Harvest for McDermott 1964 Created 19 Jan 16:20

Harvesting Log

[INFO] [2023-01-19 16:20:53] Created harvest instance #4266
[STOP] [2023-01-19 16:20:53] create_harvest_instance
[START] [2023-01-19 16:20:53] fetch_files
[STOP] [2023-01-19 16:20:53] fetch_files
[START] [2023-01-19 16:20:53] validate_each_file
[INFO] [2023-01-19 16:20:53] Looping over 3 formats...
[INFO] [2023-01-19 16:20:53] ...nodes (/app/public/data/mc_dermott_mcder/taxa.txt)
[INFO] [2023-01-19 16:20:53] Valid: /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_nodes_30046.csv (8 lines)
[INFO] [2023-01-19 16:20:53] ...occurrences (/app/public/data/mc_dermott_mcder/occurrences.txt)
[INFO] [2023-01-19 16:20:53] Valid: /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_occurrences_30047.csv (8 lines)
[INFO] [2023-01-19 16:20:53] ...measurements (/app/public/data/mc_dermott_mcder/measurementsorfacts.txt)
[INFO] [2023-01-19 16:20:53] Valid: /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_measurements_30048.csv (16 lines)
[STOP] [2023-01-19 16:20:53] validate_each_file
[START] [2023-01-19 16:20:53] convert_to_csv
[INFO] [2023-01-19 16:20:53] Looping over 3 formats...
[INFO] [2023-01-19 16:20:53] ...nodes (/app/public/data/mc_dermott_mcder/taxa.txt)
[CMD] [2023-01-19 16:20:53] /usr/bin/sort /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_nodes_30046.csv > /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_nodes_30046.csv_sorted
[INFO] [2023-01-19 16:20:53] Converted: /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_nodes_30046.csv (8 lines)
[INFO] [2023-01-19 16:20:53] ...occurrences (/app/public/data/mc_dermott_mcder/occurrences.txt)
[CMD] [2023-01-19 16:20:53] /usr/bin/sort /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_occurrences_30047.csv > /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_occurrences_30047.csv_sorted
[INFO] [2023-01-19 16:20:53] Converted: /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_occurrences_30047.csv (8 lines)
[INFO] [2023-01-19 16:20:53] ...measurements (/app/public/data/mc_dermott_mcder/measurementsorfacts.txt)
[CMD] [2023-01-19 16:20:53] /usr/bin/sort /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_measurements_30048.csv > /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_measurements_30048.csv_sorted
[INFO] [2023-01-19 16:20:53] Converted: /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_measurements_30048.csv (16 lines)
[STOP] [2023-01-19 16:20:53] convert_to_csv
[START] [2023-01-19 16:20:53] calculate_delta
[INFO] [2023-01-19 16:20:53] Looping over 3 formats...
[INFO] [2023-01-19 16:20:53] ...nodes (/app/public/data/mc_dermott_mcder/taxa.txt)
[CMD] [2023-01-19 16:20:53] echo "0a" > /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_nodes_30046.diff
[CMD] [2023-01-19 16:20:55] tail -n +1 /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_nodes_30046.csv >> /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_nodes_30046.diff
[CMD] [2023-01-19 16:20:55] echo "." >> /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_nodes_30046.diff
[INFO] [2023-01-19 16:20:55] Created diff: /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_nodes_30046.diff (10 lines)
[INFO] [2023-01-19 16:20:55] ...occurrences (/app/public/data/mc_dermott_mcder/occurrences.txt)
[CMD] [2023-01-19 16:20:55] echo "0a" > /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_occurrences_30047.diff
[CMD] [2023-01-19 16:20:55] tail -n +1 /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_occurrences_30047.csv >> /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_occurrences_30047.diff
[CMD] [2023-01-19 16:20:55] echo "." >> /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_occurrences_30047.diff
[INFO] [2023-01-19 16:20:55] Created diff: /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_occurrences_30047.diff (10 lines)
[INFO] [2023-01-19 16:20:55] ...measurements (/app/public/data/mc_dermott_mcder/measurementsorfacts.txt)
[CMD] [2023-01-19 16:20:55] echo "0a" > /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_measurements_30048.diff
[CMD] [2023-01-19 16:20:55] tail -n +1 /app/public/data/mc_dermott_mcder/converted_csv/mc_dermott_mcder_measurements_30048.csv >> /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_measurements_30048.diff
[CMD] [2023-01-19 16:20:55] echo "." >> /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_measurements_30048.diff
[INFO] [2023-01-19 16:20:55] Created diff: /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_measurements_30048.diff (18 lines)
[STOP] [2023-01-19 16:20:55] calculate_delta
[START] [2023-01-19 16:20:55] parse_diff_and_store
[INFO] [2023-01-19 16:20:55] Handling diff: /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_nodes_30046.diff (10 lines)
[INFO] [2023-01-19 16:20:55] Loading nodes diff file into memory (10 lines)...
[INFO] [2023-01-19 16:20:55] Storing 8 ScientificNames (16/8/10)
[INFO] [2023-01-19 16:20:55] Storing 8 Nodes (16/8/10)
[INFO] [2023-01-19 16:20:55] Handling diff: /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_occurrences_30047.diff (10 lines)
[INFO] [2023-01-19 16:20:55] Loading occurrences diff file into memory (10 lines)...
[INFO] [2023-01-19 16:20:55] Storing 8 Occurrences (16/8/10)
[INFO] [2023-01-19 16:20:55] Storing 8 OccurrenceMetadata (16/8/10)
[INFO] [2023-01-19 16:20:55] Handling diff: /app/public/data/mc_dermott_mcder/diff/mc_dermott_mcder_measurements_30048.diff (18 lines)
[INFO] [2023-01-19 16:20:55] Loading measurements diff file into memory (18 lines)...
[INFO] [2023-01-19 16:20:55] Storing 16 Traits (24/16/18)
[INFO] [2023-01-19 16:20:55] Storing 8 MetaTraits (24/16/18)
[STOP] [2023-01-19 16:20:55] parse_diff_and_store
[START] [2023-01-19 16:20:55] resolve_keys
[2023-01-19 16:20:55] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-19 16:21:02] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-19 16:21:02] traits to occurrences...
[INFO] [2023-01-19 16:21:02] traits to nodes (through occurrences)...
[INFO] [2023-01-19 16:21:02] Traits to sex term...
[INFO] [2023-01-19 16:21:02] Traits to lifestage term...
[INFO] [2023-01-19 16:21:02] MetaTraits to traits...
[INFO] [2023-01-19 16:21:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-19 16:21:02] Assocs to occurrences...
[INFO] [2023-01-19 16:21:02] Assocs to nodes...
[INFO] [2023-01-19 16:21:02] Assoc to sex term...
[INFO] [2023-01-19 16:21:02] Assoc to lifestage term...
[INFO] [2023-01-19 16:21:02] MetaAssoc to assocs...
[STOP] [2023-01-19 16:21:02] resolve_keys
[START] [2023-01-19 16:21:02] hold_for_later_1
[STOP] [2023-01-19 16:21:02] hold_for_later_1
[START] [2023-01-19 16:21:02] hold_for_later_2
[STOP] [2023-01-19 16:21:02] hold_for_later_2
[START] [2023-01-19 16:21:02] resolve_missing_parents
[STOP] [2023-01-19 16:21:02] resolve_missing_parents
[START] [2023-01-19 16:21:02] rebuild_nodes
[START] [2023-01-19 16:21:02] Flattener#flatten
[START] [2023-01-19 16:21:02] Flattener#study_resource
[START] [2023-01-19 16:21:02] Flattener#build_ancestry
[STOP] [2023-01-19 16:21:02] Flattener#build_ancestry
[INFO] [2023-01-19 16:21:02] 8 ancestry keys
[START] [2023-01-19 16:21:02] build_node_ancestors
[INFO] [2023-01-19 16:21:02] old ancestors deleted.
[STOP] [2023-01-19 16:21:02] build_node_ancestors
[WARN] [2023-01-19 16:21:02] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-19 16:21:02] Flattener#flatten
[STOP] [2023-01-19 16:21:02] rebuild_nodes
[START] [2023-01-19 16:21:02] resolve_missing_media_owners
[STOP] [2023-01-19 16:21:02] resolve_missing_media_owners
[START] [2023-01-19 16:21:02] sanitize_media_verbatims
[STOP] [2023-01-19 16:21:02] sanitize_media_verbatims
[START] [2023-01-19 16:21:02] queue_downloads
[STOP] [2023-01-19 16:21:02] queue_downloads
[START] [2023-01-19 16:21:02] parse_names
[WARN] [2023-01-19 16:21:02] I see 8 names which still need to be parsed.
[WARN] [2023-01-19 16:21:02] Names to parse: 8 formatted: 8 learned: 8 parsed: 8
[STOP] [2023-01-19 16:21:03] parse_names
[START] [2023-01-19 16:21:03] denormalize_canonical_names_to_nodes
[STOP] [2023-01-19 16:21:03] denormalize_canonical_names_to_nodes
[START] [2023-01-19 16:21:03] match_nodes
[START] [2023-01-19 16:21:03] map_all_nodes_to_pages
[STOP] [2023-01-19 16:21:03] map_all_nodes_to_pages
[INFO] [2023-01-19 16:21:03] ZERO unmatched nodes (of 8)! Nicely done.
[START] [2023-01-19 16:21:03] update_nodes
[STOP] [2023-01-19 16:21:03] update_nodes
[STOP] [2023-01-19 16:21:03] match_nodes
[START] [2023-01-19 16:21:03] reindex_search
[STOP] [2023-01-19 16:21:04] reindex_search
[START] [2023-01-19 16:21:04] normalize_units
[STOP] [2023-01-19 16:21:04] normalize_units
[START] [2023-01-19 16:21:04] calculate_statistics
[2023-01-19 16:21:04] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-19 16:21:04] Duplicate page_id count: 0
[STOP] [2023-01-19 16:21:04] calculate_statistics
[START] [2023-01-19 16:21:04] complete_harvest_instance
[START] [2023-01-19 16:21:04] overall_tsv_creation
[INFO] [2023-01-19 16:21:04] Exporting 8 nodes as TSV in batches of 10000...
[INFO] [2023-01-19 16:21:04] Processing group of 8 in 1 batches of 10000
[INFO] [2023-01-19 16:21:04] 8 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-19 16:21:04] Building Traits map for 8 nodes (this can take a while)...
[INFO] [2023-01-19 16:21:04] Mapped 8 traits (8 meta) for 8 nodes.
[INFO] [2023-01-19 16:21:04] Building Associations map (this can take a while)...
[INFO] [2023-01-19 16:21:04] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-19 16:21:04] Adding 8 traits...
[INFO] [2023-01-19 16:21:04] 8 metadata added.
[INFO] [2023-01-19 16:21:04] Adding 0 assocs...
[INFO] [2023-01-19 16:21:04] 0 metadata added.
[INFO] [2023-01-19 16:21:48] Processed 8/8 nodes
[INFO] [2023-01-19 16:21:48] Average Time: 43.8
[INFO] [2023-01-19 16:21:48] Total Time: 44s
[STOP] [2023-01-19 16:21:48] overall_tsv_creation
[INFO] [2023-01-19 16:21:48] Done. Check your files:
[INFO] [2023-01-19 16:21:48] (8 lines) /app/public/data/mc_dermott_mcder/publish_nodes.tsv
[INFO] [2023-01-19 16:21:48] (8 lines) /app/public/data/mc_dermott_mcder/publish_scientific_names.tsv
[INFO] [2023-01-19 16:21:48] (9 lines) /app/public/data/mc_dermott_mcder/publish_traits.tsv
[INFO] [2023-01-19 16:21:48] (9 lines) /app/public/data/mc_dermott_mcder/publish_metadata.tsv
[STOP] [2023-01-19 16:21:48] complete_harvest_instance
[START] [2023-01-19 16:21:48] completed
[STOP] [2023-01-19 16:21:48] completed
[STOP] [2023-01-19 16:21:48] logged process, took 54.75

Latest Process

19 Jan 16:20 EXITED currently processing 0