Harvest for Yager 1999 Created 14 Oct 08:32

Stage: completed
Fetched: 14 Oct 08:32
Validated: 14 Oct 08:32
Deltas Created 14 Oct 08:32
Units Normalized: 14 Oct 08:32
Ancestry Built: 14 Oct 08:32
Nodes Matched: 14 Oct 08:32
Names Parsed: 14 Oct 08:32
New Models Stored: 14 Oct 08:32
Indexed: 14 Oct 08:32
Completed: 14 Oct 08:33
Time to Harvest: less than a minute

Harvesting Log

(156 lines)
[INFO] [2023-10-14 08:32:34] Created harvest instance #4473
[STOP] [2023-10-14 08:32:34] create_harvest_instance
[START] [2023-10-14 08:32:34] fetch_files
[STOP] [2023-10-14 08:32:34] fetch_files
[START] [2023-10-14 08:32:34] validate_each_file
[INFO] [2023-10-14 08:32:34] Looping over 4 formats...
[INFO] [2023-10-14 08:32:34] ...refs (/app/public/data/yager_yager_1999/references.txt)
[INFO] [2023-10-14 08:32:34] Valid: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_refs_30900.csv (3 lines)
[INFO] [2023-10-14 08:32:34] ...nodes (/app/public/data/yager_yager_1999/taxa.txt)
[INFO] [2023-10-14 08:32:34] Valid: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_nodes_30897.csv (14 lines)
[INFO] [2023-10-14 08:32:34] ...occurrences (/app/public/data/yager_yager_1999/occurrences.txt)
[INFO] [2023-10-14 08:32:34] Valid: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_occurrences_30898.csv (14 lines)
[INFO] [2023-10-14 08:32:34] ...measurements (/app/public/data/yager_yager_1999/measurementsorfacts.txt)
[INFO] [2023-10-14 08:32:34] Valid: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_measurements_30899.csv (58 lines)
[STOP] [2023-10-14 08:32:34] validate_each_file
[START] [2023-10-14 08:32:34] convert_to_csv
[INFO] [2023-10-14 08:32:34] Looping over 4 formats...
[INFO] [2023-10-14 08:32:34] ...refs (/app/public/data/yager_yager_1999/references.txt)
[CMD] [2023-10-14 08:32:34] /usr/bin/sort /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_refs_30900.csv > /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_refs_30900.csv_sorted
[INFO] [2023-10-14 08:32:34] Converted: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_refs_30900.csv (3 lines)
[INFO] [2023-10-14 08:32:34] ...nodes (/app/public/data/yager_yager_1999/taxa.txt)
[CMD] [2023-10-14 08:32:34] /usr/bin/sort /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_nodes_30897.csv > /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_nodes_30897.csv_sorted
[INFO] [2023-10-14 08:32:34] Converted: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_nodes_30897.csv (14 lines)
[INFO] [2023-10-14 08:32:34] ...occurrences (/app/public/data/yager_yager_1999/occurrences.txt)
[CMD] [2023-10-14 08:32:34] /usr/bin/sort /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_occurrences_30898.csv > /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_occurrences_30898.csv_sorted
[INFO] [2023-10-14 08:32:34] Converted: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_occurrences_30898.csv (14 lines)
[INFO] [2023-10-14 08:32:34] ...measurements (/app/public/data/yager_yager_1999/measurementsorfacts.txt)
[CMD] [2023-10-14 08:32:34] /usr/bin/sort /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_measurements_30899.csv > /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_measurements_30899.csv_sorted
[INFO] [2023-10-14 08:32:35] Converted: /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_measurements_30899.csv (58 lines)
[STOP] [2023-10-14 08:32:35] convert_to_csv
[START] [2023-10-14 08:32:35] calculate_delta
[INFO] [2023-10-14 08:32:35] Looping over 4 formats...
[INFO] [2023-10-14 08:32:35] ...refs (/app/public/data/yager_yager_1999/references.txt)
[CMD] [2023-10-14 08:32:35] echo "0a" > /app/public/data/yager_yager_1999/diff/yager_yager_1999_refs_30900.diff
[CMD] [2023-10-14 08:32:35] tail -n +1 /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_refs_30900.csv >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_refs_30900.diff
[CMD] [2023-10-14 08:32:35] echo "." >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_refs_30900.diff
[INFO] [2023-10-14 08:32:35] Created diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_refs_30900.diff (5 lines)
[INFO] [2023-10-14 08:32:35] ...nodes (/app/public/data/yager_yager_1999/taxa.txt)
[CMD] [2023-10-14 08:32:35] echo "0a" > /app/public/data/yager_yager_1999/diff/yager_yager_1999_nodes_30897.diff
[CMD] [2023-10-14 08:32:35] tail -n +1 /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_nodes_30897.csv >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_nodes_30897.diff
[CMD] [2023-10-14 08:32:35] echo "." >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_nodes_30897.diff
[INFO] [2023-10-14 08:32:35] Created diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_nodes_30897.diff (16 lines)
[INFO] [2023-10-14 08:32:35] ...occurrences (/app/public/data/yager_yager_1999/occurrences.txt)
[CMD] [2023-10-14 08:32:35] echo "0a" > /app/public/data/yager_yager_1999/diff/yager_yager_1999_occurrences_30898.diff
[CMD] [2023-10-14 08:32:35] tail -n +1 /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_occurrences_30898.csv >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_occurrences_30898.diff
[CMD] [2023-10-14 08:32:35] echo "." >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_occurrences_30898.diff
[INFO] [2023-10-14 08:32:35] Created diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_occurrences_30898.diff (16 lines)
[INFO] [2023-10-14 08:32:35] ...measurements (/app/public/data/yager_yager_1999/measurementsorfacts.txt)
[CMD] [2023-10-14 08:32:35] echo "0a" > /app/public/data/yager_yager_1999/diff/yager_yager_1999_measurements_30899.diff
[CMD] [2023-10-14 08:32:35] tail -n +1 /app/public/data/yager_yager_1999/converted_csv/yager_yager_1999_measurements_30899.csv >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_measurements_30899.diff
[CMD] [2023-10-14 08:32:35] echo "." >> /app/public/data/yager_yager_1999/diff/yager_yager_1999_measurements_30899.diff
[INFO] [2023-10-14 08:32:35] Created diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_measurements_30899.diff (60 lines)
[STOP] [2023-10-14 08:32:35] calculate_delta
[START] [2023-10-14 08:32:35] parse_diff_and_store
[INFO] [2023-10-14 08:32:35] Handling diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_refs_30900.diff (5 lines)
[INFO] [2023-10-14 08:32:35] Loading refs diff file into memory (5 lines)...
[INFO] [2023-10-14 08:32:35] Storing 3 References (3/3/5)
[INFO] [2023-10-14 08:32:35] Handling diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_nodes_30897.diff (16 lines)
[INFO] [2023-10-14 08:32:36] Loading nodes diff file into memory (16 lines)...
[INFO] [2023-10-14 08:32:36] Storing 14 ScientificNames (28/14/16)
[INFO] [2023-10-14 08:32:36] Storing 14 Nodes (28/14/16)
[INFO] [2023-10-14 08:32:36] Handling diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_occurrences_30898.diff (16 lines)
[INFO] [2023-10-14 08:32:36] Loading occurrences diff file into memory (16 lines)...
[INFO] [2023-10-14 08:32:36] Storing 14 Occurrences (14/14/16)
[INFO] [2023-10-14 08:32:36] Handling diff: /app/public/data/yager_yager_1999/diff/yager_yager_1999_measurements_30899.diff (60 lines)
[INFO] [2023-10-14 08:32:36] Loading measurements diff file into memory (60 lines)...
[INFO] [2023-10-14 08:32:36] Storing 58 Traits (129/58/60)
[INFO] [2023-10-14 08:32:36] Storing 62 MetaTraits (129/58/60)
[INFO] [2023-10-14 08:32:36] Storing 9 TraitsReferences (129/58/60)
[STOP] [2023-10-14 08:32:36] parse_diff_and_store
[START] [2023-10-14 08:32:36] resolve_keys
[2023-10-14 08:32:36] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-10-14 08:32:44] Occurrences to nodes (through scientific_names)...
[INFO] [2023-10-14 08:32:44] traits to occurrences...
[INFO] [2023-10-14 08:32:44] traits to nodes (through occurrences)...
[INFO] [2023-10-14 08:32:44] Traits to sex term...
[INFO] [2023-10-14 08:32:44] Traits to lifestage term...
[INFO] [2023-10-14 08:32:44] MetaTraits to traits...
[INFO] [2023-10-14 08:32:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-10-14 08:32:44] Assocs to occurrences...
[INFO] [2023-10-14 08:32:44] Assocs to nodes...
[INFO] [2023-10-14 08:32:44] Assoc to sex term...
[INFO] [2023-10-14 08:32:44] Assoc to lifestage term...
[INFO] [2023-10-14 08:32:44] MetaAssoc to assocs...
[STOP] [2023-10-14 08:32:44] resolve_keys
[START] [2023-10-14 08:32:44] hold_for_later_1
[STOP] [2023-10-14 08:32:44] hold_for_later_1
[START] [2023-10-14 08:32:44] hold_for_later_2
[STOP] [2023-10-14 08:32:44] hold_for_later_2
[START] [2023-10-14 08:32:44] resolve_missing_parents
[STOP] [2023-10-14 08:32:44] resolve_missing_parents
[START] [2023-10-14 08:32:44] rebuild_nodes
[START] [2023-10-14 08:32:44] Flattener#flatten
[START] [2023-10-14 08:32:44] Flattener#study_resource
[START] [2023-10-14 08:32:44] Flattener#build_ancestry
[STOP] [2023-10-14 08:32:44] Flattener#build_ancestry
[INFO] [2023-10-14 08:32:44] 14 ancestry keys
[START] [2023-10-14 08:32:44] build_node_ancestors
[INFO] [2023-10-14 08:32:44] old ancestors deleted.
[STOP] [2023-10-14 08:32:44] build_node_ancestors
[WARN] [2023-10-14 08:32:44] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-10-14 08:32:44] Flattener#flatten
[STOP] [2023-10-14 08:32:44] rebuild_nodes
[START] [2023-10-14 08:32:44] resolve_missing_media_owners
[STOP] [2023-10-14 08:32:44] resolve_missing_media_owners
[START] [2023-10-14 08:32:44] sanitize_media_verbatims
[STOP] [2023-10-14 08:32:44] sanitize_media_verbatims
[START] [2023-10-14 08:32:44] queue_downloads
[STOP] [2023-10-14 08:32:44] queue_downloads
[START] [2023-10-14 08:32:44] parse_names
[WARN] [2023-10-14 08:32:44] I see 14 names which still need to be parsed.
[WARN] [2023-10-14 08:32:44] Names to parse: 14 formatted: 14 learned: 14 parsed: 14
[STOP] [2023-10-14 08:32:45] parse_names
[START] [2023-10-14 08:32:45] denormalize_canonical_names_to_nodes
[STOP] [2023-10-14 08:32:45] denormalize_canonical_names_to_nodes
[START] [2023-10-14 08:32:45] match_nodes
[START] [2023-10-14 08:32:45] map_all_nodes_to_pages
[STOP] [2023-10-14 08:32:45] map_all_nodes_to_pages
[INFO] [2023-10-14 08:32:45] ZERO unmatched nodes (of 14)! Nicely done.
[START] [2023-10-14 08:32:45] update_nodes
[STOP] [2023-10-14 08:32:45] update_nodes
[STOP] [2023-10-14 08:32:45] match_nodes
[START] [2023-10-14 08:32:45] reindex_search
[STOP] [2023-10-14 08:32:45] reindex_search
[START] [2023-10-14 08:32:45] normalize_units
[STOP] [2023-10-14 08:32:45] normalize_units
[START] [2023-10-14 08:32:45] calculate_statistics
[2023-10-14 08:32:45] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-10-14 08:32:45] Duplicate page_id count: 0
[STOP] [2023-10-14 08:32:45] calculate_statistics
[START] [2023-10-14 08:32:45] complete_harvest_instance
[START] [2023-10-14 08:32:45] overall_tsv_creation
[INFO] [2023-10-14 08:32:45] Exporting 14 nodes as TSV in batches of 10000...
[INFO] [2023-10-14 08:32:45] Processing group of 14 in 1 batches of 10000
[INFO] [2023-10-14 08:32:46] 28 Traits (unfiltered) and 0 associations...
[INFO] [2023-10-14 08:32:46] Building Traits map for 14 nodes (this can take a while)...
[INFO] [2023-10-14 08:32:46] Mapped 28 traits (62 meta) for 14 nodes.
[INFO] [2023-10-14 08:32:46] Building Associations map (this can take a while)...
[INFO] [2023-10-14 08:32:46] Done. 0 assocs mapped (0 meta).
[INFO] [2023-10-14 08:32:46] Adding 28 traits...
[INFO] [2023-10-14 08:32:46] 39 metadata added.
[INFO] [2023-10-14 08:32:46] Adding 0 assocs...
[INFO] [2023-10-14 08:32:46] 0 metadata added.
[INFO] [2023-10-14 08:33:30] Processed 14/14 nodes
[INFO] [2023-10-14 08:33:30] Average Time: 44.09
[INFO] [2023-10-14 08:33:30] Total Time: 45s
[STOP] [2023-10-14 08:33:30] overall_tsv_creation
[INFO] [2023-10-14 08:33:30] Done. Check your files:
[INFO] [2023-10-14 08:33:30] (14 lines) /app/public/data/yager_yager_1999/publish_nodes.tsv
[INFO] [2023-10-14 08:33:30] (14 lines) /app/public/data/yager_yager_1999/publish_scientific_names.tsv
[INFO] [2023-10-14 08:33:30] (29 lines) /app/public/data/yager_yager_1999/publish_traits.tsv
[INFO] [2023-10-14 08:33:30] (40 lines) /app/public/data/yager_yager_1999/publish_metadata.tsv
[STOP] [2023-10-14 08:33:30] complete_harvest_instance
[START] [2023-10-14 08:33:30] completed
[STOP] [2023-10-14 08:33:30] completed
[STOP] [2023-10-14 08:33:30] logged process, took 55.89

Latest Process