Harvest for Necchi 2016 Created 03 Aug 16:40

Stage: completed
Fetched: 03 Aug 16:40
Validated: 03 Aug 16:40
Deltas Created 03 Aug 16:40
Units Normalized: 03 Aug 16:40
Ancestry Built: 03 Aug 16:40
Nodes Matched: 03 Aug 16:40
Names Parsed: 03 Aug 16:40
New Models Stored: 03 Aug 16:40
Indexed: 03 Aug 16:40
Completed: 03 Aug 16:42
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
[INFO] [2022-08-03 16:40:19] Created harvest instance #4176
[STOP] [2022-08-03 16:40:19] create_harvest_instance
[START] [2022-08-03 16:40:19] fetch_files
[STOP] [2022-08-03 16:40:19] fetch_files
[START] [2022-08-03 16:40:19] validate_each_file
[INFO] [2022-08-03 16:40:19] Looping over 3 formats...
[INFO] [2022-08-03 16:40:19] ...nodes (/app/public/data/necchi_necchi_20/taxa.txt)
[INFO] [2022-08-03 16:40:19] Valid: /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_nodes_29594.csv (63 lines)
[INFO] [2022-08-03 16:40:19] ...occurrences (/app/public/data/necchi_necchi_20/occurrences.txt)
[INFO] [2022-08-03 16:40:19] Valid: /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_occurrences_29595.csv (63 lines)
[INFO] [2022-08-03 16:40:19] ...measurements (/app/public/data/necchi_necchi_20/measurementOrFact.txt)
[INFO] [2022-08-03 16:40:19] Valid: /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_measurements_29596.csv (126 lines)
[STOP] [2022-08-03 16:40:19] validate_each_file
[START] [2022-08-03 16:40:19] convert_to_csv
[INFO] [2022-08-03 16:40:19] Looping over 3 formats...
[INFO] [2022-08-03 16:40:19] ...nodes (/app/public/data/necchi_necchi_20/taxa.txt)
[CMD] [2022-08-03 16:40:19] /usr/bin/sort /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_nodes_29594.csv > /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_nodes_29594.csv_sorted
[INFO] [2022-08-03 16:40:19] Converted: /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_nodes_29594.csv (63 lines)
[INFO] [2022-08-03 16:40:19] ...occurrences (/app/public/data/necchi_necchi_20/occurrences.txt)
[CMD] [2022-08-03 16:40:19] /usr/bin/sort /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_occurrences_29595.csv > /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_occurrences_29595.csv_sorted
[INFO] [2022-08-03 16:40:19] Converted: /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_occurrences_29595.csv (63 lines)
[INFO] [2022-08-03 16:40:19] ...measurements (/app/public/data/necchi_necchi_20/measurementOrFact.txt)
[CMD] [2022-08-03 16:40:19] /usr/bin/sort /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_measurements_29596.csv > /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_measurements_29596.csv_sorted
[INFO] [2022-08-03 16:40:19] Converted: /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_measurements_29596.csv (126 lines)
[STOP] [2022-08-03 16:40:19] convert_to_csv
[START] [2022-08-03 16:40:19] calculate_delta
[INFO] [2022-08-03 16:40:19] Looping over 3 formats...
[INFO] [2022-08-03 16:40:19] ...nodes (/app/public/data/necchi_necchi_20/taxa.txt)
[CMD] [2022-08-03 16:40:19] echo "0a" > /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_nodes_29594.diff
[CMD] [2022-08-03 16:40:19] tail -n +1 /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_nodes_29594.csv >> /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_nodes_29594.diff
[CMD] [2022-08-03 16:40:19] echo "." >> /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_nodes_29594.diff
[INFO] [2022-08-03 16:40:19] Created diff: /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_nodes_29594.diff (65 lines)
[INFO] [2022-08-03 16:40:19] ...occurrences (/app/public/data/necchi_necchi_20/occurrences.txt)
[CMD] [2022-08-03 16:40:19] echo "0a" > /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_occurrences_29595.diff
[CMD] [2022-08-03 16:40:19] tail -n +1 /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_occurrences_29595.csv >> /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_occurrences_29595.diff
[CMD] [2022-08-03 16:40:19] echo "." >> /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_occurrences_29595.diff
[INFO] [2022-08-03 16:40:19] Created diff: /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_occurrences_29595.diff (65 lines)
[INFO] [2022-08-03 16:40:19] ...measurements (/app/public/data/necchi_necchi_20/measurementOrFact.txt)
[CMD] [2022-08-03 16:40:19] echo "0a" > /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_measurements_29596.diff
[CMD] [2022-08-03 16:40:19] tail -n +1 /app/public/data/necchi_necchi_20/converted_csv/necchi_necchi_20_measurements_29596.csv >> /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_measurements_29596.diff
[CMD] [2022-08-03 16:40:19] echo "." >> /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_measurements_29596.diff
[INFO] [2022-08-03 16:40:19] Created diff: /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_measurements_29596.diff (128 lines)
[STOP] [2022-08-03 16:40:19] calculate_delta
[START] [2022-08-03 16:40:19] parse_diff_and_store
[INFO] [2022-08-03 16:40:19] Handling diff: /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_nodes_29594.diff (65 lines)
[INFO] [2022-08-03 16:40:19] Loading nodes diff file into memory (65 lines)...
[INFO] [2022-08-03 16:40:19] Storing 63 ScientificNames (126/63/65)
[INFO] [2022-08-03 16:40:19] Storing 63 Nodes (126/63/65)
[INFO] [2022-08-03 16:40:19] Handling diff: /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_occurrences_29595.diff (65 lines)
[INFO] [2022-08-03 16:40:19] Loading occurrences diff file into memory (65 lines)...
[INFO] [2022-08-03 16:40:19] Storing 63 Occurrences (63/63/65)
[INFO] [2022-08-03 16:40:19] Handling diff: /app/public/data/necchi_necchi_20/diff/necchi_necchi_20_measurements_29596.diff (128 lines)
[INFO] [2022-08-03 16:40:19] Loading measurements diff file into memory (128 lines)...
[INFO] [2022-08-03 16:40:19] Storing 126 Traits (197/126/128)
[INFO] [2022-08-03 16:40:19] Storing 71 MetaTraits (197/126/128)
[STOP] [2022-08-03 16:40:19] parse_diff_and_store
[START] [2022-08-03 16:40:19] resolve_keys
[2022-08-03 16:40:20] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 16:40:27] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 16:40:28] traits to occurrences...
[INFO] [2022-08-03 16:40:28] traits to nodes (through occurrences)...
[INFO] [2022-08-03 16:40:28] Traits to sex term...
[INFO] [2022-08-03 16:40:28] Traits to lifestage term...
[INFO] [2022-08-03 16:40:28] MetaTraits to traits...
[INFO] [2022-08-03 16:40:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 16:40:28] Assocs to occurrences...
[INFO] [2022-08-03 16:40:28] Assocs to nodes...
[INFO] [2022-08-03 16:40:28] Assoc to sex term...
[INFO] [2022-08-03 16:40:28] Assoc to lifestage term...
[INFO] [2022-08-03 16:40:28] MetaAssoc to assocs...
[STOP] [2022-08-03 16:40:28] resolve_keys
[START] [2022-08-03 16:40:28] hold_for_later_1
[STOP] [2022-08-03 16:40:28] hold_for_later_1
[START] [2022-08-03 16:40:28] hold_for_later_2
[STOP] [2022-08-03 16:40:28] hold_for_later_2
[START] [2022-08-03 16:40:28] resolve_missing_parents
[STOP] [2022-08-03 16:40:28] resolve_missing_parents
[START] [2022-08-03 16:40:28] rebuild_nodes
[START] [2022-08-03 16:40:28] Flattener#flatten
[START] [2022-08-03 16:40:28] Flattener#study_resource
[START] [2022-08-03 16:40:28] Flattener#build_ancestry
[STOP] [2022-08-03 16:40:28] Flattener#build_ancestry
[INFO] [2022-08-03 16:40:28] 63 ancestry keys
[START] [2022-08-03 16:40:28] build_node_ancestors
[INFO] [2022-08-03 16:40:28] old ancestors deleted.
[STOP] [2022-08-03 16:40:28] build_node_ancestors
[WARN] [2022-08-03 16:40:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 16:40:28] Flattener#flatten
[STOP] [2022-08-03 16:40:28] rebuild_nodes
[START] [2022-08-03 16:40:28] resolve_missing_media_owners
[STOP] [2022-08-03 16:40:28] resolve_missing_media_owners
[START] [2022-08-03 16:40:28] sanitize_media_verbatims
[STOP] [2022-08-03 16:40:28] sanitize_media_verbatims
[START] [2022-08-03 16:40:28] queue_downloads
[STOP] [2022-08-03 16:40:28] queue_downloads
[START] [2022-08-03 16:40:28] parse_names
[WARN] [2022-08-03 16:40:28] I see 63 names which still need to be parsed.
[WARN] [2022-08-03 16:40:28] Names to parse: 63 formatted: 63 learned: 63 parsed: 63
[STOP] [2022-08-03 16:40:29] parse_names
[START] [2022-08-03 16:40:29] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 16:40:29] denormalize_canonical_names_to_nodes
[START] [2022-08-03 16:40:29] match_nodes
[START] [2022-08-03 16:40:29] map_all_nodes_to_pages
[STOP] [2022-08-03 16:40:29] map_all_nodes_to_pages
[INFO] [2022-08-03 16:40:29] ZERO unmatched nodes (of 63)! Nicely done.
[START] [2022-08-03 16:40:29] update_nodes
[STOP] [2022-08-03 16:40:29] update_nodes
[STOP] [2022-08-03 16:40:29] match_nodes
[START] [2022-08-03 16:40:29] reindex_search
[STOP] [2022-08-03 16:40:29] reindex_search
[START] [2022-08-03 16:40:29] normalize_units
[STOP] [2022-08-03 16:40:29] normalize_units
[START] [2022-08-03 16:40:29] calculate_statistics
[2022-08-03 16:40:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 16:40:33] Duplicate page_id count: 0
[STOP] [2022-08-03 16:40:33] calculate_statistics
[START] [2022-08-03 16:40:33] complete_harvest_instance
[START] [2022-08-03 16:40:33] overall_tsv_creation
[INFO] [2022-08-03 16:40:33] Exporting 63 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 16:40:33] Processing group of 63 in 1 batches of 10000
[INFO] [2022-08-03 16:41:16] 63 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 16:41:16] Building Traits map for 63 nodes (this can take a while)...
[INFO] [2022-08-03 16:42:08] Mapped 63 traits (71 meta) for 63 nodes.
[INFO] [2022-08-03 16:42:08] Building Associations map (this can take a while)...
[INFO] [2022-08-03 16:42:08] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 16:42:08] Adding 63 traits...
[INFO] [2022-08-03 16:42:08] 63 metadata added.
[INFO] [2022-08-03 16:42:08] Adding 0 assocs...
[INFO] [2022-08-03 16:42:08] 0 metadata added.
[INFO] [2022-08-03 16:42:50] Processed 63/63 nodes
[INFO] [2022-08-03 16:42:50] Average Time: 111.7
[INFO] [2022-08-03 16:42:50] Total Time: 2m17s
[STOP] [2022-08-03 16:42:50] overall_tsv_creation
[INFO] [2022-08-03 16:42:50] Done. Check your files:
[INFO] [2022-08-03 16:42:50] (63 lines) /app/public/data/necchi_necchi_20/publish_nodes.tsv
[INFO] [2022-08-03 16:42:50] (63 lines) /app/public/data/necchi_necchi_20/publish_scientific_names.tsv
[INFO] [2022-08-03 16:42:50] (64 lines) /app/public/data/necchi_necchi_20/publish_traits.tsv
[INFO] [2022-08-03 16:42:50] (64 lines) /app/public/data/necchi_necchi_20/publish_metadata.tsv
[STOP] [2022-08-03 16:42:50] complete_harvest_instance
[START] [2022-08-03 16:42:50] completed
[STOP] [2022-08-03 16:42:50] completed
[STOP] [2022-08-03 16:42:50] logged process, took 151.47
Latest Process

03 Aug 16:40 EXITED currently processing 0