Harvest for Hove et al 2001 Created 22 Jul 14:59

Stage: completed
Fetched: 22 Jul 14:59
Validated: 22 Jul 14:59
Deltas Created 22 Jul 14:59
Units Normalized: 22 Jul 14:59
Ancestry Built: 22 Jul 14:59
Nodes Matched: 22 Jul 14:59
Names Parsed: 22 Jul 14:59
New Models Stored: 22 Jul 14:59
Indexed: 22 Jul 14:59
Completed: 22 Jul 15:01
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:53:29 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:53:29] logged process
[START] [2020-07-22 14:53:29] Creating resource from OpenData
[START] [2020-07-22 14:53:30] logged process
[START] [2020-07-22 14:53:30] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:53:30] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:53:30] Creating resource from OpenData
[INFO] [2020-07-22 14:59:25] ## HARVEST: type = -harvest
[START] [2020-07-22 14:59:29] logged process
[START] [2020-07-22 14:59:29] create_harvest_instance
[STOP] [2020-07-22 14:59:30] create_harvest_instance
[START] [2020-07-22 14:59:30] fetch_files
[STOP] [2020-07-22 14:59:30] fetch_files
[START] [2020-07-22 14:59:30] validate_each_file
[STOP] [2020-07-22 14:59:30] validate_each_file
[START] [2020-07-22 14:59:30] convert_to_csv
[CMD] [2020-07-22 14:59:30] /usr/bin/sort /app/public/converted_csv/hove_et_al_hove__nodes_22024.csv > /app/public/converted_csv/hove_et_al_hove__nodes_22024.csv_sorted
[CMD] [2020-07-22 14:59:30] /usr/bin/sort /app/public/converted_csv/hove_et_al_hove__occurrences_22025.csv > /app/public/converted_csv/hove_et_al_hove__occurrences_22025.csv_sorted
[CMD] [2020-07-22 14:59:30] /usr/bin/sort /app/public/converted_csv/hove_et_al_hove__measurements_22026.csv > /app/public/converted_csv/hove_et_al_hove__measurements_22026.csv_sorted
[STOP] [2020-07-22 14:59:30] convert_to_csv
[START] [2020-07-22 14:59:30] calculate_delta
[CMD] [2020-07-22 14:59:30] echo "0a" > /app/public/diff/hove_et_al_hove__nodes_22024.diff
[CMD] [2020-07-22 14:59:30] tail -n +1 /app/public/converted_csv/hove_et_al_hove__nodes_22024.csv >> /app/public/diff/hove_et_al_hove__nodes_22024.diff
[CMD] [2020-07-22 14:59:30] echo "." >> /app/public/diff/hove_et_al_hove__nodes_22024.diff
[CMD] [2020-07-22 14:59:30] echo "0a" > /app/public/diff/hove_et_al_hove__occurrences_22025.diff
[CMD] [2020-07-22 14:59:30] tail -n +1 /app/public/converted_csv/hove_et_al_hove__occurrences_22025.csv >> /app/public/diff/hove_et_al_hove__occurrences_22025.diff
[CMD] [2020-07-22 14:59:30] echo "." >> /app/public/diff/hove_et_al_hove__occurrences_22025.diff
[CMD] [2020-07-22 14:59:30] echo "0a" > /app/public/diff/hove_et_al_hove__measurements_22026.diff
[CMD] [2020-07-22 14:59:30] tail -n +1 /app/public/converted_csv/hove_et_al_hove__measurements_22026.csv >> /app/public/diff/hove_et_al_hove__measurements_22026.diff
[CMD] [2020-07-22 14:59:30] echo "." >> /app/public/diff/hove_et_al_hove__measurements_22026.diff
[STOP] [2020-07-22 14:59:30] calculate_delta
[START] [2020-07-22 14:59:30] parse_diff_and_store
[INFO] [2020-07-22 14:59:30] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:59:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:59:30] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:59:30] Storing 1 ScientificNames
[INFO] [2020-07-22 14:59:30] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:59:30] Average Time: 0.0
[INFO] [2020-07-22 14:59:30] Total Time: 1s
[INFO] [2020-07-22 14:59:30] Storing 1 Nodes
[INFO] [2020-07-22 14:59:30] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:59:30] Average Time: 0.0
[INFO] [2020-07-22 14:59:30] Total Time: 1s
[INFO] [2020-07-22 14:59:30] Storing 1 Occurrences
[INFO] [2020-07-22 14:59:30] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:59:30] Average Time: 0.0
[INFO] [2020-07-22 14:59:30] Total Time: 1s
[INFO] [2020-07-22 14:59:30] Storing 2 Traits
[INFO] [2020-07-22 14:59:30] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:59:30] Average Time: 0.0
[INFO] [2020-07-22 14:59:30] Total Time: 1s
[INFO] [2020-07-22 14:59:30] Storing 2 MetaTraits
[INFO] [2020-07-22 14:59:30] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:59:30] Average Time: 0.0
[INFO] [2020-07-22 14:59:30] Total Time: 1s
[STOP] [2020-07-22 14:59:30] parse_diff_and_store
[START] [2020-07-22 14:59:30] resolve_keys
[INFO] [2020-07-22 14:59:37] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:59:37] traits to occurrences...
[INFO] [2020-07-22 14:59:37] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:59:37] Traits to sex term...
[INFO] [2020-07-22 14:59:37] Traits to lifestage term...
[INFO] [2020-07-22 14:59:37] MetaTraits to traits...
[INFO] [2020-07-22 14:59:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:59:37] Assocs to occurrences...
[INFO] [2020-07-22 14:59:37] Assocs to nodes...
[INFO] [2020-07-22 14:59:37] Assoc to sex term...
[INFO] [2020-07-22 14:59:37] Assoc to lifestage term...
[STOP] [2020-07-22 14:59:37] resolve_keys
[START] [2020-07-22 14:59:37] hold_for_later_1
[STOP] [2020-07-22 14:59:37] hold_for_later_1
[START] [2020-07-22 14:59:37] hold_for_later_2
[STOP] [2020-07-22 14:59:37] hold_for_later_2
[START] [2020-07-22 14:59:37] resolve_missing_parents
[STOP] [2020-07-22 14:59:37] resolve_missing_parents
[START] [2020-07-22 14:59:37] rebuild_nodes
[START] [2020-07-22 14:59:37] Flattener#flatten
[START] [2020-07-22 14:59:37] Flattener#study_resource
[START] [2020-07-22 14:59:37] Flattener#build_ancestry
[STOP] [2020-07-22 14:59:37] Flattener#build_ancestry
[INFO] [2020-07-22 14:59:37] 1 ancestry keys
[START] [2020-07-22 14:59:37] build_node_ancestors
[INFO] [2020-07-22 14:59:37] old ancestors deleted.
[STOP] [2020-07-22 14:59:37] build_node_ancestors
[WARN] [2020-07-22 14:59:37] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:59:37] Flattener#flatten
[STOP] [2020-07-22 14:59:37] rebuild_nodes
[START] [2020-07-22 14:59:37] resolve_missing_media_owners
[STOP] [2020-07-22 14:59:37] resolve_missing_media_owners
[START] [2020-07-22 14:59:37] sanitize_media_verbatims
[STOP] [2020-07-22 14:59:37] sanitize_media_verbatims
[START] [2020-07-22 14:59:37] queue_downloads
[STOP] [2020-07-22 14:59:37] queue_downloads
[START] [2020-07-22 14:59:37] parse_names
[WARN] [2020-07-22 14:59:37] I see 1 names which still need to be parsed.
[STOP] [2020-07-22 14:59:38] parse_names
[START] [2020-07-22 14:59:38] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:59:38] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:59:38] match_nodes
[START] [2020-07-22 14:59:38] map_all_nodes_to_pages
[STOP] [2020-07-22 14:59:38] map_all_nodes_to_pages
[INFO] [2020-07-22 14:59:38] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-22 14:59:38] update_nodes
[STOP] [2020-07-22 14:59:38] update_nodes
[STOP] [2020-07-22 14:59:38] match_nodes
[START] [2020-07-22 14:59:38] reindex_search
[STOP] [2020-07-22 14:59:38] reindex_search
[START] [2020-07-22 14:59:38] normalize_units
[STOP] [2020-07-22 14:59:38] normalize_units
[START] [2020-07-22 14:59:38] calculate_statistics
[2020-07-22 14:59:38] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:59:38] calculate_statistics
[START] [2020-07-22 14:59:38] complete_harvest_instance
[START] [2020-07-22 14:59:38] overall_tsv_creation
[INFO] [2020-07-22 14:59:38] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-22 15:00:26] 1 Traits (unfiltered)...
[INFO] [2020-07-22 15:01:00] 1 Traits (filtered)...
[INFO] [2020-07-22 15:01:00] 0 Associations (filtered)...
[INFO] [2020-07-22 15:01:00] 3 metadata added.
[INFO] [2020-07-22 15:01:00] 0 metadata added.
[INFO] [2020-07-22 15:01:00] Average Time: 55.18
[INFO] [2020-07-22 15:01:00] Total Time: 1m22s
[STOP] [2020-07-22 15:01:00] overall_tsv_creation
[INFO] [2020-07-22 15:01:00] Done. Check your files:
[INFO] [2020-07-22 15:01:00] (1 lines) /app/public/data/hove_et_al_hove_/publish_nodes.tsv
[INFO] [2020-07-22 15:01:00] (1 lines) /app/public/data/hove_et_al_hove_/publish_scientific_names.tsv
[INFO] [2020-07-22 15:01:00] (2 lines) /app/public/data/hove_et_al_hove_/publish_traits.tsv
[INFO] [2020-07-22 15:01:00] (2 lines) /app/public/data/hove_et_al_hove_/publish_metadata.tsv
[STOP] [2020-07-22 15:01:00] complete_harvest_instance
[START] [2020-07-22 15:01:00] completed
[STOP] [2020-07-22 15:01:00] completed
[STOP] [2020-07-22 15:01:00] logged process, took 91.56
Latest Process

22 Jul 14:59 EXITED currently processing 0