Harvest for Carrano 2006 Created 13 Oct 12:07

Harvesting Log

[INFO] [2023-10-13 12:07:24] Created harvest instance #4439
[STOP] [2023-10-13 12:07:24] create_harvest_instance
[START] [2023-10-13 12:07:24] fetch_files
[STOP] [2023-10-13 12:07:24] fetch_files
[START] [2023-10-13 12:07:24] validate_each_file
[INFO] [2023-10-13 12:07:24] Looping over 4 formats...
[INFO] [2023-10-13 12:07:24] ...refs (/app/public/data/carrano_carrano_/reference.tab)
[INFO] [2023-10-13 12:07:24] Valid: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__refs_30734.csv (69 lines)
[INFO] [2023-10-13 12:07:24] ...nodes (/app/public/data/carrano_carrano_/taxon.tab)
[INFO] [2023-10-13 12:07:24] Valid: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__nodes_30735.csv (454 lines)
[INFO] [2023-10-13 12:07:24] ...occurrences (/app/public/data/carrano_carrano_/occurrence_specific.tab)
[INFO] [2023-10-13 12:07:24] Valid: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__occurrences_30737.csv (829 lines)
[INFO] [2023-10-13 12:07:24] ...measurements (/app/public/data/carrano_carrano_/measurement_or_fact.tab)
[INFO] [2023-10-13 12:07:25] Valid: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__measurements_30736.csv (2724 lines)
[STOP] [2023-10-13 12:07:25] validate_each_file
[START] [2023-10-13 12:07:25] convert_to_csv
[INFO] [2023-10-13 12:07:25] Looping over 4 formats...
[INFO] [2023-10-13 12:07:25] ...refs (/app/public/data/carrano_carrano_/reference.tab)
[CMD] [2023-10-13 12:07:25] /usr/bin/sort /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__refs_30734.csv > /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__refs_30734.csv_sorted
[INFO] [2023-10-13 12:07:25] Converted: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__refs_30734.csv (69 lines)
[INFO] [2023-10-13 12:07:25] ...nodes (/app/public/data/carrano_carrano_/taxon.tab)
[CMD] [2023-10-13 12:07:25] /usr/bin/sort /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__nodes_30735.csv > /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__nodes_30735.csv_sorted
[INFO] [2023-10-13 12:07:25] Converted: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__nodes_30735.csv (454 lines)
[INFO] [2023-10-13 12:07:25] ...occurrences (/app/public/data/carrano_carrano_/occurrence_specific.tab)
[CMD] [2023-10-13 12:07:25] /usr/bin/sort /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__occurrences_30737.csv > /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__occurrences_30737.csv_sorted
[INFO] [2023-10-13 12:07:25] Converted: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__occurrences_30737.csv (829 lines)
[INFO] [2023-10-13 12:07:25] ...measurements (/app/public/data/carrano_carrano_/measurement_or_fact.tab)
[CMD] [2023-10-13 12:07:25] /usr/bin/sort /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__measurements_30736.csv > /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__measurements_30736.csv_sorted
[INFO] [2023-10-13 12:07:25] Converted: /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__measurements_30736.csv (2724 lines)
[STOP] [2023-10-13 12:07:25] convert_to_csv
[START] [2023-10-13 12:07:25] calculate_delta
[INFO] [2023-10-13 12:07:25] Looping over 4 formats...
[INFO] [2023-10-13 12:07:25] ...refs (/app/public/data/carrano_carrano_/reference.tab)
[CMD] [2023-10-13 12:07:25] echo "0a" > /app/public/data/carrano_carrano_/diff/carrano_carrano__refs_30734.diff
[CMD] [2023-10-13 12:07:25] tail -n +1 /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__refs_30734.csv >> /app/public/data/carrano_carrano_/diff/carrano_carrano__refs_30734.diff
[CMD] [2023-10-13 12:07:25] echo "." >> /app/public/data/carrano_carrano_/diff/carrano_carrano__refs_30734.diff
[INFO] [2023-10-13 12:07:25] Created diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__refs_30734.diff (71 lines)
[INFO] [2023-10-13 12:07:25] ...nodes (/app/public/data/carrano_carrano_/taxon.tab)
[CMD] [2023-10-13 12:07:25] echo "0a" > /app/public/data/carrano_carrano_/diff/carrano_carrano__nodes_30735.diff
[CMD] [2023-10-13 12:07:25] tail -n +1 /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__nodes_30735.csv >> /app/public/data/carrano_carrano_/diff/carrano_carrano__nodes_30735.diff
[CMD] [2023-10-13 12:07:25] echo "." >> /app/public/data/carrano_carrano_/diff/carrano_carrano__nodes_30735.diff
[INFO] [2023-10-13 12:07:25] Created diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__nodes_30735.diff (456 lines)
[INFO] [2023-10-13 12:07:25] ...occurrences (/app/public/data/carrano_carrano_/occurrence_specific.tab)
[CMD] [2023-10-13 12:07:25] echo "0a" > /app/public/data/carrano_carrano_/diff/carrano_carrano__occurrences_30737.diff
[CMD] [2023-10-13 12:07:25] tail -n +1 /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__occurrences_30737.csv >> /app/public/data/carrano_carrano_/diff/carrano_carrano__occurrences_30737.diff
[CMD] [2023-10-13 12:07:25] echo "." >> /app/public/data/carrano_carrano_/diff/carrano_carrano__occurrences_30737.diff
[INFO] [2023-10-13 12:07:26] Created diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__occurrences_30737.diff (831 lines)
[INFO] [2023-10-13 12:07:26] ...measurements (/app/public/data/carrano_carrano_/measurement_or_fact.tab)
[CMD] [2023-10-13 12:07:26] echo "0a" > /app/public/data/carrano_carrano_/diff/carrano_carrano__measurements_30736.diff
[CMD] [2023-10-13 12:07:26] tail -n +1 /app/public/data/carrano_carrano_/converted_csv/carrano_carrano__measurements_30736.csv >> /app/public/data/carrano_carrano_/diff/carrano_carrano__measurements_30736.diff
[CMD] [2023-10-13 12:07:26] echo "." >> /app/public/data/carrano_carrano_/diff/carrano_carrano__measurements_30736.diff
[INFO] [2023-10-13 12:07:26] Created diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__measurements_30736.diff (2726 lines)
[STOP] [2023-10-13 12:07:26] calculate_delta
[START] [2023-10-13 12:07:26] parse_diff_and_store
[INFO] [2023-10-13 12:07:26] Handling diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__refs_30734.diff (71 lines)
[INFO] [2023-10-13 12:07:26] Loading refs diff file into memory (71 lines)...
[INFO] [2023-10-13 12:07:26] Storing 69 References (69/69/71)
[INFO] [2023-10-13 12:07:26] Handling diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__nodes_30735.diff (456 lines)
[INFO] [2023-10-13 12:07:26] Loading nodes diff file into memory (456 lines)...
[INFO] [2023-10-13 12:07:26] Storing 775 ScientificNames (1550/454/456)
[INFO] [2023-10-13 12:07:26] Storing 775 Nodes (1550/454/456)
[INFO] [2023-10-13 12:07:27] Handling diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__occurrences_30737.diff (831 lines)
[INFO] [2023-10-13 12:07:27] Loading occurrences diff file into memory (831 lines)...
[INFO] [2023-10-13 12:07:27] Storing 829 Occurrences (1658/829/831)
[INFO] [2023-10-13 12:07:27] Storing 829 OccurrenceMetadata (1658/829/831)
[INFO] [2023-10-13 12:07:27] Handling diff: /app/public/data/carrano_carrano_/diff/carrano_carrano__measurements_30736.diff (2726 lines)
[INFO] [2023-10-13 12:07:27] Loading measurements diff file into memory (2726 lines)...
[INFO] [2023-10-13 12:07:28] Storing 1070 OccurrenceMetadata (6124/2724/2726)
[INFO] [2023-10-13 12:07:28] Storing 319 TraitsReferences (6124/2724/2726)
[INFO] [2023-10-13 12:07:28] Storing 1654 Traits (6124/2724/2726)
[INFO] [2023-10-13 12:07:29] Storing 3081 MetaTraits (6124/2724/2726)
[STOP] [2023-10-13 12:07:29] parse_diff_and_store
[START] [2023-10-13 12:07:29] resolve_keys
[2023-10-13 12:07:30] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 12:07:37] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 12:07:38] traits to occurrences...
[INFO] [2023-10-13 12:07:38] traits to nodes (through occurrences)...
[INFO] [2023-10-13 12:07:38] Traits to sex term...
[INFO] [2023-10-13 12:07:38] Traits to lifestage term...
[INFO] [2023-10-13 12:07:38] MetaTraits to traits...
[INFO] [2023-10-13 12:07:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 12:07:38] Assocs to occurrences...
[INFO] [2023-10-13 12:07:38] Assocs to nodes...
[INFO] [2023-10-13 12:07:38] Assoc to sex term...
[INFO] [2023-10-13 12:07:38] Assoc to lifestage term...
[INFO] [2023-10-13 12:07:38] MetaAssoc to assocs...
[STOP] [2023-10-13 12:07:38] resolve_keys
[START] [2023-10-13 12:07:38] hold_for_later_1
[STOP] [2023-10-13 12:07:38] hold_for_later_1
[START] [2023-10-13 12:07:38] hold_for_later_2
[STOP] [2023-10-13 12:07:38] hold_for_later_2
[START] [2023-10-13 12:07:38] resolve_missing_parents
[STOP] [2023-10-13 12:07:38] resolve_missing_parents
[START] [2023-10-13 12:07:38] rebuild_nodes
[START] [2023-10-13 12:07:38] Flattener#flatten
[START] [2023-10-13 12:07:38] Flattener#study_resource
[START] [2023-10-13 12:07:38] Flattener#build_ancestry
[STOP] [2023-10-13 12:07:38] Flattener#build_ancestry
[INFO] [2023-10-13 12:07:38] 775 ancestry keys
[START] [2023-10-13 12:07:38] build_node_ancestors
[INFO] [2023-10-13 12:07:38] old ancestors deleted.
[STOP] [2023-10-13 12:07:38] build_node_ancestors
[START] [2023-10-13 12:07:38] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 12:07:38] Flattener#propagate_ancestor_ids
[STOP] [2023-10-13 12:07:38] Flattener#flatten
[STOP] [2023-10-13 12:07:38] rebuild_nodes
[START] [2023-10-13 12:07:38] resolve_missing_media_owners
[STOP] [2023-10-13 12:07:38] resolve_missing_media_owners
[START] [2023-10-13 12:07:38] sanitize_media_verbatims
[STOP] [2023-10-13 12:07:38] sanitize_media_verbatims
[START] [2023-10-13 12:07:38] queue_downloads
[STOP] [2023-10-13 12:07:38] queue_downloads
[START] [2023-10-13 12:07:38] parse_names
[WARN] [2023-10-13 12:07:38] I see 775 names which still need to be parsed.
[WARN] [2023-10-13 12:07:38] Names to parse: 775 formatted: 775 learned: 716 parsed: 775
[STOP] [2023-10-13 12:07:40] parse_names
[START] [2023-10-13 12:07:40] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 12:07:40] denormalize_canonical_names_to_nodes
[START] [2023-10-13 12:07:40] match_nodes
[START] [2023-10-13 12:07:40] map_all_nodes_to_pages
[STOP] [2023-10-13 12:07:49] map_all_nodes_to_pages
[INFO] [2023-10-13 12:07:49] 189 Unmatched nodes (of 775)! That's too many to output. Full list in /app/public/data/carrano_carrano_/unmatched_nodes.txt ; First 10: Canonical: Agilisaurus multidens; Node#137159267; ResourceID: Agilisaurus_multidens; Canonical: Albertosaurus; Node#137159271; ResourceID: Albertosaurus; Canonical: Albertosaurus libratus; Node#137159272; ResourceID: Albertosaurus_libratus; Canonical: Allosaurus; Node#137159279; ResourceID: Allosaurus; Canonical: Ammosaurus; Node#137159287; ResourceID: Ammosaurus; Canonical: Ammosaurus major; Node#137159288; ResourceID: Ammosaurus_major; Canonical: Anatosaurus; Node#137159295; ResourceID: Anatosaurus; Canonical: Anatosaurus; Node#137159296; ResourceID: Anatosaurus; Canonical: Anatosaurus annectens; Node#137159297; ResourceID: Anatosaurus_annectens; Canonical: Anatotitan; Node#137159298; ResourceID: Anatotitan
[START] [2023-10-13 12:07:49] update_nodes
[STOP] [2023-10-13 12:07:49] update_nodes
[STOP] [2023-10-13 12:07:49] match_nodes
[START] [2023-10-13 12:07:49] reindex_search
[STOP] [2023-10-13 12:07:49] reindex_search
[START] [2023-10-13 12:07:49] normalize_units
[STOP] [2023-10-13 12:07:56] normalize_units
[START] [2023-10-13 12:07:56] calculate_statistics
[INFO] [2023-10-13 12:07:56] Duplicate page_id count: 0
[STOP] [2023-10-13 12:07:56] calculate_statistics
[START] [2023-10-13 12:07:56] complete_harvest_instance
[START] [2023-10-13 12:07:56] overall_tsv_creation
[INFO] [2023-10-13 12:07:56] Exporting 775 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 12:07:56] Processing group of 775 in 1 batches of 10000
[INFO] [2023-10-13 12:07:57] 1652 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 12:07:57] Building Traits map for 775 nodes (this can take a while)...
[INFO] [2023-10-13 12:07:58] Mapped 1652 traits (3077 meta) for 775 nodes.
[INFO] [2023-10-13 12:07:58] Building Associations map (this can take a while)...
[INFO] [2023-10-13 12:07:58] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 12:07:58] Adding 1652 traits...
[INFO] [2023-10-13 12:07:58] 1855 metadata added.
[INFO] [2023-10-13 12:07:58] Adding 0 assocs...
[INFO] [2023-10-13 12:07:58] 0 metadata added.
[INFO] [2023-10-13 12:08:42] Processed 775/775 nodes
[INFO] [2023-10-13 12:08:42] Average Time: 46.01
[INFO] [2023-10-13 12:08:42] Total Time: 47s
[STOP] [2023-10-13 12:08:42] overall_tsv_creation
[INFO] [2023-10-13 12:08:42] Done. Check your files:
[INFO] [2023-10-13 12:08:43] (716 lines) /app/public/data/carrano_carrano_/publish_nodes.tsv
[INFO] [2023-10-13 12:08:43] (395 lines) /app/public/data/carrano_carrano_/publish_node_ancestors.tsv
[INFO] [2023-10-13 12:08:43] (775 lines) /app/public/data/carrano_carrano_/publish_scientific_names.tsv
[INFO] [2023-10-13 12:08:43] (1653 lines) /app/public/data/carrano_carrano_/publish_traits.tsv
[INFO] [2023-10-13 12:08:43] (1856 lines) /app/public/data/carrano_carrano_/publish_metadata.tsv
[STOP] [2023-10-13 12:08:43] complete_harvest_instance
[START] [2023-10-13 12:08:43] completed
[STOP] [2023-10-13 12:08:43] completed
[STOP] [2023-10-13 12:08:43] logged process, took 78.82

Latest Process

13 Oct 12:07 EXITED currently processing 0