Harvest for Marshall and Valentine 2010 Created 03 Aug 16:28

Stage: completed
Fetched: 03 Aug 16:28
Validated: 03 Aug 16:28
Deltas Created 03 Aug 16:28
Units Normalized: 03 Aug 16:28
Ancestry Built: 03 Aug 16:28
Nodes Matched: 03 Aug 16:28
Names Parsed: 03 Aug 16:28
New Models Stored: 03 Aug 16:28
Indexed: 03 Aug 16:28
Completed: 03 Aug 16:30
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:28:09] Created harvest instance #4171
[STOP] [2022-08-03 16:28:09] create_harvest_instance
[START] [2022-08-03 16:28:09] fetch_files
[STOP] [2022-08-03 16:28:09] fetch_files
[START] [2022-08-03 16:28:09] validate_each_file
[INFO] [2022-08-03 16:28:09] Looping over 3 formats...
[INFO] [2022-08-03 16:28:09] ...nodes (/app/public/data/marshall_valenti/taxa.txt)
[INFO] [2022-08-03 16:28:10] Valid: /app/public/data/marshall_valenti/converted_csv/marshall_valenti_nodes_29576.csv (1 lines)
[INFO] [2022-08-03 16:28:10] ...occurrences (/app/public/data/marshall_valenti/occurrences.txt)
[INFO] [2022-08-03 16:28:10] Valid: /app/public/data/marshall_valenti/converted_csv/marshall_valenti_occurrences_29577.csv (1 lines)
[INFO] [2022-08-03 16:28:10] ...measurements (/app/public/data/marshall_valenti/measurementOrFact.txt)
[INFO] [2022-08-03 16:28:10] Valid: /app/public/data/marshall_valenti/converted_csv/marshall_valenti_measurements_29578.csv (4 lines)
[STOP] [2022-08-03 16:28:10] validate_each_file
[START] [2022-08-03 16:28:10] convert_to_csv
[INFO] [2022-08-03 16:28:10] Looping over 3 formats...
[INFO] [2022-08-03 16:28:10] ...nodes (/app/public/data/marshall_valenti/taxa.txt)
[CMD] [2022-08-03 16:28:10] /usr/bin/sort /app/public/data/marshall_valenti/converted_csv/marshall_valenti_nodes_29576.csv > /app/public/data/marshall_valenti/converted_csv/marshall_valenti_nodes_29576.csv_sorted
[INFO] [2022-08-03 16:28:10] Converted: /app/public/data/marshall_valenti/converted_csv/marshall_valenti_nodes_29576.csv (1 lines)
[INFO] [2022-08-03 16:28:10] ...occurrences (/app/public/data/marshall_valenti/occurrences.txt)
[CMD] [2022-08-03 16:28:10] /usr/bin/sort /app/public/data/marshall_valenti/converted_csv/marshall_valenti_occurrences_29577.csv > /app/public/data/marshall_valenti/converted_csv/marshall_valenti_occurrences_29577.csv_sorted
[INFO] [2022-08-03 16:28:10] Converted: /app/public/data/marshall_valenti/converted_csv/marshall_valenti_occurrences_29577.csv (1 lines)
[INFO] [2022-08-03 16:28:10] ...measurements (/app/public/data/marshall_valenti/measurementOrFact.txt)
[CMD] [2022-08-03 16:28:10] /usr/bin/sort /app/public/data/marshall_valenti/converted_csv/marshall_valenti_measurements_29578.csv > /app/public/data/marshall_valenti/converted_csv/marshall_valenti_measurements_29578.csv_sorted
[INFO] [2022-08-03 16:28:10] Converted: /app/public/data/marshall_valenti/converted_csv/marshall_valenti_measurements_29578.csv (4 lines)
[STOP] [2022-08-03 16:28:10] convert_to_csv
[START] [2022-08-03 16:28:10] calculate_delta
[INFO] [2022-08-03 16:28:10] Looping over 3 formats...
[INFO] [2022-08-03 16:28:10] ...nodes (/app/public/data/marshall_valenti/taxa.txt)
[CMD] [2022-08-03 16:28:10] echo "0a" > /app/public/data/marshall_valenti/diff/marshall_valenti_nodes_29576.diff
[CMD] [2022-08-03 16:28:10] tail -n +1 /app/public/data/marshall_valenti/converted_csv/marshall_valenti_nodes_29576.csv >> /app/public/data/marshall_valenti/diff/marshall_valenti_nodes_29576.diff
[CMD] [2022-08-03 16:28:10] echo "." >> /app/public/data/marshall_valenti/diff/marshall_valenti_nodes_29576.diff
[INFO] [2022-08-03 16:28:10] Created diff: /app/public/data/marshall_valenti/diff/marshall_valenti_nodes_29576.diff (3 lines)
[INFO] [2022-08-03 16:28:10] ...occurrences (/app/public/data/marshall_valenti/occurrences.txt)
[CMD] [2022-08-03 16:28:10] echo "0a" > /app/public/data/marshall_valenti/diff/marshall_valenti_occurrences_29577.diff
[CMD] [2022-08-03 16:28:10] tail -n +1 /app/public/data/marshall_valenti/converted_csv/marshall_valenti_occurrences_29577.csv >> /app/public/data/marshall_valenti/diff/marshall_valenti_occurrences_29577.diff
[CMD] [2022-08-03 16:28:10] echo "." >> /app/public/data/marshall_valenti/diff/marshall_valenti_occurrences_29577.diff
[INFO] [2022-08-03 16:28:10] Created diff: /app/public/data/marshall_valenti/diff/marshall_valenti_occurrences_29577.diff (3 lines)
[INFO] [2022-08-03 16:28:10] ...measurements (/app/public/data/marshall_valenti/measurementOrFact.txt)
[CMD] [2022-08-03 16:28:10] echo "0a" > /app/public/data/marshall_valenti/diff/marshall_valenti_measurements_29578.diff
[CMD] [2022-08-03 16:28:10] tail -n +1 /app/public/data/marshall_valenti/converted_csv/marshall_valenti_measurements_29578.csv >> /app/public/data/marshall_valenti/diff/marshall_valenti_measurements_29578.diff
[CMD] [2022-08-03 16:28:10] echo "." >> /app/public/data/marshall_valenti/diff/marshall_valenti_measurements_29578.diff
[INFO] [2022-08-03 16:28:10] Created diff: /app/public/data/marshall_valenti/diff/marshall_valenti_measurements_29578.diff (6 lines)
[STOP] [2022-08-03 16:28:10] calculate_delta
[START] [2022-08-03 16:28:10] parse_diff_and_store
[INFO] [2022-08-03 16:28:10] Handling diff: /app/public/data/marshall_valenti/diff/marshall_valenti_nodes_29576.diff (3 lines)
[INFO] [2022-08-03 16:28:10] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:28:10] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:28:10] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:28:10] Handling diff: /app/public/data/marshall_valenti/diff/marshall_valenti_occurrences_29577.diff (3 lines)
[INFO] [2022-08-03 16:28:10] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:28:10] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:28:10] Handling diff: /app/public/data/marshall_valenti/diff/marshall_valenti_measurements_29578.diff (6 lines)
[INFO] [2022-08-03 16:28:10] Loading measurements diff file into memory (6 lines)...
[INFO] [2022-08-03 16:28:10] Storing 4 Traits (6/4/6)
[INFO] [2022-08-03 16:28:10] Storing 2 MetaTraits (6/4/6)
[STOP] [2022-08-03 16:28:10] parse_diff_and_store
[START] [2022-08-03 16:28:10] resolve_keys
[2022-08-03 16:28:10] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:28:17] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:28:17] traits to occurrences...
[INFO] [2022-08-03 16:28:17] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:28:17] Traits to sex term...
[INFO] [2022-08-03 16:28:17] Traits to lifestage term...
[INFO] [2022-08-03 16:28:17] MetaTraits to traits...
[INFO] [2022-08-03 16:28:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:28:17] Assocs to occurrences...
[INFO] [2022-08-03 16:28:17] Assocs to nodes...
[INFO] [2022-08-03 16:28:17] Assoc to sex term...
[INFO] [2022-08-03 16:28:17] Assoc to lifestage term...
[INFO] [2022-08-03 16:28:17] MetaAssoc to assocs...
[STOP] [2022-08-03 16:28:17] resolve_keys
[START] [2022-08-03 16:28:17] hold_for_later_1
[STOP] [2022-08-03 16:28:17] hold_for_later_1
[START] [2022-08-03 16:28:17] hold_for_later_2
[STOP] [2022-08-03 16:28:17] hold_for_later_2
[START] [2022-08-03 16:28:17] resolve_missing_parents
[STOP] [2022-08-03 16:28:17] resolve_missing_parents
[START] [2022-08-03 16:28:17] rebuild_nodes
[START] [2022-08-03 16:28:17] Flattener#flatten
[START] [2022-08-03 16:28:17] Flattener#study_resource
[START] [2022-08-03 16:28:17] Flattener#build_ancestry
[STOP] [2022-08-03 16:28:17] Flattener#build_ancestry
[INFO] [2022-08-03 16:28:17] 1 ancestry keys
[START] [2022-08-03 16:28:17] build_node_ancestors
[INFO] [2022-08-03 16:28:17] old ancestors deleted.
[STOP] [2022-08-03 16:28:17] build_node_ancestors
[WARN] [2022-08-03 16:28:17] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:28:17] Flattener#flatten
[STOP] [2022-08-03 16:28:17] rebuild_nodes
[START] [2022-08-03 16:28:17] resolve_missing_media_owners
[STOP] [2022-08-03 16:28:17] resolve_missing_media_owners
[START] [2022-08-03 16:28:17] sanitize_media_verbatims
[STOP] [2022-08-03 16:28:17] sanitize_media_verbatims
[START] [2022-08-03 16:28:17] queue_downloads
[STOP] [2022-08-03 16:28:17] queue_downloads
[START] [2022-08-03 16:28:17] parse_names
[WARN] [2022-08-03 16:28:17] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:28:17] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:28:18] parse_names
[START] [2022-08-03 16:28:18] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:28:18] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:28:18] match_nodes
[START] [2022-08-03 16:28:18] map_all_nodes_to_pages
[STOP] [2022-08-03 16:28:18] map_all_nodes_to_pages
[INFO] [2022-08-03 16:28:18] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:28:18] update_nodes
[STOP] [2022-08-03 16:28:18] update_nodes
[STOP] [2022-08-03 16:28:18] match_nodes
[START] [2022-08-03 16:28:18] reindex_search
[STOP] [2022-08-03 16:28:18] reindex_search
[START] [2022-08-03 16:28:18] normalize_units
[STOP] [2022-08-03 16:28:18] normalize_units
[START] [2022-08-03 16:28:18] calculate_statistics
[2022-08-03 16:28:18] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:28:18] Duplicate page_id count: 0
[STOP] [2022-08-03 16:28:18] calculate_statistics
[START] [2022-08-03 16:28:18] complete_harvest_instance
[START] [2022-08-03 16:28:18] overall_tsv_creation
[INFO] [2022-08-03 16:28:18] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:28:18] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:28:59] 2 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:28:59] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:29:50] Mapped 2 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 16:29:50] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:29:50] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:29:50] Adding 2 traits...
[INFO] [2022-08-03 16:29:50] 2 metadata added.
[INFO] [2022-08-03 16:29:50] Adding 0 assocs...
[INFO] [2022-08-03 16:29:50] 0 metadata added.
[INFO] [2022-08-03 16:30:34] Processed 1/1 nodes
[INFO] [2022-08-03 16:30:34] Average Time: 110.88
[INFO] [2022-08-03 16:30:34] Total Time: 2m16s
[STOP] [2022-08-03 16:30:34] overall_tsv_creation
[INFO] [2022-08-03 16:30:34] Done. Check your files:
[INFO] [2022-08-03 16:30:34] (1 lines) /app/public/data/marshall_valenti/publish_nodes.tsv
[INFO] [2022-08-03 16:30:34] (1 lines) /app/public/data/marshall_valenti/publish_scientific_names.tsv
[INFO] [2022-08-03 16:30:34] (3 lines) /app/public/data/marshall_valenti/publish_traits.tsv
[INFO] [2022-08-03 16:30:34] (3 lines) /app/public/data/marshall_valenti/publish_metadata.tsv
[STOP] [2022-08-03 16:30:34] complete_harvest_instance
[START] [2022-08-03 16:30:34] completed
[STOP] [2022-08-03 16:30:34] completed
[STOP] [2022-08-03 16:30:34] logged process, took 144.78
Latest Process

03 Aug 16:28 EXITED currently processing 0