Harvest for English Vernaculars for Landmark Taxa Created 11 Mar 13:13

Harvesting Log

[INFO] [2025-03-11 13:13:09] Created harvest instance #4569
[STOP] [2025-03-11 13:13:09] create_harvest_instance
[START] [2025-03-11 13:13:09] fetch_files
[STOP] [2025-03-11 13:13:09] fetch_files
[START] [2025-03-11 13:13:09] validate_each_file
[INFO] [2025-03-11 13:13:09] Looping over 2 formats...
[INFO] [2025-03-11 13:13:09] ...nodes (/app/public/data/English_Vernacul/taxa.txt)
[INFO] [2025-03-11 13:13:10] Valid: /app/public/data/English_Vernacul/converted_csv/English_Vernacul_nodes_31232.csv (2556 lines)
[INFO] [2025-03-11 13:13:10] ...vernaculars (/app/public/data/English_Vernacul/vernacular.txt)
[INFO] [2025-03-11 13:13:10] Valid: /app/public/data/English_Vernacul/converted_csv/English_Vernacul_vernaculars_31233.csv (2556 lines)
[STOP] [2025-03-11 13:13:10] validate_each_file
[START] [2025-03-11 13:13:10] convert_to_csv
[INFO] [2025-03-11 13:13:10] Looping over 2 formats...
[INFO] [2025-03-11 13:13:10] ...nodes (/app/public/data/English_Vernacul/taxa.txt)
[CMD] [2025-03-11 13:13:10] /usr/bin/sort /app/public/data/English_Vernacul/converted_csv/English_Vernacul_nodes_31232.csv > /app/public/data/English_Vernacul/converted_csv/English_Vernacul_nodes_31232.csv_sorted
[INFO] [2025-03-11 13:13:10] Converted: /app/public/data/English_Vernacul/converted_csv/English_Vernacul_nodes_31232.csv (2556 lines)
[INFO] [2025-03-11 13:13:10] ...vernaculars (/app/public/data/English_Vernacul/vernacular.txt)
[CMD] [2025-03-11 13:13:10] /usr/bin/sort /app/public/data/English_Vernacul/converted_csv/English_Vernacul_vernaculars_31233.csv > /app/public/data/English_Vernacul/converted_csv/English_Vernacul_vernaculars_31233.csv_sorted
[INFO] [2025-03-11 13:13:10] Converted: /app/public/data/English_Vernacul/converted_csv/English_Vernacul_vernaculars_31233.csv (2556 lines)
[STOP] [2025-03-11 13:13:10] convert_to_csv
[START] [2025-03-11 13:13:10] calculate_delta
[INFO] [2025-03-11 13:13:10] Looping over 2 formats...
[INFO] [2025-03-11 13:13:10] ...nodes (/app/public/data/English_Vernacul/taxa.txt)
[CMD] [2025-03-11 13:13:10] echo "0a" > /app/public/data/English_Vernacul/diff/English_Vernacul_nodes_31232.diff
[CMD] [2025-03-11 13:13:10] tail -n +1 /app/public/data/English_Vernacul/converted_csv/English_Vernacul_nodes_31232.csv >> /app/public/data/English_Vernacul/diff/English_Vernacul_nodes_31232.diff
[CMD] [2025-03-11 13:13:10] echo "." >> /app/public/data/English_Vernacul/diff/English_Vernacul_nodes_31232.diff
[INFO] [2025-03-11 13:13:10] Created diff: /app/public/data/English_Vernacul/diff/English_Vernacul_nodes_31232.diff (2558 lines)
[INFO] [2025-03-11 13:13:10] ...vernaculars (/app/public/data/English_Vernacul/vernacular.txt)
[CMD] [2025-03-11 13:13:10] echo "0a" > /app/public/data/English_Vernacul/diff/English_Vernacul_vernaculars_31233.diff
[CMD] [2025-03-11 13:13:10] tail -n +1 /app/public/data/English_Vernacul/converted_csv/English_Vernacul_vernaculars_31233.csv >> /app/public/data/English_Vernacul/diff/English_Vernacul_vernaculars_31233.diff
[CMD] [2025-03-11 13:13:10] echo "." >> /app/public/data/English_Vernacul/diff/English_Vernacul_vernaculars_31233.diff
[INFO] [2025-03-11 13:13:10] Created diff: /app/public/data/English_Vernacul/diff/English_Vernacul_vernaculars_31233.diff (2558 lines)
[STOP] [2025-03-11 13:13:10] calculate_delta
[START] [2025-03-11 13:13:10] parse_diff_and_store
[INFO] [2025-03-11 13:13:10] Handling diff: /app/public/data/English_Vernacul/diff/English_Vernacul_nodes_31232.diff (2558 lines)
[INFO] [2025-03-11 13:13:10] Loading nodes diff file into memory (2558 lines)...
[INFO] [2025-03-11 13:13:11] Storing 2556 ScientificNames (5112/2556/2558)
[INFO] [2025-03-11 13:13:12] Storing 2556 Nodes (5112/2556/2558)
[INFO] [2025-03-11 13:13:13] Handling diff: /app/public/data/English_Vernacul/diff/English_Vernacul_vernaculars_31233.diff (2558 lines)
[INFO] [2025-03-11 13:13:13] Loading vernaculars diff file into memory (2558 lines)...
[INFO] [2025-03-11 13:13:13] Storing 2556 Vernaculars (2556/2556/2558)
[STOP] [2025-03-11 13:13:14] parse_diff_and_store
[START] [2025-03-11 13:13:14] resolve_keys
[2025-03-11 13:13:20] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2025-03-11 13:13:30] Occurrences to nodes (through scientific_names)...
[INFO] [2025-03-11 13:13:30] traits to occurrences...
[INFO] [2025-03-11 13:13:30] traits to nodes (through occurrences)...
[INFO] [2025-03-11 13:13:30] Traits to sex term...
[INFO] [2025-03-11 13:13:30] Traits to lifestage term...
[INFO] [2025-03-11 13:13:30] MetaTraits to traits...
[INFO] [2025-03-11 13:13:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2025-03-11 13:13:30] Assocs to occurrences...
[INFO] [2025-03-11 13:13:30] Assocs to nodes...
[INFO] [2025-03-11 13:13:30] Assoc to sex term...
[INFO] [2025-03-11 13:13:30] Assoc to lifestage term...
[INFO] [2025-03-11 13:13:30] MetaAssoc to assocs...
[STOP] [2025-03-11 13:13:30] resolve_keys
[START] [2025-03-11 13:13:30] hold_for_later_1
[STOP] [2025-03-11 13:13:30] hold_for_later_1
[START] [2025-03-11 13:13:30] hold_for_later_2
[STOP] [2025-03-11 13:13:30] hold_for_later_2
[START] [2025-03-11 13:13:30] resolve_missing_parents
[STOP] [2025-03-11 13:13:30] resolve_missing_parents
[START] [2025-03-11 13:13:30] rebuild_nodes
[START] [2025-03-11 13:13:30] Flattener#flatten
[START] [2025-03-11 13:13:30] Flattener#study_resource
[START] [2025-03-11 13:13:30] Flattener#build_ancestry
[STOP] [2025-03-11 13:13:31] Flattener#build_ancestry
[INFO] [2025-03-11 13:13:31] 2556 ancestry keys
[START] [2025-03-11 13:13:31] build_node_ancestors
[INFO] [2025-03-11 13:13:31] old ancestors deleted.
[STOP] [2025-03-11 13:13:31] build_node_ancestors
[WARN] [2025-03-11 13:13:31] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2025-03-11 13:13:31] Flattener#flatten
[STOP] [2025-03-11 13:13:31] rebuild_nodes
[START] [2025-03-11 13:13:31] resolve_missing_media_owners
[STOP] [2025-03-11 13:13:31] resolve_missing_media_owners
[START] [2025-03-11 13:13:31] sanitize_media_verbatims
[STOP] [2025-03-11 13:13:31] sanitize_media_verbatims
[START] [2025-03-11 13:13:31] queue_downloads
[STOP] [2025-03-11 13:13:31] queue_downloads
[START] [2025-03-11 13:13:31] parse_names
[WARN] [2025-03-11 13:13:31] I see 2556 names which still need to be parsed.
[WARN] [2025-03-11 13:13:31] Names to parse: 2556 formatted: 2556 learned: 2556 parsed: 2556
[STOP] [2025-03-11 13:13:35] parse_names
[START] [2025-03-11 13:13:35] denormalize_canonical_names_to_nodes
[STOP] [2025-03-11 13:13:36] denormalize_canonical_names_to_nodes
[START] [2025-03-11 13:13:36] match_nodes
[START] [2025-03-11 13:13:36] map_all_nodes_to_pages
[STOP] [2025-03-11 13:13:38] map_all_nodes_to_pages
[INFO] [2025-03-11 13:13:38] ZERO unmatched nodes (of 2556)! Nicely done.
[START] [2025-03-11 13:13:38] update_nodes
[STOP] [2025-03-11 13:13:38] update_nodes
[STOP] [2025-03-11 13:13:38] match_nodes
[START] [2025-03-11 13:13:38] reindex_search
[STOP] [2025-03-11 13:13:43] reindex_search
[START] [2025-03-11 13:13:43] normalize_units
[STOP] [2025-03-11 13:13:43] normalize_units
[START] [2025-03-11 13:13:43] calculate_statistics
[2025-03-11 13:13:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2025-03-11 13:16:02] Duplicate page_id count: 0
[STOP] [2025-03-11 13:16:02] calculate_statistics
[START] [2025-03-11 13:16:02] complete_harvest_instance
[START] [2025-03-11 13:16:02] overall_tsv_creation
[INFO] [2025-03-11 13:16:03] Exporting 2556 nodes as TSV in batches of 10000...
[INFO] [2025-03-11 13:16:03] Processing group of 2556 in 1 batches of 10000
[INFO] [2025-03-11 13:16:08] Processed 2556/2556 nodes
[INFO] [2025-03-11 13:16:08] Average Time: 4.01
[INFO] [2025-03-11 13:16:08] Total Time: 6s
[STOP] [2025-03-11 13:16:08] overall_tsv_creation
[INFO] [2025-03-11 13:16:08] Done. Check your files:
[INFO] [2025-03-11 13:16:09] (2556 lines) /app/public/data/English_Vernacul/publish_nodes.tsv
[INFO] [2025-03-11 13:16:09] (2556 lines) /app/public/data/English_Vernacul/publish_scientific_names.tsv
[INFO] [2025-03-11 13:16:09] (2556 lines) /app/public/data/English_Vernacul/publish_vernaculars.tsv
[STOP] [2025-03-11 13:16:09] complete_harvest_instance
[START] [2025-03-11 13:16:09] completed
[STOP] [2025-03-11 13:16:09] completed
[STOP] [2025-03-11 13:16:09] logged process, took 179.7

Latest Process

11 Mar 13:13 EXITED currently processing 0