Harvest for Hoffman and Wiklund 2006 Created 09 Jul 14:45

Stage: completed
Fetched: 09 Jul 14:45
Validated: 09 Jul 14:45
Deltas Created 09 Jul 14:45
Units Normalized: 09 Jul 14:45
Ancestry Built: 09 Jul 14:45
Nodes Matched: 09 Jul 14:45
Names Parsed: 09 Jul 14:45
New Models Stored: 09 Jul 14:45
Indexed: 09 Jul 14:45
Completed: 09 Jul 14:47
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2020-07-09 14:45:36 -0400 by logger.rb/v1.4.2
[INFO] [2020-07-09 14:45:36] ## HARVEST: type = -harvest
[START] [2020-07-09 14:45:36] logged process
[START] [2020-07-09 14:45:36] create_harvest_instance
[STOP] [2020-07-09 14:45:37] create_harvest_instance
[START] [2020-07-09 14:45:37] fetch_files
[STOP] [2020-07-09 14:45:37] fetch_files
[START] [2020-07-09 14:45:37] validate_each_file
[STOP] [2020-07-09 14:45:37] validate_each_file
[START] [2020-07-09 14:45:37] convert_to_csv
[CMD] [2020-07-09 14:45:37] /usr/bin/sort /app/public/converted_csv/hoffman_wiklund__nodes_21545.csv > /app/public/converted_csv/hoffman_wiklund__nodes_21545.csv_sorted
[CMD] [2020-07-09 14:45:37] /usr/bin/sort /app/public/converted_csv/hoffman_wiklund__occurrences_21546.csv > /app/public/converted_csv/hoffman_wiklund__occurrences_21546.csv_sorted
[CMD] [2020-07-09 14:45:37] /usr/bin/sort /app/public/converted_csv/hoffman_wiklund__measurements_21547.csv > /app/public/converted_csv/hoffman_wiklund__measurements_21547.csv_sorted
[STOP] [2020-07-09 14:45:37] convert_to_csv
[START] [2020-07-09 14:45:37] calculate_delta
[CMD] [2020-07-09 14:45:37] echo "0a" > /app/public/diff/hoffman_wiklund__nodes_21545.diff
[CMD] [2020-07-09 14:45:37] tail -n +1 /app/public/converted_csv/hoffman_wiklund__nodes_21545.csv >> /app/public/diff/hoffman_wiklund__nodes_21545.diff
[CMD] [2020-07-09 14:45:37] echo "." >> /app/public/diff/hoffman_wiklund__nodes_21545.diff
[CMD] [2020-07-09 14:45:37] echo "0a" > /app/public/diff/hoffman_wiklund__occurrences_21546.diff
[CMD] [2020-07-09 14:45:37] tail -n +1 /app/public/converted_csv/hoffman_wiklund__occurrences_21546.csv >> /app/public/diff/hoffman_wiklund__occurrences_21546.diff
[CMD] [2020-07-09 14:45:37] echo "." >> /app/public/diff/hoffman_wiklund__occurrences_21546.diff
[CMD] [2020-07-09 14:45:37] echo "0a" > /app/public/diff/hoffman_wiklund__measurements_21547.diff
[CMD] [2020-07-09 14:45:37] tail -n +1 /app/public/converted_csv/hoffman_wiklund__measurements_21547.csv >> /app/public/diff/hoffman_wiklund__measurements_21547.diff
[CMD] [2020-07-09 14:45:37] echo "." >> /app/public/diff/hoffman_wiklund__measurements_21547.diff
[STOP] [2020-07-09 14:45:37] calculate_delta
[START] [2020-07-09 14:45:37] parse_diff_and_store
[INFO] [2020-07-09 14:45:38] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-09 14:45:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-09 14:45:38] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-09 14:45:38] Storing 15 ScientificNames
[INFO] [2020-07-09 14:45:38] Processing group of 15 in 1 groups of 1000
[INFO] [2020-07-09 14:45:38] Average Time: 0.01
[INFO] [2020-07-09 14:45:38] Total Time: 1s
[INFO] [2020-07-09 14:45:38] Storing 15 Nodes
[INFO] [2020-07-09 14:45:38] Processing group of 15 in 1 groups of 1000
[INFO] [2020-07-09 14:45:38] Average Time: 0.03
[INFO] [2020-07-09 14:45:38] Total Time: 1s
[INFO] [2020-07-09 14:45:38] Storing 15 Occurrences
[INFO] [2020-07-09 14:45:38] Processing group of 15 in 1 groups of 1000
[INFO] [2020-07-09 14:45:38] Average Time: 0.02
[INFO] [2020-07-09 14:45:38] Total Time: 1s
[INFO] [2020-07-09 14:45:38] Storing 43 Traits
[INFO] [2020-07-09 14:45:38] Processing group of 43 in 1 groups of 1000
[INFO] [2020-07-09 14:45:38] Average Time: 0.02
[INFO] [2020-07-09 14:45:38] Total Time: 1s
[INFO] [2020-07-09 14:45:38] Storing 86 MetaTraits
[INFO] [2020-07-09 14:45:38] Processing group of 86 in 1 groups of 1000
[INFO] [2020-07-09 14:45:38] Average Time: 0.02
[INFO] [2020-07-09 14:45:38] Total Time: 1s
[STOP] [2020-07-09 14:45:38] parse_diff_and_store
[START] [2020-07-09 14:45:38] resolve_keys
[INFO] [2020-07-09 14:45:45] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-09 14:45:45] traits to occurrences...
[INFO] [2020-07-09 14:45:45] traits to nodes (through occurrences)...
[INFO] [2020-07-09 14:45:45] Traits to sex term...
[INFO] [2020-07-09 14:45:45] Traits to lifestage term...
[INFO] [2020-07-09 14:45:45] MetaTraits to traits...
[INFO] [2020-07-09 14:45:45] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-09 14:45:45] Assocs to occurrences...
[INFO] [2020-07-09 14:45:45] Assocs to nodes...
[INFO] [2020-07-09 14:45:45] Assoc to sex term...
[INFO] [2020-07-09 14:45:45] Assoc to lifestage term...
[STOP] [2020-07-09 14:45:45] resolve_keys
[START] [2020-07-09 14:45:45] hold_for_later_1
[STOP] [2020-07-09 14:45:45] hold_for_later_1
[START] [2020-07-09 14:45:45] hold_for_later_2
[STOP] [2020-07-09 14:45:45] hold_for_later_2
[START] [2020-07-09 14:45:45] resolve_missing_parents
[STOP] [2020-07-09 14:45:45] resolve_missing_parents
[START] [2020-07-09 14:45:45] rebuild_nodes
[START] [2020-07-09 14:45:45] Flattener#flatten
[START] [2020-07-09 14:45:45] Flattener#study_resource
[START] [2020-07-09 14:45:45] Flattener#build_ancestry
[STOP] [2020-07-09 14:45:45] Flattener#build_ancestry
[INFO] [2020-07-09 14:45:45] 15 ancestry keys
[START] [2020-07-09 14:45:45] build_node_ancestors
[INFO] [2020-07-09 14:45:45] old ancestors deleted.
[STOP] [2020-07-09 14:45:45] build_node_ancestors
[WARN] [2020-07-09 14:45:45] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-09 14:45:45] Flattener#flatten
[STOP] [2020-07-09 14:45:45] rebuild_nodes
[START] [2020-07-09 14:45:45] resolve_missing_media_owners
[STOP] [2020-07-09 14:45:45] resolve_missing_media_owners
[START] [2020-07-09 14:45:45] sanitize_media_verbatims
[STOP] [2020-07-09 14:45:45] sanitize_media_verbatims
[START] [2020-07-09 14:45:45] queue_downloads
[STOP] [2020-07-09 14:45:45] queue_downloads
[START] [2020-07-09 14:45:45] parse_names
[WARN] [2020-07-09 14:45:45] I see 15 names which still need to be parsed.
[STOP] [2020-07-09 14:45:46] parse_names
[START] [2020-07-09 14:45:46] denormalize_canonical_names_to_nodes
[STOP] [2020-07-09 14:45:46] denormalize_canonical_names_to_nodes
[START] [2020-07-09 14:45:46] match_nodes
[START] [2020-07-09 14:45:46] map_all_nodes_to_pages
[STOP] [2020-07-09 14:45:46] map_all_nodes_to_pages
[INFO] [2020-07-09 14:45:46] ZERO unmatched nodes (of 15)! Nicely done.
[START] [2020-07-09 14:45:46] update_nodes
[STOP] [2020-07-09 14:45:46] update_nodes
[STOP] [2020-07-09 14:45:46] match_nodes
[START] [2020-07-09 14:45:46] reindex_search
[STOP] [2020-07-09 14:45:46] reindex_search
[START] [2020-07-09 14:45:46] normalize_units
[STOP] [2020-07-09 14:45:46] normalize_units
[START] [2020-07-09 14:45:46] calculate_statistics
[2020-07-09 14:45:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-09 14:45:46] calculate_statistics
[START] [2020-07-09 14:45:46] complete_harvest_instance
[START] [2020-07-09 14:45:46] overall_tsv_creation
[INFO] [2020-07-09 14:45:46] Processing group of 15 in 1 batches of 10000
[INFO] [2020-07-09 14:46:34] 43 Traits (unfiltered)...
[INFO] [2020-07-09 14:46:47] 43 Traits (filtered)...
[INFO] [2020-07-09 14:46:47] 0 Associations (filtered)...
[INFO] [2020-07-09 14:47:23] 86 metadata added.
[INFO] [2020-07-09 14:47:23] 0 metadata added.
[INFO] [2020-07-09 14:47:23] Average Time: 70.45
[INFO] [2020-07-09 14:47:23] Total Time: 1m38s
[STOP] [2020-07-09 14:47:23] overall_tsv_creation
[INFO] [2020-07-09 14:47:23] Done. Check your files:
[INFO] [2020-07-09 14:47:23] (15 lines) /app/public/data/hoffman_wiklund_/publish_nodes.tsv
[INFO] [2020-07-09 14:47:23] (15 lines) /app/public/data/hoffman_wiklund_/publish_scientific_names.tsv
[INFO] [2020-07-09 14:47:23] (44 lines) /app/public/data/hoffman_wiklund_/publish_traits.tsv
[INFO] [2020-07-09 14:47:23] (87 lines) /app/public/data/hoffman_wiklund_/publish_metadata.tsv
[STOP] [2020-07-09 14:47:23] complete_harvest_instance
[START] [2020-07-09 14:47:23] completed
[STOP] [2020-07-09 14:47:23] completed
[STOP] [2020-07-09 14:47:23] logged process, took 106.97
Latest Process

09 Jul 14:45 EXITED currently processing 0