Harvest for Schmidt Rhaesa 2012 Created 03 Aug 16:18

Harvesting Log

[INFO] [2022-08-03 16:18:33] Created harvest instance #4167
[STOP] [2022-08-03 16:18:33] create_harvest_instance
[START] [2022-08-03 16:18:33] fetch_files
[STOP] [2022-08-03 16:18:33] fetch_files
[START] [2022-08-03 16:18:33] validate_each_file
[INFO] [2022-08-03 16:18:33] Looping over 3 formats...
[INFO] [2022-08-03 16:18:33] ...nodes (/app/public/data/schmidt_rhaesa_s/taxa.txt)
[INFO] [2022-08-03 16:18:33] Valid: /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_nodes_29564.csv (1 lines)
[INFO] [2022-08-03 16:18:33] ...occurrences (/app/public/data/schmidt_rhaesa_s/occurrences.txt)
[INFO] [2022-08-03 16:18:33] Valid: /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_occurrences_29565.csv (1 lines)
[INFO] [2022-08-03 16:18:33] ...measurements (/app/public/data/schmidt_rhaesa_s/measurementOrFact.txt)
[INFO] [2022-08-03 16:18:33] Valid: /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_measurements_29566.csv (2 lines)
[STOP] [2022-08-03 16:18:33] validate_each_file
[START] [2022-08-03 16:18:33] convert_to_csv
[INFO] [2022-08-03 16:18:33] Looping over 3 formats...
[INFO] [2022-08-03 16:18:33] ...nodes (/app/public/data/schmidt_rhaesa_s/taxa.txt)
[CMD] [2022-08-03 16:18:33] /usr/bin/sort /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_nodes_29564.csv > /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_nodes_29564.csv_sorted
[INFO] [2022-08-03 16:18:33] Converted: /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_nodes_29564.csv (1 lines)
[INFO] [2022-08-03 16:18:33] ...occurrences (/app/public/data/schmidt_rhaesa_s/occurrences.txt)
[CMD] [2022-08-03 16:18:33] /usr/bin/sort /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_occurrences_29565.csv > /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_occurrences_29565.csv_sorted
[INFO] [2022-08-03 16:18:33] Converted: /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_occurrences_29565.csv (1 lines)
[INFO] [2022-08-03 16:18:33] ...measurements (/app/public/data/schmidt_rhaesa_s/measurementOrFact.txt)
[CMD] [2022-08-03 16:18:33] /usr/bin/sort /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_measurements_29566.csv > /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_measurements_29566.csv_sorted
[INFO] [2022-08-03 16:18:33] Converted: /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_measurements_29566.csv (2 lines)
[STOP] [2022-08-03 16:18:33] convert_to_csv
[START] [2022-08-03 16:18:33] calculate_delta
[INFO] [2022-08-03 16:18:33] Looping over 3 formats...
[INFO] [2022-08-03 16:18:33] ...nodes (/app/public/data/schmidt_rhaesa_s/taxa.txt)
[CMD] [2022-08-03 16:18:33] echo "0a" > /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_nodes_29564.diff
[CMD] [2022-08-03 16:18:33] tail -n +1 /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_nodes_29564.csv >> /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_nodes_29564.diff
[CMD] [2022-08-03 16:18:33] echo "." >> /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_nodes_29564.diff
[INFO] [2022-08-03 16:18:33] Created diff: /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_nodes_29564.diff (3 lines)
[INFO] [2022-08-03 16:18:33] ...occurrences (/app/public/data/schmidt_rhaesa_s/occurrences.txt)
[CMD] [2022-08-03 16:18:33] echo "0a" > /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_occurrences_29565.diff
[CMD] [2022-08-03 16:18:33] tail -n +1 /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_occurrences_29565.csv >> /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_occurrences_29565.diff
[CMD] [2022-08-03 16:18:33] echo "." >> /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_occurrences_29565.diff
[INFO] [2022-08-03 16:18:33] Created diff: /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_occurrences_29565.diff (3 lines)
[INFO] [2022-08-03 16:18:33] ...measurements (/app/public/data/schmidt_rhaesa_s/measurementOrFact.txt)
[CMD] [2022-08-03 16:18:33] echo "0a" > /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_measurements_29566.diff
[CMD] [2022-08-03 16:18:33] tail -n +1 /app/public/data/schmidt_rhaesa_s/converted_csv/schmidt_rhaesa_s_measurements_29566.csv >> /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_measurements_29566.diff
[CMD] [2022-08-03 16:18:33] echo "." >> /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_measurements_29566.diff
[INFO] [2022-08-03 16:18:33] Created diff: /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_measurements_29566.diff (4 lines)
[STOP] [2022-08-03 16:18:33] calculate_delta
[START] [2022-08-03 16:18:33] parse_diff_and_store
[INFO] [2022-08-03 16:18:33] Handling diff: /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_nodes_29564.diff (3 lines)
[INFO] [2022-08-03 16:18:33] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:18:33] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:18:33] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:18:33] Handling diff: /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_occurrences_29565.diff (3 lines)
[INFO] [2022-08-03 16:18:33] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:18:33] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:18:33] Handling diff: /app/public/data/schmidt_rhaesa_s/diff/schmidt_rhaesa_s_measurements_29566.diff (4 lines)
[INFO] [2022-08-03 16:18:33] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:18:33] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:18:33] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:18:33] parse_diff_and_store
[START] [2022-08-03 16:18:33] resolve_keys
[2022-08-03 16:18:33] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:18:41] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:18:41] traits to occurrences...
[INFO] [2022-08-03 16:18:41] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:18:41] Traits to sex term...
[INFO] [2022-08-03 16:18:41] Traits to lifestage term...
[INFO] [2022-08-03 16:18:41] MetaTraits to traits...
[INFO] [2022-08-03 16:18:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:18:41] Assocs to occurrences...
[INFO] [2022-08-03 16:18:41] Assocs to nodes...
[INFO] [2022-08-03 16:18:41] Assoc to sex term...
[INFO] [2022-08-03 16:18:41] Assoc to lifestage term...
[INFO] [2022-08-03 16:18:41] MetaAssoc to assocs...
[STOP] [2022-08-03 16:18:41] resolve_keys
[START] [2022-08-03 16:18:41] hold_for_later_1
[STOP] [2022-08-03 16:18:41] hold_for_later_1
[START] [2022-08-03 16:18:41] hold_for_later_2
[STOP] [2022-08-03 16:18:41] hold_for_later_2
[START] [2022-08-03 16:18:41] resolve_missing_parents
[STOP] [2022-08-03 16:18:41] resolve_missing_parents
[START] [2022-08-03 16:18:41] rebuild_nodes
[START] [2022-08-03 16:18:41] Flattener#flatten
[START] [2022-08-03 16:18:41] Flattener#study_resource
[START] [2022-08-03 16:18:41] Flattener#build_ancestry
[STOP] [2022-08-03 16:18:41] Flattener#build_ancestry
[INFO] [2022-08-03 16:18:41] 1 ancestry keys
[START] [2022-08-03 16:18:41] build_node_ancestors
[INFO] [2022-08-03 16:18:41] old ancestors deleted.
[STOP] [2022-08-03 16:18:41] build_node_ancestors
[WARN] [2022-08-03 16:18:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:18:41] Flattener#flatten
[STOP] [2022-08-03 16:18:41] rebuild_nodes
[START] [2022-08-03 16:18:41] resolve_missing_media_owners
[STOP] [2022-08-03 16:18:41] resolve_missing_media_owners
[START] [2022-08-03 16:18:41] sanitize_media_verbatims
[STOP] [2022-08-03 16:18:41] sanitize_media_verbatims
[START] [2022-08-03 16:18:41] queue_downloads
[STOP] [2022-08-03 16:18:41] queue_downloads
[START] [2022-08-03 16:18:41] parse_names
[WARN] [2022-08-03 16:18:41] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:18:41] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:18:42] parse_names
[START] [2022-08-03 16:18:42] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:18:42] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:18:42] match_nodes
[START] [2022-08-03 16:18:42] map_all_nodes_to_pages
[STOP] [2022-08-03 16:18:42] map_all_nodes_to_pages
[INFO] [2022-08-03 16:18:42] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:18:42] update_nodes
[STOP] [2022-08-03 16:18:42] update_nodes
[STOP] [2022-08-03 16:18:42] match_nodes
[START] [2022-08-03 16:18:42] reindex_search
[STOP] [2022-08-03 16:18:42] reindex_search
[START] [2022-08-03 16:18:42] normalize_units
[STOP] [2022-08-03 16:18:42] normalize_units
[START] [2022-08-03 16:18:42] calculate_statistics
[2022-08-03 16:18:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:18:42] Duplicate page_id count: 0
[STOP] [2022-08-03 16:18:42] calculate_statistics
[START] [2022-08-03 16:18:42] complete_harvest_instance
[START] [2022-08-03 16:18:42] overall_tsv_creation
[INFO] [2022-08-03 16:18:42] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:18:42] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:19:23] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:19:23] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:20:15] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:20:15] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:20:15] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:20:15] Adding 1 traits...
[INFO] [2022-08-03 16:20:15] 1 metadata added.
[INFO] [2022-08-03 16:20:15] Adding 0 assocs...
[INFO] [2022-08-03 16:20:15] 0 metadata added.
[INFO] [2022-08-03 16:20:57] Processed 1/1 nodes
[INFO] [2022-08-03 16:20:57] Average Time: 109.46
[INFO] [2022-08-03 16:20:57] Total Time: 2m15s
[STOP] [2022-08-03 16:20:57] overall_tsv_creation
[INFO] [2022-08-03 16:20:57] Done. Check your files:
[INFO] [2022-08-03 16:20:57] (1 lines) /app/public/data/schmidt_rhaesa_s/publish_nodes.tsv
[INFO] [2022-08-03 16:20:57] (1 lines) /app/public/data/schmidt_rhaesa_s/publish_scientific_names.tsv
[INFO] [2022-08-03 16:20:57] (2 lines) /app/public/data/schmidt_rhaesa_s/publish_traits.tsv
[INFO] [2022-08-03 16:20:57] (2 lines) /app/public/data/schmidt_rhaesa_s/publish_metadata.tsv
[STOP] [2022-08-03 16:20:57] complete_harvest_instance
[START] [2022-08-03 16:20:57] completed
[STOP] [2022-08-03 16:20:57] completed
[STOP] [2022-08-03 16:20:57] logged process, took 143.71

Latest Process

03 Aug 16:18 EXITED currently processing 0