Harvest for Dunn et al 2015 Created 03 Aug 17:07

Stage: completed
Fetched: 03 Aug 17:07
Validated: 03 Aug 17:07
Deltas Created 03 Aug 17:07
Units Normalized: 03 Aug 17:07
Ancestry Built: 03 Aug 17:07
Nodes Matched: 03 Aug 17:07
Names Parsed: 03 Aug 17:07
New Models Stored: 03 Aug 17:07
Indexed: 03 Aug 17:07
Completed: 03 Aug 17:09
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2022-08-03 17:07:31] Created harvest instance #4189
[STOP] [2022-08-03 17:07:31] create_harvest_instance
[START] [2022-08-03 17:07:31] fetch_files
[STOP] [2022-08-03 17:07:31] fetch_files
[START] [2022-08-03 17:07:31] validate_each_file
[INFO] [2022-08-03 17:07:31] Looping over 3 formats...
[INFO] [2022-08-03 17:07:31] ...nodes (/app/public/data/dunn_et_al_dunn_/taxa.txt)
[INFO] [2022-08-03 17:07:31] Valid: /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__nodes_29633.csv (1 lines)
[INFO] [2022-08-03 17:07:31] ...occurrences (/app/public/data/dunn_et_al_dunn_/occurrences.txt)
[INFO] [2022-08-03 17:07:31] Valid: /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__occurrences_29634.csv (1 lines)
[INFO] [2022-08-03 17:07:31] ...measurements (/app/public/data/dunn_et_al_dunn_/measurementOrFact.txt)
[INFO] [2022-08-03 17:07:31] Valid: /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__measurements_29635.csv (2 lines)
[STOP] [2022-08-03 17:07:31] validate_each_file
[START] [2022-08-03 17:07:31] convert_to_csv
[INFO] [2022-08-03 17:07:31] Looping over 3 formats...
[INFO] [2022-08-03 17:07:31] ...nodes (/app/public/data/dunn_et_al_dunn_/taxa.txt)
[CMD] [2022-08-03 17:07:31] /usr/bin/sort /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__nodes_29633.csv > /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__nodes_29633.csv_sorted
[INFO] [2022-08-03 17:07:31] Converted: /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__nodes_29633.csv (1 lines)
[INFO] [2022-08-03 17:07:31] ...occurrences (/app/public/data/dunn_et_al_dunn_/occurrences.txt)
[CMD] [2022-08-03 17:07:31] /usr/bin/sort /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__occurrences_29634.csv > /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__occurrences_29634.csv_sorted
[INFO] [2022-08-03 17:07:31] Converted: /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__occurrences_29634.csv (1 lines)
[INFO] [2022-08-03 17:07:31] ...measurements (/app/public/data/dunn_et_al_dunn_/measurementOrFact.txt)
[CMD] [2022-08-03 17:07:31] /usr/bin/sort /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__measurements_29635.csv > /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__measurements_29635.csv_sorted
[INFO] [2022-08-03 17:07:31] Converted: /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__measurements_29635.csv (2 lines)
[STOP] [2022-08-03 17:07:31] convert_to_csv
[START] [2022-08-03 17:07:31] calculate_delta
[INFO] [2022-08-03 17:07:31] Looping over 3 formats...
[INFO] [2022-08-03 17:07:31] ...nodes (/app/public/data/dunn_et_al_dunn_/taxa.txt)
[CMD] [2022-08-03 17:07:31] echo "0a" > /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__nodes_29633.diff
[CMD] [2022-08-03 17:07:31] tail -n +1 /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__nodes_29633.csv >> /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__nodes_29633.diff
[CMD] [2022-08-03 17:07:31] echo "." >> /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__nodes_29633.diff
[INFO] [2022-08-03 17:07:31] Created diff: /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__nodes_29633.diff (3 lines)
[INFO] [2022-08-03 17:07:31] ...occurrences (/app/public/data/dunn_et_al_dunn_/occurrences.txt)
[CMD] [2022-08-03 17:07:31] echo "0a" > /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__occurrences_29634.diff
[CMD] [2022-08-03 17:07:31] tail -n +1 /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__occurrences_29634.csv >> /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__occurrences_29634.diff
[CMD] [2022-08-03 17:07:31] echo "." >> /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__occurrences_29634.diff
[INFO] [2022-08-03 17:07:31] Created diff: /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__occurrences_29634.diff (3 lines)
[INFO] [2022-08-03 17:07:31] ...measurements (/app/public/data/dunn_et_al_dunn_/measurementOrFact.txt)
[CMD] [2022-08-03 17:07:31] echo "0a" > /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__measurements_29635.diff
[CMD] [2022-08-03 17:07:31] tail -n +1 /app/public/data/dunn_et_al_dunn_/converted_csv/dunn_et_al_dunn__measurements_29635.csv >> /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__measurements_29635.diff
[CMD] [2022-08-03 17:07:31] echo "." >> /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__measurements_29635.diff
[INFO] [2022-08-03 17:07:31] Created diff: /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__measurements_29635.diff (4 lines)
[STOP] [2022-08-03 17:07:31] calculate_delta
[START] [2022-08-03 17:07:31] parse_diff_and_store
[INFO] [2022-08-03 17:07:31] Handling diff: /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__nodes_29633.diff (3 lines)
[INFO] [2022-08-03 17:07:31] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 17:07:31] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 17:07:31] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 17:07:31] Handling diff: /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__occurrences_29634.diff (3 lines)
[INFO] [2022-08-03 17:07:31] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 17:07:31] Storing 1 Occurrences (2/1/3)
[INFO] [2022-08-03 17:07:31] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2022-08-03 17:07:31] Handling diff: /app/public/data/dunn_et_al_dunn_/diff/dunn_et_al_dunn__measurements_29635.diff (4 lines)
[INFO] [2022-08-03 17:07:31] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 17:07:31] Storing 2 Traits (4/2/4)
[INFO] [2022-08-03 17:07:31] Storing 2 MetaTraits (4/2/4)
[STOP] [2022-08-03 17:07:31] parse_diff_and_store
[START] [2022-08-03 17:07:31] resolve_keys
[2022-08-03 17:07:31] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:07:39] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:07:39] traits to occurrences...
[INFO] [2022-08-03 17:07:39] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:07:39] Traits to sex term...
[INFO] [2022-08-03 17:07:39] Traits to lifestage term...
[INFO] [2022-08-03 17:07:39] MetaTraits to traits...
[INFO] [2022-08-03 17:07:39] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:07:39] Assocs to occurrences...
[INFO] [2022-08-03 17:07:39] Assocs to nodes...
[INFO] [2022-08-03 17:07:39] Assoc to sex term...
[INFO] [2022-08-03 17:07:39] Assoc to lifestage term...
[INFO] [2022-08-03 17:07:39] MetaAssoc to assocs...
[STOP] [2022-08-03 17:07:39] resolve_keys
[START] [2022-08-03 17:07:39] hold_for_later_1
[STOP] [2022-08-03 17:07:39] hold_for_later_1
[START] [2022-08-03 17:07:39] hold_for_later_2
[STOP] [2022-08-03 17:07:39] hold_for_later_2
[START] [2022-08-03 17:07:39] resolve_missing_parents
[STOP] [2022-08-03 17:07:39] resolve_missing_parents
[START] [2022-08-03 17:07:39] rebuild_nodes
[START] [2022-08-03 17:07:39] Flattener#flatten
[START] [2022-08-03 17:07:39] Flattener#study_resource
[START] [2022-08-03 17:07:39] Flattener#build_ancestry
[STOP] [2022-08-03 17:07:39] Flattener#build_ancestry
[INFO] [2022-08-03 17:07:39] 1 ancestry keys
[START] [2022-08-03 17:07:39] build_node_ancestors
[INFO] [2022-08-03 17:07:39] old ancestors deleted.
[STOP] [2022-08-03 17:07:39] build_node_ancestors
[WARN] [2022-08-03 17:07:39] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:07:39] Flattener#flatten
[STOP] [2022-08-03 17:07:39] rebuild_nodes
[START] [2022-08-03 17:07:39] resolve_missing_media_owners
[STOP] [2022-08-03 17:07:39] resolve_missing_media_owners
[START] [2022-08-03 17:07:39] sanitize_media_verbatims
[STOP] [2022-08-03 17:07:39] sanitize_media_verbatims
[START] [2022-08-03 17:07:39] queue_downloads
[STOP] [2022-08-03 17:07:39] queue_downloads
[START] [2022-08-03 17:07:39] parse_names
[WARN] [2022-08-03 17:07:39] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 17:07:39] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 17:07:40] parse_names
[START] [2022-08-03 17:07:40] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:07:40] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:07:40] match_nodes
[START] [2022-08-03 17:07:40] map_all_nodes_to_pages
[STOP] [2022-08-03 17:07:40] map_all_nodes_to_pages
[INFO] [2022-08-03 17:07:40] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 17:07:40] update_nodes
[STOP] [2022-08-03 17:07:40] update_nodes
[STOP] [2022-08-03 17:07:40] match_nodes
[START] [2022-08-03 17:07:40] reindex_search
[STOP] [2022-08-03 17:07:41] reindex_search
[START] [2022-08-03 17:07:41] normalize_units
[STOP] [2022-08-03 17:07:41] normalize_units
[START] [2022-08-03 17:07:41] calculate_statistics
[2022-08-03 17:07:41] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:07:41] Duplicate page_id count: 0
[STOP] [2022-08-03 17:07:41] calculate_statistics
[START] [2022-08-03 17:07:41] complete_harvest_instance
[START] [2022-08-03 17:07:41] overall_tsv_creation
[INFO] [2022-08-03 17:07:41] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:07:41] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 17:08:22] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:08:22] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 17:09:16] Mapped 1 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 17:09:16] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:09:16] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:09:16] Adding 1 traits...
[INFO] [2022-08-03 17:09:16] 1 metadata added.
[INFO] [2022-08-03 17:09:16] Adding 0 assocs...
[INFO] [2022-08-03 17:09:16] 0 metadata added.
[INFO] [2022-08-03 17:09:59] Processed 1/1 nodes
[INFO] [2022-08-03 17:09:59] Average Time: 112.82
[INFO] [2022-08-03 17:09:59] Total Time: 2m18s
[STOP] [2022-08-03 17:09:59] overall_tsv_creation
[INFO] [2022-08-03 17:09:59] Done. Check your files:
[INFO] [2022-08-03 17:09:59] (1 lines) /app/public/data/dunn_et_al_dunn_/publish_nodes.tsv
[INFO] [2022-08-03 17:09:59] (1 lines) /app/public/data/dunn_et_al_dunn_/publish_scientific_names.tsv
[INFO] [2022-08-03 17:09:59] (2 lines) /app/public/data/dunn_et_al_dunn_/publish_traits.tsv
[INFO] [2022-08-03 17:09:59] (2 lines) /app/public/data/dunn_et_al_dunn_/publish_metadata.tsv
[STOP] [2022-08-03 17:09:59] complete_harvest_instance
[START] [2022-08-03 17:09:59] completed
[STOP] [2022-08-03 17:09:59] completed
[STOP] [2022-08-03 17:09:59] logged process, took 147.94
Latest Process

03 Aug 17:07 EXITED currently processing 0