Harvest for Hughes 1970 Created 13 Oct 13:49

Harvesting Log

[INFO] [2023-10-13 13:49:57] Created harvest instance #4459
[STOP] [2023-10-13 13:49:57] create_harvest_instance
[START] [2023-10-13 13:49:57] fetch_files
[STOP] [2023-10-13 13:49:57] fetch_files
[START] [2023-10-13 13:49:57] validate_each_file
[INFO] [2023-10-13 13:49:57] Looping over 4 formats...
[INFO] [2023-10-13 13:49:57] ...refs (/app/public/data/hughes_hughes_19/references.tsv)
[INFO] [2023-10-13 13:49:57] Valid: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_refs_30844.csv (1 lines)
[INFO] [2023-10-13 13:49:57] ...nodes (/app/public/data/hughes_hughes_19/taxa.txt)
[INFO] [2023-10-13 13:49:57] Valid: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_nodes_30841.csv (1 lines)
[INFO] [2023-10-13 13:49:57] ...occurrences (/app/public/data/hughes_hughes_19/occurrences.txt)
[INFO] [2023-10-13 13:49:57] Valid: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_occurrences_30842.csv (1 lines)
[INFO] [2023-10-13 13:49:57] ...measurements (/app/public/data/hughes_hughes_19/measurementsorfacts.txt)
[INFO] [2023-10-13 13:49:57] Valid: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_measurements_30843.csv (3 lines)
[STOP] [2023-10-13 13:49:57] validate_each_file
[START] [2023-10-13 13:49:57] convert_to_csv
[INFO] [2023-10-13 13:49:57] Looping over 4 formats...
[INFO] [2023-10-13 13:49:57] ...refs (/app/public/data/hughes_hughes_19/references.tsv)
[CMD] [2023-10-13 13:49:57] /usr/bin/sort /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_refs_30844.csv > /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_refs_30844.csv_sorted
[INFO] [2023-10-13 13:49:57] Converted: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_refs_30844.csv (1 lines)
[INFO] [2023-10-13 13:49:57] ...nodes (/app/public/data/hughes_hughes_19/taxa.txt)
[CMD] [2023-10-13 13:49:57] /usr/bin/sort /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_nodes_30841.csv > /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_nodes_30841.csv_sorted
[INFO] [2023-10-13 13:49:57] Converted: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_nodes_30841.csv (1 lines)
[INFO] [2023-10-13 13:49:57] ...occurrences (/app/public/data/hughes_hughes_19/occurrences.txt)
[CMD] [2023-10-13 13:49:57] /usr/bin/sort /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_occurrences_30842.csv > /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_occurrences_30842.csv_sorted
[INFO] [2023-10-13 13:49:57] Converted: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_occurrences_30842.csv (1 lines)
[INFO] [2023-10-13 13:49:57] ...measurements (/app/public/data/hughes_hughes_19/measurementsorfacts.txt)
[CMD] [2023-10-13 13:49:57] /usr/bin/sort /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_measurements_30843.csv > /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_measurements_30843.csv_sorted
[INFO] [2023-10-13 13:49:57] Converted: /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_measurements_30843.csv (3 lines)
[STOP] [2023-10-13 13:49:57] convert_to_csv
[START] [2023-10-13 13:49:57] calculate_delta
[INFO] [2023-10-13 13:49:57] Looping over 4 formats...
[INFO] [2023-10-13 13:49:57] ...refs (/app/public/data/hughes_hughes_19/references.tsv)
[CMD] [2023-10-13 13:49:57] echo "0a" > /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_refs_30844.diff
[CMD] [2023-10-13 13:49:58] tail -n +1 /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_refs_30844.csv >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_refs_30844.diff
[CMD] [2023-10-13 13:49:58] echo "." >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_refs_30844.diff
[INFO] [2023-10-13 13:49:58] Created diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_refs_30844.diff (3 lines)
[INFO] [2023-10-13 13:49:58] ...nodes (/app/public/data/hughes_hughes_19/taxa.txt)
[CMD] [2023-10-13 13:49:58] echo "0a" > /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_nodes_30841.diff
[CMD] [2023-10-13 13:49:58] tail -n +1 /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_nodes_30841.csv >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_nodes_30841.diff
[CMD] [2023-10-13 13:49:58] echo "." >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_nodes_30841.diff
[INFO] [2023-10-13 13:49:58] Created diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_nodes_30841.diff (3 lines)
[INFO] [2023-10-13 13:49:58] ...occurrences (/app/public/data/hughes_hughes_19/occurrences.txt)
[CMD] [2023-10-13 13:49:58] echo "0a" > /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_occurrences_30842.diff
[CMD] [2023-10-13 13:49:58] tail -n +1 /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_occurrences_30842.csv >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_occurrences_30842.diff
[CMD] [2023-10-13 13:49:58] echo "." >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_occurrences_30842.diff
[INFO] [2023-10-13 13:49:58] Created diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_occurrences_30842.diff (3 lines)
[INFO] [2023-10-13 13:49:58] ...measurements (/app/public/data/hughes_hughes_19/measurementsorfacts.txt)
[CMD] [2023-10-13 13:49:58] echo "0a" > /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_measurements_30843.diff
[CMD] [2023-10-13 13:49:58] tail -n +1 /app/public/data/hughes_hughes_19/converted_csv/hughes_hughes_19_measurements_30843.csv >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_measurements_30843.diff
[CMD] [2023-10-13 13:49:58] echo "." >> /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_measurements_30843.diff
[INFO] [2023-10-13 13:49:58] Created diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_measurements_30843.diff (5 lines)
[STOP] [2023-10-13 13:49:58] calculate_delta
[START] [2023-10-13 13:49:58] parse_diff_and_store
[INFO] [2023-10-13 13:49:58] Handling diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_refs_30844.diff (3 lines)
[INFO] [2023-10-13 13:49:58] Loading refs diff file into memory (3 lines)...
[INFO] [2023-10-13 13:49:58] Storing 1 References (1/1/3)
[INFO] [2023-10-13 13:49:58] Handling diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_nodes_30841.diff (3 lines)
[INFO] [2023-10-13 13:49:59] Loading nodes diff file into memory (3 lines)...
[INFO] [2023-10-13 13:49:59] Storing 1 ScientificNames (2/1/3)
[INFO] [2023-10-13 13:49:59] Storing 1 Nodes (2/1/3)
[INFO] [2023-10-13 13:49:59] Handling diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_occurrences_30842.diff (3 lines)
[INFO] [2023-10-13 13:49:59] Loading occurrences diff file into memory (3 lines)...
[INFO] [2023-10-13 13:49:59] Storing 1 Occurrences (1/1/3)
[INFO] [2023-10-13 13:49:59] Handling diff: /app/public/data/hughes_hughes_19/diff/hughes_hughes_19_measurements_30843.diff (5 lines)
[INFO] [2023-10-13 13:49:59] Loading measurements diff file into memory (5 lines)...
[INFO] [2023-10-13 13:49:59] Storing 1 TraitsReferences (6/3/5)
[INFO] [2023-10-13 13:49:59] Storing 3 Traits (6/3/5)
[INFO] [2023-10-13 13:49:59] Storing 2 MetaTraits (6/3/5)
[STOP] [2023-10-13 13:49:59] parse_diff_and_store
[START] [2023-10-13 13:49:59] resolve_keys
[2023-10-13 13:49:59] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-13 13:50:06] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-13 13:50:06] traits to occurrences...
[INFO] [2023-10-13 13:50:06] traits to nodes (through occurrences)...
[INFO] [2023-10-13 13:50:06] Traits to sex term...
[INFO] [2023-10-13 13:50:06] Traits to lifestage term...
[INFO] [2023-10-13 13:50:06] MetaTraits to traits...
[INFO] [2023-10-13 13:50:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-13 13:50:06] Assocs to occurrences...
[INFO] [2023-10-13 13:50:06] Assocs to nodes...
[INFO] [2023-10-13 13:50:06] Assoc to sex term...
[INFO] [2023-10-13 13:50:06] Assoc to lifestage term...
[INFO] [2023-10-13 13:50:06] MetaAssoc to assocs...
[STOP] [2023-10-13 13:50:06] resolve_keys
[START] [2023-10-13 13:50:06] hold_for_later_1
[STOP] [2023-10-13 13:50:06] hold_for_later_1
[START] [2023-10-13 13:50:06] hold_for_later_2
[STOP] [2023-10-13 13:50:06] hold_for_later_2
[START] [2023-10-13 13:50:07] resolve_missing_parents
[STOP] [2023-10-13 13:50:07] resolve_missing_parents
[START] [2023-10-13 13:50:07] rebuild_nodes
[START] [2023-10-13 13:50:07] Flattener#flatten
[START] [2023-10-13 13:50:07] Flattener#study_resource
[START] [2023-10-13 13:50:07] Flattener#build_ancestry
[STOP] [2023-10-13 13:50:07] Flattener#build_ancestry
[INFO] [2023-10-13 13:50:07] 1 ancestry keys
[START] [2023-10-13 13:50:07] build_node_ancestors
[INFO] [2023-10-13 13:50:07] old ancestors deleted.
[STOP] [2023-10-13 13:50:07] build_node_ancestors
[WARN] [2023-10-13 13:50:07] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-13 13:50:07] Flattener#flatten
[STOP] [2023-10-13 13:50:07] rebuild_nodes
[START] [2023-10-13 13:50:07] resolve_missing_media_owners
[STOP] [2023-10-13 13:50:07] resolve_missing_media_owners
[START] [2023-10-13 13:50:07] sanitize_media_verbatims
[STOP] [2023-10-13 13:50:07] sanitize_media_verbatims
[START] [2023-10-13 13:50:07] queue_downloads
[STOP] [2023-10-13 13:50:07] queue_downloads
[START] [2023-10-13 13:50:07] parse_names
[WARN] [2023-10-13 13:50:07] I see 1 names which still need to be parsed.
[WARN] [2023-10-13 13:50:07] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2023-10-13 13:50:08] parse_names
[START] [2023-10-13 13:50:08] denormalize_canonical_names_to_nodes
[STOP] [2023-10-13 13:50:08] denormalize_canonical_names_to_nodes
[START] [2023-10-13 13:50:08] match_nodes
[START] [2023-10-13 13:50:08] map_all_nodes_to_pages
[STOP] [2023-10-13 13:50:08] map_all_nodes_to_pages
[INFO] [2023-10-13 13:50:08] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2023-10-13 13:50:08] update_nodes
[STOP] [2023-10-13 13:50:08] update_nodes
[STOP] [2023-10-13 13:50:08] match_nodes
[START] [2023-10-13 13:50:08] reindex_search
[STOP] [2023-10-13 13:50:08] reindex_search
[START] [2023-10-13 13:50:08] normalize_units
[STOP] [2023-10-13 13:50:08] normalize_units
[START] [2023-10-13 13:50:08] calculate_statistics
[2023-10-13 13:50:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-13 13:50:08] Duplicate page_id count: 0
[STOP] [2023-10-13 13:50:08] calculate_statistics
[START] [2023-10-13 13:50:08] complete_harvest_instance
[START] [2023-10-13 13:50:08] overall_tsv_creation
[INFO] [2023-10-13 13:50:08] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2023-10-13 13:50:08] Processing group of 1 in 1 batches of 10000
[INFO] [2023-10-13 13:50:08] 1 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-13 13:50:08] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2023-10-13 13:50:08] Mapped 1 traits (2 meta) for 1 nodes.
[INFO] [2023-10-13 13:50:08] Building Associations map (this can take a while)...
[INFO] [2023-10-13 13:50:08] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-13 13:50:08] Adding 1 traits...
[INFO] [2023-10-13 13:50:08] 3 metadata added.
[INFO] [2023-10-13 13:50:08] Adding 0 assocs...
[INFO] [2023-10-13 13:50:08] 0 metadata added.
[INFO] [2023-10-13 13:50:52] Processed 1/1 nodes
[INFO] [2023-10-13 13:50:52] Average Time: 43.94
[INFO] [2023-10-13 13:50:52] Total Time: 44s
[STOP] [2023-10-13 13:50:52] overall_tsv_creation
[INFO] [2023-10-13 13:50:52] Done. Check your files:
[INFO] [2023-10-13 13:50:52] (1 lines) /app/public/data/hughes_hughes_19/publish_nodes.tsv
[INFO] [2023-10-13 13:50:52] (1 lines) /app/public/data/hughes_hughes_19/publish_scientific_names.tsv
[INFO] [2023-10-13 13:50:52] (2 lines) /app/public/data/hughes_hughes_19/publish_traits.tsv
[INFO] [2023-10-13 13:50:52] (4 lines) /app/public/data/hughes_hughes_19/publish_metadata.tsv
[STOP] [2023-10-13 13:50:52] complete_harvest_instance
[START] [2023-10-13 13:50:52] completed
[STOP] [2023-10-13 13:50:52] completed
[STOP] [2023-10-13 13:50:52] logged process, took 55.35

Latest Process

13 Oct 13:49 EXITED currently processing 0