Harvest for Kaulfuss et al, 2013 Created 31 Jan 12:14

Stage: completed
Fetched: 31 Jan 12:14
Validated: 31 Jan 12:14
Deltas Created 31 Jan 12:14
Units Normalized: 31 Jan 12:14
Ancestry Built: 31 Jan 12:14
Nodes Matched: 31 Jan 12:14
Names Parsed: 31 Jan 12:14
New Models Stored: 31 Jan 12:14
Indexed: 31 Jan 12:14
Completed: 31 Jan 12:15
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2023-01-31 12:14:32] Created harvest instance #4288
[STOP] [2023-01-31 12:14:32] create_harvest_instance
[START] [2023-01-31 12:14:32] fetch_files
[STOP] [2023-01-31 12:14:32] fetch_files
[START] [2023-01-31 12:14:32] validate_each_file
[INFO] [2023-01-31 12:14:32] Looping over 3 formats...
[INFO] [2023-01-31 12:14:32] ...nodes (/app/public/data/kaulfuss_et_al_k/taxa.tsv)
[INFO] [2023-01-31 12:14:32] Valid: /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_nodes_30167.csv (16 lines)
[INFO] [2023-01-31 12:14:32] ...occurrences (/app/public/data/kaulfuss_et_al_k/occurrences.tsv)
[INFO] [2023-01-31 12:14:32] Valid: /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_occurrences_30168.csv (16 lines)
[INFO] [2023-01-31 12:14:32] ...measurements (/app/public/data/kaulfuss_et_al_k/measurementOrFact.tsv)
[INFO] [2023-01-31 12:14:32] Valid: /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_measurements_30169.csv (30 lines)
[STOP] [2023-01-31 12:14:32] validate_each_file
[START] [2023-01-31 12:14:32] convert_to_csv
[INFO] [2023-01-31 12:14:32] Looping over 3 formats...
[INFO] [2023-01-31 12:14:32] ...nodes (/app/public/data/kaulfuss_et_al_k/taxa.tsv)
[CMD] [2023-01-31 12:14:32] /usr/bin/sort /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_nodes_30167.csv > /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_nodes_30167.csv_sorted
[INFO] [2023-01-31 12:14:32] Converted: /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_nodes_30167.csv (16 lines)
[INFO] [2023-01-31 12:14:32] ...occurrences (/app/public/data/kaulfuss_et_al_k/occurrences.tsv)
[CMD] [2023-01-31 12:14:32] /usr/bin/sort /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_occurrences_30168.csv > /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_occurrences_30168.csv_sorted
[INFO] [2023-01-31 12:14:32] Converted: /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_occurrences_30168.csv (16 lines)
[INFO] [2023-01-31 12:14:32] ...measurements (/app/public/data/kaulfuss_et_al_k/measurementOrFact.tsv)
[CMD] [2023-01-31 12:14:32] /usr/bin/sort /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_measurements_30169.csv > /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_measurements_30169.csv_sorted
[INFO] [2023-01-31 12:14:32] Converted: /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_measurements_30169.csv (30 lines)
[STOP] [2023-01-31 12:14:32] convert_to_csv
[START] [2023-01-31 12:14:32] calculate_delta
[INFO] [2023-01-31 12:14:32] Looping over 3 formats...
[INFO] [2023-01-31 12:14:32] ...nodes (/app/public/data/kaulfuss_et_al_k/taxa.tsv)
[CMD] [2023-01-31 12:14:32] echo "0a" > /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_nodes_30167.diff
[CMD] [2023-01-31 12:14:32] tail -n +1 /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_nodes_30167.csv >> /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_nodes_30167.diff
[CMD] [2023-01-31 12:14:32] echo "." >> /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_nodes_30167.diff
[INFO] [2023-01-31 12:14:32] Created diff: /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_nodes_30167.diff (18 lines)
[INFO] [2023-01-31 12:14:32] ...occurrences (/app/public/data/kaulfuss_et_al_k/occurrences.tsv)
[CMD] [2023-01-31 12:14:32] echo "0a" > /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_occurrences_30168.diff
[CMD] [2023-01-31 12:14:32] tail -n +1 /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_occurrences_30168.csv >> /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_occurrences_30168.diff
[CMD] [2023-01-31 12:14:32] echo "." >> /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_occurrences_30168.diff
[INFO] [2023-01-31 12:14:32] Created diff: /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_occurrences_30168.diff (18 lines)
[INFO] [2023-01-31 12:14:32] ...measurements (/app/public/data/kaulfuss_et_al_k/measurementOrFact.tsv)
[CMD] [2023-01-31 12:14:32] echo "0a" > /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_measurements_30169.diff
[CMD] [2023-01-31 12:14:32] tail -n +1 /app/public/data/kaulfuss_et_al_k/converted_csv/kaulfuss_et_al_k_measurements_30169.csv >> /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_measurements_30169.diff
[CMD] [2023-01-31 12:14:32] echo "." >> /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_measurements_30169.diff
[INFO] [2023-01-31 12:14:32] Created diff: /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_measurements_30169.diff (32 lines)
[STOP] [2023-01-31 12:14:32] calculate_delta
[START] [2023-01-31 12:14:32] parse_diff_and_store
[INFO] [2023-01-31 12:14:32] Handling diff: /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_nodes_30167.diff (18 lines)
[INFO] [2023-01-31 12:14:32] Loading nodes diff file into memory (18 lines)...
[INFO] [2023-01-31 12:14:32] Storing 16 ScientificNames (32/16/18)
[INFO] [2023-01-31 12:14:32] Storing 16 Nodes (32/16/18)
[INFO] [2023-01-31 12:14:32] Handling diff: /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_occurrences_30168.diff (18 lines)
[INFO] [2023-01-31 12:14:32] Loading occurrences diff file into memory (18 lines)...
[INFO] [2023-01-31 12:14:32] Storing 16 Occurrences (16/16/18)
[INFO] [2023-01-31 12:14:32] Handling diff: /app/public/data/kaulfuss_et_al_k/diff/kaulfuss_et_al_k_measurements_30169.diff (32 lines)
[INFO] [2023-01-31 12:14:32] Loading measurements diff file into memory (32 lines)...
[INFO] [2023-01-31 12:14:32] Storing 30 Traits (50/30/32)
[INFO] [2023-01-31 12:14:32] Storing 20 MetaTraits (50/30/32)
[STOP] [2023-01-31 12:14:32] parse_diff_and_store
[START] [2023-01-31 12:14:32] resolve_keys
[2023-01-31 12:14:32] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-31 12:14:40] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-31 12:14:40] traits to occurrences...
[INFO] [2023-01-31 12:14:40] traits to nodes (through occurrences)...
[INFO] [2023-01-31 12:14:40] Traits to sex term...
[INFO] [2023-01-31 12:14:40] Traits to lifestage term...
[INFO] [2023-01-31 12:14:40] MetaTraits to traits...
[INFO] [2023-01-31 12:14:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-31 12:14:40] Assocs to occurrences...
[INFO] [2023-01-31 12:14:40] Assocs to nodes...
[INFO] [2023-01-31 12:14:40] Assoc to sex term...
[INFO] [2023-01-31 12:14:40] Assoc to lifestage term...
[INFO] [2023-01-31 12:14:40] MetaAssoc to assocs...
[STOP] [2023-01-31 12:14:40] resolve_keys
[START] [2023-01-31 12:14:40] hold_for_later_1
[STOP] [2023-01-31 12:14:40] hold_for_later_1
[START] [2023-01-31 12:14:40] hold_for_later_2
[STOP] [2023-01-31 12:14:40] hold_for_later_2
[START] [2023-01-31 12:14:40] resolve_missing_parents
[STOP] [2023-01-31 12:14:40] resolve_missing_parents
[START] [2023-01-31 12:14:40] rebuild_nodes
[START] [2023-01-31 12:14:40] Flattener#flatten
[START] [2023-01-31 12:14:40] Flattener#study_resource
[START] [2023-01-31 12:14:40] Flattener#build_ancestry
[STOP] [2023-01-31 12:14:40] Flattener#build_ancestry
[INFO] [2023-01-31 12:14:40] 16 ancestry keys
[START] [2023-01-31 12:14:40] build_node_ancestors
[INFO] [2023-01-31 12:14:40] old ancestors deleted.
[STOP] [2023-01-31 12:14:40] build_node_ancestors
[WARN] [2023-01-31 12:14:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-31 12:14:40] Flattener#flatten
[STOP] [2023-01-31 12:14:40] rebuild_nodes
[START] [2023-01-31 12:14:40] resolve_missing_media_owners
[STOP] [2023-01-31 12:14:40] resolve_missing_media_owners
[START] [2023-01-31 12:14:40] sanitize_media_verbatims
[STOP] [2023-01-31 12:14:40] sanitize_media_verbatims
[START] [2023-01-31 12:14:40] queue_downloads
[STOP] [2023-01-31 12:14:40] queue_downloads
[START] [2023-01-31 12:14:40] parse_names
[WARN] [2023-01-31 12:14:40] I see 16 names which still need to be parsed.
[WARN] [2023-01-31 12:14:40] Names to parse: 16 formatted: 16 learned: 16 parsed: 16
[STOP] [2023-01-31 12:14:41] parse_names
[START] [2023-01-31 12:14:41] denormalize_canonical_names_to_nodes
[STOP] [2023-01-31 12:14:41] denormalize_canonical_names_to_nodes
[START] [2023-01-31 12:14:41] match_nodes
[START] [2023-01-31 12:14:41] map_all_nodes_to_pages
[STOP] [2023-01-31 12:14:41] map_all_nodes_to_pages
[INFO] [2023-01-31 12:14:41] ZERO unmatched nodes (of 16)! Nicely done.
[START] [2023-01-31 12:14:41] update_nodes
[STOP] [2023-01-31 12:14:41] update_nodes
[STOP] [2023-01-31 12:14:41] match_nodes
[START] [2023-01-31 12:14:41] reindex_search
[STOP] [2023-01-31 12:14:41] reindex_search
[START] [2023-01-31 12:14:41] normalize_units
[STOP] [2023-01-31 12:14:41] normalize_units
[START] [2023-01-31 12:14:41] calculate_statistics
[2023-01-31 12:14:41] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-31 12:14:41] Duplicate page_id count: 0
[STOP] [2023-01-31 12:14:41] calculate_statistics
[START] [2023-01-31 12:14:41] complete_harvest_instance
[START] [2023-01-31 12:14:41] overall_tsv_creation
[INFO] [2023-01-31 12:14:41] Exporting 16 nodes as TSV in batches of 10000...
[INFO] [2023-01-31 12:14:41] Processing group of 16 in 1 batches of 10000
[INFO] [2023-01-31 12:14:41] 16 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-31 12:14:41] Building Traits map for 16 nodes (this can take a while)...
[INFO] [2023-01-31 12:14:41] Mapped 16 traits (20 meta) for 16 nodes.
[INFO] [2023-01-31 12:14:41] Building Associations map (this can take a while)...
[INFO] [2023-01-31 12:14:41] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-31 12:14:41] Adding 16 traits...
[INFO] [2023-01-31 12:14:41] 14 metadata added.
[INFO] [2023-01-31 12:14:41] Adding 0 assocs...
[INFO] [2023-01-31 12:14:41] 0 metadata added.
[INFO] [2023-01-31 12:15:26] Processed 16/16 nodes
[INFO] [2023-01-31 12:15:26] Average Time: 44.99
[INFO] [2023-01-31 12:15:26] Total Time: 46s
[STOP] [2023-01-31 12:15:26] overall_tsv_creation
[INFO] [2023-01-31 12:15:26] Done. Check your files:
[INFO] [2023-01-31 12:15:26] (16 lines) /app/public/data/kaulfuss_et_al_k/publish_nodes.tsv
[INFO] [2023-01-31 12:15:26] (16 lines) /app/public/data/kaulfuss_et_al_k/publish_scientific_names.tsv
[INFO] [2023-01-31 12:15:26] (17 lines) /app/public/data/kaulfuss_et_al_k/publish_traits.tsv
[INFO] [2023-01-31 12:15:26] (15 lines) /app/public/data/kaulfuss_et_al_k/publish_metadata.tsv
[STOP] [2023-01-31 12:15:26] complete_harvest_instance
[START] [2023-01-31 12:15:26] completed
[STOP] [2023-01-31 12:15:26] completed
[STOP] [2023-01-31 12:15:26] logged process, took 54.66
Latest Process

31 Jan 12:14 EXITED currently processing 0