Harvest for Lavrov et al 2004 Created 03 Aug 16:47

Stage: completed
Fetched: 03 Aug 16:47
Validated: 03 Aug 16:47
Deltas Created 03 Aug 16:47
Units Normalized: 03 Aug 16:47
Ancestry Built: 03 Aug 16:47
Nodes Matched: 03 Aug 16:47
Names Parsed: 03 Aug 16:47
New Models Stored: 03 Aug 16:47
Indexed: 03 Aug 16:47
Completed: 03 Aug 16:50
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:47:47] Created harvest instance #4180
[STOP] [2022-08-03 16:47:47] create_harvest_instance
[START] [2022-08-03 16:47:47] fetch_files
[STOP] [2022-08-03 16:47:47] fetch_files
[START] [2022-08-03 16:47:47] validate_each_file
[INFO] [2022-08-03 16:47:47] Looping over 3 formats...
[INFO] [2022-08-03 16:47:47] ...nodes (/app/public/data/lavrov_et_al_lav/taxa.txt)
[INFO] [2022-08-03 16:47:47] Valid: /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_nodes_29606.csv (1 lines)
[INFO] [2022-08-03 16:47:47] ...occurrences (/app/public/data/lavrov_et_al_lav/occurrences.txt)
[INFO] [2022-08-03 16:47:47] Valid: /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_occurrences_29607.csv (1 lines)
[INFO] [2022-08-03 16:47:47] ...measurements (/app/public/data/lavrov_et_al_lav/measurementOrFact.txt)
[INFO] [2022-08-03 16:47:47] Valid: /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_measurements_29608.csv (2 lines)
[STOP] [2022-08-03 16:47:47] validate_each_file
[START] [2022-08-03 16:47:47] convert_to_csv
[INFO] [2022-08-03 16:47:47] Looping over 3 formats...
[INFO] [2022-08-03 16:47:47] ...nodes (/app/public/data/lavrov_et_al_lav/taxa.txt)
[CMD] [2022-08-03 16:47:47] /usr/bin/sort /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_nodes_29606.csv > /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_nodes_29606.csv_sorted
[INFO] [2022-08-03 16:47:47] Converted: /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_nodes_29606.csv (1 lines)
[INFO] [2022-08-03 16:47:47] ...occurrences (/app/public/data/lavrov_et_al_lav/occurrences.txt)
[CMD] [2022-08-03 16:47:47] /usr/bin/sort /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_occurrences_29607.csv > /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_occurrences_29607.csv_sorted
[INFO] [2022-08-03 16:47:47] Converted: /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_occurrences_29607.csv (1 lines)
[INFO] [2022-08-03 16:47:47] ...measurements (/app/public/data/lavrov_et_al_lav/measurementOrFact.txt)
[CMD] [2022-08-03 16:47:47] /usr/bin/sort /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_measurements_29608.csv > /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_measurements_29608.csv_sorted
[INFO] [2022-08-03 16:47:47] Converted: /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_measurements_29608.csv (2 lines)
[STOP] [2022-08-03 16:47:47] convert_to_csv
[START] [2022-08-03 16:47:47] calculate_delta
[INFO] [2022-08-03 16:47:47] Looping over 3 formats...
[INFO] [2022-08-03 16:47:47] ...nodes (/app/public/data/lavrov_et_al_lav/taxa.txt)
[CMD] [2022-08-03 16:47:47] echo "0a" > /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_nodes_29606.diff
[CMD] [2022-08-03 16:47:47] tail -n +1 /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_nodes_29606.csv >> /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_nodes_29606.diff
[CMD] [2022-08-03 16:47:47] echo "." >> /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_nodes_29606.diff
[INFO] [2022-08-03 16:47:47] Created diff: /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_nodes_29606.diff (3 lines)
[INFO] [2022-08-03 16:47:47] ...occurrences (/app/public/data/lavrov_et_al_lav/occurrences.txt)
[CMD] [2022-08-03 16:47:47] echo "0a" > /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_occurrences_29607.diff
[CMD] [2022-08-03 16:47:47] tail -n +1 /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_occurrences_29607.csv >> /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_occurrences_29607.diff
[CMD] [2022-08-03 16:47:47] echo "." >> /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_occurrences_29607.diff
[INFO] [2022-08-03 16:47:47] Created diff: /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_occurrences_29607.diff (3 lines)
[INFO] [2022-08-03 16:47:47] ...measurements (/app/public/data/lavrov_et_al_lav/measurementOrFact.txt)
[CMD] [2022-08-03 16:47:47] echo "0a" > /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_measurements_29608.diff
[CMD] [2022-08-03 16:47:47] tail -n +1 /app/public/data/lavrov_et_al_lav/converted_csv/lavrov_et_al_lav_measurements_29608.csv >> /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_measurements_29608.diff
[CMD] [2022-08-03 16:47:47] echo "." >> /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_measurements_29608.diff
[INFO] [2022-08-03 16:47:47] Created diff: /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_measurements_29608.diff (4 lines)
[STOP] [2022-08-03 16:47:47] calculate_delta
[START] [2022-08-03 16:47:47] parse_diff_and_store
[INFO] [2022-08-03 16:47:47] Handling diff: /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_nodes_29606.diff (3 lines)
[INFO] [2022-08-03 16:47:47] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:47:48] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:47:48] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:47:48] Handling diff: /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_occurrences_29607.diff (3 lines)
[INFO] [2022-08-03 16:47:48] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:47:48] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:47:48] Handling diff: /app/public/data/lavrov_et_al_lav/diff/lavrov_et_al_lav_measurements_29608.diff (4 lines)
[INFO] [2022-08-03 16:47:48] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:47:48] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:47:48] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:47:48] parse_diff_and_store
[START] [2022-08-03 16:47:48] resolve_keys
[2022-08-03 16:47:48] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:47:55] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:47:55] traits to occurrences...
[INFO] [2022-08-03 16:47:55] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:47:55] Traits to sex term...
[INFO] [2022-08-03 16:47:55] Traits to lifestage term...
[INFO] [2022-08-03 16:47:55] MetaTraits to traits...
[INFO] [2022-08-03 16:47:55] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:47:55] Assocs to occurrences...
[INFO] [2022-08-03 16:47:55] Assocs to nodes...
[INFO] [2022-08-03 16:47:55] Assoc to sex term...
[INFO] [2022-08-03 16:47:55] Assoc to lifestage term...
[INFO] [2022-08-03 16:47:55] MetaAssoc to assocs...
[STOP] [2022-08-03 16:47:55] resolve_keys
[START] [2022-08-03 16:47:55] hold_for_later_1
[STOP] [2022-08-03 16:47:55] hold_for_later_1
[START] [2022-08-03 16:47:55] hold_for_later_2
[STOP] [2022-08-03 16:47:55] hold_for_later_2
[START] [2022-08-03 16:47:55] resolve_missing_parents
[STOP] [2022-08-03 16:47:55] resolve_missing_parents
[START] [2022-08-03 16:47:55] rebuild_nodes
[START] [2022-08-03 16:47:55] Flattener#flatten
[START] [2022-08-03 16:47:55] Flattener#study_resource
[START] [2022-08-03 16:47:55] Flattener#build_ancestry
[STOP] [2022-08-03 16:47:55] Flattener#build_ancestry
[INFO] [2022-08-03 16:47:55] 1 ancestry keys
[START] [2022-08-03 16:47:55] build_node_ancestors
[INFO] [2022-08-03 16:47:55] old ancestors deleted.
[STOP] [2022-08-03 16:47:55] build_node_ancestors
[WARN] [2022-08-03 16:47:55] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:47:55] Flattener#flatten
[STOP] [2022-08-03 16:47:55] rebuild_nodes
[START] [2022-08-03 16:47:55] resolve_missing_media_owners
[STOP] [2022-08-03 16:47:55] resolve_missing_media_owners
[START] [2022-08-03 16:47:55] sanitize_media_verbatims
[STOP] [2022-08-03 16:47:55] sanitize_media_verbatims
[START] [2022-08-03 16:47:55] queue_downloads
[STOP] [2022-08-03 16:47:55] queue_downloads
[START] [2022-08-03 16:47:55] parse_names
[WARN] [2022-08-03 16:47:55] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:47:55] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:47:56] parse_names
[START] [2022-08-03 16:47:56] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:47:56] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:47:56] match_nodes
[START] [2022-08-03 16:47:56] map_all_nodes_to_pages
[STOP] [2022-08-03 16:47:56] map_all_nodes_to_pages
[INFO] [2022-08-03 16:47:56] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:47:56] update_nodes
[STOP] [2022-08-03 16:47:56] update_nodes
[STOP] [2022-08-03 16:47:56] match_nodes
[START] [2022-08-03 16:47:56] reindex_search
[STOP] [2022-08-03 16:47:56] reindex_search
[START] [2022-08-03 16:47:56] normalize_units
[STOP] [2022-08-03 16:47:56] normalize_units
[START] [2022-08-03 16:47:56] calculate_statistics
[2022-08-03 16:47:56] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:47:56] Duplicate page_id count: 0
[STOP] [2022-08-03 16:47:56] calculate_statistics
[START] [2022-08-03 16:47:56] complete_harvest_instance
[START] [2022-08-03 16:47:56] overall_tsv_creation
[INFO] [2022-08-03 16:47:56] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:47:56] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:48:37] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:48:37] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:49:31] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:49:31] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:49:31] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:49:31] Adding 1 traits...
[INFO] [2022-08-03 16:49:31] 1 metadata added.
[INFO] [2022-08-03 16:49:31] Adding 0 assocs...
[INFO] [2022-08-03 16:49:31] 0 metadata added.
[INFO] [2022-08-03 16:50:15] Processed 1/1 nodes
[INFO] [2022-08-03 16:50:15] Average Time: 113.56
[INFO] [2022-08-03 16:50:15] Total Time: 2m19s
[STOP] [2022-08-03 16:50:15] overall_tsv_creation
[INFO] [2022-08-03 16:50:15] Done. Check your files:
[INFO] [2022-08-03 16:50:15] (1 lines) /app/public/data/lavrov_et_al_lav/publish_nodes.tsv
[INFO] [2022-08-03 16:50:15] (1 lines) /app/public/data/lavrov_et_al_lav/publish_scientific_names.tsv
[INFO] [2022-08-03 16:50:15] (2 lines) /app/public/data/lavrov_et_al_lav/publish_traits.tsv
[INFO] [2022-08-03 16:50:15] (2 lines) /app/public/data/lavrov_et_al_lav/publish_metadata.tsv
[STOP] [2022-08-03 16:50:15] complete_harvest_instance
[START] [2022-08-03 16:50:15] completed
[STOP] [2022-08-03 16:50:15] completed
[STOP] [2022-08-03 16:50:15] logged process, took 147.81
Latest Process

03 Aug 16:47 EXITED currently processing 0