Harvest for Budelmann 1992 Created 31 May 19:32

Stage: completed
Fetched: 31 May 19:32
Validated: 31 May 19:32
Deltas Created 31 May 19:32
Units Normalized: 31 May 19:32
Ancestry Built: 31 May 19:32
Nodes Matched: 31 May 19:32
Names Parsed: 31 May 19:32
New Models Stored: 31 May 19:32
Indexed: 31 May 19:32
Completed: 31 May 19:33
Time to Harvest: less than a minute

Harvesting Log

(168 lines)
[INFO] [2021-05-31 19:32:19] Created harvest instance #3953
[STOP] [2021-05-31 19:32:19] create_harvest_instance
[START] [2021-05-31 19:32:19] fetch_files
[STOP] [2021-05-31 19:32:19] fetch_files
[START] [2021-05-31 19:32:19] validate_each_file
[INFO] [2021-05-31 19:32:19] Looping over 4 formats...
[INFO] [2021-05-31 19:32:19] ...refs (/app/public/data/budelmann_budelm/references.txt)
[INFO] [2021-05-31 19:32:19] Valid: /app/public/converted_csv/budelmann_budelm_refs_3953.csv (2 lines)
[INFO] [2021-05-31 19:32:19] ...nodes (/app/public/data/budelmann_budelm/taxa.txt)
[INFO] [2021-05-31 19:32:19] Valid: /app/public/converted_csv/budelmann_budelm_nodes_3953.csv (1 lines)
[INFO] [2021-05-31 19:32:19] ...occurrences (/app/public/data/budelmann_budelm/occurrences.txt)
[INFO] [2021-05-31 19:32:19] Valid: /app/public/converted_csv/budelmann_budelm_occurrences_3953.csv (1 lines)
[INFO] [2021-05-31 19:32:19] ...measurements (/app/public/data/budelmann_budelm/measurementsorfacts.txt)
[INFO] [2021-05-31 19:32:19] Valid: /app/public/converted_csv/budelmann_budelm_measurements_3953.csv (11 lines)
[STOP] [2021-05-31 19:32:19] validate_each_file
[START] [2021-05-31 19:32:19] convert_to_csv
[INFO] [2021-05-31 19:32:19] Looping over 4 formats...
[INFO] [2021-05-31 19:32:19] ...refs (/app/public/data/budelmann_budelm/references.txt)
[CMD] [2021-05-31 19:32:19] /usr/bin/sort /app/public/converted_csv/budelmann_budelm_refs_3953.csv > /app/public/converted_csv/budelmann_budelm_refs_3953.csv_sorted
[INFO] [2021-05-31 19:32:19] Converted: /app/public/converted_csv/budelmann_budelm_refs_3953.csv (2 lines)
[INFO] [2021-05-31 19:32:19] ...nodes (/app/public/data/budelmann_budelm/taxa.txt)
[CMD] [2021-05-31 19:32:19] /usr/bin/sort /app/public/converted_csv/budelmann_budelm_nodes_3953.csv > /app/public/converted_csv/budelmann_budelm_nodes_3953.csv_sorted
[INFO] [2021-05-31 19:32:20] Converted: /app/public/converted_csv/budelmann_budelm_nodes_3953.csv (1 lines)
[INFO] [2021-05-31 19:32:20] ...occurrences (/app/public/data/budelmann_budelm/occurrences.txt)
[CMD] [2021-05-31 19:32:20] /usr/bin/sort /app/public/converted_csv/budelmann_budelm_occurrences_3953.csv > /app/public/converted_csv/budelmann_budelm_occurrences_3953.csv_sorted
[INFO] [2021-05-31 19:32:20] Converted: /app/public/converted_csv/budelmann_budelm_occurrences_3953.csv (1 lines)
[INFO] [2021-05-31 19:32:20] ...measurements (/app/public/data/budelmann_budelm/measurementsorfacts.txt)
[CMD] [2021-05-31 19:32:20] /usr/bin/sort /app/public/converted_csv/budelmann_budelm_measurements_3953.csv > /app/public/converted_csv/budelmann_budelm_measurements_3953.csv_sorted
[INFO] [2021-05-31 19:32:20] Converted: /app/public/converted_csv/budelmann_budelm_measurements_3953.csv (11 lines)
[STOP] [2021-05-31 19:32:20] convert_to_csv
[START] [2021-05-31 19:32:20] calculate_delta
[INFO] [2021-05-31 19:32:20] Looping over 4 formats...
[INFO] [2021-05-31 19:32:20] ...refs (/app/public/data/budelmann_budelm/references.txt)
[CMD] [2021-05-31 19:32:20] echo "0a" > /app/public/diff/budelmann_budelm_refs_3953.diff
[CMD] [2021-05-31 19:32:21] tail -n +1 /app/public/converted_csv/budelmann_budelm_refs_3953.csv >> /app/public/diff/budelmann_budelm_refs_3953.diff
[CMD] [2021-05-31 19:32:21] echo "." >> /app/public/diff/budelmann_budelm_refs_3953.diff
[INFO] [2021-05-31 19:32:22] Created diff: /app/public/diff/budelmann_budelm_refs_3953.diff (4 lines)
[INFO] [2021-05-31 19:32:22] ...nodes (/app/public/data/budelmann_budelm/taxa.txt)
[CMD] [2021-05-31 19:32:22] echo "0a" > /app/public/diff/budelmann_budelm_nodes_3953.diff
[CMD] [2021-05-31 19:32:22] tail -n +1 /app/public/converted_csv/budelmann_budelm_nodes_3953.csv >> /app/public/diff/budelmann_budelm_nodes_3953.diff
[CMD] [2021-05-31 19:32:22] echo "." >> /app/public/diff/budelmann_budelm_nodes_3953.diff
[INFO] [2021-05-31 19:32:23] Created diff: /app/public/diff/budelmann_budelm_nodes_3953.diff (3 lines)
[INFO] [2021-05-31 19:32:23] ...occurrences (/app/public/data/budelmann_budelm/occurrences.txt)
[CMD] [2021-05-31 19:32:23] echo "0a" > /app/public/diff/budelmann_budelm_occurrences_3953.diff
[CMD] [2021-05-31 19:32:23] tail -n +1 /app/public/converted_csv/budelmann_budelm_occurrences_3953.csv >> /app/public/diff/budelmann_budelm_occurrences_3953.diff
[CMD] [2021-05-31 19:32:24] echo "." >> /app/public/diff/budelmann_budelm_occurrences_3953.diff
[INFO] [2021-05-31 19:32:24] Created diff: /app/public/diff/budelmann_budelm_occurrences_3953.diff (3 lines)
[INFO] [2021-05-31 19:32:24] ...measurements (/app/public/data/budelmann_budelm/measurementsorfacts.txt)
[CMD] [2021-05-31 19:32:24] echo "0a" > /app/public/diff/budelmann_budelm_measurements_3953.diff
[CMD] [2021-05-31 19:32:24] tail -n +1 /app/public/converted_csv/budelmann_budelm_measurements_3953.csv >> /app/public/diff/budelmann_budelm_measurements_3953.diff
[CMD] [2021-05-31 19:32:25] echo "." >> /app/public/diff/budelmann_budelm_measurements_3953.diff
[INFO] [2021-05-31 19:32:25] Created diff: /app/public/diff/budelmann_budelm_measurements_3953.diff (13 lines)
[STOP] [2021-05-31 19:32:25] calculate_delta
[START] [2021-05-31 19:32:25] parse_diff_and_store
[INFO] [2021-05-31 19:32:25] Handling diff: /app/public/diff/budelmann_budelm_refs_3953.diff (4 lines)
[INFO] [2021-05-31 19:32:25] Loading refs diff file into memory (4 /app/public/diff/budelmann_budelm_refs_3953.diff lines)...
[INFO] [2021-05-31 19:32:26] Handling diff: /app/public/diff/budelmann_budelm_nodes_3953.diff (3 lines)
[INFO] [2021-05-31 19:32:26] Loading nodes diff file into memory (3 /app/public/diff/budelmann_budelm_nodes_3953.diff lines)...
[INFO] [2021-05-31 19:32:27] Handling diff: /app/public/diff/budelmann_budelm_occurrences_3953.diff (3 lines)
[INFO] [2021-05-31 19:32:27] Loading occurrences diff file into memory (3 /app/public/diff/budelmann_budelm_occurrences_3953.diff lines)...
[INFO] [2021-05-31 19:32:27] Handling diff: /app/public/diff/budelmann_budelm_measurements_3953.diff (13 lines)
[INFO] [2021-05-31 19:32:28] Loading measurements diff file into memory (13 /app/public/diff/budelmann_budelm_measurements_3953.diff lines)...
[INFO] [2021-05-31 19:32:28] Storing 2 References
[INFO] [2021-05-31 19:32:28] Processing group of 2 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[INFO] [2021-05-31 19:32:28] Storing 1 ScientificNames
[INFO] [2021-05-31 19:32:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[INFO] [2021-05-31 19:32:28] Storing 1 Nodes
[INFO] [2021-05-31 19:32:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[INFO] [2021-05-31 19:32:28] Storing 1 Occurrences
[INFO] [2021-05-31 19:32:28] Processing group of 1 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[INFO] [2021-05-31 19:32:28] Storing 8 TraitsReferences
[INFO] [2021-05-31 19:32:28] Processing group of 8 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[INFO] [2021-05-31 19:32:28] Storing 11 Traits
[INFO] [2021-05-31 19:32:28] Processing group of 11 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[INFO] [2021-05-31 19:32:28] Storing 8 MetaTraits
[INFO] [2021-05-31 19:32:28] Processing group of 8 in 1 groups of 1000
[INFO] [2021-05-31 19:32:28] Average Time: 0.0
[INFO] [2021-05-31 19:32:28] Total Time: 1s
[STOP] [2021-05-31 19:32:28] parse_diff_and_store
[START] [2021-05-31 19:32:28] resolve_keys
[INFO] [2021-05-31 19:32:34] Occurrences to nodes (through scientific_names)...
[INFO] [2021-05-31 19:32:34] traits to occurrences...
[INFO] [2021-05-31 19:32:34] traits to nodes (through occurrences)...
[INFO] [2021-05-31 19:32:34] Traits to sex term...
[INFO] [2021-05-31 19:32:34] Traits to lifestage term...
[INFO] [2021-05-31 19:32:34] MetaTraits to traits...
[INFO] [2021-05-31 19:32:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-05-31 19:32:34] Assocs to occurrences...
[INFO] [2021-05-31 19:32:34] Assocs to nodes...
[INFO] [2021-05-31 19:32:34] Assoc to sex term...
[INFO] [2021-05-31 19:32:34] Assoc to lifestage term...
[INFO] [2021-05-31 19:32:34] MetaAssoc to assocs...
[STOP] [2021-05-31 19:32:34] resolve_keys
[START] [2021-05-31 19:32:34] hold_for_later_1
[STOP] [2021-05-31 19:32:34] hold_for_later_1
[START] [2021-05-31 19:32:34] hold_for_later_2
[STOP] [2021-05-31 19:32:34] hold_for_later_2
[START] [2021-05-31 19:32:34] resolve_missing_parents
[STOP] [2021-05-31 19:32:34] resolve_missing_parents
[START] [2021-05-31 19:32:34] rebuild_nodes
[START] [2021-05-31 19:32:34] Flattener#flatten
[START] [2021-05-31 19:32:34] Flattener#study_resource
[START] [2021-05-31 19:32:34] Flattener#build_ancestry
[STOP] [2021-05-31 19:32:34] Flattener#build_ancestry
[INFO] [2021-05-31 19:32:34] 1 ancestry keys
[START] [2021-05-31 19:32:34] build_node_ancestors
[INFO] [2021-05-31 19:32:34] old ancestors deleted.
[STOP] [2021-05-31 19:32:34] build_node_ancestors
[WARN] [2021-05-31 19:32:34] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-05-31 19:32:34] Flattener#flatten
[STOP] [2021-05-31 19:32:34] rebuild_nodes
[START] [2021-05-31 19:32:34] resolve_missing_media_owners
[STOP] [2021-05-31 19:32:34] resolve_missing_media_owners
[START] [2021-05-31 19:32:34] sanitize_media_verbatims
[STOP] [2021-05-31 19:32:34] sanitize_media_verbatims
[START] [2021-05-31 19:32:34] queue_downloads
[STOP] [2021-05-31 19:32:34] queue_downloads
[START] [2021-05-31 19:32:34] parse_names
[WARN] [2021-05-31 19:32:34] I see 1 names which still need to be parsed.
[STOP] [2021-05-31 19:32:35] parse_names
[START] [2021-05-31 19:32:35] denormalize_canonical_names_to_nodes
[STOP] [2021-05-31 19:32:35] denormalize_canonical_names_to_nodes
[START] [2021-05-31 19:32:35] match_nodes
[START] [2021-05-31 19:32:35] map_all_nodes_to_pages
[STOP] [2021-05-31 19:32:35] map_all_nodes_to_pages
[INFO] [2021-05-31 19:32:35] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-05-31 19:32:35] update_nodes
[STOP] [2021-05-31 19:32:35] update_nodes
[STOP] [2021-05-31 19:32:35] match_nodes
[START] [2021-05-31 19:32:35] reindex_search
[STOP] [2021-05-31 19:32:35] reindex_search
[START] [2021-05-31 19:32:35] normalize_units
[STOP] [2021-05-31 19:32:35] normalize_units
[START] [2021-05-31 19:32:35] calculate_statistics
[2021-05-31 19:32:35] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-05-31 19:32:35] calculate_statistics
[START] [2021-05-31 19:32:35] complete_harvest_instance
[START] [2021-05-31 19:32:35] overall_tsv_creation
[INFO] [2021-05-31 19:32:35] Processing group of 1 in 1 batches of 10000
[INFO] [2021-05-31 19:33:07] 4 Traits (unfiltered)...
[INFO] [2021-05-31 19:33:33] 4 Traits (filtered)...
[INFO] [2021-05-31 19:33:33] 0 Associations (filtered)...
[INFO] [2021-05-31 19:33:33] 15 metadata added.
[INFO] [2021-05-31 19:33:33] 0 metadata added.
[INFO] [2021-05-31 19:33:56] Average Time: 58.81
[INFO] [2021-05-31 19:33:56] Total Time: 1m21s
[STOP] [2021-05-31 19:33:56] overall_tsv_creation
[INFO] [2021-05-31 19:33:56] Done. Check your files:
[INFO] [2021-05-31 19:33:56] (1 lines) /app/public/data/budelmann_budelm/publish_nodes.tsv
[INFO] [2021-05-31 19:33:57] (1 lines) /app/public/data/budelmann_budelm/publish_scientific_names.tsv
[INFO] [2021-05-31 19:33:57] (5 lines) /app/public/data/budelmann_budelm/publish_traits.tsv
[INFO] [2021-05-31 19:33:57] (16 lines) /app/public/data/budelmann_budelm/publish_metadata.tsv
[STOP] [2021-05-31 19:33:57] complete_harvest_instance
[START] [2021-05-31 19:33:57] completed
[STOP] [2021-05-31 19:33:57] completed
[STOP] [2021-05-31 19:33:57] logged process, took 98.87

Latest Process