Harvest for Body length data for North American Syrphidae, Tabanidae Created 30 Dec 10:40

Stage: completed
Fetched: 30 Dec 10:40
Validated: 30 Dec 10:40
Deltas Created 30 Dec 10:40
Units Normalized: 30 Dec 10:41
Ancestry Built: 30 Dec 10:40
Nodes Matched: 30 Dec 10:41
Names Parsed: 30 Dec 10:40
New Models Stored: 30 Dec 10:40
Indexed: 30 Dec 10:41
Completed: 30 Dec 10:41
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2022-12-30 10:40:44] Created harvest instance #4249
[STOP] [2022-12-30 10:40:44] create_harvest_instance
[START] [2022-12-30 10:40:44] fetch_files
[STOP] [2022-12-30 10:40:44] fetch_files
[START] [2022-12-30 10:40:44] validate_each_file
[INFO] [2022-12-30 10:40:44] Looping over 3 formats...
[INFO] [2022-12-30 10:40:44] ...nodes (/app/public/data/bldnas/taxon.tab)
[INFO] [2022-12-30 10:40:44] Valid: /app/public/data/bldnas/converted_csv/bldnas_nodes_29993.csv (325 lines)
[INFO] [2022-12-30 10:40:44] ...occurrences (/app/public/data/bldnas/occurrence_specific.tab)
[INFO] [2022-12-30 10:40:44] Valid: /app/public/data/bldnas/converted_csv/bldnas_occurrences_29994.csv (644 lines)
[INFO] [2022-12-30 10:40:44] ...measurements (/app/public/data/bldnas/measurement_or_fact_specific.tab)
[INFO] [2022-12-30 10:40:45] Valid: /app/public/data/bldnas/converted_csv/bldnas_measurements_29995.csv (644 lines)
[STOP] [2022-12-30 10:40:45] validate_each_file
[START] [2022-12-30 10:40:45] convert_to_csv
[INFO] [2022-12-30 10:40:45] Looping over 3 formats...
[INFO] [2022-12-30 10:40:45] ...nodes (/app/public/data/bldnas/taxon.tab)
[CMD] [2022-12-30 10:40:45] /usr/bin/sort /app/public/data/bldnas/converted_csv/bldnas_nodes_29993.csv > /app/public/data/bldnas/converted_csv/bldnas_nodes_29993.csv_sorted
[INFO] [2022-12-30 10:40:45] Converted: /app/public/data/bldnas/converted_csv/bldnas_nodes_29993.csv (325 lines)
[INFO] [2022-12-30 10:40:45] ...occurrences (/app/public/data/bldnas/occurrence_specific.tab)
[CMD] [2022-12-30 10:40:45] /usr/bin/sort /app/public/data/bldnas/converted_csv/bldnas_occurrences_29994.csv > /app/public/data/bldnas/converted_csv/bldnas_occurrences_29994.csv_sorted
[INFO] [2022-12-30 10:40:45] Converted: /app/public/data/bldnas/converted_csv/bldnas_occurrences_29994.csv (644 lines)
[INFO] [2022-12-30 10:40:45] ...measurements (/app/public/data/bldnas/measurement_or_fact_specific.tab)
[CMD] [2022-12-30 10:40:45] /usr/bin/sort /app/public/data/bldnas/converted_csv/bldnas_measurements_29995.csv > /app/public/data/bldnas/converted_csv/bldnas_measurements_29995.csv_sorted
[INFO] [2022-12-30 10:40:45] Converted: /app/public/data/bldnas/converted_csv/bldnas_measurements_29995.csv (644 lines)
[STOP] [2022-12-30 10:40:45] convert_to_csv
[START] [2022-12-30 10:40:45] calculate_delta
[INFO] [2022-12-30 10:40:45] Looping over 3 formats...
[INFO] [2022-12-30 10:40:45] ...nodes (/app/public/data/bldnas/taxon.tab)
[CMD] [2022-12-30 10:40:45] echo "0a" > /app/public/data/bldnas/diff/bldnas_nodes_29993.diff
[CMD] [2022-12-30 10:40:45] tail -n +1 /app/public/data/bldnas/converted_csv/bldnas_nodes_29993.csv >> /app/public/data/bldnas/diff/bldnas_nodes_29993.diff
[CMD] [2022-12-30 10:40:45] echo "." >> /app/public/data/bldnas/diff/bldnas_nodes_29993.diff
[INFO] [2022-12-30 10:40:46] Created diff: /app/public/data/bldnas/diff/bldnas_nodes_29993.diff (327 lines)
[INFO] [2022-12-30 10:40:46] ...occurrences (/app/public/data/bldnas/occurrence_specific.tab)
[CMD] [2022-12-30 10:40:46] echo "0a" > /app/public/data/bldnas/diff/bldnas_occurrences_29994.diff
[CMD] [2022-12-30 10:40:46] tail -n +1 /app/public/data/bldnas/converted_csv/bldnas_occurrences_29994.csv >> /app/public/data/bldnas/diff/bldnas_occurrences_29994.diff
[CMD] [2022-12-30 10:40:46] echo "." >> /app/public/data/bldnas/diff/bldnas_occurrences_29994.diff
[INFO] [2022-12-30 10:40:46] Created diff: /app/public/data/bldnas/diff/bldnas_occurrences_29994.diff (646 lines)
[INFO] [2022-12-30 10:40:46] ...measurements (/app/public/data/bldnas/measurement_or_fact_specific.tab)
[CMD] [2022-12-30 10:40:46] echo "0a" > /app/public/data/bldnas/diff/bldnas_measurements_29995.diff
[CMD] [2022-12-30 10:40:46] tail -n +1 /app/public/data/bldnas/converted_csv/bldnas_measurements_29995.csv >> /app/public/data/bldnas/diff/bldnas_measurements_29995.diff
[CMD] [2022-12-30 10:40:47] echo "." >> /app/public/data/bldnas/diff/bldnas_measurements_29995.diff
[INFO] [2022-12-30 10:40:47] Created diff: /app/public/data/bldnas/diff/bldnas_measurements_29995.diff (646 lines)
[STOP] [2022-12-30 10:40:47] calculate_delta
[START] [2022-12-30 10:40:47] parse_diff_and_store
[INFO] [2022-12-30 10:40:47] Handling diff: /app/public/data/bldnas/diff/bldnas_nodes_29993.diff (327 lines)
[INFO] [2022-12-30 10:40:47] Loading nodes diff file into memory (327 lines)...
[INFO] [2022-12-30 10:40:47] Storing 327 ScientificNames (654/325/327)
[INFO] [2022-12-30 10:40:47] Storing 327 Nodes (654/325/327)
[INFO] [2022-12-30 10:40:47] Handling diff: /app/public/data/bldnas/diff/bldnas_occurrences_29994.diff (646 lines)
[INFO] [2022-12-30 10:40:47] Loading occurrences diff file into memory (646 lines)...
[INFO] [2022-12-30 10:40:48] Storing 644 Occurrences (1585/644/646)
[INFO] [2022-12-30 10:40:48] Storing 941 OccurrenceMetadata (1585/644/646)
[INFO] [2022-12-30 10:40:48] Handling diff: /app/public/data/bldnas/diff/bldnas_measurements_29995.diff (646 lines)
[INFO] [2022-12-30 10:40:48] Loading measurements diff file into memory (646 lines)...
[INFO] [2022-12-30 10:40:48] Storing 644 Traits (1288/644/646)
[INFO] [2022-12-30 10:40:49] Storing 644 MetaTraits (1288/644/646)
[STOP] [2022-12-30 10:40:49] parse_diff_and_store
[START] [2022-12-30 10:40:49] resolve_keys
[2022-12-30 10:40:49] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-12-30 10:40:56] Occurrences to nodes (through scientific_names)...
[INFO] [2022-12-30 10:40:56] traits to occurrences...
[INFO] [2022-12-30 10:40:56] traits to nodes (through occurrences)...
[INFO] [2022-12-30 10:40:56] Traits to sex term...
[INFO] [2022-12-30 10:40:56] Traits to lifestage term...
[INFO] [2022-12-30 10:40:56] MetaTraits to traits...
[INFO] [2022-12-30 10:40:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-12-30 10:40:56] Assocs to occurrences...
[INFO] [2022-12-30 10:40:56] Assocs to nodes...
[INFO] [2022-12-30 10:40:56] Assoc to sex term...
[INFO] [2022-12-30 10:40:56] Assoc to lifestage term...
[INFO] [2022-12-30 10:40:56] MetaAssoc to assocs...
[STOP] [2022-12-30 10:40:56] resolve_keys
[START] [2022-12-30 10:40:56] hold_for_later_1
[STOP] [2022-12-30 10:40:56] hold_for_later_1
[START] [2022-12-30 10:40:56] hold_for_later_2
[STOP] [2022-12-30 10:40:56] hold_for_later_2
[START] [2022-12-30 10:40:56] resolve_missing_parents
[STOP] [2022-12-30 10:40:56] resolve_missing_parents
[START] [2022-12-30 10:40:56] rebuild_nodes
[START] [2022-12-30 10:40:56] Flattener#flatten
[START] [2022-12-30 10:40:56] Flattener#study_resource
[START] [2022-12-30 10:40:56] Flattener#build_ancestry
[STOP] [2022-12-30 10:40:56] Flattener#build_ancestry
[INFO] [2022-12-30 10:40:56] 327 ancestry keys
[START] [2022-12-30 10:40:56] build_node_ancestors
[INFO] [2022-12-30 10:40:56] old ancestors deleted.
[STOP] [2022-12-30 10:40:56] build_node_ancestors
[START] [2022-12-30 10:40:56] Flattener#propagate_ancestor_ids
[STOP] [2022-12-30 10:40:56] Flattener#propagate_ancestor_ids
[STOP] [2022-12-30 10:40:56] Flattener#flatten
[STOP] [2022-12-30 10:40:56] rebuild_nodes
[START] [2022-12-30 10:40:56] resolve_missing_media_owners
[STOP] [2022-12-30 10:40:56] resolve_missing_media_owners
[START] [2022-12-30 10:40:56] sanitize_media_verbatims
[STOP] [2022-12-30 10:40:56] sanitize_media_verbatims
[START] [2022-12-30 10:40:56] queue_downloads
[STOP] [2022-12-30 10:40:56] queue_downloads
[START] [2022-12-30 10:40:56] parse_names
[WARN] [2022-12-30 10:40:56] I see 327 names which still need to be parsed.
[WARN] [2022-12-30 10:40:56] Names to parse: 327 formatted: 327 learned: 327 parsed: 327
[STOP] [2022-12-30 10:40:58] parse_names
[START] [2022-12-30 10:40:58] denormalize_canonical_names_to_nodes
[STOP] [2022-12-30 10:40:58] denormalize_canonical_names_to_nodes
[START] [2022-12-30 10:40:58] match_nodes
[START] [2022-12-30 10:40:58] map_all_nodes_to_pages
[STOP] [2022-12-30 10:41:01] map_all_nodes_to_pages
[INFO] [2022-12-30 10:41:01] Unmatched nodes (1 of 327): Canonical: Tabanus sequax; Node#122394852; ResourceID: Tabanus_sequax
[START] [2022-12-30 10:41:01] update_nodes
[STOP] [2022-12-30 10:41:01] update_nodes
[STOP] [2022-12-30 10:41:01] match_nodes
[START] [2022-12-30 10:41:01] reindex_search
[STOP] [2022-12-30 10:41:01] reindex_search
[START] [2022-12-30 10:41:01] normalize_units
[STOP] [2022-12-30 10:41:04] normalize_units
[START] [2022-12-30 10:41:04] calculate_statistics
[INFO] [2022-12-30 10:41:04] Duplicate page_id count: 0
[STOP] [2022-12-30 10:41:04] calculate_statistics
[START] [2022-12-30 10:41:04] complete_harvest_instance
[START] [2022-12-30 10:41:04] overall_tsv_creation
[INFO] [2022-12-30 10:41:04] Exporting 327 nodes as TSV in batches of 10000...
[INFO] [2022-12-30 10:41:04] Processing group of 327 in 1 batches of 10000
[INFO] [2022-12-30 10:41:04] 644 Traits (unfiltered) and 0 associations...
[INFO] [2022-12-30 10:41:04] Building Traits map for 327 nodes (this can take a while)...
[INFO] [2022-12-30 10:41:05] Mapped 644 traits (644 meta) for 327 nodes.
[INFO] [2022-12-30 10:41:05] Building Associations map (this can take a while)...
[INFO] [2022-12-30 10:41:05] Done. 0 assocs mapped (0 meta).
[INFO] [2022-12-30 10:41:05] Adding 644 traits...
[INFO] [2022-12-30 10:41:05] 0 metadata added.
[INFO] [2022-12-30 10:41:05] Adding 0 assocs...
[INFO] [2022-12-30 10:41:05] 0 metadata added.
[INFO] [2022-12-30 10:41:49] Processed 327/327 nodes
[INFO] [2022-12-30 10:41:49] Average Time: 44.52
[INFO] [2022-12-30 10:41:49] Total Time: 45s
[STOP] [2022-12-30 10:41:49] overall_tsv_creation
[INFO] [2022-12-30 10:41:49] Done. Check your files:
[INFO] [2022-12-30 10:41:49] (327 lines) /app/public/data/bldnas/publish_nodes.tsv
[INFO] [2022-12-30 10:41:49] (325 lines) /app/public/data/bldnas/publish_node_ancestors.tsv
[INFO] [2022-12-30 10:41:49] (327 lines) /app/public/data/bldnas/publish_scientific_names.tsv
[INFO] [2022-12-30 10:41:49] (645 lines) /app/public/data/bldnas/publish_traits.tsv
[INFO] [2022-12-30 10:41:49] (1 lines) /app/public/data/bldnas/publish_metadata.tsv
[STOP] [2022-12-30 10:41:49] complete_harvest_instance
[START] [2022-12-30 10:41:49] completed
[STOP] [2022-12-30 10:41:49] completed
[STOP] [2022-12-30 10:41:49] logged process, took 65.41
Latest Process

30 Dec 10:40 EXITED currently processing 0