Harvest for Paul and Smith 1984 Created 03 Aug 17:20

Stage: completed
Fetched: 03 Aug 17:20
Validated: 03 Aug 17:20
Deltas Created 03 Aug 17:20
Units Normalized: 03 Aug 17:20
Ancestry Built: 03 Aug 17:20
Nodes Matched: 03 Aug 17:20
Names Parsed: 03 Aug 17:20
New Models Stored: 03 Aug 17:20
Indexed: 03 Aug 17:20
Completed: 03 Aug 17:23
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2022-08-03 17:20:38] Created harvest instance #4196
[STOP] [2022-08-03 17:20:38] create_harvest_instance
[START] [2022-08-03 17:20:38] fetch_files
[STOP] [2022-08-03 17:20:38] fetch_files
[START] [2022-08-03 17:20:38] validate_each_file
[INFO] [2022-08-03 17:20:38] Looping over 3 formats...
[INFO] [2022-08-03 17:20:38] ...nodes (/app/public/data/paul_smith_paul_/taxa.txt)
[INFO] [2022-08-03 17:20:38] Valid: /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__nodes_29650.csv (1 lines)
[INFO] [2022-08-03 17:20:38] ...occurrences (/app/public/data/paul_smith_paul_/occurrences.txt)
[INFO] [2022-08-03 17:20:38] Valid: /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__occurrences_29651.csv (1 lines)
[INFO] [2022-08-03 17:20:38] ...measurements (/app/public/data/paul_smith_paul_/measurementOrFact.txt)
[INFO] [2022-08-03 17:20:38] Valid: /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__measurements_29652.csv (21 lines)
[STOP] [2022-08-03 17:20:38] validate_each_file
[START] [2022-08-03 17:20:38] convert_to_csv
[INFO] [2022-08-03 17:20:38] Looping over 3 formats...
[INFO] [2022-08-03 17:20:38] ...nodes (/app/public/data/paul_smith_paul_/taxa.txt)
[CMD] [2022-08-03 17:20:38] /usr/bin/sort /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__nodes_29650.csv > /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__nodes_29650.csv_sorted
[INFO] [2022-08-03 17:20:38] Converted: /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__nodes_29650.csv (1 lines)
[INFO] [2022-08-03 17:20:38] ...occurrences (/app/public/data/paul_smith_paul_/occurrences.txt)
[CMD] [2022-08-03 17:20:38] /usr/bin/sort /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__occurrences_29651.csv > /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__occurrences_29651.csv_sorted
[INFO] [2022-08-03 17:20:38] Converted: /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__occurrences_29651.csv (1 lines)
[INFO] [2022-08-03 17:20:38] ...measurements (/app/public/data/paul_smith_paul_/measurementOrFact.txt)
[CMD] [2022-08-03 17:20:38] /usr/bin/sort /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__measurements_29652.csv > /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__measurements_29652.csv_sorted
[INFO] [2022-08-03 17:20:38] Converted: /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__measurements_29652.csv (21 lines)
[STOP] [2022-08-03 17:20:38] convert_to_csv
[START] [2022-08-03 17:20:38] calculate_delta
[INFO] [2022-08-03 17:20:38] Looping over 3 formats...
[INFO] [2022-08-03 17:20:38] ...nodes (/app/public/data/paul_smith_paul_/taxa.txt)
[CMD] [2022-08-03 17:20:39] echo "0a" > /app/public/data/paul_smith_paul_/diff/paul_smith_paul__nodes_29650.diff
[CMD] [2022-08-03 17:20:39] tail -n +1 /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__nodes_29650.csv >> /app/public/data/paul_smith_paul_/diff/paul_smith_paul__nodes_29650.diff
[CMD] [2022-08-03 17:20:39] echo "." >> /app/public/data/paul_smith_paul_/diff/paul_smith_paul__nodes_29650.diff
[INFO] [2022-08-03 17:20:39] Created diff: /app/public/data/paul_smith_paul_/diff/paul_smith_paul__nodes_29650.diff (3 lines)
[INFO] [2022-08-03 17:20:39] ...occurrences (/app/public/data/paul_smith_paul_/occurrences.txt)
[CMD] [2022-08-03 17:20:39] echo "0a" > /app/public/data/paul_smith_paul_/diff/paul_smith_paul__occurrences_29651.diff
[CMD] [2022-08-03 17:20:39] tail -n +1 /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__occurrences_29651.csv >> /app/public/data/paul_smith_paul_/diff/paul_smith_paul__occurrences_29651.diff
[CMD] [2022-08-03 17:20:39] echo "." >> /app/public/data/paul_smith_paul_/diff/paul_smith_paul__occurrences_29651.diff
[INFO] [2022-08-03 17:20:39] Created diff: /app/public/data/paul_smith_paul_/diff/paul_smith_paul__occurrences_29651.diff (3 lines)
[INFO] [2022-08-03 17:20:39] ...measurements (/app/public/data/paul_smith_paul_/measurementOrFact.txt)
[CMD] [2022-08-03 17:20:39] echo "0a" > /app/public/data/paul_smith_paul_/diff/paul_smith_paul__measurements_29652.diff
[CMD] [2022-08-03 17:20:39] tail -n +1 /app/public/data/paul_smith_paul_/converted_csv/paul_smith_paul__measurements_29652.csv >> /app/public/data/paul_smith_paul_/diff/paul_smith_paul__measurements_29652.diff
[CMD] [2022-08-03 17:20:39] echo "." >> /app/public/data/paul_smith_paul_/diff/paul_smith_paul__measurements_29652.diff
[INFO] [2022-08-03 17:20:39] Created diff: /app/public/data/paul_smith_paul_/diff/paul_smith_paul__measurements_29652.diff (23 lines)
[STOP] [2022-08-03 17:20:39] calculate_delta
[START] [2022-08-03 17:20:39] parse_diff_and_store
[INFO] [2022-08-03 17:20:39] Handling diff: /app/public/data/paul_smith_paul_/diff/paul_smith_paul__nodes_29650.diff (3 lines)
[INFO] [2022-08-03 17:20:39] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 17:20:39] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 17:20:39] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 17:20:39] Handling diff: /app/public/data/paul_smith_paul_/diff/paul_smith_paul__occurrences_29651.diff (3 lines)
[INFO] [2022-08-03 17:20:39] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 17:20:39] Storing 1 Occurrences (2/1/3)
[INFO] [2022-08-03 17:20:39] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2022-08-03 17:20:39] Handling diff: /app/public/data/paul_smith_paul_/diff/paul_smith_paul__measurements_29652.diff (23 lines)
[INFO] [2022-08-03 17:20:39] Loading measurements diff file into memory (23 lines)...
[INFO] [2022-08-03 17:20:39] Storing 21 Traits (22/21/23)
[INFO] [2022-08-03 17:20:39] Storing 1 MetaTraits (22/21/23)
[STOP] [2022-08-03 17:20:39] parse_diff_and_store
[START] [2022-08-03 17:20:39] resolve_keys
[2022-08-03 17:20:39] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:20:46] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:20:46] traits to occurrences...
[INFO] [2022-08-03 17:20:46] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:20:46] Traits to sex term...
[INFO] [2022-08-03 17:20:46] Traits to lifestage term...
[INFO] [2022-08-03 17:20:46] MetaTraits to traits...
[INFO] [2022-08-03 17:20:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:20:46] Assocs to occurrences...
[INFO] [2022-08-03 17:20:46] Assocs to nodes...
[INFO] [2022-08-03 17:20:46] Assoc to sex term...
[INFO] [2022-08-03 17:20:46] Assoc to lifestage term...
[INFO] [2022-08-03 17:20:46] MetaAssoc to assocs...
[STOP] [2022-08-03 17:20:46] resolve_keys
[START] [2022-08-03 17:20:46] hold_for_later_1
[STOP] [2022-08-03 17:20:46] hold_for_later_1
[START] [2022-08-03 17:20:46] hold_for_later_2
[STOP] [2022-08-03 17:20:46] hold_for_later_2
[START] [2022-08-03 17:20:46] resolve_missing_parents
[STOP] [2022-08-03 17:20:46] resolve_missing_parents
[START] [2022-08-03 17:20:46] rebuild_nodes
[START] [2022-08-03 17:20:46] Flattener#flatten
[START] [2022-08-03 17:20:46] Flattener#study_resource
[START] [2022-08-03 17:20:46] Flattener#build_ancestry
[STOP] [2022-08-03 17:20:46] Flattener#build_ancestry
[INFO] [2022-08-03 17:20:46] 1 ancestry keys
[START] [2022-08-03 17:20:46] build_node_ancestors
[INFO] [2022-08-03 17:20:46] old ancestors deleted.
[STOP] [2022-08-03 17:20:46] build_node_ancestors
[WARN] [2022-08-03 17:20:46] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:20:46] Flattener#flatten
[STOP] [2022-08-03 17:20:46] rebuild_nodes
[START] [2022-08-03 17:20:46] resolve_missing_media_owners
[STOP] [2022-08-03 17:20:46] resolve_missing_media_owners
[START] [2022-08-03 17:20:46] sanitize_media_verbatims
[STOP] [2022-08-03 17:20:46] sanitize_media_verbatims
[START] [2022-08-03 17:20:46] queue_downloads
[STOP] [2022-08-03 17:20:46] queue_downloads
[START] [2022-08-03 17:20:46] parse_names
[WARN] [2022-08-03 17:20:46] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 17:20:46] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 17:20:47] parse_names
[START] [2022-08-03 17:20:47] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:20:47] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:20:47] match_nodes
[START] [2022-08-03 17:20:47] map_all_nodes_to_pages
[STOP] [2022-08-03 17:20:47] map_all_nodes_to_pages
[INFO] [2022-08-03 17:20:47] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 17:20:47] update_nodes
[STOP] [2022-08-03 17:20:47] update_nodes
[STOP] [2022-08-03 17:20:47] match_nodes
[START] [2022-08-03 17:20:47] reindex_search
[STOP] [2022-08-03 17:20:47] reindex_search
[START] [2022-08-03 17:20:47] normalize_units
[STOP] [2022-08-03 17:20:47] normalize_units
[START] [2022-08-03 17:20:47] calculate_statistics
[2022-08-03 17:20:47] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:20:47] Duplicate page_id count: 0
[STOP] [2022-08-03 17:20:47] calculate_statistics
[START] [2022-08-03 17:20:47] complete_harvest_instance
[START] [2022-08-03 17:20:47] overall_tsv_creation
[INFO] [2022-08-03 17:20:47] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:20:47] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 17:21:29] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:21:29] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 17:22:22] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 17:22:22] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:22:22] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:22:22] Adding 1 traits...
[INFO] [2022-08-03 17:22:22] Trait #278707113 in key 278707113 has 22 metadata... that seems high?
[INFO] [2022-08-03 17:22:22] 20 metadata added.
[INFO] [2022-08-03 17:22:22] Adding 0 assocs...
[INFO] [2022-08-03 17:22:22] 0 metadata added.
[INFO] [2022-08-03 17:23:04] Processed 1/1 nodes
[INFO] [2022-08-03 17:23:04] Average Time: 111.94
[INFO] [2022-08-03 17:23:04] Total Time: 2m18s
[STOP] [2022-08-03 17:23:04] overall_tsv_creation
[INFO] [2022-08-03 17:23:04] Done. Check your files:
[INFO] [2022-08-03 17:23:04] (1 lines) /app/public/data/paul_smith_paul_/publish_nodes.tsv
[INFO] [2022-08-03 17:23:04] (1 lines) /app/public/data/paul_smith_paul_/publish_scientific_names.tsv
[INFO] [2022-08-03 17:23:04] (2 lines) /app/public/data/paul_smith_paul_/publish_traits.tsv
[INFO] [2022-08-03 17:23:04] (21 lines) /app/public/data/paul_smith_paul_/publish_metadata.tsv
[STOP] [2022-08-03 17:23:04] complete_harvest_instance
[START] [2022-08-03 17:23:05] completed
[STOP] [2022-08-03 17:23:05] completed
[STOP] [2022-08-03 17:23:05] logged process, took 146.95
Latest Process

03 Aug 17:20 EXITED currently processing 0