Harvest for Ax and Dörjes, 1966 Created 31 Jan 12:44

Harvesting Log

[INFO] [2023-01-31 12:44:13] Created harvest instance #4293
[STOP] [2023-01-31 12:44:13] create_harvest_instance
[START] [2023-01-31 12:44:13] fetch_files
[STOP] [2023-01-31 12:44:13] fetch_files
[START] [2023-01-31 12:44:13] validate_each_file
[INFO] [2023-01-31 12:44:13] Looping over 3 formats...
[INFO] [2023-01-31 12:44:13] ...nodes (/app/public/data/ax_ax_and_d_rjes/taxa.tsv)
[INFO] [2023-01-31 12:44:13] Valid: /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_nodes_30182.csv (1 lines)
[INFO] [2023-01-31 12:44:13] ...occurrences (/app/public/data/ax_ax_and_d_rjes/occurrences.tsv)
[INFO] [2023-01-31 12:44:13] Valid: /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_occurrences_30183.csv (1 lines)
[INFO] [2023-01-31 12:44:13] ...measurements (/app/public/data/ax_ax_and_d_rjes/measurementOrFact.tsv)
[INFO] [2023-01-31 12:44:13] Valid: /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_measurements_30184.csv (2 lines)
[STOP] [2023-01-31 12:44:13] validate_each_file
[START] [2023-01-31 12:44:13] convert_to_csv
[INFO] [2023-01-31 12:44:13] Looping over 3 formats...
[INFO] [2023-01-31 12:44:13] ...nodes (/app/public/data/ax_ax_and_d_rjes/taxa.tsv)
[CMD] [2023-01-31 12:44:13] /usr/bin/sort /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_nodes_30182.csv > /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_nodes_30182.csv_sorted
[INFO] [2023-01-31 12:44:13] Converted: /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_nodes_30182.csv (1 lines)
[INFO] [2023-01-31 12:44:13] ...occurrences (/app/public/data/ax_ax_and_d_rjes/occurrences.tsv)
[CMD] [2023-01-31 12:44:13] /usr/bin/sort /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_occurrences_30183.csv > /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_occurrences_30183.csv_sorted
[INFO] [2023-01-31 12:44:13] Converted: /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_occurrences_30183.csv (1 lines)
[INFO] [2023-01-31 12:44:13] ...measurements (/app/public/data/ax_ax_and_d_rjes/measurementOrFact.tsv)
[CMD] [2023-01-31 12:44:13] /usr/bin/sort /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_measurements_30184.csv > /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_measurements_30184.csv_sorted
[INFO] [2023-01-31 12:44:13] Converted: /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_measurements_30184.csv (2 lines)
[STOP] [2023-01-31 12:44:13] convert_to_csv
[START] [2023-01-31 12:44:13] calculate_delta
[INFO] [2023-01-31 12:44:13] Looping over 3 formats...
[INFO] [2023-01-31 12:44:13] ...nodes (/app/public/data/ax_ax_and_d_rjes/taxa.tsv)
[CMD] [2023-01-31 12:44:13] echo "0a" > /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_nodes_30182.diff
[CMD] [2023-01-31 12:44:13] tail -n +1 /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_nodes_30182.csv >> /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_nodes_30182.diff
[CMD] [2023-01-31 12:44:13] echo "." >> /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_nodes_30182.diff
[INFO] [2023-01-31 12:44:13] Created diff: /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_nodes_30182.diff (3 lines)
[INFO] [2023-01-31 12:44:13] ...occurrences (/app/public/data/ax_ax_and_d_rjes/occurrences.tsv)
[CMD] [2023-01-31 12:44:13] echo "0a" > /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_occurrences_30183.diff
[CMD] [2023-01-31 12:44:13] tail -n +1 /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_occurrences_30183.csv >> /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_occurrences_30183.diff
[CMD] [2023-01-31 12:44:13] echo "." >> /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_occurrences_30183.diff
[INFO] [2023-01-31 12:44:13] Created diff: /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_occurrences_30183.diff (3 lines)
[INFO] [2023-01-31 12:44:13] ...measurements (/app/public/data/ax_ax_and_d_rjes/measurementOrFact.tsv)
[CMD] [2023-01-31 12:44:13] echo "0a" > /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_measurements_30184.diff
[CMD] [2023-01-31 12:44:13] tail -n +1 /app/public/data/ax_ax_and_d_rjes/converted_csv/ax_ax_and_d_rjes_measurements_30184.csv >> /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_measurements_30184.diff
[CMD] [2023-01-31 12:44:13] echo "." >> /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_measurements_30184.diff
[INFO] [2023-01-31 12:44:13] Created diff: /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_measurements_30184.diff (4 lines)
[STOP] [2023-01-31 12:44:13] calculate_delta
[START] [2023-01-31 12:44:13] parse_diff_and_store
[INFO] [2023-01-31 12:44:13] Handling diff: /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_nodes_30182.diff (3 lines)
[INFO] [2023-01-31 12:44:13] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-01-31 12:44:13] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-01-31 12:44:13] Storing 1 Nodes (2/1/3)
[INFO] [2023-01-31 12:44:13] Handling diff: /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_occurrences_30183.diff (3 lines)
[INFO] [2023-01-31 12:44:13] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-01-31 12:44:13] Storing 1 Occurrences (1/1/3)
[INFO] [2023-01-31 12:44:13] Handling diff: /app/public/data/ax_ax_and_d_rjes/diff/ax_ax_and_d_rjes_measurements_30184.diff (4 lines)
[INFO] [2023-01-31 12:44:13] Loading measurements diff file into memory (4 lines)...
[INFO] [2023-01-31 12:44:13] Storing 2 Traits (4/2/4)
[INFO] [2023-01-31 12:44:13] Storing 2 MetaTraits (4/2/4)
[STOP] [2023-01-31 12:44:13] parse_diff_and_store
[START] [2023-01-31 12:44:13] resolve_keys
[2023-01-31 12:44:13] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 12:44:20] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 12:44:20] traits to occurrences...
[INFO] [2023-01-31 12:44:20] traits to nodes (through occurrences)...
[INFO] [2023-01-31 12:44:20] Traits to sex term...
[INFO] [2023-01-31 12:44:20] Traits to lifestage term...
[INFO] [2023-01-31 12:44:20] MetaTraits to traits...
[INFO] [2023-01-31 12:44:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 12:44:20] Assocs to occurrences...
[INFO] [2023-01-31 12:44:20] Assocs to nodes...
[INFO] [2023-01-31 12:44:20] Assoc to sex term...
[INFO] [2023-01-31 12:44:20] Assoc to lifestage term...
[INFO] [2023-01-31 12:44:20] MetaAssoc to assocs...
[STOP] [2023-01-31 12:44:20] resolve_keys
[START] [2023-01-31 12:44:20] hold_for_later_1
[STOP] [2023-01-31 12:44:20] hold_for_later_1
[START] [2023-01-31 12:44:20] hold_for_later_2
[STOP] [2023-01-31 12:44:21] hold_for_later_2
[START] [2023-01-31 12:44:21] resolve_missing_parents
[STOP] [2023-01-31 12:44:21] resolve_missing_parents
[START] [2023-01-31 12:44:21] rebuild_nodes
[START] [2023-01-31 12:44:21] Flattener#flatten
[START] [2023-01-31 12:44:21] Flattener#study_resource
[START] [2023-01-31 12:44:21] Flattener#build_ancestry
[STOP] [2023-01-31 12:44:21] Flattener#build_ancestry
[INFO] [2023-01-31 12:44:21] 1 ancestry keys
[START] [2023-01-31 12:44:21] build_node_ancestors
[INFO] [2023-01-31 12:44:21] old ancestors deleted.
[STOP] [2023-01-31 12:44:21] build_node_ancestors
[WARN] [2023-01-31 12:44:21] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-31 12:44:21] Flattener#flatten
[STOP] [2023-01-31 12:44:21] rebuild_nodes
[START] [2023-01-31 12:44:21] resolve_missing_media_owners
[STOP] [2023-01-31 12:44:21] resolve_missing_media_owners
[START] [2023-01-31 12:44:21] sanitize_media_verbatims
[STOP] [2023-01-31 12:44:21] sanitize_media_verbatims
[START] [2023-01-31 12:44:21] queue_downloads
[STOP] [2023-01-31 12:44:21] queue_downloads
[START] [2023-01-31 12:44:21] parse_names
[WARN] [2023-01-31 12:44:21] I see 1 names which still need to be parsed.
[WARN] [2023-01-31 12:44:21] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-01-31 12:44:22] parse_names
[START] [2023-01-31 12:44:22] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 12:44:22] denormalize_canonical_names_to_nodes
[START] [2023-01-31 12:44:22] match_nodes
[START] [2023-01-31 12:44:22] map_all_nodes_to_pages
[STOP] [2023-01-31 12:44:22] map_all_nodes_to_pages
[INFO] [2023-01-31 12:44:22] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-01-31 12:44:22] update_nodes
[STOP] [2023-01-31 12:44:22] update_nodes
[STOP] [2023-01-31 12:44:22] match_nodes
[START] [2023-01-31 12:44:22] reindex_search
[STOP] [2023-01-31 12:44:22] reindex_search
[START] [2023-01-31 12:44:22] normalize_units
[STOP] [2023-01-31 12:44:22] normalize_units
[START] [2023-01-31 12:44:22] calculate_statistics
[2023-01-31 12:44:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-31 12:44:22] Duplicate page_id count: 0
[STOP] [2023-01-31 12:44:22] calculate_statistics
[START] [2023-01-31 12:44:22] complete_harvest_instance
[START] [2023-01-31 12:44:22] overall_tsv_creation
[INFO] [2023-01-31 12:44:22] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 12:44:22] Processing group of 1 in 1 batches of 10000
[INFO] [2023-01-31 12:44:22] 2 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 12:44:22] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-01-31 12:44:22] Mapped 2 traits (2 meta) for 1 nodes.
[INFO] [2023-01-31 12:44:22] Building Associations map (this can take a while)...
[INFO] [2023-01-31 12:44:22] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 12:44:22] Adding 2 traits...
[INFO] [2023-01-31 12:44:22] 0 metadata added.
[INFO] [2023-01-31 12:44:22] Adding 0 assocs...
[INFO] [2023-01-31 12:44:22] 0 metadata added.
[INFO] [2023-01-31 12:45:07] Processed 1/1 nodes
[INFO] [2023-01-31 12:45:07] Average Time: 44.74
[INFO] [2023-01-31 12:45:07] Total Time: 45s
[STOP] [2023-01-31 12:45:07] overall_tsv_creation
[INFO] [2023-01-31 12:45:07] Done. Check your files:
[INFO] [2023-01-31 12:45:07] (1 lines) /app/public/data/ax_ax_and_d_rjes/publish_nodes.tsv
[INFO] [2023-01-31 12:45:07] (1 lines) /app/public/data/ax_ax_and_d_rjes/publish_scientific_names.tsv
[INFO] [2023-01-31 12:45:07] (3 lines) /app/public/data/ax_ax_and_d_rjes/publish_traits.tsv
[INFO] [2023-01-31 12:45:07] (1 lines) /app/public/data/ax_ax_and_d_rjes/publish_metadata.tsv
[STOP] [2023-01-31 12:45:07] complete_harvest_instance
[START] [2023-01-31 12:45:07] completed
[STOP] [2023-01-31 12:45:07] completed
[STOP] [2023-01-31 12:45:07] logged process, took 54.34

Latest Process

31 Jan 12:42 EXITED currently processing 0