Harvest for Yamano et al 2000 Created 05 Jan 17:28

Stage: completed
Fetched: 05 Jan 17:28
Validated: 05 Jan 17:28
Deltas Created 05 Jan 17:28
Units Normalized: 05 Jan 17:28
Ancestry Built: 05 Jan 17:28
Nodes Matched: 05 Jan 17:28
Names Parsed: 05 Jan 17:28
New Models Stored: 05 Jan 17:28
Indexed: 05 Jan 17:28
Completed: 05 Jan 17:29
Time to Harvest: less than a minute

Harvesting Log

(143 lines)
[INFO] [2023-01-05 17:28:43] Created harvest instance #4251
[STOP] [2023-01-05 17:28:43] create_harvest_instance
[START] [2023-01-05 17:28:43] fetch_files
[STOP] [2023-01-05 17:28:43] fetch_files
[START] [2023-01-05 17:28:43] validate_each_file
[INFO] [2023-01-05 17:28:43] Looping over 3 formats...
[INFO] [2023-01-05 17:28:43] ...nodes (/app/public/data/yamano_et_al_yam/taxa.txt)
[INFO] [2023-01-05 17:28:43] Valid: /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_nodes_29999.csv (7 lines)
[INFO] [2023-01-05 17:28:43] ...occurrences (/app/public/data/yamano_et_al_yam/occurrences.txt)
[INFO] [2023-01-05 17:28:43] Valid: /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_occurrences_30000.csv (7 lines)
[INFO] [2023-01-05 17:28:43] ...measurements (/app/public/data/yamano_et_al_yam/measurementsorfacts.txt)
[INFO] [2023-01-05 17:28:43] Valid: /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_measurements_30001.csv (32 lines)
[STOP] [2023-01-05 17:28:43] validate_each_file
[START] [2023-01-05 17:28:43] convert_to_csv
[INFO] [2023-01-05 17:28:43] Looping over 3 formats...
[INFO] [2023-01-05 17:28:43] ...nodes (/app/public/data/yamano_et_al_yam/taxa.txt)
[CMD] [2023-01-05 17:28:43] /usr/bin/sort /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_nodes_29999.csv > /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_nodes_29999.csv_sorted
[INFO] [2023-01-05 17:28:43] Converted: /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_nodes_29999.csv (7 lines)
[INFO] [2023-01-05 17:28:43] ...occurrences (/app/public/data/yamano_et_al_yam/occurrences.txt)
[CMD] [2023-01-05 17:28:43] /usr/bin/sort /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_occurrences_30000.csv > /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_occurrences_30000.csv_sorted
[INFO] [2023-01-05 17:28:43] Converted: /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_occurrences_30000.csv (7 lines)
[INFO] [2023-01-05 17:28:43] ...measurements (/app/public/data/yamano_et_al_yam/measurementsorfacts.txt)
[CMD] [2023-01-05 17:28:43] /usr/bin/sort /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_measurements_30001.csv > /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_measurements_30001.csv_sorted
[INFO] [2023-01-05 17:28:43] Converted: /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_measurements_30001.csv (32 lines)
[STOP] [2023-01-05 17:28:43] convert_to_csv
[START] [2023-01-05 17:28:43] calculate_delta
[INFO] [2023-01-05 17:28:43] Looping over 3 formats...
[INFO] [2023-01-05 17:28:43] ...nodes (/app/public/data/yamano_et_al_yam/taxa.txt)
[CMD] [2023-01-05 17:28:43] echo "0a" > /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_nodes_29999.diff
[CMD] [2023-01-05 17:28:43] tail -n +1 /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_nodes_29999.csv >> /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_nodes_29999.diff
[CMD] [2023-01-05 17:28:43] echo "." >> /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_nodes_29999.diff
[INFO] [2023-01-05 17:28:43] Created diff: /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_nodes_29999.diff (9 lines)
[INFO] [2023-01-05 17:28:43] ...occurrences (/app/public/data/yamano_et_al_yam/occurrences.txt)
[CMD] [2023-01-05 17:28:43] echo "0a" > /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_occurrences_30000.diff
[CMD] [2023-01-05 17:28:43] tail -n +1 /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_occurrences_30000.csv >> /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_occurrences_30000.diff
[CMD] [2023-01-05 17:28:43] echo "." >> /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_occurrences_30000.diff
[INFO] [2023-01-05 17:28:43] Created diff: /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_occurrences_30000.diff (9 lines)
[INFO] [2023-01-05 17:28:43] ...measurements (/app/public/data/yamano_et_al_yam/measurementsorfacts.txt)
[CMD] [2023-01-05 17:28:43] echo "0a" > /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_measurements_30001.diff
[CMD] [2023-01-05 17:28:43] tail -n +1 /app/public/data/yamano_et_al_yam/converted_csv/yamano_et_al_yam_measurements_30001.csv >> /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_measurements_30001.diff
[CMD] [2023-01-05 17:28:43] echo "." >> /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_measurements_30001.diff
[INFO] [2023-01-05 17:28:43] Created diff: /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_measurements_30001.diff (34 lines)
[STOP] [2023-01-05 17:28:43] calculate_delta
[START] [2023-01-05 17:28:43] parse_diff_and_store
[INFO] [2023-01-05 17:28:43] Handling diff: /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_nodes_29999.diff (9 lines)
[INFO] [2023-01-05 17:28:43] Loading nodes diff file into memory (9 lines)...
[INFO] [2023-01-05 17:28:43] Storing 7 ScientificNames (14/7/9)
[INFO] [2023-01-05 17:28:43] Storing 7 Nodes (14/7/9)
[INFO] [2023-01-05 17:28:43] Handling diff: /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_occurrences_30000.diff (9 lines)
[INFO] [2023-01-05 17:28:44] Loading occurrences diff file into memory (9 lines)...
[INFO] [2023-01-05 17:28:45] Storing 7 Occurrences (14/7/9)
[INFO] [2023-01-05 17:28:45] Storing 7 OccurrenceMetadata (14/7/9)
[INFO] [2023-01-05 17:28:45] Handling diff: /app/public/data/yamano_et_al_yam/diff/yamano_et_al_yam_measurements_30001.diff (34 lines)
[INFO] [2023-01-05 17:28:45] Loading measurements diff file into memory (34 lines)...
[INFO] [2023-01-05 17:28:45] Storing 32 Traits (39/32/34)
[INFO] [2023-01-05 17:28:45] Storing 7 MetaTraits (39/32/34)
[STOP] [2023-01-05 17:28:45] parse_diff_and_store
[START] [2023-01-05 17:28:45] resolve_keys
[2023-01-05 17:28:45] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-01-05 17:28:53] Occurrences to nodes (through scientific_names)...
[INFO] [2023-01-05 17:28:53] traits to occurrences...
[INFO] [2023-01-05 17:28:53] traits to nodes (through occurrences)...
[INFO] [2023-01-05 17:28:53] Traits to sex term...
[INFO] [2023-01-05 17:28:53] Traits to lifestage term...
[INFO] [2023-01-05 17:28:53] MetaTraits to traits...
[INFO] [2023-01-05 17:28:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-01-05 17:28:53] Assocs to occurrences...
[INFO] [2023-01-05 17:28:53] Assocs to nodes...
[INFO] [2023-01-05 17:28:53] Assoc to sex term...
[INFO] [2023-01-05 17:28:53] Assoc to lifestage term...
[INFO] [2023-01-05 17:28:53] MetaAssoc to assocs...
[STOP] [2023-01-05 17:28:53] resolve_keys
[START] [2023-01-05 17:28:53] hold_for_later_1
[STOP] [2023-01-05 17:28:53] hold_for_later_1
[START] [2023-01-05 17:28:53] hold_for_later_2
[STOP] [2023-01-05 17:28:53] hold_for_later_2
[START] [2023-01-05 17:28:53] resolve_missing_parents
[STOP] [2023-01-05 17:28:53] resolve_missing_parents
[START] [2023-01-05 17:28:53] rebuild_nodes
[START] [2023-01-05 17:28:53] Flattener#flatten
[START] [2023-01-05 17:28:53] Flattener#study_resource
[START] [2023-01-05 17:28:53] Flattener#build_ancestry
[STOP] [2023-01-05 17:28:54] Flattener#build_ancestry
[INFO] [2023-01-05 17:28:54] 7 ancestry keys
[START] [2023-01-05 17:28:54] build_node_ancestors
[INFO] [2023-01-05 17:28:54] old ancestors deleted.
[STOP] [2023-01-05 17:28:54] build_node_ancestors
[WARN] [2023-01-05 17:28:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2023-01-05 17:28:54] Flattener#flatten
[STOP] [2023-01-05 17:28:54] rebuild_nodes
[START] [2023-01-05 17:28:54] resolve_missing_media_owners
[STOP] [2023-01-05 17:28:54] resolve_missing_media_owners
[START] [2023-01-05 17:28:54] sanitize_media_verbatims
[STOP] [2023-01-05 17:28:54] sanitize_media_verbatims
[START] [2023-01-05 17:28:54] queue_downloads
[STOP] [2023-01-05 17:28:54] queue_downloads
[START] [2023-01-05 17:28:54] parse_names
[WARN] [2023-01-05 17:28:54] I see 7 names which still need to be parsed.
[WARN] [2023-01-05 17:28:54] Names to parse: 7 formatted: 7 learned: 7 parsed: 7
[STOP] [2023-01-05 17:28:55] parse_names
[START] [2023-01-05 17:28:55] denormalize_canonical_names_to_nodes
[STOP] [2023-01-05 17:28:55] denormalize_canonical_names_to_nodes
[START] [2023-01-05 17:28:55] match_nodes
[START] [2023-01-05 17:28:55] map_all_nodes_to_pages
[STOP] [2023-01-05 17:28:55] map_all_nodes_to_pages
[INFO] [2023-01-05 17:28:55] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2023-01-05 17:28:55] update_nodes
[STOP] [2023-01-05 17:28:55] update_nodes
[STOP] [2023-01-05 17:28:55] match_nodes
[START] [2023-01-05 17:28:55] reindex_search
[STOP] [2023-01-05 17:28:55] reindex_search
[START] [2023-01-05 17:28:55] normalize_units
[STOP] [2023-01-05 17:28:55] normalize_units
[START] [2023-01-05 17:28:55] calculate_statistics
[2023-01-05 17:28:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2023-01-05 17:28:55] Duplicate page_id count: 0
[STOP] [2023-01-05 17:28:55] calculate_statistics
[START] [2023-01-05 17:28:55] complete_harvest_instance
[START] [2023-01-05 17:28:55] overall_tsv_creation
[INFO] [2023-01-05 17:28:55] Exporting 7 nodes as TSV in batches of 10000...
[INFO] [2023-01-05 17:28:55] Processing group of 7 in 1 batches of 10000
[INFO] [2023-01-05 17:28:56] 7 Traits (unfiltered) and 0 associations...
[INFO] [2023-01-05 17:28:56] Building Traits map for 7 nodes (this can take a while)...
[INFO] [2023-01-05 17:28:56] Mapped 7 traits (7 meta) for 7 nodes.
[INFO] [2023-01-05 17:28:56] Building Associations map (this can take a while)...
[INFO] [2023-01-05 17:28:56] Done. 0 assocs mapped (0 meta).
[INFO] [2023-01-05 17:28:56] Adding 7 traits...
[INFO] [2023-01-05 17:28:56] 25 metadata added.
[INFO] [2023-01-05 17:28:56] Adding 0 assocs...
[INFO] [2023-01-05 17:28:56] 0 metadata added.
[INFO] [2023-01-05 17:29:57] Processed 7/7 nodes
[INFO] [2023-01-05 17:29:57] Average Time: 61.48
[INFO] [2023-01-05 17:29:57] Total Time: 1m2s
[STOP] [2023-01-05 17:29:57] overall_tsv_creation
[INFO] [2023-01-05 17:29:57] Done. Check your files:
[INFO] [2023-01-05 17:29:57] (7 lines) /app/public/data/yamano_et_al_yam/publish_nodes.tsv
[INFO] [2023-01-05 17:29:57] (7 lines) /app/public/data/yamano_et_al_yam/publish_scientific_names.tsv
[INFO] [2023-01-05 17:29:57] (8 lines) /app/public/data/yamano_et_al_yam/publish_traits.tsv
[INFO] [2023-01-05 17:29:57] (26 lines) /app/public/data/yamano_et_al_yam/publish_metadata.tsv
[STOP] [2023-01-05 17:29:57] complete_harvest_instance
[START] [2023-01-05 17:29:57] completed
[STOP] [2023-01-05 17:29:57] completed
[STOP] [2023-01-05 17:29:57] logged process, took 74.04

Latest Process