Harvest for Geisler et al 2014 Created 13 Oct 13:57

Harvesting Log

[INFO] [2023-10-13 13:57:39] Created harvest instance #4464
[STOP] [2023-10-13 13:57:39] create_harvest_instance
[START] [2023-10-13 13:57:39] fetch_files
[STOP] [2023-10-13 13:57:39] fetch_files
[START] [2023-10-13 13:57:39] validate_each_file
[INFO] [2023-10-13 13:57:39] Looping over 4 formats...
[INFO] [2023-10-13 13:57:39] ...refs (/app/public/data/geisler_et_al_ge/references.txt)
[INFO] [2023-10-13 13:57:39] Valid: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_refs_30864.csv (2 lines)
[INFO] [2023-10-13 13:57:39] ...nodes (/app/public/data/geisler_et_al_ge/taxa.txt)
[INFO] [2023-10-13 13:57:39] Valid: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_nodes_30861.csv (1 lines)
[INFO] [2023-10-13 13:57:39] ...occurrences (/app/public/data/geisler_et_al_ge/occurrences.txt)
[INFO] [2023-10-13 13:57:39] Valid: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_occurrences_30862.csv (1 lines)
[INFO] [2023-10-13 13:57:39] ...measurements (/app/public/data/geisler_et_al_ge/measurementsorfacts.txt)
[INFO] [2023-10-13 13:57:39] Valid: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_measurements_30863.csv (2 lines)
[STOP] [2023-10-13 13:57:39] validate_each_file
[START] [2023-10-13 13:57:39] convert_to_csv
[INFO] [2023-10-13 13:57:39] Looping over 4 formats...
[INFO] [2023-10-13 13:57:39] ...refs (/app/public/data/geisler_et_al_ge/references.txt)
[CMD] [2023-10-13 13:57:39] /usr/bin/sort /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_refs_30864.csv > /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_refs_30864.csv_sorted
[INFO] [2023-10-13 13:57:39] Converted: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_refs_30864.csv (2 lines)
[INFO] [2023-10-13 13:57:39] ...nodes (/app/public/data/geisler_et_al_ge/taxa.txt)
[CMD] [2023-10-13 13:57:39] /usr/bin/sort /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_nodes_30861.csv > /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_nodes_30861.csv_sorted
[INFO] [2023-10-13 13:57:39] Converted: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_nodes_30861.csv (1 lines)
[INFO] [2023-10-13 13:57:39] ...occurrences (/app/public/data/geisler_et_al_ge/occurrences.txt)
[CMD] [2023-10-13 13:57:39] /usr/bin/sort /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_occurrences_30862.csv > /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_occurrences_30862.csv_sorted
[INFO] [2023-10-13 13:57:39] Converted: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_occurrences_30862.csv (1 lines)
[INFO] [2023-10-13 13:57:39] ...measurements (/app/public/data/geisler_et_al_ge/measurementsorfacts.txt)
[CMD] [2023-10-13 13:57:39] /usr/bin/sort /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_measurements_30863.csv > /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_measurements_30863.csv_sorted
[INFO] [2023-10-13 13:57:39] Converted: /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_measurements_30863.csv (2 lines)
[STOP] [2023-10-13 13:57:39] convert_to_csv
[START] [2023-10-13 13:57:39] calculate_delta
[INFO] [2023-10-13 13:57:39] Looping over 4 formats...
[INFO] [2023-10-13 13:57:39] ...refs (/app/public/data/geisler_et_al_ge/references.txt)
[CMD] [2023-10-13 13:57:39] echo "0a" > /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_refs_30864.diff
[CMD] [2023-10-13 13:57:39] tail -n +1 /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_refs_30864.csv >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_refs_30864.diff
[CMD] [2023-10-13 13:57:39] echo "." >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_refs_30864.diff
[INFO] [2023-10-13 13:57:40] Created diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_refs_30864.diff (4 lines)
[INFO] [2023-10-13 13:57:40] ...nodes (/app/public/data/geisler_et_al_ge/taxa.txt)
[CMD] [2023-10-13 13:57:40] echo "0a" > /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_nodes_30861.diff
[CMD] [2023-10-13 13:57:40] tail -n +1 /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_nodes_30861.csv >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_nodes_30861.diff
[CMD] [2023-10-13 13:57:40] echo "." >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_nodes_30861.diff
[INFO] [2023-10-13 13:57:40] Created diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_nodes_30861.diff (3 lines)
[INFO] [2023-10-13 13:57:40] ...occurrences (/app/public/data/geisler_et_al_ge/occurrences.txt)
[CMD] [2023-10-13 13:57:40] echo "0a" > /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_occurrences_30862.diff
[CMD] [2023-10-13 13:57:40] tail -n +1 /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_occurrences_30862.csv >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_occurrences_30862.diff
[CMD] [2023-10-13 13:57:40] echo "." >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_occurrences_30862.diff
[INFO] [2023-10-13 13:57:40] Created diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_occurrences_30862.diff (3 lines)
[INFO] [2023-10-13 13:57:40] ...measurements (/app/public/data/geisler_et_al_ge/measurementsorfacts.txt)
[CMD] [2023-10-13 13:57:40] echo "0a" > /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_measurements_30863.diff
[CMD] [2023-10-13 13:57:40] tail -n +1 /app/public/data/geisler_et_al_ge/converted_csv/geisler_et_al_ge_measurements_30863.csv >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_measurements_30863.diff
[CMD] [2023-10-13 13:57:40] echo "." >> /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_measurements_30863.diff
[INFO] [2023-10-13 13:57:40] Created diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_measurements_30863.diff (4 lines)
[STOP] [2023-10-13 13:57:40] calculate_delta
[START] [2023-10-13 13:57:40] parse_diff_and_store
[INFO] [2023-10-13 13:57:40] Handling diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_refs_30864.diff (4 lines)
[INFO] [2023-10-13 13:57:40] Loading refs diff file into memory (4 lines)...
[INFO] [2023-10-13 13:57:40] Storing 2 References (2/2/4)
[INFO] [2023-10-13 13:57:40] Handling diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_nodes_30861.diff (3 lines)
[INFO] [2023-10-13 13:57:40] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-13 13:57:40] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-13 13:57:40] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-13 13:57:40] Handling diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_occurrences_30862.diff (3 lines)
[INFO] [2023-10-13 13:57:40] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-13 13:57:40] Storing 1 Occurrences (1/1/3)
[INFO] [2023-10-13 13:57:40] Handling diff: /app/public/data/geisler_et_al_ge/diff/geisler_et_al_ge_measurements_30863.diff (4 lines)
[INFO] [2023-10-13 13:57:41] Loading measurements diff file into memory (4 lines)...
[INFO] [2023-10-13 13:57:41] Storing 2 TraitsReferences (7/2/4)
[INFO] [2023-10-13 13:57:41] Storing 2 Traits (7/2/4)
[INFO] [2023-10-13 13:57:41] Storing 3 MetaTraits (7/2/4)
[STOP] [2023-10-13 13:57:41] parse_diff_and_store
[START] [2023-10-13 13:57:41] resolve_keys
[2023-10-13 13:57:41] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:57:48] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:57:48] traits to occurrences...
[INFO] [2023-10-13 13:57:48] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:57:48] Traits to sex term...
[INFO] [2023-10-13 13:57:48] Traits to lifestage term...
[INFO] [2023-10-13 13:57:48] MetaTraits to traits...
[INFO] [2023-10-13 13:57:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:57:48] Assocs to occurrences...
[INFO] [2023-10-13 13:57:48] Assocs to nodes...
[INFO] [2023-10-13 13:57:48] Assoc to sex term...
[INFO] [2023-10-13 13:57:48] Assoc to lifestage term...
[INFO] [2023-10-13 13:57:48] MetaAssoc to assocs...
[STOP] [2023-10-13 13:57:48] resolve_keys
[START] [2023-10-13 13:57:48] hold_for_later_1
[STOP] [2023-10-13 13:57:48] hold_for_later_1
[START] [2023-10-13 13:57:48] hold_for_later_2
[STOP] [2023-10-13 13:57:48] hold_for_later_2
[START] [2023-10-13 13:57:48] resolve_missing_parents
[STOP] [2023-10-13 13:57:48] resolve_missing_parents
[START] [2023-10-13 13:57:48] rebuild_nodes
[START] [2023-10-13 13:57:48] Flattener#flatten
[START] [2023-10-13 13:57:48] Flattener#study_resource
[START] [2023-10-13 13:57:48] Flattener#build_ancestry
[STOP] [2023-10-13 13:57:48] Flattener#build_ancestry
[INFO] [2023-10-13 13:57:48] 1 ancestry keys
[START] [2023-10-13 13:57:48] build_node_ancestors
[INFO] [2023-10-13 13:57:48] old ancestors deleted.
[STOP] [2023-10-13 13:57:48] build_node_ancestors
[WARN] [2023-10-13 13:57:48] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:57:48] Flattener#flatten
[STOP] [2023-10-13 13:57:48] rebuild_nodes
[START] [2023-10-13 13:57:48] resolve_missing_media_owners
[STOP] [2023-10-13 13:57:48] resolve_missing_media_owners
[START] [2023-10-13 13:57:48] sanitize_media_verbatims
[STOP] [2023-10-13 13:57:48] sanitize_media_verbatims
[START] [2023-10-13 13:57:48] queue_downloads
[STOP] [2023-10-13 13:57:49] queue_downloads
[START] [2023-10-13 13:57:49] parse_names
[WARN] [2023-10-13 13:57:49] I see 1 names which still need to be parsed.
[WARN] [2023-10-13 13:57:49] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-13 13:57:50] parse_names
[START] [2023-10-13 13:57:50] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:57:50] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:57:50] match_nodes
[START] [2023-10-13 13:57:50] map_all_nodes_to_pages
[STOP] [2023-10-13 13:57:50] map_all_nodes_to_pages
[INFO] [2023-10-13 13:57:50] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-13 13:57:50] update_nodes
[STOP] [2023-10-13 13:57:50] update_nodes
[STOP] [2023-10-13 13:57:50] match_nodes
[START] [2023-10-13 13:57:50] reindex_search
[STOP] [2023-10-13 13:57:50] reindex_search
[START] [2023-10-13 13:57:50] normalize_units
[STOP] [2023-10-13 13:57:50] normalize_units
[START] [2023-10-13 13:57:50] calculate_statistics
[2023-10-13 13:57:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:57:50] Duplicate page_id count: 0
[STOP] [2023-10-13 13:57:50] calculate_statistics
[START] [2023-10-13 13:57:50] complete_harvest_instance
[START] [2023-10-13 13:57:50] overall_tsv_creation
[INFO] [2023-10-13 13:57:50] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:57:50] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-13 13:57:50] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:57:50] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-13 13:57:50] Mapped 1 traits (3 meta) for 1 nodes.
[INFO] [2023-10-13 13:57:50] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:57:50] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:57:50] Adding 1 traits...
[INFO] [2023-10-13 13:57:50] 3 metadata added.
[INFO] [2023-10-13 13:57:50] Adding 0 assocs...
[INFO] [2023-10-13 13:57:50] 0 metadata added.
[INFO] [2023-10-13 13:58:34] Processed 1/1 nodes
[INFO] [2023-10-13 13:58:34] Average Time: 43.99
[INFO] [2023-10-13 13:58:34] Total Time: 45s
[STOP] [2023-10-13 13:58:34] overall_tsv_creation
[INFO] [2023-10-13 13:58:34] Done. Check your files:
[INFO] [2023-10-13 13:58:34] (1 lines) /app/public/data/geisler_et_al_ge/publish_nodes.tsv
[INFO] [2023-10-13 13:58:34] (1 lines) /app/public/data/geisler_et_al_ge/publish_scientific_names.tsv
[INFO] [2023-10-13 13:58:34] (2 lines) /app/public/data/geisler_et_al_ge/publish_traits.tsv
[INFO] [2023-10-13 13:58:34] (4 lines) /app/public/data/geisler_et_al_ge/publish_metadata.tsv
[STOP] [2023-10-13 13:58:34] complete_harvest_instance
[START] [2023-10-13 13:58:34] completed
[STOP] [2023-10-13 13:58:34] completed
[STOP] [2023-10-13 13:58:34] logged process, took 55.28

Latest Process

13 Oct 13:57 EXITED currently processing 0