Harvest for Edmondst 2000 Created 03 Aug 17:12

Stage: completed
Fetched: 03 Aug 17:12
Validated: 03 Aug 17:12
Deltas Created 03 Aug 17:12
Units Normalized: 03 Aug 17:12
Ancestry Built: 03 Aug 17:12
Nodes Matched: 03 Aug 17:12
Names Parsed: 03 Aug 17:12
New Models Stored: 03 Aug 17:12
Indexed: 03 Aug 17:12
Completed: 03 Aug 17:14
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 17:12:31] Created harvest instance #4191
[STOP] [2022-08-03 17:12:31] create_harvest_instance
[START] [2022-08-03 17:12:31] fetch_files
[STOP] [2022-08-03 17:12:31] fetch_files
[START] [2022-08-03 17:12:31] validate_each_file
[INFO] [2022-08-03 17:12:31] Looping over 3 formats...
[INFO] [2022-08-03 17:12:31] ...nodes (/app/public/data/edmondst_edmonds/taxa.txt)
[INFO] [2022-08-03 17:12:31] Valid: /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_nodes_29588.csv (1 lines)
[INFO] [2022-08-03 17:12:31] ...occurrences (/app/public/data/edmondst_edmonds/occurrences.txt)
[INFO] [2022-08-03 17:12:31] Valid: /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_occurrences_29589.csv (1 lines)
[INFO] [2022-08-03 17:12:31] ...measurements (/app/public/data/edmondst_edmonds/measurementOrFact.txt)
[INFO] [2022-08-03 17:12:31] Valid: /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_measurements_29590.csv (4 lines)
[STOP] [2022-08-03 17:12:31] validate_each_file
[START] [2022-08-03 17:12:31] convert_to_csv
[INFO] [2022-08-03 17:12:31] Looping over 3 formats...
[INFO] [2022-08-03 17:12:31] ...nodes (/app/public/data/edmondst_edmonds/taxa.txt)
[CMD] [2022-08-03 17:12:31] /usr/bin/sort /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_nodes_29588.csv > /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_nodes_29588.csv_sorted
[INFO] [2022-08-03 17:12:31] Converted: /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_nodes_29588.csv (1 lines)
[INFO] [2022-08-03 17:12:31] ...occurrences (/app/public/data/edmondst_edmonds/occurrences.txt)
[CMD] [2022-08-03 17:12:31] /usr/bin/sort /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_occurrences_29589.csv > /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_occurrences_29589.csv_sorted
[INFO] [2022-08-03 17:12:31] Converted: /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_occurrences_29589.csv (1 lines)
[INFO] [2022-08-03 17:12:31] ...measurements (/app/public/data/edmondst_edmonds/measurementOrFact.txt)
[CMD] [2022-08-03 17:12:31] /usr/bin/sort /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_measurements_29590.csv > /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_measurements_29590.csv_sorted
[INFO] [2022-08-03 17:12:31] Converted: /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_measurements_29590.csv (4 lines)
[STOP] [2022-08-03 17:12:31] convert_to_csv
[START] [2022-08-03 17:12:31] calculate_delta
[INFO] [2022-08-03 17:12:31] Looping over 3 formats...
[INFO] [2022-08-03 17:12:31] ...nodes (/app/public/data/edmondst_edmonds/taxa.txt)
[CMD] [2022-08-03 17:12:31] echo "0a" > /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_nodes_29588.diff
[CMD] [2022-08-03 17:12:31] tail -n +1 /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_nodes_29588.csv >> /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_nodes_29588.diff
[CMD] [2022-08-03 17:12:31] echo "." >> /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_nodes_29588.diff
[INFO] [2022-08-03 17:12:31] Created diff: /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_nodes_29588.diff (3 lines)
[INFO] [2022-08-03 17:12:31] ...occurrences (/app/public/data/edmondst_edmonds/occurrences.txt)
[CMD] [2022-08-03 17:12:31] echo "0a" > /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_occurrences_29589.diff
[CMD] [2022-08-03 17:12:31] tail -n +1 /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_occurrences_29589.csv >> /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_occurrences_29589.diff
[CMD] [2022-08-03 17:12:31] echo "." >> /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_occurrences_29589.diff
[INFO] [2022-08-03 17:12:31] Created diff: /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_occurrences_29589.diff (3 lines)
[INFO] [2022-08-03 17:12:31] ...measurements (/app/public/data/edmondst_edmonds/measurementOrFact.txt)
[CMD] [2022-08-03 17:12:31] echo "0a" > /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_measurements_29590.diff
[CMD] [2022-08-03 17:12:31] tail -n +1 /app/public/data/edmondst_edmonds/converted_csv/edmondst_edmonds_measurements_29590.csv >> /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_measurements_29590.diff
[CMD] [2022-08-03 17:12:31] echo "." >> /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_measurements_29590.diff
[INFO] [2022-08-03 17:12:31] Created diff: /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_measurements_29590.diff (6 lines)
[STOP] [2022-08-03 17:12:32] calculate_delta
[START] [2022-08-03 17:12:32] parse_diff_and_store
[INFO] [2022-08-03 17:12:32] Handling diff: /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_nodes_29588.diff (3 lines)
[INFO] [2022-08-03 17:12:32] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 17:12:32] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 17:12:32] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 17:12:32] Handling diff: /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_occurrences_29589.diff (3 lines)
[INFO] [2022-08-03 17:12:32] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 17:12:32] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 17:12:32] Handling diff: /app/public/data/edmondst_edmonds/diff/edmondst_edmonds_measurements_29590.diff (6 lines)
[INFO] [2022-08-03 17:12:32] Loading measurements diff file into memory (6 lines)...
[INFO] [2022-08-03 17:12:32] Storing 4 Traits (6/4/6)
[INFO] [2022-08-03 17:12:32] Storing 2 MetaTraits (6/4/6)
[STOP] [2022-08-03 17:12:32] parse_diff_and_store
[START] [2022-08-03 17:12:32] resolve_keys
[2022-08-03 17:12:32] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:12:39] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:12:39] traits to occurrences...
[INFO] [2022-08-03 17:12:39] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:12:39] Traits to sex term...
[INFO] [2022-08-03 17:12:39] Traits to lifestage term...
[INFO] [2022-08-03 17:12:39] MetaTraits to traits...
[INFO] [2022-08-03 17:12:39] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:12:39] Assocs to occurrences...
[INFO] [2022-08-03 17:12:39] Assocs to nodes...
[INFO] [2022-08-03 17:12:39] Assoc to sex term...
[INFO] [2022-08-03 17:12:39] Assoc to lifestage term...
[INFO] [2022-08-03 17:12:39] MetaAssoc to assocs...
[STOP] [2022-08-03 17:12:39] resolve_keys
[START] [2022-08-03 17:12:39] hold_for_later_1
[STOP] [2022-08-03 17:12:39] hold_for_later_1
[START] [2022-08-03 17:12:39] hold_for_later_2
[STOP] [2022-08-03 17:12:39] hold_for_later_2
[START] [2022-08-03 17:12:39] resolve_missing_parents
[STOP] [2022-08-03 17:12:39] resolve_missing_parents
[START] [2022-08-03 17:12:39] rebuild_nodes
[START] [2022-08-03 17:12:39] Flattener#flatten
[START] [2022-08-03 17:12:39] Flattener#study_resource
[START] [2022-08-03 17:12:39] Flattener#build_ancestry
[STOP] [2022-08-03 17:12:39] Flattener#build_ancestry
[INFO] [2022-08-03 17:12:39] 1 ancestry keys
[START] [2022-08-03 17:12:39] build_node_ancestors
[INFO] [2022-08-03 17:12:39] old ancestors deleted.
[STOP] [2022-08-03 17:12:39] build_node_ancestors
[WARN] [2022-08-03 17:12:39] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:12:39] Flattener#flatten
[STOP] [2022-08-03 17:12:39] rebuild_nodes
[START] [2022-08-03 17:12:39] resolve_missing_media_owners
[STOP] [2022-08-03 17:12:39] resolve_missing_media_owners
[START] [2022-08-03 17:12:39] sanitize_media_verbatims
[STOP] [2022-08-03 17:12:39] sanitize_media_verbatims
[START] [2022-08-03 17:12:39] queue_downloads
[STOP] [2022-08-03 17:12:39] queue_downloads
[START] [2022-08-03 17:12:39] parse_names
[WARN] [2022-08-03 17:12:39] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 17:12:39] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 17:12:40] parse_names
[START] [2022-08-03 17:12:40] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:12:40] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:12:40] match_nodes
[START] [2022-08-03 17:12:40] map_all_nodes_to_pages
[STOP] [2022-08-03 17:12:40] map_all_nodes_to_pages
[INFO] [2022-08-03 17:12:40] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 17:12:40] update_nodes
[STOP] [2022-08-03 17:12:40] update_nodes
[STOP] [2022-08-03 17:12:40] match_nodes
[START] [2022-08-03 17:12:40] reindex_search
[STOP] [2022-08-03 17:12:40] reindex_search
[START] [2022-08-03 17:12:40] normalize_units
[STOP] [2022-08-03 17:12:40] normalize_units
[START] [2022-08-03 17:12:40] calculate_statistics
[2022-08-03 17:12:40] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:12:40] Duplicate page_id count: 0
[STOP] [2022-08-03 17:12:40] calculate_statistics
[START] [2022-08-03 17:12:40] complete_harvest_instance
[START] [2022-08-03 17:12:40] overall_tsv_creation
[INFO] [2022-08-03 17:12:40] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:12:40] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 17:13:21] 2 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:13:21] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 17:14:13] Mapped 2 traits (2 meta) for 1 nodes.
[INFO] [2022-08-03 17:14:13] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:14:13] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:14:13] Adding 2 traits...
[INFO] [2022-08-03 17:14:13] 2 metadata added.
[INFO] [2022-08-03 17:14:13] Adding 0 assocs...
[INFO] [2022-08-03 17:14:13] 0 metadata added.
[INFO] [2022-08-03 17:14:54] Processed 1/1 nodes
[INFO] [2022-08-03 17:14:54] Average Time: 109.4
[INFO] [2022-08-03 17:14:54] Total Time: 2m15s
[STOP] [2022-08-03 17:14:54] overall_tsv_creation
[INFO] [2022-08-03 17:14:54] Done. Check your files:
[INFO] [2022-08-03 17:14:54] (1 lines) /app/public/data/edmondst_edmonds/publish_nodes.tsv
[INFO] [2022-08-03 17:14:54] (1 lines) /app/public/data/edmondst_edmonds/publish_scientific_names.tsv
[INFO] [2022-08-03 17:14:54] (3 lines) /app/public/data/edmondst_edmonds/publish_traits.tsv
[INFO] [2022-08-03 17:14:54] (3 lines) /app/public/data/edmondst_edmonds/publish_metadata.tsv
[STOP] [2022-08-03 17:14:54] complete_harvest_instance
[START] [2022-08-03 17:14:54] completed
[STOP] [2022-08-03 17:14:54] completed
[STOP] [2022-08-03 17:14:54] logged process, took 143.49
Latest Process

03 Aug 17:12 EXITED currently processing 0