Harvest for Baumiller and Messing 2007 Created 30 Jul 15:03

Stage: completed
Fetched: 30 Jul 15:03
Validated: 30 Jul 15:03
Deltas Created 30 Jul 15:03
Units Normalized: 30 Jul 15:03
Ancestry Built: 30 Jul 15:03
Nodes Matched: 30 Jul 15:03
Names Parsed: 30 Jul 15:03
New Models Stored: 30 Jul 15:03
Indexed: 30 Jul 15:03
Completed: 30 Jul 15:05
Time to Harvest: less than a minute
Harvesting Log

(145 lines)
# Logfile created on 2020-07-30 15:03:08 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 15:03:08] logged process
[START] [2020-07-30 15:03:08] Creating resource from OpenData
[START] [2020-07-30 15:03:08] logged process
[START] [2020-07-30 15:03:08] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:03:08] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:03:08] Creating resource from OpenData
[INFO] [2020-07-30 15:03:23] ## HARVEST: type = -harvest
[START] [2020-07-30 15:03:24] logged process
[START] [2020-07-30 15:03:24] create_harvest_instance
[STOP] [2020-07-30 15:03:26] create_harvest_instance
[START] [2020-07-30 15:03:26] fetch_files
[STOP] [2020-07-30 15:03:26] fetch_files
[START] [2020-07-30 15:03:26] validate_each_file
[STOP] [2020-07-30 15:03:26] validate_each_file
[START] [2020-07-30 15:03:26] convert_to_csv
[CMD] [2020-07-30 15:03:26] /usr/bin/sort /app/public/converted_csv/baumiller_messin_refs_22356.csv > /app/public/converted_csv/baumiller_messin_refs_22356.csv_sorted
[CMD] [2020-07-30 15:03:26] /usr/bin/sort /app/public/converted_csv/baumiller_messin_nodes_22357.csv > /app/public/converted_csv/baumiller_messin_nodes_22357.csv_sorted
[CMD] [2020-07-30 15:03:26] /usr/bin/sort /app/public/converted_csv/baumiller_messin_occurrences_22358.csv > /app/public/converted_csv/baumiller_messin_occurrences_22358.csv_sorted
[CMD] [2020-07-30 15:03:26] /usr/bin/sort /app/public/converted_csv/baumiller_messin_measurements_22359.csv > /app/public/converted_csv/baumiller_messin_measurements_22359.csv_sorted
[STOP] [2020-07-30 15:03:26] convert_to_csv
[START] [2020-07-30 15:03:26] calculate_delta
[CMD] [2020-07-30 15:03:26] echo "0a" > /app/public/diff/baumiller_messin_refs_22356.diff
[CMD] [2020-07-30 15:03:26] tail -n +1 /app/public/converted_csv/baumiller_messin_refs_22356.csv >> /app/public/diff/baumiller_messin_refs_22356.diff
[CMD] [2020-07-30 15:03:26] echo "." >> /app/public/diff/baumiller_messin_refs_22356.diff
[CMD] [2020-07-30 15:03:26] echo "0a" > /app/public/diff/baumiller_messin_nodes_22357.diff
[CMD] [2020-07-30 15:03:26] tail -n +1 /app/public/converted_csv/baumiller_messin_nodes_22357.csv >> /app/public/diff/baumiller_messin_nodes_22357.diff
[CMD] [2020-07-30 15:03:26] echo "." >> /app/public/diff/baumiller_messin_nodes_22357.diff
[CMD] [2020-07-30 15:03:26] echo "0a" > /app/public/diff/baumiller_messin_occurrences_22358.diff
[CMD] [2020-07-30 15:03:26] tail -n +1 /app/public/converted_csv/baumiller_messin_occurrences_22358.csv >> /app/public/diff/baumiller_messin_occurrences_22358.diff
[CMD] [2020-07-30 15:03:26] echo "." >> /app/public/diff/baumiller_messin_occurrences_22358.diff
[CMD] [2020-07-30 15:03:26] echo "0a" > /app/public/diff/baumiller_messin_measurements_22359.diff
[CMD] [2020-07-30 15:03:26] tail -n +1 /app/public/converted_csv/baumiller_messin_measurements_22359.csv >> /app/public/diff/baumiller_messin_measurements_22359.diff
[CMD] [2020-07-30 15:03:26] echo "." >> /app/public/diff/baumiller_messin_measurements_22359.diff
[STOP] [2020-07-30 15:03:26] calculate_delta
[START] [2020-07-30 15:03:26] parse_diff_and_store
[INFO] [2020-07-30 15:03:26] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 15:03:26] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 15:03:26] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 15:03:26] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 15:03:26] Storing 11 References
[INFO] [2020-07-30 15:03:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[INFO] [2020-07-30 15:03:26] Storing 2 ScientificNames
[INFO] [2020-07-30 15:03:26] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[INFO] [2020-07-30 15:03:26] Storing 2 Nodes
[INFO] [2020-07-30 15:03:26] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[INFO] [2020-07-30 15:03:26] Storing 2 Occurrences
[INFO] [2020-07-30 15:03:26] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[INFO] [2020-07-30 15:03:26] Storing 11 Traits
[INFO] [2020-07-30 15:03:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[INFO] [2020-07-30 15:03:26] Storing 9 MetaTraits
[INFO] [2020-07-30 15:03:26] Processing group of 9 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[INFO] [2020-07-30 15:03:26] Storing 11 TraitsReferences
[INFO] [2020-07-30 15:03:26] Processing group of 11 in 1 groups of 1000
[INFO] [2020-07-30 15:03:26] Average Time: 0.0
[INFO] [2020-07-30 15:03:26] Total Time: 1s
[STOP] [2020-07-30 15:03:26] parse_diff_and_store
[START] [2020-07-30 15:03:26] resolve_keys
[INFO] [2020-07-30 15:03:33] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 15:03:33] traits to occurrences...
[INFO] [2020-07-30 15:03:33] traits to nodes (through occurrences)...
[INFO] [2020-07-30 15:03:33] Traits to sex term...
[INFO] [2020-07-30 15:03:33] Traits to lifestage term...
[INFO] [2020-07-30 15:03:33] MetaTraits to traits...
[INFO] [2020-07-30 15:03:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 15:03:33] Assocs to occurrences...
[INFO] [2020-07-30 15:03:33] Assocs to nodes...
[INFO] [2020-07-30 15:03:33] Assoc to sex term...
[INFO] [2020-07-30 15:03:33] Assoc to lifestage term...
[STOP] [2020-07-30 15:03:33] resolve_keys
[START] [2020-07-30 15:03:33] hold_for_later_1
[STOP] [2020-07-30 15:03:33] hold_for_later_1
[START] [2020-07-30 15:03:33] hold_for_later_2
[STOP] [2020-07-30 15:03:33] hold_for_later_2
[START] [2020-07-30 15:03:33] resolve_missing_parents
[STOP] [2020-07-30 15:03:33] resolve_missing_parents
[START] [2020-07-30 15:03:33] rebuild_nodes
[START] [2020-07-30 15:03:33] Flattener#flatten
[START] [2020-07-30 15:03:33] Flattener#study_resource
[START] [2020-07-30 15:03:33] Flattener#build_ancestry
[STOP] [2020-07-30 15:03:33] Flattener#build_ancestry
[INFO] [2020-07-30 15:03:33] 2 ancestry keys
[START] [2020-07-30 15:03:33] build_node_ancestors
[INFO] [2020-07-30 15:03:33] old ancestors deleted.
[STOP] [2020-07-30 15:03:33] build_node_ancestors
[WARN] [2020-07-30 15:03:33] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 15:03:33] Flattener#flatten
[STOP] [2020-07-30 15:03:33] rebuild_nodes
[START] [2020-07-30 15:03:33] resolve_missing_media_owners
[STOP] [2020-07-30 15:03:33] resolve_missing_media_owners
[START] [2020-07-30 15:03:33] sanitize_media_verbatims
[STOP] [2020-07-30 15:03:33] sanitize_media_verbatims
[START] [2020-07-30 15:03:33] queue_downloads
[STOP] [2020-07-30 15:03:33] queue_downloads
[START] [2020-07-30 15:03:33] parse_names
[WARN] [2020-07-30 15:03:33] I see 2 names which still need to be parsed.
[STOP] [2020-07-30 15:03:34] parse_names
[START] [2020-07-30 15:03:34] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 15:03:34] denormalize_canonical_names_to_nodes
[START] [2020-07-30 15:03:34] match_nodes
[START] [2020-07-30 15:03:34] map_all_nodes_to_pages
[STOP] [2020-07-30 15:03:34] map_all_nodes_to_pages
[INFO] [2020-07-30 15:03:34] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-07-30 15:03:34] update_nodes
[STOP] [2020-07-30 15:03:34] update_nodes
[STOP] [2020-07-30 15:03:34] match_nodes
[START] [2020-07-30 15:03:34] reindex_search
[STOP] [2020-07-30 15:03:34] reindex_search
[START] [2020-07-30 15:03:34] normalize_units
[STOP] [2020-07-30 15:03:34] normalize_units
[START] [2020-07-30 15:03:34] calculate_statistics
[2020-07-30 15:03:34] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 15:03:34] calculate_statistics
[START] [2020-07-30 15:03:34] complete_harvest_instance
[START] [2020-07-30 15:03:34] overall_tsv_creation
[INFO] [2020-07-30 15:03:34] Processing group of 2 in 1 batches of 10000
[INFO] [2020-07-30 15:04:24] 4 Traits (unfiltered)...
[INFO] [2020-07-30 15:05:01] 4 Traits (filtered)...
[INFO] [2020-07-30 15:05:01] 0 Associations (filtered)...
[INFO] [2020-07-30 15:05:01] 27 metadata added.
[INFO] [2020-07-30 15:05:01] 0 metadata added.
[INFO] [2020-07-30 15:05:01] Average Time: 58.84
[INFO] [2020-07-30 15:05:01] Total Time: 1m27s
[STOP] [2020-07-30 15:05:01] overall_tsv_creation
[INFO] [2020-07-30 15:05:01] Done. Check your files:
[INFO] [2020-07-30 15:05:01] (2 lines) /app/public/data/baumiller_messin/publish_nodes.tsv
[INFO] [2020-07-30 15:05:01] (2 lines) /app/public/data/baumiller_messin/publish_scientific_names.tsv
[INFO] [2020-07-30 15:05:01] (5 lines) /app/public/data/baumiller_messin/publish_traits.tsv
[INFO] [2020-07-30 15:05:01] (19 lines) /app/public/data/baumiller_messin/publish_metadata.tsv
[STOP] [2020-07-30 15:05:01] complete_harvest_instance
[START] [2020-07-30 15:05:01] completed
[STOP] [2020-07-30 15:05:01] completed
[STOP] [2020-07-30 15:05:01] logged process, took 96.4
Latest Process

30 Jul 15:03 EXITED currently processing 0