Harvest for Lindsey 1978 Created 22 Jul 15:02

Stage: completed
Fetched: 22 Jul 15:02
Validated: 22 Jul 15:02
Deltas Created 22 Jul 15:02
Units Normalized: 22 Jul 15:02
Ancestry Built: 22 Jul 15:02
Nodes Matched: 22 Jul 15:02
Names Parsed: 22 Jul 15:02
New Models Stored: 22 Jul 15:02
Indexed: 22 Jul 15:02
Completed: 22 Jul 15:04
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:55:35 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:55:35] logged process
[START] [2020-07-22 14:55:35] Creating resource from OpenData
[START] [2020-07-22 14:55:35] logged process
[START] [2020-07-22 14:55:35] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:55:35] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:55:35] Creating resource from OpenData
[INFO] [2020-07-22 15:02:45] ## HARVEST: type = -harvest
[START] [2020-07-22 15:02:49] logged process
[START] [2020-07-22 15:02:49] create_harvest_instance
[STOP] [2020-07-22 15:02:50] create_harvest_instance
[START] [2020-07-22 15:02:50] fetch_files
[STOP] [2020-07-22 15:02:51] fetch_files
[START] [2020-07-22 15:02:51] validate_each_file
[STOP] [2020-07-22 15:02:51] validate_each_file
[START] [2020-07-22 15:02:51] convert_to_csv
[CMD] [2020-07-22 15:02:51] /usr/bin/sort /app/public/converted_csv/lindsey_lindsey__nodes_22030.csv > /app/public/converted_csv/lindsey_lindsey__nodes_22030.csv_sorted
[CMD] [2020-07-22 15:02:51] /usr/bin/sort /app/public/converted_csv/lindsey_lindsey__occurrences_22031.csv > /app/public/converted_csv/lindsey_lindsey__occurrences_22031.csv_sorted
[CMD] [2020-07-22 15:02:51] /usr/bin/sort /app/public/converted_csv/lindsey_lindsey__measurements_22032.csv > /app/public/converted_csv/lindsey_lindsey__measurements_22032.csv_sorted
[STOP] [2020-07-22 15:02:51] convert_to_csv
[START] [2020-07-22 15:02:51] calculate_delta
[CMD] [2020-07-22 15:02:51] echo "0a" > /app/public/diff/lindsey_lindsey__nodes_22030.diff
[CMD] [2020-07-22 15:02:51] tail -n +1 /app/public/converted_csv/lindsey_lindsey__nodes_22030.csv >> /app/public/diff/lindsey_lindsey__nodes_22030.diff
[CMD] [2020-07-22 15:02:51] echo "." >> /app/public/diff/lindsey_lindsey__nodes_22030.diff
[CMD] [2020-07-22 15:02:51] echo "0a" > /app/public/diff/lindsey_lindsey__occurrences_22031.diff
[CMD] [2020-07-22 15:02:51] tail -n +1 /app/public/converted_csv/lindsey_lindsey__occurrences_22031.csv >> /app/public/diff/lindsey_lindsey__occurrences_22031.diff
[CMD] [2020-07-22 15:02:51] echo "." >> /app/public/diff/lindsey_lindsey__occurrences_22031.diff
[CMD] [2020-07-22 15:02:51] echo "0a" > /app/public/diff/lindsey_lindsey__measurements_22032.diff
[CMD] [2020-07-22 15:02:51] tail -n +1 /app/public/converted_csv/lindsey_lindsey__measurements_22032.csv >> /app/public/diff/lindsey_lindsey__measurements_22032.diff
[CMD] [2020-07-22 15:02:51] echo "." >> /app/public/diff/lindsey_lindsey__measurements_22032.diff
[STOP] [2020-07-22 15:02:51] calculate_delta
[START] [2020-07-22 15:02:51] parse_diff_and_store
[INFO] [2020-07-22 15:02:51] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:02:51] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:02:51] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:02:51] Storing 12 ScientificNames
[INFO] [2020-07-22 15:02:51] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-22 15:02:51] Average Time: 0.01
[INFO] [2020-07-22 15:02:51] Total Time: 1s
[INFO] [2020-07-22 15:02:51] Storing 12 Nodes
[INFO] [2020-07-22 15:02:51] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-22 15:02:51] Average Time: 0.0
[INFO] [2020-07-22 15:02:51] Total Time: 1s
[INFO] [2020-07-22 15:02:51] Storing 12 Occurrences
[INFO] [2020-07-22 15:02:51] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-22 15:02:51] Average Time: 0.0
[INFO] [2020-07-22 15:02:51] Total Time: 1s
[INFO] [2020-07-22 15:02:51] Storing 24 Traits
[INFO] [2020-07-22 15:02:51] Processing group of 24 in 1 groups of 1000
[INFO] [2020-07-22 15:02:51] Average Time: 0.01
[INFO] [2020-07-22 15:02:51] Total Time: 1s
[INFO] [2020-07-22 15:02:51] Storing 24 MetaTraits
[INFO] [2020-07-22 15:02:51] Processing group of 24 in 1 groups of 1000
[INFO] [2020-07-22 15:02:51] Average Time: 0.01
[INFO] [2020-07-22 15:02:51] Total Time: 1s
[STOP] [2020-07-22 15:02:51] parse_diff_and_store
[START] [2020-07-22 15:02:51] resolve_keys
[INFO] [2020-07-22 15:02:58] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:02:58] traits to occurrences...
[INFO] [2020-07-22 15:02:58] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:02:58] Traits to sex term...
[INFO] [2020-07-22 15:02:58] Traits to lifestage term...
[INFO] [2020-07-22 15:02:58] MetaTraits to traits...
[INFO] [2020-07-22 15:02:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:02:58] Assocs to occurrences...
[INFO] [2020-07-22 15:02:58] Assocs to nodes...
[INFO] [2020-07-22 15:02:58] Assoc to sex term...
[INFO] [2020-07-22 15:02:58] Assoc to lifestage term...
[STOP] [2020-07-22 15:02:58] resolve_keys
[START] [2020-07-22 15:02:58] hold_for_later_1
[STOP] [2020-07-22 15:02:58] hold_for_later_1
[START] [2020-07-22 15:02:58] hold_for_later_2
[STOP] [2020-07-22 15:02:58] hold_for_later_2
[START] [2020-07-22 15:02:58] resolve_missing_parents
[STOP] [2020-07-22 15:02:58] resolve_missing_parents
[START] [2020-07-22 15:02:58] rebuild_nodes
[START] [2020-07-22 15:02:58] Flattener#flatten
[START] [2020-07-22 15:02:58] Flattener#study_resource
[START] [2020-07-22 15:02:58] Flattener#build_ancestry
[STOP] [2020-07-22 15:02:58] Flattener#build_ancestry
[INFO] [2020-07-22 15:02:58] 12 ancestry keys
[START] [2020-07-22 15:02:58] build_node_ancestors
[INFO] [2020-07-22 15:02:58] old ancestors deleted.
[STOP] [2020-07-22 15:02:58] build_node_ancestors
[WARN] [2020-07-22 15:02:58] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:02:58] Flattener#flatten
[STOP] [2020-07-22 15:02:58] rebuild_nodes
[START] [2020-07-22 15:02:58] resolve_missing_media_owners
[STOP] [2020-07-22 15:02:58] resolve_missing_media_owners
[START] [2020-07-22 15:02:58] sanitize_media_verbatims
[STOP] [2020-07-22 15:02:58] sanitize_media_verbatims
[START] [2020-07-22 15:02:58] queue_downloads
[STOP] [2020-07-22 15:02:58] queue_downloads
[START] [2020-07-22 15:02:58] parse_names
[WARN] [2020-07-22 15:02:58] I see 12 names which still need to be parsed.
[STOP] [2020-07-22 15:02:59] parse_names
[START] [2020-07-22 15:02:59] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:02:59] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:02:59] match_nodes
[START] [2020-07-22 15:02:59] map_all_nodes_to_pages
[STOP] [2020-07-22 15:02:59] map_all_nodes_to_pages
[INFO] [2020-07-22 15:02:59] ZERO unmatched nodes (of 12)! Nicely done.
[START] [2020-07-22 15:02:59] update_nodes
[STOP] [2020-07-22 15:02:59] update_nodes
[STOP] [2020-07-22 15:02:59] match_nodes
[START] [2020-07-22 15:02:59] reindex_search
[STOP] [2020-07-22 15:02:59] reindex_search
[START] [2020-07-22 15:02:59] normalize_units
[STOP] [2020-07-22 15:02:59] normalize_units
[START] [2020-07-22 15:02:59] calculate_statistics
[2020-07-22 15:02:59] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:02:59] calculate_statistics
[START] [2020-07-22 15:02:59] complete_harvest_instance
[START] [2020-07-22 15:02:59] overall_tsv_creation
[INFO] [2020-07-22 15:02:59] Processing group of 12 in 1 batches of 10000
[INFO] [2020-07-22 15:03:48] 12 Traits (unfiltered)...
[INFO] [2020-07-22 15:04:25] 12 Traits (filtered)...
[INFO] [2020-07-22 15:04:25] 0 Associations (filtered)...
[INFO] [2020-07-22 15:04:25] 36 metadata added.
[INFO] [2020-07-22 15:04:25] 0 metadata added.
[INFO] [2020-07-22 15:04:25] Average Time: 58.29
[INFO] [2020-07-22 15:04:25] Total Time: 1m26s
[STOP] [2020-07-22 15:04:25] overall_tsv_creation
[INFO] [2020-07-22 15:04:25] Done. Check your files:
[INFO] [2020-07-22 15:04:25] (12 lines) /app/public/data/lindsey_lindsey_/publish_nodes.tsv
[INFO] [2020-07-22 15:04:25] (12 lines) /app/public/data/lindsey_lindsey_/publish_scientific_names.tsv
[INFO] [2020-07-22 15:04:25] (13 lines) /app/public/data/lindsey_lindsey_/publish_traits.tsv
[INFO] [2020-07-22 15:04:25] (13 lines) /app/public/data/lindsey_lindsey_/publish_metadata.tsv
[STOP] [2020-07-22 15:04:25] complete_harvest_instance
[START] [2020-07-22 15:04:25] completed
[STOP] [2020-07-22 15:04:25] completed
[STOP] [2020-07-22 15:04:25] logged process, took 95.45
Latest Process

22 Jul 15:02 EXITED currently processing 0