Harvest for GILBERT 1985 Created 13 Oct 09:10

Harvesting Log

[INFO] [2023-10-13 09:10:14] Created harvest instance #4414
[STOP] [2023-10-13 09:10:14] create_harvest_instance
[START] [2023-10-13 09:10:14] fetch_files
[STOP] [2023-10-13 09:10:14] fetch_files
[START] [2023-10-13 09:10:14] validate_each_file
[INFO] [2023-10-13 09:10:14] Looping over 4 formats...
[INFO] [2023-10-13 09:10:14] ...refs (/app/public/data/gilbert_1985_gil/references.txt)
[INFO] [2023-10-13 09:10:14] Valid: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_refs_30605.csv (2 lines)
[INFO] [2023-10-13 09:10:14] ...nodes (/app/public/data/gilbert_1985_gil/taxa.txt)
[INFO] [2023-10-13 09:10:14] Valid: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_nodes_30604.csv (1 lines)
[INFO] [2023-10-13 09:10:14] ...occurrences (/app/public/data/gilbert_1985_gil/occurrences.txt)
[INFO] [2023-10-13 09:10:14] Valid: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_occurrences_30606.csv (1 lines)
[INFO] [2023-10-13 09:10:14] ...measurements (/app/public/data/gilbert_1985_gil/measurementsorfacts.txt)
[INFO] [2023-10-13 09:10:14] Valid: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_measurements_30607.csv (2 lines)
[STOP] [2023-10-13 09:10:14] validate_each_file
[START] [2023-10-13 09:10:14] convert_to_csv
[INFO] [2023-10-13 09:10:14] Looping over 4 formats...
[INFO] [2023-10-13 09:10:14] ...refs (/app/public/data/gilbert_1985_gil/references.txt)
[CMD] [2023-10-13 09:10:14] /usr/bin/sort /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_refs_30605.csv > /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_refs_30605.csv_sorted
[INFO] [2023-10-13 09:10:14] Converted: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_refs_30605.csv (2 lines)
[INFO] [2023-10-13 09:10:14] ...nodes (/app/public/data/gilbert_1985_gil/taxa.txt)
[CMD] [2023-10-13 09:10:14] /usr/bin/sort /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_nodes_30604.csv > /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_nodes_30604.csv_sorted
[INFO] [2023-10-13 09:10:14] Converted: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_nodes_30604.csv (1 lines)
[INFO] [2023-10-13 09:10:14] ...occurrences (/app/public/data/gilbert_1985_gil/occurrences.txt)
[CMD] [2023-10-13 09:10:14] /usr/bin/sort /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_occurrences_30606.csv > /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_occurrences_30606.csv_sorted
[INFO] [2023-10-13 09:10:15] Converted: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_occurrences_30606.csv (1 lines)
[INFO] [2023-10-13 09:10:15] ...measurements (/app/public/data/gilbert_1985_gil/measurementsorfacts.txt)
[CMD] [2023-10-13 09:10:15] /usr/bin/sort /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_measurements_30607.csv > /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_measurements_30607.csv_sorted
[INFO] [2023-10-13 09:10:15] Converted: /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_measurements_30607.csv (2 lines)
[STOP] [2023-10-13 09:10:15] convert_to_csv
[START] [2023-10-13 09:10:15] calculate_delta
[INFO] [2023-10-13 09:10:15] Looping over 4 formats...
[INFO] [2023-10-13 09:10:15] ...refs (/app/public/data/gilbert_1985_gil/references.txt)
[CMD] [2023-10-13 09:10:15] echo "0a" > /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_refs_30605.diff
[CMD] [2023-10-13 09:10:15] tail -n +1 /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_refs_30605.csv >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_refs_30605.diff
[CMD] [2023-10-13 09:10:15] echo "." >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_refs_30605.diff
[INFO] [2023-10-13 09:10:15] Created diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_refs_30605.diff (4 lines)
[INFO] [2023-10-13 09:10:15] ...nodes (/app/public/data/gilbert_1985_gil/taxa.txt)
[CMD] [2023-10-13 09:10:15] echo "0a" > /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_nodes_30604.diff
[CMD] [2023-10-13 09:10:15] tail -n +1 /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_nodes_30604.csv >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_nodes_30604.diff
[CMD] [2023-10-13 09:10:15] echo "." >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_nodes_30604.diff
[INFO] [2023-10-13 09:10:15] Created diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_nodes_30604.diff (3 lines)
[INFO] [2023-10-13 09:10:15] ...occurrences (/app/public/data/gilbert_1985_gil/occurrences.txt)
[CMD] [2023-10-13 09:10:15] echo "0a" > /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_occurrences_30606.diff
[CMD] [2023-10-13 09:10:15] tail -n +1 /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_occurrences_30606.csv >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_occurrences_30606.diff
[CMD] [2023-10-13 09:10:15] echo "." >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_occurrences_30606.diff
[INFO] [2023-10-13 09:10:15] Created diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_occurrences_30606.diff (3 lines)
[INFO] [2023-10-13 09:10:15] ...measurements (/app/public/data/gilbert_1985_gil/measurementsorfacts.txt)
[CMD] [2023-10-13 09:10:15] echo "0a" > /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_measurements_30607.diff
[CMD] [2023-10-13 09:10:15] tail -n +1 /app/public/data/gilbert_1985_gil/converted_csv/gilbert_1985_gil_measurements_30607.csv >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_measurements_30607.diff
[CMD] [2023-10-13 09:10:15] echo "." >> /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_measurements_30607.diff
[INFO] [2023-10-13 09:10:16] Created diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_measurements_30607.diff (4 lines)
[STOP] [2023-10-13 09:10:16] calculate_delta
[START] [2023-10-13 09:10:16] parse_diff_and_store
[INFO] [2023-10-13 09:10:16] Handling diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_refs_30605.diff (4 lines)
[INFO] [2023-10-13 09:10:16] Loading refs diff file into memory (4 lines)...
[INFO] [2023-10-13 09:10:16] Storing 2 References (2/2/4)
[INFO] [2023-10-13 09:10:16] Handling diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_nodes_30604.diff (3 lines)
[INFO] [2023-10-13 09:10:16] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-13 09:10:16] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-13 09:10:16] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-13 09:10:16] Handling diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_occurrences_30606.diff (3 lines)
[INFO] [2023-10-13 09:10:16] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-13 09:10:16] Storing 1 Occurrences (2/1/3)
[INFO] [2023-10-13 09:10:16] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2023-10-13 09:10:16] Handling diff: /app/public/data/gilbert_1985_gil/diff/gilbert_1985_gil_measurements_30607.diff (4 lines)
[INFO] [2023-10-13 09:10:16] Loading measurements diff file into memory (4 lines)...
[INFO] [2023-10-13 09:10:16] Storing 2 TraitsReferences (7/2/4)
[INFO] [2023-10-13 09:10:16] Storing 2 Traits (7/2/4)
[INFO] [2023-10-13 09:10:16] Storing 3 MetaTraits (7/2/4)
[STOP] [2023-10-13 09:10:16] parse_diff_and_store
[START] [2023-10-13 09:10:16] resolve_keys
[2023-10-13 09:10:16] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 09:10:24] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 09:10:24] traits to occurrences...
[INFO] [2023-10-13 09:10:24] traits to nodes (through occurrences)...
[INFO] [2023-10-13 09:10:24] Traits to sex term...
[INFO] [2023-10-13 09:10:24] Traits to lifestage term...
[INFO] [2023-10-13 09:10:24] MetaTraits to traits...
[INFO] [2023-10-13 09:10:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 09:10:24] Assocs to occurrences...
[INFO] [2023-10-13 09:10:24] Assocs to nodes...
[INFO] [2023-10-13 09:10:24] Assoc to sex term...
[INFO] [2023-10-13 09:10:24] Assoc to lifestage term...
[INFO] [2023-10-13 09:10:24] MetaAssoc to assocs...
[STOP] [2023-10-13 09:10:24] resolve_keys
[START] [2023-10-13 09:10:24] hold_for_later_1
[STOP] [2023-10-13 09:10:24] hold_for_later_1
[START] [2023-10-13 09:10:24] hold_for_later_2
[STOP] [2023-10-13 09:10:24] hold_for_later_2
[START] [2023-10-13 09:10:24] resolve_missing_parents
[STOP] [2023-10-13 09:10:24] resolve_missing_parents
[START] [2023-10-13 09:10:24] rebuild_nodes
[START] [2023-10-13 09:10:24] Flattener#flatten
[START] [2023-10-13 09:10:24] Flattener#study_resource
[START] [2023-10-13 09:10:24] Flattener#build_ancestry
[STOP] [2023-10-13 09:10:24] Flattener#build_ancestry
[INFO] [2023-10-13 09:10:24] 1 ancestry keys
[START] [2023-10-13 09:10:24] build_node_ancestors
[INFO] [2023-10-13 09:10:24] old ancestors deleted.
[STOP] [2023-10-13 09:10:24] build_node_ancestors
[WARN] [2023-10-13 09:10:24] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 09:10:24] Flattener#flatten
[STOP] [2023-10-13 09:10:24] rebuild_nodes
[START] [2023-10-13 09:10:24] resolve_missing_media_owners
[STOP] [2023-10-13 09:10:24] resolve_missing_media_owners
[START] [2023-10-13 09:10:24] sanitize_media_verbatims
[STOP] [2023-10-13 09:10:24] sanitize_media_verbatims
[START] [2023-10-13 09:10:24] queue_downloads
[STOP] [2023-10-13 09:10:24] queue_downloads
[START] [2023-10-13 09:10:24] parse_names
[WARN] [2023-10-13 09:10:24] I see 1 names which still need to be parsed.
[WARN] [2023-10-13 09:10:24] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-13 09:10:25] parse_names
[START] [2023-10-13 09:10:25] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 09:10:25] denormalize_canonical_names_to_nodes
[START] [2023-10-13 09:10:25] match_nodes
[START] [2023-10-13 09:10:25] map_all_nodes_to_pages
[STOP] [2023-10-13 09:10:25] map_all_nodes_to_pages
[INFO] [2023-10-13 09:10:25] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-13 09:10:25] update_nodes
[STOP] [2023-10-13 09:10:25] update_nodes
[STOP] [2023-10-13 09:10:25] match_nodes
[START] [2023-10-13 09:10:25] reindex_search
[STOP] [2023-10-13 09:10:25] reindex_search
[START] [2023-10-13 09:10:25] normalize_units
[STOP] [2023-10-13 09:10:25] normalize_units
[START] [2023-10-13 09:10:25] calculate_statistics
[2023-10-13 09:10:25] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 09:10:25] Duplicate page_id count: 0
[STOP] [2023-10-13 09:10:25] calculate_statistics
[START] [2023-10-13 09:10:25] complete_harvest_instance
[START] [2023-10-13 09:10:25] overall_tsv_creation
[INFO] [2023-10-13 09:10:25] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 09:10:25] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-13 09:10:25] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 09:10:25] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-13 09:10:25] Mapped 1 traits (3 meta) for 1 nodes.
[INFO] [2023-10-13 09:10:25] Building Associations map (this can take a while)...
[INFO] [2023-10-13 09:10:25] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 09:10:25] Adding 1 traits...
[INFO] [2023-10-13 09:10:25] 3 metadata added.
[INFO] [2023-10-13 09:10:25] Adding 0 assocs...
[INFO] [2023-10-13 09:10:25] 0 metadata added.
[INFO] [2023-10-13 09:11:09] Processed 1/1 nodes
[INFO] [2023-10-13 09:11:09] Average Time: 44.44
[INFO] [2023-10-13 09:11:09] Total Time: 45s
[STOP] [2023-10-13 09:11:09] overall_tsv_creation
[INFO] [2023-10-13 09:11:09] Done. Check your files:
[INFO] [2023-10-13 09:11:10] (1 lines) /app/public/data/gilbert_1985_gil/publish_nodes.tsv
[INFO] [2023-10-13 09:11:10] (1 lines) /app/public/data/gilbert_1985_gil/publish_scientific_names.tsv
[INFO] [2023-10-13 09:11:10] (2 lines) /app/public/data/gilbert_1985_gil/publish_traits.tsv
[INFO] [2023-10-13 09:11:10] (4 lines) /app/public/data/gilbert_1985_gil/publish_metadata.tsv
[STOP] [2023-10-13 09:11:10] complete_harvest_instance
[START] [2023-10-13 09:11:10] completed
[STOP] [2023-10-13 09:11:10] completed
[STOP] [2023-10-13 09:11:10] logged process, took 55.69

Latest Process

13 Oct 09:10 EXITED currently processing 0