Harvest for Grabowsky 1994b Created 03 Aug 17:15

Stage: completed
Fetched: 03 Aug 17:15
Validated: 03 Aug 17:15
Deltas Created 03 Aug 17:15
Units Normalized: 03 Aug 17:15
Ancestry Built: 03 Aug 17:15
Nodes Matched: 03 Aug 17:15
Names Parsed: 03 Aug 17:15
New Models Stored: 03 Aug 17:15
Indexed: 03 Aug 17:15
Completed: 03 Aug 17:18
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 17:15:45] Created harvest instance #4194
[STOP] [2022-08-03 17:15:45] create_harvest_instance
[START] [2022-08-03 17:15:45] fetch_files
[STOP] [2022-08-03 17:15:45] fetch_files
[START] [2022-08-03 17:15:45] validate_each_file
[INFO] [2022-08-03 17:15:45] Looping over 3 formats...
[INFO] [2022-08-03 17:15:45] ...nodes (/app/public/data/grabowsky_1994b/taxa.txt)
[INFO] [2022-08-03 17:15:45] Valid: /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_nodes_29644.csv (5 lines)
[INFO] [2022-08-03 17:15:45] ...occurrences (/app/public/data/grabowsky_1994b/occurrences.txt)
[INFO] [2022-08-03 17:15:45] Valid: /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_occurrences_29645.csv (5 lines)
[INFO] [2022-08-03 17:15:45] ...measurements (/app/public/data/grabowsky_1994b/measurementOrFact.txt)
[INFO] [2022-08-03 17:15:45] Valid: /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_measurements_29646.csv (9 lines)
[STOP] [2022-08-03 17:15:45] validate_each_file
[START] [2022-08-03 17:15:45] convert_to_csv
[INFO] [2022-08-03 17:15:45] Looping over 3 formats...
[INFO] [2022-08-03 17:15:45] ...nodes (/app/public/data/grabowsky_1994b/taxa.txt)
[CMD] [2022-08-03 17:15:45] /usr/bin/sort /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_nodes_29644.csv > /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_nodes_29644.csv_sorted
[INFO] [2022-08-03 17:15:45] Converted: /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_nodes_29644.csv (5 lines)
[INFO] [2022-08-03 17:15:45] ...occurrences (/app/public/data/grabowsky_1994b/occurrences.txt)
[CMD] [2022-08-03 17:15:45] /usr/bin/sort /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_occurrences_29645.csv > /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_occurrences_29645.csv_sorted
[INFO] [2022-08-03 17:15:45] Converted: /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_occurrences_29645.csv (5 lines)
[INFO] [2022-08-03 17:15:45] ...measurements (/app/public/data/grabowsky_1994b/measurementOrFact.txt)
[CMD] [2022-08-03 17:15:45] /usr/bin/sort /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_measurements_29646.csv > /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_measurements_29646.csv_sorted
[INFO] [2022-08-03 17:15:45] Converted: /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_measurements_29646.csv (9 lines)
[STOP] [2022-08-03 17:15:45] convert_to_csv
[START] [2022-08-03 17:15:45] calculate_delta
[INFO] [2022-08-03 17:15:45] Looping over 3 formats...
[INFO] [2022-08-03 17:15:45] ...nodes (/app/public/data/grabowsky_1994b/taxa.txt)
[CMD] [2022-08-03 17:15:45] echo "0a" > /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_nodes_29644.diff
[CMD] [2022-08-03 17:15:45] tail -n +1 /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_nodes_29644.csv >> /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_nodes_29644.diff
[CMD] [2022-08-03 17:15:45] echo "." >> /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_nodes_29644.diff
[INFO] [2022-08-03 17:15:45] Created diff: /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_nodes_29644.diff (7 lines)
[INFO] [2022-08-03 17:15:45] ...occurrences (/app/public/data/grabowsky_1994b/occurrences.txt)
[CMD] [2022-08-03 17:15:45] echo "0a" > /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_occurrences_29645.diff
[CMD] [2022-08-03 17:15:45] tail -n +1 /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_occurrences_29645.csv >> /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_occurrences_29645.diff
[CMD] [2022-08-03 17:15:45] echo "." >> /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_occurrences_29645.diff
[INFO] [2022-08-03 17:15:45] Created diff: /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_occurrences_29645.diff (7 lines)
[INFO] [2022-08-03 17:15:45] ...measurements (/app/public/data/grabowsky_1994b/measurementOrFact.txt)
[CMD] [2022-08-03 17:15:45] echo "0a" > /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_measurements_29646.diff
[CMD] [2022-08-03 17:15:45] tail -n +1 /app/public/data/grabowsky_1994b/converted_csv/grabowsky_1994b_measurements_29646.csv >> /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_measurements_29646.diff
[CMD] [2022-08-03 17:15:45] echo "." >> /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_measurements_29646.diff
[INFO] [2022-08-03 17:15:45] Created diff: /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_measurements_29646.diff (11 lines)
[STOP] [2022-08-03 17:15:45] calculate_delta
[START] [2022-08-03 17:15:45] parse_diff_and_store
[INFO] [2022-08-03 17:15:45] Handling diff: /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_nodes_29644.diff (7 lines)
[INFO] [2022-08-03 17:15:46] Loading nodes diff file into memory (7 lines)...
[INFO] [2022-08-03 17:15:46] Storing 5 ScientificNames (10/5/7)
[INFO] [2022-08-03 17:15:46] Storing 5 Nodes (10/5/7)
[INFO] [2022-08-03 17:15:46] Handling diff: /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_occurrences_29645.diff (7 lines)
[INFO] [2022-08-03 17:15:46] Loading occurrences diff file into memory (7 lines)...
[INFO] [2022-08-03 17:15:46] Storing 5 Occurrences (5/5/7)
[INFO] [2022-08-03 17:15:46] Handling diff: /app/public/data/grabowsky_1994b/diff/grabowsky_1994b_measurements_29646.diff (11 lines)
[INFO] [2022-08-03 17:15:46] Loading measurements diff file into memory (11 lines)...
[INFO] [2022-08-03 17:15:46] Storing 9 Traits (14/9/11)
[INFO] [2022-08-03 17:15:46] Storing 5 MetaTraits (14/9/11)
[STOP] [2022-08-03 17:15:46] parse_diff_and_store
[START] [2022-08-03 17:15:46] resolve_keys
[2022-08-03 17:15:46] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 17:15:53] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 17:15:53] traits to occurrences...
[INFO] [2022-08-03 17:15:53] traits to nodes (through occurrences)...
[INFO] [2022-08-03 17:15:53] Traits to sex term...
[INFO] [2022-08-03 17:15:53] Traits to lifestage term...
[INFO] [2022-08-03 17:15:53] MetaTraits to traits...
[INFO] [2022-08-03 17:15:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 17:15:53] Assocs to occurrences...
[INFO] [2022-08-03 17:15:53] Assocs to nodes...
[INFO] [2022-08-03 17:15:53] Assoc to sex term...
[INFO] [2022-08-03 17:15:53] Assoc to lifestage term...
[INFO] [2022-08-03 17:15:53] MetaAssoc to assocs...
[STOP] [2022-08-03 17:15:53] resolve_keys
[START] [2022-08-03 17:15:53] hold_for_later_1
[STOP] [2022-08-03 17:15:53] hold_for_later_1
[START] [2022-08-03 17:15:53] hold_for_later_2
[STOP] [2022-08-03 17:15:53] hold_for_later_2
[START] [2022-08-03 17:15:53] resolve_missing_parents
[STOP] [2022-08-03 17:15:53] resolve_missing_parents
[START] [2022-08-03 17:15:53] rebuild_nodes
[START] [2022-08-03 17:15:53] Flattener#flatten
[START] [2022-08-03 17:15:53] Flattener#study_resource
[START] [2022-08-03 17:15:53] Flattener#build_ancestry
[STOP] [2022-08-03 17:15:53] Flattener#build_ancestry
[INFO] [2022-08-03 17:15:53] 5 ancestry keys
[START] [2022-08-03 17:15:53] build_node_ancestors
[INFO] [2022-08-03 17:15:53] old ancestors deleted.
[STOP] [2022-08-03 17:15:53] build_node_ancestors
[WARN] [2022-08-03 17:15:53] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 17:15:53] Flattener#flatten
[STOP] [2022-08-03 17:15:53] rebuild_nodes
[START] [2022-08-03 17:15:53] resolve_missing_media_owners
[STOP] [2022-08-03 17:15:53] resolve_missing_media_owners
[START] [2022-08-03 17:15:53] sanitize_media_verbatims
[STOP] [2022-08-03 17:15:53] sanitize_media_verbatims
[START] [2022-08-03 17:15:53] queue_downloads
[STOP] [2022-08-03 17:15:53] queue_downloads
[START] [2022-08-03 17:15:53] parse_names
[WARN] [2022-08-03 17:15:53] I see 5 names which still need to be parsed.
[WARN] [2022-08-03 17:15:53] Names to parse: 5 formatted: 5 learned: 5 parsed: 5
[STOP] [2022-08-03 17:15:54] parse_names
[START] [2022-08-03 17:15:54] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 17:15:54] denormalize_canonical_names_to_nodes
[START] [2022-08-03 17:15:54] match_nodes
[START] [2022-08-03 17:15:54] map_all_nodes_to_pages
[STOP] [2022-08-03 17:15:54] map_all_nodes_to_pages
[INFO] [2022-08-03 17:15:54] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2022-08-03 17:15:54] update_nodes
[STOP] [2022-08-03 17:15:54] update_nodes
[STOP] [2022-08-03 17:15:54] match_nodes
[START] [2022-08-03 17:15:54] reindex_search
[STOP] [2022-08-03 17:15:54] reindex_search
[START] [2022-08-03 17:15:54] normalize_units
[STOP] [2022-08-03 17:15:54] normalize_units
[START] [2022-08-03 17:15:54] calculate_statistics
[2022-08-03 17:15:54] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 17:15:54] Duplicate page_id count: 0
[STOP] [2022-08-03 17:15:54] calculate_statistics
[START] [2022-08-03 17:15:54] complete_harvest_instance
[START] [2022-08-03 17:15:54] overall_tsv_creation
[INFO] [2022-08-03 17:15:54] Exporting 5 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 17:15:54] Processing group of 5 in 1 batches of 10000
[INFO] [2022-08-03 17:16:36] 5 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 17:16:36] Building Traits map for 5 nodes (this can take a while)...
[INFO] [2022-08-03 17:17:31] Mapped 5 traits (5 meta) for 5 nodes.
[INFO] [2022-08-03 17:17:31] Building Associations map (this can take a while)...
[INFO] [2022-08-03 17:17:31] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 17:17:31] Adding 5 traits...
[INFO] [2022-08-03 17:17:31] 4 metadata added.
[INFO] [2022-08-03 17:17:31] Adding 0 assocs...
[INFO] [2022-08-03 17:17:31] 0 metadata added.
[INFO] [2022-08-03 17:18:13] Processed 5/5 nodes
[INFO] [2022-08-03 17:18:13] Average Time: 113.45
[INFO] [2022-08-03 17:18:13] Total Time: 2m19s
[STOP] [2022-08-03 17:18:13] overall_tsv_creation
[INFO] [2022-08-03 17:18:13] Done. Check your files:
[INFO] [2022-08-03 17:18:13] (5 lines) /app/public/data/grabowsky_1994b/publish_nodes.tsv
[INFO] [2022-08-03 17:18:13] (5 lines) /app/public/data/grabowsky_1994b/publish_scientific_names.tsv
[INFO] [2022-08-03 17:18:13] (6 lines) /app/public/data/grabowsky_1994b/publish_traits.tsv
[INFO] [2022-08-03 17:18:13] (5 lines) /app/public/data/grabowsky_1994b/publish_metadata.tsv
[STOP] [2022-08-03 17:18:13] complete_harvest_instance
[START] [2022-08-03 17:18:13] completed
[STOP] [2022-08-03 17:18:13] completed
[STOP] [2022-08-03 17:18:13] logged process, took 147.89
Latest Process

03 Aug 17:15 EXITED currently processing 0