Harvest for Hetherington and Lindquist 1999 Created 31 May 19:38

Harvesting Log

[INFO] [2021-05-31 19:38:56] Created harvest instance #3956
[STOP] [2021-05-31 19:38:56] create_harvest_instance
[START] [2021-05-31 19:38:56] fetch_files
[STOP] [2021-05-31 19:38:56] fetch_files
[START] [2021-05-31 19:38:56] validate_each_file
[INFO] [2021-05-31 19:38:56] Looping over 4 formats...
[INFO] [2021-05-31 19:38:56] ...refs (/app/public/data/hetherington_lin/references.txt)
[INFO] [2021-05-31 19:38:56] Valid: /app/public/converted_csv/hetherington_lin_refs_3956.csv (0 lines)
[INFO] [2021-05-31 19:38:56] ...nodes (/app/public/data/hetherington_lin/taxa.txt)
[INFO] [2021-05-31 19:38:56] Valid: /app/public/converted_csv/hetherington_lin_nodes_3956.csv (1 lines)
[INFO] [2021-05-31 19:38:56] ...occurrences (/app/public/data/hetherington_lin/occurrences.txt)
[INFO] [2021-05-31 19:38:56] Valid: /app/public/converted_csv/hetherington_lin_occurrences_3956.csv (1 lines)
[INFO] [2021-05-31 19:38:56] ...measurements (/app/public/data/hetherington_lin/measurementsorfacts.txt)
[INFO] [2021-05-31 19:38:56] Valid: /app/public/converted_csv/hetherington_lin_measurements_3956.csv (3 lines)
[STOP] [2021-05-31 19:38:56] validate_each_file
[START] [2021-05-31 19:38:56] convert_to_csv
[INFO] [2021-05-31 19:38:56] Looping over 4 formats...
[INFO] [2021-05-31 19:38:56] ...refs (/app/public/data/hetherington_lin/references.txt)
[CMD] [2021-05-31 19:38:56] /usr/bin/sort /app/public/converted_csv/hetherington_lin_refs_3956.csv > /app/public/converted_csv/hetherington_lin_refs_3956.csv_sorted
[INFO] [2021-05-31 19:38:56] Converted: /app/public/converted_csv/hetherington_lin_refs_3956.csv (0 lines)
[INFO] [2021-05-31 19:38:56] ...nodes (/app/public/data/hetherington_lin/taxa.txt)
[CMD] [2021-05-31 19:38:56] /usr/bin/sort /app/public/converted_csv/hetherington_lin_nodes_3956.csv > /app/public/converted_csv/hetherington_lin_nodes_3956.csv_sorted
[INFO] [2021-05-31 19:38:57] Converted: /app/public/converted_csv/hetherington_lin_nodes_3956.csv (1 lines)
[INFO] [2021-05-31 19:38:57] ...occurrences (/app/public/data/hetherington_lin/occurrences.txt)
[CMD] [2021-05-31 19:38:57] /usr/bin/sort /app/public/converted_csv/hetherington_lin_occurrences_3956.csv > /app/public/converted_csv/hetherington_lin_occurrences_3956.csv_sorted
[INFO] [2021-05-31 19:38:57] Converted: /app/public/converted_csv/hetherington_lin_occurrences_3956.csv (1 lines)
[INFO] [2021-05-31 19:38:57] ...measurements (/app/public/data/hetherington_lin/measurementsorfacts.txt)
[CMD] [2021-05-31 19:38:57] /usr/bin/sort /app/public/converted_csv/hetherington_lin_measurements_3956.csv > /app/public/converted_csv/hetherington_lin_measurements_3956.csv_sorted
[INFO] [2021-05-31 19:38:57] Converted: /app/public/converted_csv/hetherington_lin_measurements_3956.csv (3 lines)
[STOP] [2021-05-31 19:38:57] convert_to_csv
[START] [2021-05-31 19:38:57] calculate_delta
[INFO] [2021-05-31 19:38:57] Looping over 4 formats...
[INFO] [2021-05-31 19:38:57] ...refs (/app/public/data/hetherington_lin/references.txt)
[CMD] [2021-05-31 19:38:57] echo "0a" > /app/public/diff/hetherington_lin_refs_3956.diff
[CMD] [2021-05-31 19:38:58] tail -n +1 /app/public/converted_csv/hetherington_lin_refs_3956.csv >> /app/public/diff/hetherington_lin_refs_3956.diff
[CMD] [2021-05-31 19:38:58] echo "." >> /app/public/diff/hetherington_lin_refs_3956.diff
[INFO] [2021-05-31 19:38:59] Created diff: /app/public/diff/hetherington_lin_refs_3956.diff (2 lines)
[INFO] [2021-05-31 19:38:59] ...nodes (/app/public/data/hetherington_lin/taxa.txt)
[CMD] [2021-05-31 19:38:59] echo "0a" > /app/public/diff/hetherington_lin_nodes_3956.diff
[CMD] [2021-05-31 19:38:59] tail -n +1 /app/public/converted_csv/hetherington_lin_nodes_3956.csv >> /app/public/diff/hetherington_lin_nodes_3956.diff
[CMD] [2021-05-31 19:38:59] echo "." >> /app/public/diff/hetherington_lin_nodes_3956.diff
[INFO] [2021-05-31 19:39:00] Created diff: /app/public/diff/hetherington_lin_nodes_3956.diff (3 lines)
[INFO] [2021-05-31 19:39:00] ...occurrences (/app/public/data/hetherington_lin/occurrences.txt)
[CMD] [2021-05-31 19:39:00] echo "0a" > /app/public/diff/hetherington_lin_occurrences_3956.diff
[CMD] [2021-05-31 19:39:00] tail -n +1 /app/public/converted_csv/hetherington_lin_occurrences_3956.csv >> /app/public/diff/hetherington_lin_occurrences_3956.diff
[CMD] [2021-05-31 19:39:01] echo "." >> /app/public/diff/hetherington_lin_occurrences_3956.diff
[INFO] [2021-05-31 19:39:01] Created diff: /app/public/diff/hetherington_lin_occurrences_3956.diff (3 lines)
[INFO] [2021-05-31 19:39:01] ...measurements (/app/public/data/hetherington_lin/measurementsorfacts.txt)
[CMD] [2021-05-31 19:39:01] echo "0a" > /app/public/diff/hetherington_lin_measurements_3956.diff
[CMD] [2021-05-31 19:39:01] tail -n +1 /app/public/converted_csv/hetherington_lin_measurements_3956.csv >> /app/public/diff/hetherington_lin_measurements_3956.diff
[CMD] [2021-05-31 19:39:02] echo "." >> /app/public/diff/hetherington_lin_measurements_3956.diff
[INFO] [2021-05-31 19:39:02] Created diff: /app/public/diff/hetherington_lin_measurements_3956.diff (5 lines)
[STOP] [2021-05-31 19:39:02] calculate_delta
[START] [2021-05-31 19:39:02] parse_diff_and_store
[INFO] [2021-05-31 19:39:02] Handling diff: /app/public/diff/hetherington_lin_refs_3956.diff (2 lines)
[INFO] [2021-05-31 19:39:03] Loading refs diff file into memory (2 /app/public/diff/hetherington_lin_refs_3956.diff lines)...
[INFO] [2021-05-31 19:39:03] Handling diff: /app/public/diff/hetherington_lin_nodes_3956.diff (3 lines)
[INFO] [2021-05-31 19:39:03] Loading nodes diff file into memory (3 /app/public/diff/hetherington_lin_nodes_3956.diff lines)...
[INFO] [2021-05-31 19:39:04] Handling diff: /app/public/diff/hetherington_lin_occurrences_3956.diff (3 lines)
[INFO] [2021-05-31 19:39:04] Loading occurrences diff file into memory (3 /app/public/diff/hetherington_lin_occurrences_3956.diff lines)...
[INFO] [2021-05-31 19:39:04] Handling diff: /app/public/diff/hetherington_lin_measurements_3956.diff (5 lines)
[INFO] [2021-05-31 19:39:05] Loading measurements diff file into memory (5 /app/public/diff/hetherington_lin_measurements_3956.diff lines)...
[INFO] [2021-05-31 19:39:05] Storing 1 ScientificNames
[INFO] [2021-05-31 19:39:05] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:39:05] Average Time: 0.0
[INFO] [2021-05-31 19:39:05] Total Time: 1s
[INFO] [2021-05-31 19:39:05] Storing 1 Nodes
[INFO] [2021-05-31 19:39:05] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:39:05] Average Time: 0.0
[INFO] [2021-05-31 19:39:05] Total Time: 1s
[INFO] [2021-05-31 19:39:05] Storing 1 Occurrences
[INFO] [2021-05-31 19:39:05] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:39:05] Average Time: 0.0
[INFO] [2021-05-31 19:39:05] Total Time: 1s
[INFO] [2021-05-31 19:39:05] Storing 1 OccurrenceMetadata
[INFO] [2021-05-31 19:39:05] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:39:05] Average Time: 0.0
[INFO] [2021-05-31 19:39:05] Total Time: 1s
[INFO] [2021-05-31 19:39:05] Storing 3 Traits
[INFO] [2021-05-31 19:39:05] Processing group of 3 in 1 groups of 1000
[INFO] [2021-05-31 19:39:05] Average Time: 0.0
[INFO] [2021-05-31 19:39:05] Total Time: 1s
[INFO] [2021-05-31 19:39:05] Storing 4 MetaTraits
[INFO] [2021-05-31 19:39:05] Processing group of 4 in 1 groups of 1000
[INFO] [2021-05-31 19:39:05] Average Time: 0.0
[INFO] [2021-05-31 19:39:05] Total Time: 1s
[STOP] [2021-05-31 19:39:05] parse_diff_and_store
[START] [2021-05-31 19:39:05] resolve_keys
[INFO] [2021-05-31 19:39:11] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:39:11] traits to occurrences...
[INFO] [2021-05-31 19:39:11] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:39:11] Traits to sex term...
[INFO] [2021-05-31 19:39:11] Traits to lifestage term...
[INFO] [2021-05-31 19:39:11] MetaTraits to traits...
[INFO] [2021-05-31 19:39:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:39:11] Assocs to occurrences...
[INFO] [2021-05-31 19:39:11] Assocs to nodes...
[INFO] [2021-05-31 19:39:11] Assoc to sex term...
[INFO] [2021-05-31 19:39:11] Assoc to lifestage term...
[INFO] [2021-05-31 19:39:11] MetaAssoc to assocs...
[STOP] [2021-05-31 19:39:11] resolve_keys
[START] [2021-05-31 19:39:11] hold_for_later_1
[STOP] [2021-05-31 19:39:11] hold_for_later_1
[START] [2021-05-31 19:39:11] hold_for_later_2
[STOP] [2021-05-31 19:39:11] hold_for_later_2
[START] [2021-05-31 19:39:11] resolve_missing_parents
[STOP] [2021-05-31 19:39:11] resolve_missing_parents
[START] [2021-05-31 19:39:11] rebuild_nodes
[START] [2021-05-31 19:39:11] Flattener#flatten
[START] [2021-05-31 19:39:11] Flattener#study_resource
[START] [2021-05-31 19:39:11] Flattener#build_ancestry
[STOP] [2021-05-31 19:39:11] Flattener#build_ancestry
[INFO] [2021-05-31 19:39:11] 1 ancestry keys
[START] [2021-05-31 19:39:11] build_node_ancestors
[INFO] [2021-05-31 19:39:11] old ancestors deleted.
[STOP] [2021-05-31 19:39:11] build_node_ancestors
[WARN] [2021-05-31 19:39:11] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:39:11] Flattener#flatten
[STOP] [2021-05-31 19:39:11] rebuild_nodes
[START] [2021-05-31 19:39:11] resolve_missing_media_owners
[STOP] [2021-05-31 19:39:11] resolve_missing_media_owners
[START] [2021-05-31 19:39:11] sanitize_media_verbatims
[STOP] [2021-05-31 19:39:11] sanitize_media_verbatims
[START] [2021-05-31 19:39:11] queue_downloads
[STOP] [2021-05-31 19:39:11] queue_downloads
[START] [2021-05-31 19:39:11] parse_names
[WARN] [2021-05-31 19:39:11] I see 1 names which still need to be parsed.
[STOP] [2021-05-31 19:39:12] parse_names
[START] [2021-05-31 19:39:12] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:39:12] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:39:12] match_nodes
[START] [2021-05-31 19:39:12] map_all_nodes_to_pages
[STOP] [2021-05-31 19:39:12] map_all_nodes_to_pages
[INFO] [2021-05-31 19:39:12] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-05-31 19:39:12] update_nodes
[STOP] [2021-05-31 19:39:12] update_nodes
[STOP] [2021-05-31 19:39:12] match_nodes
[START] [2021-05-31 19:39:12] reindex_search
[STOP] [2021-05-31 19:39:12] reindex_search
[START] [2021-05-31 19:39:12] normalize_units
[STOP] [2021-05-31 19:39:12] normalize_units
[START] [2021-05-31 19:39:12] calculate_statistics
[2021-05-31 19:39:12] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:39:12] calculate_statistics
[START] [2021-05-31 19:39:12] complete_harvest_instance
[START] [2021-05-31 19:39:12] overall_tsv_creation
[INFO] [2021-05-31 19:39:13] Processing group of 1 in 1 batches of 10000
[INFO] [2021-05-31 19:39:44] 3 Traits (unfiltered)...
[INFO] [2021-05-31 19:40:09] 3 Traits (filtered)...
[INFO] [2021-05-31 19:40:09] 0 Associations (filtered)...
[INFO] [2021-05-31 19:40:09] 0 metadata added.
[INFO] [2021-05-31 19:40:09] 0 metadata added.
[INFO] [2021-05-31 19:40:32] Average Time: 57.83
[INFO] [2021-05-31 19:40:32] Total Time: 1m20s
[STOP] [2021-05-31 19:40:32] overall_tsv_creation
[INFO] [2021-05-31 19:40:32] Done. Check your files:
[INFO] [2021-05-31 19:40:32] (1 lines) /app/public/data/hetherington_lin/publish_nodes.tsv
[INFO] [2021-05-31 19:40:33] (1 lines) /app/public/data/hetherington_lin/publish_scientific_names.tsv
[INFO] [2021-05-31 19:40:33] (4 lines) /app/public/data/hetherington_lin/publish_traits.tsv
[INFO] [2021-05-31 19:40:33] (1 lines) /app/public/data/hetherington_lin/publish_metadata.tsv
[STOP] [2021-05-31 19:40:33] complete_harvest_instance
[START] [2021-05-31 19:40:33] completed
[STOP] [2021-05-31 19:40:33] completed
[STOP] [2021-05-31 19:40:33] logged process, took 98.05

Latest Process

31 May 19:38 EXITED currently processing 0