Harvest for Hageman 2003 Created 03 Aug 16:52

Stage: completed
Fetched: 03 Aug 16:52
Validated: 03 Aug 16:52
Deltas Created 03 Aug 16:52
Units Normalized: 03 Aug 16:52
Ancestry Built: 03 Aug 16:52
Nodes Matched: 03 Aug 16:52
Names Parsed: 03 Aug 16:52
New Models Stored: 03 Aug 16:52
Indexed: 03 Aug 16:52
Completed: 03 Aug 16:55
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
[INFO] [2022-08-03 16:52:48] Created harvest instance #4182
[STOP] [2022-08-03 16:52:48] create_harvest_instance
[START] [2022-08-03 16:52:48] fetch_files
[STOP] [2022-08-03 16:52:48] fetch_files
[START] [2022-08-03 16:52:48] validate_each_file
[INFO] [2022-08-03 16:52:48] Looping over 3 formats...
[INFO] [2022-08-03 16:52:48] ...nodes (/app/public/data/hageman_hageman_/taxa.txt)
[INFO] [2022-08-03 16:52:48] Valid: /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__nodes_29612.csv (1 lines)
[INFO] [2022-08-03 16:52:48] ...occurrences (/app/public/data/hageman_hageman_/occurrences.txt)
[INFO] [2022-08-03 16:52:48] Valid: /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__occurrences_29613.csv (1 lines)
[INFO] [2022-08-03 16:52:48] ...measurements (/app/public/data/hageman_hageman_/measurementOrFact.txt)
[INFO] [2022-08-03 16:52:48] Valid: /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__measurements_29614.csv (2 lines)
[STOP] [2022-08-03 16:52:48] validate_each_file
[START] [2022-08-03 16:52:48] convert_to_csv
[INFO] [2022-08-03 16:52:48] Looping over 3 formats...
[INFO] [2022-08-03 16:52:48] ...nodes (/app/public/data/hageman_hageman_/taxa.txt)
[CMD] [2022-08-03 16:52:48] /usr/bin/sort /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__nodes_29612.csv > /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__nodes_29612.csv_sorted
[INFO] [2022-08-03 16:52:48] Converted: /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__nodes_29612.csv (1 lines)
[INFO] [2022-08-03 16:52:48] ...occurrences (/app/public/data/hageman_hageman_/occurrences.txt)
[CMD] [2022-08-03 16:52:48] /usr/bin/sort /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__occurrences_29613.csv > /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__occurrences_29613.csv_sorted
[INFO] [2022-08-03 16:52:48] Converted: /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__occurrences_29613.csv (1 lines)
[INFO] [2022-08-03 16:52:48] ...measurements (/app/public/data/hageman_hageman_/measurementOrFact.txt)
[CMD] [2022-08-03 16:52:48] /usr/bin/sort /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__measurements_29614.csv > /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__measurements_29614.csv_sorted
[INFO] [2022-08-03 16:52:48] Converted: /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__measurements_29614.csv (2 lines)
[STOP] [2022-08-03 16:52:48] convert_to_csv
[START] [2022-08-03 16:52:48] calculate_delta
[INFO] [2022-08-03 16:52:48] Looping over 3 formats...
[INFO] [2022-08-03 16:52:48] ...nodes (/app/public/data/hageman_hageman_/taxa.txt)
[CMD] [2022-08-03 16:52:48] echo "0a" > /app/public/data/hageman_hageman_/diff/hageman_hageman__nodes_29612.diff
[CMD] [2022-08-03 16:52:49] tail -n +1 /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__nodes_29612.csv >> /app/public/data/hageman_hageman_/diff/hageman_hageman__nodes_29612.diff
[CMD] [2022-08-03 16:52:49] echo "." >> /app/public/data/hageman_hageman_/diff/hageman_hageman__nodes_29612.diff
[INFO] [2022-08-03 16:52:49] Created diff: /app/public/data/hageman_hageman_/diff/hageman_hageman__nodes_29612.diff (3 lines)
[INFO] [2022-08-03 16:52:49] ...occurrences (/app/public/data/hageman_hageman_/occurrences.txt)
[CMD] [2022-08-03 16:52:49] echo "0a" > /app/public/data/hageman_hageman_/diff/hageman_hageman__occurrences_29613.diff
[CMD] [2022-08-03 16:52:49] tail -n +1 /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__occurrences_29613.csv >> /app/public/data/hageman_hageman_/diff/hageman_hageman__occurrences_29613.diff
[CMD] [2022-08-03 16:52:49] echo "." >> /app/public/data/hageman_hageman_/diff/hageman_hageman__occurrences_29613.diff
[INFO] [2022-08-03 16:52:49] Created diff: /app/public/data/hageman_hageman_/diff/hageman_hageman__occurrences_29613.diff (3 lines)
[INFO] [2022-08-03 16:52:49] ...measurements (/app/public/data/hageman_hageman_/measurementOrFact.txt)
[CMD] [2022-08-03 16:52:49] echo "0a" > /app/public/data/hageman_hageman_/diff/hageman_hageman__measurements_29614.diff
[CMD] [2022-08-03 16:52:49] tail -n +1 /app/public/data/hageman_hageman_/converted_csv/hageman_hageman__measurements_29614.csv >> /app/public/data/hageman_hageman_/diff/hageman_hageman__measurements_29614.diff
[CMD] [2022-08-03 16:52:49] echo "." >> /app/public/data/hageman_hageman_/diff/hageman_hageman__measurements_29614.diff
[INFO] [2022-08-03 16:52:49] Created diff: /app/public/data/hageman_hageman_/diff/hageman_hageman__measurements_29614.diff (4 lines)
[STOP] [2022-08-03 16:52:49] calculate_delta
[START] [2022-08-03 16:52:49] parse_diff_and_store
[INFO] [2022-08-03 16:52:49] Handling diff: /app/public/data/hageman_hageman_/diff/hageman_hageman__nodes_29612.diff (3 lines)
[INFO] [2022-08-03 16:52:49] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 16:52:49] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 16:52:49] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 16:52:49] Handling diff: /app/public/data/hageman_hageman_/diff/hageman_hageman__occurrences_29613.diff (3 lines)
[INFO] [2022-08-03 16:52:49] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 16:52:49] Storing 1 Occurrences (2/1/3)
[INFO] [2022-08-03 16:52:49] Storing 1 OccurrenceMetadata (2/1/3)
[INFO] [2022-08-03 16:52:49] Handling diff: /app/public/data/hageman_hageman_/diff/hageman_hageman__measurements_29614.diff (4 lines)
[INFO] [2022-08-03 16:52:49] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 16:52:49] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 16:52:49] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 16:52:49] parse_diff_and_store
[START] [2022-08-03 16:52:49] resolve_keys
[2022-08-03 16:52:49] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:52:56] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:52:56] traits to occurrences...
[INFO] [2022-08-03 16:52:56] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:52:56] Traits to sex term...
[INFO] [2022-08-03 16:52:56] Traits to lifestage term...
[INFO] [2022-08-03 16:52:56] MetaTraits to traits...
[INFO] [2022-08-03 16:52:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:52:56] Assocs to occurrences...
[INFO] [2022-08-03 16:52:56] Assocs to nodes...
[INFO] [2022-08-03 16:52:56] Assoc to sex term...
[INFO] [2022-08-03 16:52:56] Assoc to lifestage term...
[INFO] [2022-08-03 16:52:56] MetaAssoc to assocs...
[STOP] [2022-08-03 16:52:56] resolve_keys
[START] [2022-08-03 16:52:56] hold_for_later_1
[STOP] [2022-08-03 16:52:56] hold_for_later_1
[START] [2022-08-03 16:52:56] hold_for_later_2
[STOP] [2022-08-03 16:52:56] hold_for_later_2
[START] [2022-08-03 16:52:56] resolve_missing_parents
[STOP] [2022-08-03 16:52:56] resolve_missing_parents
[START] [2022-08-03 16:52:56] rebuild_nodes
[START] [2022-08-03 16:52:56] Flattener#flatten
[START] [2022-08-03 16:52:56] Flattener#study_resource
[START] [2022-08-03 16:52:56] Flattener#build_ancestry
[STOP] [2022-08-03 16:52:56] Flattener#build_ancestry
[INFO] [2022-08-03 16:52:56] 1 ancestry keys
[START] [2022-08-03 16:52:56] build_node_ancestors
[INFO] [2022-08-03 16:52:56] old ancestors deleted.
[STOP] [2022-08-03 16:52:56] build_node_ancestors
[WARN] [2022-08-03 16:52:56] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:52:56] Flattener#flatten
[STOP] [2022-08-03 16:52:56] rebuild_nodes
[START] [2022-08-03 16:52:56] resolve_missing_media_owners
[STOP] [2022-08-03 16:52:56] resolve_missing_media_owners
[START] [2022-08-03 16:52:56] sanitize_media_verbatims
[STOP] [2022-08-03 16:52:56] sanitize_media_verbatims
[START] [2022-08-03 16:52:56] queue_downloads
[STOP] [2022-08-03 16:52:56] queue_downloads
[START] [2022-08-03 16:52:56] parse_names
[WARN] [2022-08-03 16:52:56] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 16:52:56] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 16:52:57] parse_names
[START] [2022-08-03 16:52:57] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:52:57] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:52:57] match_nodes
[START] [2022-08-03 16:52:57] map_all_nodes_to_pages
[STOP] [2022-08-03 16:52:57] map_all_nodes_to_pages
[INFO] [2022-08-03 16:52:57] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 16:52:57] update_nodes
[STOP] [2022-08-03 16:52:57] update_nodes
[STOP] [2022-08-03 16:52:57] match_nodes
[START] [2022-08-03 16:52:57] reindex_search
[STOP] [2022-08-03 16:52:57] reindex_search
[START] [2022-08-03 16:52:57] normalize_units
[STOP] [2022-08-03 16:52:57] normalize_units
[START] [2022-08-03 16:52:57] calculate_statistics
[2022-08-03 16:52:57] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:52:57] Duplicate page_id count: 0
[STOP] [2022-08-03 16:52:57] calculate_statistics
[START] [2022-08-03 16:52:57] complete_harvest_instance
[START] [2022-08-03 16:52:57] overall_tsv_creation
[INFO] [2022-08-03 16:52:57] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:52:57] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 16:53:39] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:53:39] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 16:54:31] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 16:54:31] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:54:31] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:54:31] Adding 1 traits...
[INFO] [2022-08-03 16:54:31] 1 metadata added.
[INFO] [2022-08-03 16:54:31] Adding 0 assocs...
[INFO] [2022-08-03 16:54:31] 0 metadata added.
[INFO] [2022-08-03 16:55:13] Processed 1/1 nodes
[INFO] [2022-08-03 16:55:13] Average Time: 111.17
[INFO] [2022-08-03 16:55:13] Total Time: 2m17s
[STOP] [2022-08-03 16:55:13] overall_tsv_creation
[INFO] [2022-08-03 16:55:13] Done. Check your files:
[INFO] [2022-08-03 16:55:13] (1 lines) /app/public/data/hageman_hageman_/publish_nodes.tsv
[INFO] [2022-08-03 16:55:14] (1 lines) /app/public/data/hageman_hageman_/publish_scientific_names.tsv
[INFO] [2022-08-03 16:55:14] (2 lines) /app/public/data/hageman_hageman_/publish_traits.tsv
[INFO] [2022-08-03 16:55:14] (2 lines) /app/public/data/hageman_hageman_/publish_metadata.tsv
[STOP] [2022-08-03 16:55:14] complete_harvest_instance
[START] [2022-08-03 16:55:14] completed
[STOP] [2022-08-03 16:55:14] completed
[STOP] [2022-08-03 16:55:14] logged process, took 145.35
Latest Process

03 Aug 16:52 EXITED currently processing 0