Harvest for Hu et al 2009 Created 14 Oct 08:33

Harvesting Log

[INFO] [2023-10-14 08:33:38] Created harvest instance #4474
[STOP] [2023-10-14 08:33:38] create_harvest_instance
[START] [2023-10-14 08:33:38] fetch_files
[STOP] [2023-10-14 08:33:38] fetch_files
[START] [2023-10-14 08:33:38] validate_each_file
[INFO] [2023-10-14 08:33:38] Looping over 4 formats...
[INFO] [2023-10-14 08:33:38] ...refs (/app/public/data/hu_et_al_hu_et_a/references.txt)
[INFO] [2023-10-14 08:33:38] Valid: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_refs_30904.csv (2 lines)
[INFO] [2023-10-14 08:33:38] ...nodes (/app/public/data/hu_et_al_hu_et_a/taxa.txt)
[INFO] [2023-10-14 08:33:38] Valid: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_nodes_30901.csv (3 lines)
[INFO] [2023-10-14 08:33:38] ...occurrences (/app/public/data/hu_et_al_hu_et_a/occurrences.txt)
[INFO] [2023-10-14 08:33:38] Valid: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_occurrences_30902.csv (3 lines)
[INFO] [2023-10-14 08:33:38] ...measurements (/app/public/data/hu_et_al_hu_et_a/measurementsorfacts.txt)
[INFO] [2023-10-14 08:33:38] Valid: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_measurements_30903.csv (14 lines)
[STOP] [2023-10-14 08:33:38] validate_each_file
[START] [2023-10-14 08:33:38] convert_to_csv
[INFO] [2023-10-14 08:33:38] Looping over 4 formats...
[INFO] [2023-10-14 08:33:38] ...refs (/app/public/data/hu_et_al_hu_et_a/references.txt)
[CMD] [2023-10-14 08:33:38] /usr/bin/sort /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_refs_30904.csv > /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_refs_30904.csv_sorted
[INFO] [2023-10-14 08:33:38] Converted: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_refs_30904.csv (2 lines)
[INFO] [2023-10-14 08:33:38] ...nodes (/app/public/data/hu_et_al_hu_et_a/taxa.txt)
[CMD] [2023-10-14 08:33:38] /usr/bin/sort /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_nodes_30901.csv > /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_nodes_30901.csv_sorted
[INFO] [2023-10-14 08:33:38] Converted: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_nodes_30901.csv (3 lines)
[INFO] [2023-10-14 08:33:38] ...occurrences (/app/public/data/hu_et_al_hu_et_a/occurrences.txt)
[CMD] [2023-10-14 08:33:38] /usr/bin/sort /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_occurrences_30902.csv > /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_occurrences_30902.csv_sorted
[INFO] [2023-10-14 08:33:38] Converted: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_occurrences_30902.csv (3 lines)
[INFO] [2023-10-14 08:33:38] ...measurements (/app/public/data/hu_et_al_hu_et_a/measurementsorfacts.txt)
[CMD] [2023-10-14 08:33:38] /usr/bin/sort /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_measurements_30903.csv > /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_measurements_30903.csv_sorted
[INFO] [2023-10-14 08:33:38] Converted: /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_measurements_30903.csv (14 lines)
[STOP] [2023-10-14 08:33:38] convert_to_csv
[START] [2023-10-14 08:33:38] calculate_delta
[INFO] [2023-10-14 08:33:38] Looping over 4 formats...
[INFO] [2023-10-14 08:33:38] ...refs (/app/public/data/hu_et_al_hu_et_a/references.txt)
[CMD] [2023-10-14 08:33:38] echo "0a" > /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_refs_30904.diff
[CMD] [2023-10-14 08:33:38] tail -n +1 /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_refs_30904.csv >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_refs_30904.diff
[CMD] [2023-10-14 08:33:38] echo "." >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_refs_30904.diff
[INFO] [2023-10-14 08:33:38] Created diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_refs_30904.diff (4 lines)
[INFO] [2023-10-14 08:33:38] ...nodes (/app/public/data/hu_et_al_hu_et_a/taxa.txt)
[CMD] [2023-10-14 08:33:38] echo "0a" > /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_nodes_30901.diff
[CMD] [2023-10-14 08:33:38] tail -n +1 /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_nodes_30901.csv >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_nodes_30901.diff
[CMD] [2023-10-14 08:33:38] echo "." >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_nodes_30901.diff
[INFO] [2023-10-14 08:33:38] Created diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_nodes_30901.diff (5 lines)
[INFO] [2023-10-14 08:33:38] ...occurrences (/app/public/data/hu_et_al_hu_et_a/occurrences.txt)
[CMD] [2023-10-14 08:33:38] echo "0a" > /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_occurrences_30902.diff
[CMD] [2023-10-14 08:33:39] tail -n +1 /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_occurrences_30902.csv >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_occurrences_30902.diff
[CMD] [2023-10-14 08:33:39] echo "." >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_occurrences_30902.diff
[INFO] [2023-10-14 08:33:39] Created diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_occurrences_30902.diff (5 lines)
[INFO] [2023-10-14 08:33:39] ...measurements (/app/public/data/hu_et_al_hu_et_a/measurementsorfacts.txt)
[CMD] [2023-10-14 08:33:39] echo "0a" > /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_measurements_30903.diff
[CMD] [2023-10-14 08:33:39] tail -n +1 /app/public/data/hu_et_al_hu_et_a/converted_csv/hu_et_al_hu_et_a_measurements_30903.csv >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_measurements_30903.diff
[CMD] [2023-10-14 08:33:39] echo "." >> /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_measurements_30903.diff
[INFO] [2023-10-14 08:33:39] Created diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_measurements_30903.diff (16 lines)
[STOP] [2023-10-14 08:33:39] calculate_delta
[START] [2023-10-14 08:33:39] parse_diff_and_store
[INFO] [2023-10-14 08:33:39] Handling diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_refs_30904.diff (4 lines)
[INFO] [2023-10-14 08:33:39] Loading refs diff file into memory (4 lines)...
[INFO] [2023-10-14 08:33:39] Storing 2 References (2/2/4)
[INFO] [2023-10-14 08:33:39] Handling diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_nodes_30901.diff (5 lines)
[INFO] [2023-10-14 08:33:39] Loading nodes diff file into memory (5 lines)...
[INFO] [2023-10-14 08:33:39] Storing 3 ScientificNames (6/3/5)
[INFO] [2023-10-14 08:33:39] Storing 3 Nodes (6/3/5)
[INFO] [2023-10-14 08:33:39] Handling diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_occurrences_30902.diff (5 lines)
[INFO] [2023-10-14 08:33:39] Loading occurrences diff file into memory (5 lines)...
[INFO] [2023-10-14 08:33:39] Storing 3 Occurrences (3/3/5)
[INFO] [2023-10-14 08:33:39] Handling diff: /app/public/data/hu_et_al_hu_et_a/diff/hu_et_al_hu_et_a_measurements_30903.diff (16 lines)
[INFO] [2023-10-14 08:33:39] Loading measurements diff file into memory (16 lines)...
[INFO] [2023-10-14 08:33:39] Storing 2 TraitsReferences (30/14/16)
[INFO] [2023-10-14 08:33:39] Storing 14 Traits (30/14/16)
[INFO] [2023-10-14 08:33:39] Storing 14 MetaTraits (30/14/16)
[STOP] [2023-10-14 08:33:39] parse_diff_and_store
[START] [2023-10-14 08:33:39] resolve_keys
[2023-10-14 08:33:39] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:33:47] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:33:47] traits to occurrences...
[INFO] [2023-10-14 08:33:47] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:33:47] Traits to sex term...
[INFO] [2023-10-14 08:33:47] Traits to lifestage term...
[INFO] [2023-10-14 08:33:47] MetaTraits to traits...
[INFO] [2023-10-14 08:33:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:33:47] Assocs to occurrences...
[INFO] [2023-10-14 08:33:47] Assocs to nodes...
[INFO] [2023-10-14 08:33:47] Assoc to sex term...
[INFO] [2023-10-14 08:33:47] Assoc to lifestage term...
[INFO] [2023-10-14 08:33:47] MetaAssoc to assocs...
[STOP] [2023-10-14 08:33:47] resolve_keys
[START] [2023-10-14 08:33:47] hold_for_later_1
[STOP] [2023-10-14 08:33:47] hold_for_later_1
[START] [2023-10-14 08:33:47] hold_for_later_2
[STOP] [2023-10-14 08:33:47] hold_for_later_2
[START] [2023-10-14 08:33:47] resolve_missing_parents
[STOP] [2023-10-14 08:33:47] resolve_missing_parents
[START] [2023-10-14 08:33:47] rebuild_nodes
[START] [2023-10-14 08:33:47] Flattener#flatten
[START] [2023-10-14 08:33:47] Flattener#study_resource
[START] [2023-10-14 08:33:47] Flattener#build_ancestry
[STOP] [2023-10-14 08:33:47] Flattener#build_ancestry
[INFO] [2023-10-14 08:33:47] 3 ancestry keys
[START] [2023-10-14 08:33:47] build_node_ancestors
[INFO] [2023-10-14 08:33:47] old ancestors deleted.
[STOP] [2023-10-14 08:33:47] build_node_ancestors
[WARN] [2023-10-14 08:33:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:33:47] Flattener#flatten
[STOP] [2023-10-14 08:33:47] rebuild_nodes
[START] [2023-10-14 08:33:47] resolve_missing_media_owners
[STOP] [2023-10-14 08:33:47] resolve_missing_media_owners
[START] [2023-10-14 08:33:47] sanitize_media_verbatims
[STOP] [2023-10-14 08:33:47] sanitize_media_verbatims
[START] [2023-10-14 08:33:47] queue_downloads
[STOP] [2023-10-14 08:33:47] queue_downloads
[START] [2023-10-14 08:33:47] parse_names
[WARN] [2023-10-14 08:33:47] I see 3 names which still need to be parsed.
[WARN] [2023-10-14 08:33:47] Names to parse: 3 formatted: 3 learned: 3 parsed: 3
[STOP] [2023-10-14 08:33:48] parse_names
[START] [2023-10-14 08:33:48] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:33:48] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:33:48] match_nodes
[START] [2023-10-14 08:33:48] map_all_nodes_to_pages
[STOP] [2023-10-14 08:33:48] map_all_nodes_to_pages
[INFO] [2023-10-14 08:33:48] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2023-10-14 08:33:48] update_nodes
[STOP] [2023-10-14 08:33:48] update_nodes
[STOP] [2023-10-14 08:33:48] match_nodes
[START] [2023-10-14 08:33:48] reindex_search
[STOP] [2023-10-14 08:33:48] reindex_search
[START] [2023-10-14 08:33:48] normalize_units
[STOP] [2023-10-14 08:33:48] normalize_units
[START] [2023-10-14 08:33:48] calculate_statistics
[2023-10-14 08:33:48] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:33:48] Duplicate page_id count: 0
[STOP] [2023-10-14 08:33:48] calculate_statistics
[START] [2023-10-14 08:33:48] complete_harvest_instance
[START] [2023-10-14 08:33:48] overall_tsv_creation
[INFO] [2023-10-14 08:33:48] Exporting 3 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:33:48] Processing group of 3 in 1 batches of 10000
[INFO] [2023-10-14 08:33:48] 7 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:33:48] Building Traits map for 3 nodes (this can take a while)...
[INFO] [2023-10-14 08:33:48] Mapped 7 traits (14 meta) for 3 nodes.
[INFO] [2023-10-14 08:33:48] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:33:48] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:33:48] Adding 7 traits...
[INFO] [2023-10-14 08:33:48] 9 metadata added.
[INFO] [2023-10-14 08:33:48] Adding 0 assocs...
[INFO] [2023-10-14 08:33:48] 0 metadata added.
[INFO] [2023-10-14 08:34:32] Processed 3/3 nodes
[INFO] [2023-10-14 08:34:32] Average Time: 43.82
[INFO] [2023-10-14 08:34:32] Total Time: 44s
[STOP] [2023-10-14 08:34:32] overall_tsv_creation
[INFO] [2023-10-14 08:34:32] Done. Check your files:
[INFO] [2023-10-14 08:34:32] (3 lines) /app/public/data/hu_et_al_hu_et_a/publish_nodes.tsv
[INFO] [2023-10-14 08:34:32] (3 lines) /app/public/data/hu_et_al_hu_et_a/publish_scientific_names.tsv
[INFO] [2023-10-14 08:34:32] (8 lines) /app/public/data/hu_et_al_hu_et_a/publish_traits.tsv
[INFO] [2023-10-14 08:34:33] (10 lines) /app/public/data/hu_et_al_hu_et_a/publish_metadata.tsv
[STOP] [2023-10-14 08:34:33] complete_harvest_instance
[START] [2023-10-14 08:34:33] completed
[STOP] [2023-10-14 08:34:33] completed
[STOP] [2023-10-14 08:34:33] logged process, took 55.08

Latest Process

14 Oct 08:33 EXITED currently processing 0