Harvest for Body Size Data for North American Hemiptera Created 16 Feb 14:45

Stage: completed
Fetched: 16 Feb 14:45
Validated: 16 Feb 14:45
Deltas Created 16 Feb 14:45
Units Normalized: 16 Feb 14:45
Ancestry Built: 16 Feb 14:45
Nodes Matched: 16 Feb 14:45
Names Parsed: 16 Feb 14:45
New Models Stored: 16 Feb 14:45
Indexed: 16 Feb 14:45
Completed: 16 Feb 14:46
Time to Harvest: less than a minute
Harvesting Log

(144 lines)
[INFO] [2023-02-16 14:45:00] Created harvest instance #4303
[STOP] [2023-02-16 14:45:00] create_harvest_instance
[START] [2023-02-16 14:45:00] fetch_files
[STOP] [2023-02-16 14:45:00] fetch_files
[START] [2023-02-16 14:45:00] validate_each_file
[INFO] [2023-02-16 14:45:00] Looping over 3 formats...
[INFO] [2023-02-16 14:45:00] ...nodes (/app/public/data/bsdnah/taxon.tab)
[INFO] [2023-02-16 14:45:00] Valid: /app/public/data/bsdnah/converted_csv/bsdnah_nodes_30208.csv (446 lines)
[INFO] [2023-02-16 14:45:00] ...occurrences (/app/public/data/bsdnah/occurrence_specific.tab)
[INFO] [2023-02-16 14:45:00] Valid: /app/public/data/bsdnah/converted_csv/bsdnah_occurrences_30209.csv (1981 lines)
[INFO] [2023-02-16 14:45:00] ...measurements (/app/public/data/bsdnah/measurement_or_fact_specific.tab)
[INFO] [2023-02-16 14:45:00] Valid: /app/public/data/bsdnah/converted_csv/bsdnah_measurements_30210.csv (1982 lines)
[STOP] [2023-02-16 14:45:00] validate_each_file
[START] [2023-02-16 14:45:00] convert_to_csv
[INFO] [2023-02-16 14:45:00] Looping over 3 formats...
[INFO] [2023-02-16 14:45:00] ...nodes (/app/public/data/bsdnah/taxon.tab)
[CMD] [2023-02-16 14:45:00] /usr/bin/sort /app/public/data/bsdnah/converted_csv/bsdnah_nodes_30208.csv > /app/public/data/bsdnah/converted_csv/bsdnah_nodes_30208.csv_sorted
[INFO] [2023-02-16 14:45:00] Converted: /app/public/data/bsdnah/converted_csv/bsdnah_nodes_30208.csv (446 lines)
[INFO] [2023-02-16 14:45:00] ...occurrences (/app/public/data/bsdnah/occurrence_specific.tab)
[CMD] [2023-02-16 14:45:00] /usr/bin/sort /app/public/data/bsdnah/converted_csv/bsdnah_occurrences_30209.csv > /app/public/data/bsdnah/converted_csv/bsdnah_occurrences_30209.csv_sorted
[INFO] [2023-02-16 14:45:00] Converted: /app/public/data/bsdnah/converted_csv/bsdnah_occurrences_30209.csv (1981 lines)
[INFO] [2023-02-16 14:45:00] ...measurements (/app/public/data/bsdnah/measurement_or_fact_specific.tab)
[CMD] [2023-02-16 14:45:00] /usr/bin/sort /app/public/data/bsdnah/converted_csv/bsdnah_measurements_30210.csv > /app/public/data/bsdnah/converted_csv/bsdnah_measurements_30210.csv_sorted
[INFO] [2023-02-16 14:45:01] Converted: /app/public/data/bsdnah/converted_csv/bsdnah_measurements_30210.csv (1982 lines)
[STOP] [2023-02-16 14:45:01] convert_to_csv
[START] [2023-02-16 14:45:01] calculate_delta
[INFO] [2023-02-16 14:45:01] Looping over 3 formats...
[INFO] [2023-02-16 14:45:01] ...nodes (/app/public/data/bsdnah/taxon.tab)
[CMD] [2023-02-16 14:45:01] echo "0a" > /app/public/data/bsdnah/diff/bsdnah_nodes_30208.diff
[CMD] [2023-02-16 14:45:01] tail -n +1 /app/public/data/bsdnah/converted_csv/bsdnah_nodes_30208.csv >> /app/public/data/bsdnah/diff/bsdnah_nodes_30208.diff
[CMD] [2023-02-16 14:45:01] echo "." >> /app/public/data/bsdnah/diff/bsdnah_nodes_30208.diff
[INFO] [2023-02-16 14:45:01] Created diff: /app/public/data/bsdnah/diff/bsdnah_nodes_30208.diff (448 lines)
[INFO] [2023-02-16 14:45:01] ...occurrences (/app/public/data/bsdnah/occurrence_specific.tab)
[CMD] [2023-02-16 14:45:01] echo "0a" > /app/public/data/bsdnah/diff/bsdnah_occurrences_30209.diff
[CMD] [2023-02-16 14:45:01] tail -n +1 /app/public/data/bsdnah/converted_csv/bsdnah_occurrences_30209.csv >> /app/public/data/bsdnah/diff/bsdnah_occurrences_30209.diff
[CMD] [2023-02-16 14:45:01] echo "." >> /app/public/data/bsdnah/diff/bsdnah_occurrences_30209.diff
[INFO] [2023-02-16 14:45:02] Created diff: /app/public/data/bsdnah/diff/bsdnah_occurrences_30209.diff (1983 lines)
[INFO] [2023-02-16 14:45:02] ...measurements (/app/public/data/bsdnah/measurement_or_fact_specific.tab)
[CMD] [2023-02-16 14:45:02] echo "0a" > /app/public/data/bsdnah/diff/bsdnah_measurements_30210.diff
[CMD] [2023-02-16 14:45:02] tail -n +1 /app/public/data/bsdnah/converted_csv/bsdnah_measurements_30210.csv >> /app/public/data/bsdnah/diff/bsdnah_measurements_30210.diff
[CMD] [2023-02-16 14:45:02] echo "." >> /app/public/data/bsdnah/diff/bsdnah_measurements_30210.diff
[INFO] [2023-02-16 14:45:02] Created diff: /app/public/data/bsdnah/diff/bsdnah_measurements_30210.diff (1984 lines)
[STOP] [2023-02-16 14:45:02] calculate_delta
[START] [2023-02-16 14:45:02] parse_diff_and_store
[INFO] [2023-02-16 14:45:02] Handling diff: /app/public/data/bsdnah/diff/bsdnah_nodes_30208.diff (448 lines)
[INFO] [2023-02-16 14:45:02] Loading nodes diff file into memory (448 lines)...
[INFO] [2023-02-16 14:45:03] Storing 451 ScientificNames (902/446/448)
[INFO] [2023-02-16 14:45:03] Storing 451 Nodes (902/446/448)
[INFO] [2023-02-16 14:45:03] Handling diff: /app/public/data/bsdnah/diff/bsdnah_occurrences_30209.diff (1983 lines)
[INFO] [2023-02-16 14:45:03] Loading occurrences diff file into memory (1983 lines)...
[INFO] [2023-02-16 14:45:04] Storing 1981 Occurrences (4705/1981/1983)
[INFO] [2023-02-16 14:45:04] Storing 2724 OccurrenceMetadata (4705/1981/1983)
[INFO] [2023-02-16 14:45:04] Handling diff: /app/public/data/bsdnah/diff/bsdnah_measurements_30210.diff (1984 lines)
[INFO] [2023-02-16 14:45:04] Loading measurements diff file into memory (1984 lines)...
[INFO] [2023-02-16 14:45:05] Storing 1982 Traits (4002/1982/1984)
[INFO] [2023-02-16 14:45:06] Storing 2020 MetaTraits (4002/1982/1984)
[STOP] [2023-02-16 14:45:06] parse_diff_and_store
[START] [2023-02-16 14:45:06] resolve_keys
[2023-02-16 14:45:06] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2023-02-16 14:45:14] Occurrences to nodes (through scientific_names)...
[INFO] [2023-02-16 14:45:14] traits to occurrences...
[INFO] [2023-02-16 14:45:14] traits to nodes (through occurrences)...
[INFO] [2023-02-16 14:45:14] Traits to sex term...
[INFO] [2023-02-16 14:45:14] Traits to lifestage term...
[INFO] [2023-02-16 14:45:14] MetaTraits to traits...
[INFO] [2023-02-16 14:45:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2023-02-16 14:45:14] Assocs to occurrences...
[INFO] [2023-02-16 14:45:14] Assocs to nodes...
[INFO] [2023-02-16 14:45:14] Assoc to sex term...
[INFO] [2023-02-16 14:45:14] Assoc to lifestage term...
[INFO] [2023-02-16 14:45:14] MetaAssoc to assocs...
[STOP] [2023-02-16 14:45:14] resolve_keys
[START] [2023-02-16 14:45:14] hold_for_later_1
[STOP] [2023-02-16 14:45:14] hold_for_later_1
[START] [2023-02-16 14:45:14] hold_for_later_2
[STOP] [2023-02-16 14:45:14] hold_for_later_2
[START] [2023-02-16 14:45:14] resolve_missing_parents
[STOP] [2023-02-16 14:45:14] resolve_missing_parents
[START] [2023-02-16 14:45:14] rebuild_nodes
[START] [2023-02-16 14:45:14] Flattener#flatten
[START] [2023-02-16 14:45:14] Flattener#study_resource
[START] [2023-02-16 14:45:14] Flattener#build_ancestry
[STOP] [2023-02-16 14:45:14] Flattener#build_ancestry
[INFO] [2023-02-16 14:45:14] 451 ancestry keys
[START] [2023-02-16 14:45:14] build_node_ancestors
[INFO] [2023-02-16 14:45:14] old ancestors deleted.
[STOP] [2023-02-16 14:45:14] build_node_ancestors
[START] [2023-02-16 14:45:14] Flattener#propagate_ancestor_ids
[STOP] [2023-02-16 14:45:14] Flattener#propagate_ancestor_ids
[STOP] [2023-02-16 14:45:14] Flattener#flatten
[STOP] [2023-02-16 14:45:14] rebuild_nodes
[START] [2023-02-16 14:45:14] resolve_missing_media_owners
[STOP] [2023-02-16 14:45:14] resolve_missing_media_owners
[START] [2023-02-16 14:45:14] sanitize_media_verbatims
[STOP] [2023-02-16 14:45:14] sanitize_media_verbatims
[START] [2023-02-16 14:45:14] queue_downloads
[STOP] [2023-02-16 14:45:14] queue_downloads
[START] [2023-02-16 14:45:14] parse_names
[WARN] [2023-02-16 14:45:14] I see 451 names which still need to be parsed.
[WARN] [2023-02-16 14:45:14] Names to parse: 451 formatted: 451 learned: 451 parsed: 451
[STOP] [2023-02-16 14:45:16] parse_names
[START] [2023-02-16 14:45:16] denormalize_canonical_names_to_nodes
[STOP] [2023-02-16 14:45:16] denormalize_canonical_names_to_nodes
[START] [2023-02-16 14:45:16] match_nodes
[START] [2023-02-16 14:45:16] map_all_nodes_to_pages
[STOP] [2023-02-16 14:45:33] map_all_nodes_to_pages
[INFO] [2023-02-16 14:45:33] ZERO unmatched nodes (of 451)! Nicely done.
[START] [2023-02-16 14:45:33] update_nodes
[STOP] [2023-02-16 14:45:33] update_nodes
[STOP] [2023-02-16 14:45:33] match_nodes
[START] [2023-02-16 14:45:33] reindex_search
[STOP] [2023-02-16 14:45:33] reindex_search
[START] [2023-02-16 14:45:33] normalize_units
[STOP] [2023-02-16 14:45:40] normalize_units
[START] [2023-02-16 14:45:40] calculate_statistics
[INFO] [2023-02-16 14:45:40] Duplicate page_id count: 16
[STOP] [2023-02-16 14:45:40] calculate_statistics
[START] [2023-02-16 14:45:40] complete_harvest_instance
[START] [2023-02-16 14:45:40] overall_tsv_creation
[INFO] [2023-02-16 14:45:40] Exporting 451 nodes as TSV in batches of 10000...
[INFO] [2023-02-16 14:45:40] Processing group of 451 in 1 batches of 10000
[INFO] [2023-02-16 14:45:41] 1982 Traits (unfiltered) and 0 associations...
[INFO] [2023-02-16 14:45:41] Building Traits map for 451 nodes (this can take a while)...
[INFO] [2023-02-16 14:45:42] Mapped 1982 traits (2020 meta) for 451 nodes.
[INFO] [2023-02-16 14:45:42] Building Associations map (this can take a while)...
[INFO] [2023-02-16 14:45:42] Done. 0 assocs mapped (0 meta).
[INFO] [2023-02-16 14:45:42] Adding 1982 traits...
[INFO] [2023-02-16 14:45:42] 0 metadata added.
[INFO] [2023-02-16 14:45:42] Adding 0 assocs...
[INFO] [2023-02-16 14:45:42] 0 metadata added.
[INFO] [2023-02-16 14:46:26] Processed 451/451 nodes
[INFO] [2023-02-16 14:46:26] Average Time: 45.5
[INFO] [2023-02-16 14:46:26] Total Time: 46s
[STOP] [2023-02-16 14:46:26] overall_tsv_creation
[INFO] [2023-02-16 14:46:26] Done. Check your files:
[INFO] [2023-02-16 14:46:26] (451 lines) /app/public/data/bsdnah/publish_nodes.tsv
[INFO] [2023-02-16 14:46:26] (1302 lines) /app/public/data/bsdnah/publish_node_ancestors.tsv
[INFO] [2023-02-16 14:46:26] (451 lines) /app/public/data/bsdnah/publish_scientific_names.tsv
[INFO] [2023-02-16 14:46:27] (1983 lines) /app/public/data/bsdnah/publish_traits.tsv
[INFO] [2023-02-16 14:46:27] (1 lines) /app/public/data/bsdnah/publish_metadata.tsv
[STOP] [2023-02-16 14:46:27] complete_harvest_instance
[START] [2023-02-16 14:46:27] completed
[STOP] [2023-02-16 14:46:27] completed
[STOP] [2023-02-16 14:46:27] logged process, took 87.35
Latest Process

16 Feb 14:44 EXITED currently processing 0