize_media_verbatims
[START] [2021-05-31 19:22:10] queue_downloads
[STOP] [2021-05-31 19:22:10] queue_downloads
[START] [2021-05-31 19:22:10] parse_names
[WARN] [2021-05-31 19:22:10] I see 4 names which still need to be parsed.
[STOP] [2021-05-31 19:22:11] parse_names
[START] [2021-05-31 19:22:11] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:22:11] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:22:11] match_nodes
[START] [2021-05-31 19:22:11] map_all_nodes_to_pages
[STOP] [2021-05-31 19:22:11] map_all_nodes_to_pages
[INFO] [2021-05-31 19:22:11] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2021-05-31 19:22:11] update_nodes
[STOP] [2021-05-31 19:22:11] update_nodes
[STOP] [2021-05-31 19:22:11] match_nodes
[START] [2021-05-31 19:22:11] reindex_search
[STOP] [2021-05-31 19:22:11] reindex_search
[START] [2021-05-31 19:22:11] normalize_units
[STOP] [2021-05-31 19:22:11] normalize_units
[START] [2021-05-31 19:22:11] calculate_statistics
[2021-05-31 19:22:11] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:22:11] calculate_statistics
[START] [2021-05-31 19:22:11] complete_harvest_instance
[START] [2021-05-31 19:22:11] overall_tsv_creation
[INFO] [2021-05-31 19:22:11] Processing group of 4 in 1 batches of 10000
[INFO] [2021-05-31 19:22:44] 16 Traits (unfiltered)...
[INFO] [2021-05-31 19:23:10] 16 Traits (filtered)...
[INFO] [2021-05-31 19:23:10] 0 Associations (filtered)...
[INFO] [2021-05-31 19:23:10] 0 metadata added.
[INFO] [2021-05-31 19:23:10] 0 metadata added.
[INFO] [2021-05-31 19:23:32] Average Time: 59.02
[INFO] [2021-05-31 19:23:32] Total Time: 1m21s
[STOP] [2021-05-31 19:23:32] overall_tsv_creation
[INFO] [2021-05-31 19:23:32] Done. Check your files:
[INFO] [2021-05-31 19:23:33] (4 lines) /app/public/data/womack_et_al_wom/publish_nodes.tsv
[INFO] [2021-05-31 19:23:33] (4 lines) /app/public/data/womack_et_al_wom/publish_scientific_names.tsv
[INFO] [2021-05-31 19:23:33] (17 lines) /app/public/data/womack_et_al_wom/publish_traits.tsv
[INFO] [2021-05-31 19:23:34] (1 lines) /app/public/data/womack_et_al_wom/publish_metadata.tsv
[STOP] [2021-05-31 19:23:34] complete_harvest_instance
[START] [2021-05-31 19:23:34] completed
[STOP] [2021-05-31 19:23:34] completed
[STOP] [2021-05-31 19:23:34] logged process, took 99.01

Latest Process

31 May 19:21 EXITED currently processing 0