Harvest for Ryland 1997 Created 03 Aug 16:57

Stage: completed
Fetched: 03 Aug 16:57
Validated: 03 Aug 16:57
Deltas Created 03 Aug 16:57
Units Normalized: 03 Aug 16:57
Ancestry Built: 03 Aug 16:57
Nodes Matched: 03 Aug 16:57
Names Parsed: 03 Aug 16:57
New Models Stored: 03 Aug 16:57
Indexed: 03 Aug 16:57
Completed: 03 Aug 17:00
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:57:36] Created harvest instance #4184
[STOP] [2022-08-03 16:57:36] create_harvest_instance
[START] [2022-08-03 16:57:36] fetch_files
[STOP] [2022-08-03 16:57:36] fetch_files
[START] [2022-08-03 16:57:36] validate_each_file
[INFO] [2022-08-03 16:57:36] Looping over 3 formats...
[INFO] [2022-08-03 16:57:36] ...nodes (/app/public/data/ryland_ryland_19/taxa.txt)
[INFO] [2022-08-03 16:57:37] Valid: /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_nodes_29618.csv (1 lines)
[INFO] [2022-08-03 16:57:37] ...occurrences (/app/public/data/ryland_ryland_19/occurrences.txt)
[INFO] [2022-08-03 16:57:37] Valid: /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_occurrences_29619.csv (1 lines)
[INFO] [2022-08-03 16:57:37] ...measurements (/app/public/data/ryland_ryland_19/measurementOrFact.txt)
[INFO] [2022-08-03 16:57:37] Valid: /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_measurements_29620.csv (2 lines)
[STOP] [2022-08-03 16:57:37] validate_each_file
[START] [2022-08-03 16:57:37] convert_to_csv
[INFO] [2022-08-03 16:57:37] Looping over 3 formats...
[INFO] [2022-08-03 16:57:37] ...nodes (/app/public/data/ryland_ryland_19/taxa.txt)
[CMD] [2022-08-03 16:57:37] /usr/bin/sort /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_nodes_29618.csv > /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_nodes_29618.csv_sorted
[INFO] [2022-08-03 16:57:37] Converted: /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_nodes_29618.csv (1 lines)
[INFO] [2022-08-03 16:57:37] ...occurrences (/app/public/data/ryland_ryland_19/occurrences.txt)
[CMD] [2022-08-03 16:57:37] /usr/bin/sort /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_occurrences_29619.csv > /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_occurrences_29619.csv_sorted
[INFO] [2022-08-03 16:57:37] Converted: /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_occurrences_29619.csv (1 lines)
[INFO] [2022-08-03 16:57:37] ...measurements (/app/public/data/ryland_ryland_19/measurementOrFact.txt)
[CMD] [2022-08-03 16:57:37] /usr/bin/sort /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_measurements_29620.csv > /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_measurements_29620.csv_sorted
[INFO] [2022-08-03 16:57:37] Converted: /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_measurements_29620.csv (2 lines)
[STOP] [2022-08-03 16:57:37] convert_to_csv
[START] [2022-08-03 16:57:37] calculate_delta
[INFO] [2022-08-03 16:57:37] Looping over 3 formats...
[INFO] [2022-08-03 16:57:37] ...nodes (/app/public/data/ryland_ryland_19/taxa.txt)
[CMD] [2022-08-03 16:57:37] echo "0a" > /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_nodes_29618.diff
[CMD] [2022-08-03 16:57:38] tail -n +1 /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_nodes_29618.csv >> /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_nodes_29618.diff
[CMD] [2022-08-03 16:57:38] echo "." >> /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_nodes_29618.diff
[INFO] [2022-08-03 16:57:38] Created diff: /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_nodes_29618.diff (3 lines)
[INFO] [2022-08-03 16:57:38] ...occurrences (/app/public/data/ryland_ryland_19/occurrences.txt)
[CMD] [2022-08-03 16:57:38] echo "0a" > /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_occurrences_29619.diff
[CMD] [2022-08-03 16:57:38] tail -n +1 /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_occurrences_29619.csv >> /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_occurrences_29619.diff
[CMD] [2022-08-03 16:57:38] echo "." >> /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_occurrences_29619.diff
[INFO] [2022-08-03 16:57:38] Created diff: /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_occurrences_29619.diff (3 lines)
[INFO] [2022-08-03 16:57:38] ...measurements (/app/public/data/ryland_ryland_19/measurementOrFact.txt)
[CMD] [2022-08-03 16:57:38] echo "0a" > /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_measurements_29620.diff
[CMD] [2022-08-03 16:57:38] tail -n +1 /app/public/data/ryland_ryland_19/converted_csv/ryland_ryland_19_measurements_29620.csv >> /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_measurements_29620.diff
[CMD] [2022-08-03 16:57:38] echo "." >> /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_measurements_29620.diff
[INFO] [2022-08-03 16:57:38] Created diff: /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_measurements_29620.diff (4 lines)
[STOP] [2022-08-03 16:57:38] calculate_delta
[START] [2022-08-03 16:57:38] parse_diff_and_store
[INFO] [2022-08-03 16:57:38] Handling diff: /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_nodes_29618.diff (3 lines)
[INFO] [2022-08-03 16:57:38] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:57:38] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:57:38] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:57:38] Handling diff: /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_occurrences_29619.diff (3 lines)
[INFO] [2022-08-03 16:57:38] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:57:38] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 16:57:38] Handling diff: /app/public/data/ryland_ryland_19/diff/ryland_ryland_19_measurements_29620.diff (4 lines)
[INFO] [2022-08-03 16:57:38] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:57:38] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:57:38] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:57:38] parse_diff_and_store
[START] [2022-08-03 16:57:38] resolve_keys
[2022-08-03 16:57:38] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:57:45] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:57:45] traits to occurrences...
[INFO] [2022-08-03 16:57:45] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:57:45] Traits to sex term...
[INFO] [2022-08-03 16:57:45] Traits to lifestage term...
[INFO] [2022-08-03 16:57:45] MetaTraits to traits...
[INFO] [2022-08-03 16:57:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:57:45] Assocs to occurrences...
[INFO] [2022-08-03 16:57:45] Assocs to nodes...
[INFO] [2022-08-03 16:57:45] Assoc to sex term...
[INFO] [2022-08-03 16:57:45] Assoc to lifestage term...
[INFO] [2022-08-03 16:57:45] MetaAssoc to assocs...
[STOP] [2022-08-03 16:57:45] resolve_keys
[START] [2022-08-03 16:57:45] hold_for_later_1
[STOP] [2022-08-03 16:57:45] hold_for_later_1
[START] [2022-08-03 16:57:45] hold_for_later_2
[STOP] [2022-08-03 16:57:45] hold_for_later_2
[START] [2022-08-03 16:57:45] resolve_missing_parents
[STOP] [2022-08-03 16:57:45] resolve_missing_parents
[START] [2022-08-03 16:57:45] rebuild_nodes
[START] [2022-08-03 16:57:45] Flattener#flatten
[START] [2022-08-03 16:57:45] Flattener#study_resource
[START] [2022-08-03 16:57:45] Flattener#build_ancestry
[STOP] [2022-08-03 16:57:45] Flattener#build_ancestry
[INFO] [2022-08-03 16:57:45] 1 ancestry keys
[START] [2022-08-03 16:57:45] build_node_ancestors
[INFO] [2022-08-03 16:57:45] old ancestors deleted.
[STOP] [2022-08-03 16:57:45] build_node_ancestors
[WARN] [2022-08-03 16:57:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:57:45] Flattener#flatten
[STOP] [2022-08-03 16:57:45] rebuild_nodes
[START] [2022-08-03 16:57:45] resolve_missing_media_owners
[STOP] [2022-08-03 16:57:45] resolve_missing_media_owners
[START] [2022-08-03 16:57:45] sanitize_media_verbatims
[STOP] [2022-08-03 16:57:45] sanitize_media_verbatims
[START] [2022-08-03 16:57:45] queue_downloads
[STOP] [2022-08-03 16:57:45] queue_downloads
[START] [2022-08-03 16:57:45] parse_names
[WARN] [2022-08-03 16:57:45] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:57:45] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:57:46] parse_names
[START] [2022-08-03 16:57:46] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:57:46] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:57:46] match_nodes
[START] [2022-08-03 16:57:46] map_all_nodes_to_pages
[STOP] [2022-08-03 16:57:46] map_all_nodes_to_pages
[INFO] [2022-08-03 16:57:46] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:57:46] update_nodes
[STOP] [2022-08-03 16:57:46] update_nodes
[STOP] [2022-08-03 16:57:46] match_nodes
[START] [2022-08-03 16:57:46] reindex_search
[STOP] [2022-08-03 16:57:46] reindex_search
[START] [2022-08-03 16:57:46] normalize_units
[STOP] [2022-08-03 16:57:46] normalize_units
[START] [2022-08-03 16:57:46] calculate_statistics
[2022-08-03 16:57:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:57:46] Duplicate page_id count: 0
[STOP] [2022-08-03 16:57:46] calculate_statistics
[START] [2022-08-03 16:57:46] complete_harvest_instance
[START] [2022-08-03 16:57:46] overall_tsv_creation
[INFO] [2022-08-03 16:57:46] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:57:46] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:58:28] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:58:28] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:59:19] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:59:19] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:59:19] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:59:19] Adding 1 traits...
[INFO] [2022-08-03 16:59:19] 1 metadata added.
[INFO] [2022-08-03 16:59:19] Adding 0 assocs...
[INFO] [2022-08-03 16:59:19] 0 metadata added.
[INFO] [2022-08-03 17:00:03] Processed 1/1 nodes
[INFO] [2022-08-03 17:00:03] Average Time: 111.15
[INFO] [2022-08-03 17:00:03] Total Time: 2m17s
[STOP] [2022-08-03 17:00:03] overall_tsv_creation
[INFO] [2022-08-03 17:00:03] Done. Check your files:
[INFO] [2022-08-03 17:00:03] (1 lines) /app/public/data/ryland_ryland_19/publish_nodes.tsv
[INFO] [2022-08-03 17:00:03] (1 lines) /app/public/data/ryland_ryland_19/publish_scientific_names.tsv
[INFO] [2022-08-03 17:00:03] (2 lines) /app/public/data/ryland_ryland_19/publish_traits.tsv
[INFO] [2022-08-03 17:00:03] (2 lines) /app/public/data/ryland_ryland_19/publish_metadata.tsv
[STOP] [2022-08-03 17:00:03] complete_harvest_instance
[START] [2022-08-03 17:00:03] completed
[STOP] [2022-08-03 17:00:03] completed
[STOP] [2022-08-03 17:00:03] logged process, took 146.26
Latest Process

03 Aug 16:57 EXITED currently processing 0