Harvest for Boyle and Rice 2018 Created 03 Aug 16:20

Stage: completed
Fetched: 03 Aug 16:20
Validated: 03 Aug 16:20
Deltas Created 03 Aug 16:20
Units Normalized: 03 Aug 16:21
Ancestry Built: 03 Aug 16:21
Nodes Matched: 03 Aug 16:21
Names Parsed: 03 Aug 16:21
New Models Stored: 03 Aug 16:20
Indexed: 03 Aug 16:21
Completed: 03 Aug 16:23
Time to Harvest: less than a minute

Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:20:57] Created harvest instance #4168
[STOP] [2022-08-03 16:20:57] create_harvest_instance
[START] [2022-08-03 16:20:57] fetch_files
[STOP] [2022-08-03 16:20:57] fetch_files
[START] [2022-08-03 16:20:57] validate_each_file
[INFO] [2022-08-03 16:20:57] Looping over 3 formats...
[INFO] [2022-08-03 16:20:57] ...nodes (/app/public/data/boyle_rice_boyle/taxa.txt)
[INFO] [2022-08-03 16:20:57] Valid: /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_nodes_29567.csv (1 lines)
[INFO] [2022-08-03 16:20:57] ...occurrences (/app/public/data/boyle_rice_boyle/occurrences.txt)
[INFO] [2022-08-03 16:20:57] Valid: /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_occurrences_29568.csv (1 lines)
[INFO] [2022-08-03 16:20:57] ...measurements (/app/public/data/boyle_rice_boyle/measurementOrFact.txt)
[INFO] [2022-08-03 16:20:57] Valid: /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_measurements_29569.csv (2 lines)
[STOP] [2022-08-03 16:20:57] validate_each_file
[START] [2022-08-03 16:20:57] convert_to_csv
[INFO] [2022-08-03 16:20:57] Looping over 3 formats...
[INFO] [2022-08-03 16:20:57] ...nodes (/app/public/data/boyle_rice_boyle/taxa.txt)
[CMD] [2022-08-03 16:20:57] /usr/bin/sort /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_nodes_29567.csv > /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_nodes_29567.csv_sorted
[INFO] [2022-08-03 16:20:57] Converted: /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_nodes_29567.csv (1 lines)
[INFO] [2022-08-03 16:20:57] ...occurrences (/app/public/data/boyle_rice_boyle/occurrences.txt)
[CMD] [2022-08-03 16:20:57] /usr/bin/sort /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_occurrences_29568.csv > /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_occurrences_29568.csv_sorted
[INFO] [2022-08-03 16:20:57] Converted: /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_occurrences_29568.csv (1 lines)
[INFO] [2022-08-03 16:20:57] ...measurements (/app/public/data/boyle_rice_boyle/measurementOrFact.txt)
[CMD] [2022-08-03 16:20:57] /usr/bin/sort /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_measurements_29569.csv > /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_measurements_29569.csv_sorted
[INFO] [2022-08-03 16:20:57] Converted: /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_measurements_29569.csv (2 lines)
[STOP] [2022-08-03 16:20:57] convert_to_csv
[START] [2022-08-03 16:20:57] calculate_delta
[INFO] [2022-08-03 16:20:57] Looping over 3 formats...
[INFO] [2022-08-03 16:20:57] ...nodes (/app/public/data/boyle_rice_boyle/taxa.txt)
[CMD] [2022-08-03 16:20:57] echo "0a" > /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_nodes_29567.diff
[CMD] [2022-08-03 16:20:57] tail -n +1 /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_nodes_29567.csv >> /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_nodes_29567.diff
[CMD] [2022-08-03 16:20:57] echo "." >> /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_nodes_29567.diff
[INFO] [2022-08-03 16:20:57] Created diff: /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_nodes_29567.diff (3 lines)
[INFO] [2022-08-03 16:20:57] ...occurrences (/app/public/data/boyle_rice_boyle/occurrences.txt)
[CMD] [2022-08-03 16:20:57] echo "0a" > /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_occurrences_29568.diff
[CMD] [2022-08-03 16:20:57] tail -n +1 /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_occurrences_29568.csv >> /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_occurrences_29568.diff
[CMD] [2022-08-03 16:20:57] echo "." >> /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_occurrences_29568.diff
[INFO] [2022-08-03 16:20:57] Created diff: /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_occurrences_29568.diff (3 lines)
[INFO] [2022-08-03 16:20:57] ...measurements (/app/public/data/boyle_rice_boyle/measurementOrFact.txt)
[CMD] [2022-08-03 16:20:57] echo "0a" > /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_measurements_29569.diff
[CMD] [2022-08-03 16:20:57] tail -n +1 /app/public/data/boyle_rice_boyle/converted_csv/boyle_rice_boyle_measurements_29569.csv >> /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_measurements_29569.diff
[CMD] [2022-08-03 16:20:57] echo "." >> /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_measurements_29569.diff
[INFO] [2022-08-03 16:20:57] Created diff: /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_measurements_29569.diff (4 lines)
[STOP] [2022-08-03 16:20:57] calculate_delta
[START] [2022-08-03 16:20:57] parse_diff_and_store
[INFO] [2022-08-03 16:20:57] Handling diff: /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_nodes_29567.diff (3 lines)
[INFO] [2022-08-03 16:20:57] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:20:57] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:20:57] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:20:57] Handling diff: /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_occurrences_29568.diff (3 lines)
[INFO] [2022-08-03 16:20:57] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:20:57] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:20:57] Handling diff: /app/public/data/boyle_rice_boyle/diff/boyle_rice_boyle_measurements_29569.diff (4 lines)
[INFO] [2022-08-03 16:20:57] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:20:57] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:20:57] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:20:57] parse_diff_and_store
[START] [2022-08-03 16:20:57] resolve_keys
[2022-08-03 16:20:57] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:21:04] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:21:04] traits to occurrences...
[INFO] [2022-08-03 16:21:04] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:21:04] Traits to sex term...
[INFO] [2022-08-03 16:21:04] Traits to lifestage term...
[INFO] [2022-08-03 16:21:04] MetaTraits to traits...
[INFO] [2022-08-03 16:21:04] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:21:04] Assocs to occurrences...
[INFO] [2022-08-03 16:21:04] Assocs to nodes...
[INFO] [2022-08-03 16:21:04] Assoc to sex term...
[INFO] [2022-08-03 16:21:04] Assoc to lifestage term...
[INFO] [2022-08-03 16:21:04] MetaAssoc to assocs...
[STOP] [2022-08-03 16:21:04] resolve_keys
[START] [2022-08-03 16:21:04] hold_for_later_1
[STOP] [2022-08-03 16:21:04] hold_for_later_1
[START] [2022-08-03 16:21:04] hold_for_later_2
[STOP] [2022-08-03 16:21:04] hold_for_later_2
[START] [2022-08-03 16:21:04] resolve_missing_parents
[STOP] [2022-08-03 16:21:04] resolve_missing_parents
[START] [2022-08-03 16:21:04] rebuild_nodes
[START] [2022-08-03 16:21:04] Flattener#flatten
[START] [2022-08-03 16:21:04] Flattener#study_resource
[START] [2022-08-03 16:21:04] Flattener#build_ancestry
[STOP] [2022-08-03 16:21:04] Flattener#build_ancestry
[INFO] [2022-08-03 16:21:04] 1 ancestry keys
[START] [2022-08-03 16:21:04] build_node_ancestors
[INFO] [2022-08-03 16:21:04] old ancestors deleted.
[STOP] [2022-08-03 16:21:04] build_node_ancestors
[WARN] [2022-08-03 16:21:04] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:21:04] Flattener#flatten
[STOP] [2022-08-03 16:21:04] rebuild_nodes
[START] [2022-08-03 16:21:04] resolve_missing_media_owners
[STOP] [2022-08-03 16:21:04] resolve_missing_media_owners
[START] [2022-08-03 16:21:04] sanitize_media_verbatims
[STOP] [2022-08-03 16:21:04] sanitize_media_verbatims
[START] [2022-08-03 16:21:04] queue_downloads
[STOP] [2022-08-03 16:21:04] queue_downloads
[START] [2022-08-03 16:21:04] parse_names
[WARN] [2022-08-03 16:21:04] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:21:04] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:21:05] parse_names
[START] [2022-08-03 16:21:05] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:21:05] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:21:05] match_nodes
[START] [2022-08-03 16:21:05] map_all_nodes_to_pages
[STOP] [2022-08-03 16:21:05] map_all_nodes_to_pages
[INFO] [2022-08-03 16:21:06] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:21:06] update_nodes
[STOP] [2022-08-03 16:21:06] update_nodes
[STOP] [2022-08-03 16:21:06] match_nodes
[START] [2022-08-03 16:21:06] reindex_search
[STOP] [2022-08-03 16:21:06] reindex_search
[START] [2022-08-03 16:21:06] normalize_units
[STOP] [2022-08-03 16:21:06] normalize_units
[START] [2022-08-03 16:21:06] calculate_statistics
[2022-08-03 16:21:06] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:21:06] Duplicate page_id count: 0
[STOP] [2022-08-03 16:21:06] calculate_statistics
[START] [2022-08-03 16:21:06] complete_harvest_instance
[START] [2022-08-03 16:21:06] overall_tsv_creation
[INFO] [2022-08-03 16:21:06] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:21:06] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:21:47] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:21:47] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:22:39] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:22:39] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:22:39] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:22:39] Adding 1 traits...
[INFO] [2022-08-03 16:22:39] 1 metadata added.
[INFO] [2022-08-03 16:22:39] Adding 0 assocs...
[INFO] [2022-08-03 16:22:39] 0 metadata added.
[INFO] [2022-08-03 16:23:22] Processed 1/1 nodes
[INFO] [2022-08-03 16:23:22] Average Time: 111.03
[INFO] [2022-08-03 16:23:22] Total Time: 2m16s
[STOP] [2022-08-03 16:23:22] overall_tsv_creation
[INFO] [2022-08-03 16:23:22] Done. Check your files:
[INFO] [2022-08-03 16:23:22] (1 lines) /app/public/data/boyle_rice_boyle/publish_nodes.tsv
[INFO] [2022-08-03 16:23:22] (1 lines) /app/public/data/boyle_rice_boyle/publish_scientific_names.tsv
[INFO] [2022-08-03 16:23:22] (2 lines) /app/public/data/boyle_rice_boyle/publish_traits.tsv
[INFO] [2022-08-03 16:23:22] (2 lines) /app/public/data/boyle_rice_boyle/publish_metadata.tsv
[STOP] [2022-08-03 16:23:22] complete_harvest_instance
[START] [2022-08-03 16:23:22] completed
[STOP] [2022-08-03 16:23:22] completed
[STOP] [2022-08-03 16:23:22] logged process, took 145.01

Latest Process