Harvest for Lauga 2006 Created 30 Jul 15:09

Stage: completed
Fetched: 30 Jul 15:09
Validated: 30 Jul 15:09
Deltas Created 30 Jul 15:09
Units Normalized: 30 Jul 15:09
Ancestry Built: 30 Jul 15:09
Nodes Matched: 30 Jul 15:09
Names Parsed: 30 Jul 15:09
New Models Stored: 30 Jul 15:09
Indexed: 30 Jul 15:09
Completed: 30 Jul 15:11
Time to Harvest: less than a minute
Harvesting Log

(141 lines)
# Logfile created on 2020-07-30 15:04:27 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 15:04:27] logged process
[START] [2020-07-30 15:04:27] Creating resource from OpenData
[START] [2020-07-30 15:04:28] logged process
[START] [2020-07-30 15:04:28] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:04:28] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:04:28] Creating resource from OpenData
[INFO] [2020-07-30 15:09:40] ## HARVEST: type = -harvest
[START] [2020-07-30 15:09:44] logged process
[START] [2020-07-30 15:09:44] create_harvest_instance
[STOP] [2020-07-30 15:09:46] create_harvest_instance
[START] [2020-07-30 15:09:46] fetch_files
[STOP] [2020-07-30 15:09:46] fetch_files
[START] [2020-07-30 15:09:46] validate_each_file
[STOP] [2020-07-30 15:09:46] validate_each_file
[START] [2020-07-30 15:09:46] convert_to_csv
[CMD] [2020-07-30 15:09:46] /usr/bin/sort /app/public/converted_csv/lauga_lauga_2006_refs_22380.csv > /app/public/converted_csv/lauga_lauga_2006_refs_22380.csv_sorted
[CMD] [2020-07-30 15:09:46] /usr/bin/sort /app/public/converted_csv/lauga_lauga_2006_nodes_22381.csv > /app/public/converted_csv/lauga_lauga_2006_nodes_22381.csv_sorted
[CMD] [2020-07-30 15:09:46] /usr/bin/sort /app/public/converted_csv/lauga_lauga_2006_occurrences_22382.csv > /app/public/converted_csv/lauga_lauga_2006_occurrences_22382.csv_sorted
[CMD] [2020-07-30 15:09:46] /usr/bin/sort /app/public/converted_csv/lauga_lauga_2006_measurements_22383.csv > /app/public/converted_csv/lauga_lauga_2006_measurements_22383.csv_sorted
[STOP] [2020-07-30 15:09:46] convert_to_csv
[START] [2020-07-30 15:09:46] calculate_delta
[CMD] [2020-07-30 15:09:46] echo "0a" > /app/public/diff/lauga_lauga_2006_refs_22380.diff
[CMD] [2020-07-30 15:09:46] tail -n +1 /app/public/converted_csv/lauga_lauga_2006_refs_22380.csv >> /app/public/diff/lauga_lauga_2006_refs_22380.diff
[CMD] [2020-07-30 15:09:46] echo "." >> /app/public/diff/lauga_lauga_2006_refs_22380.diff
[CMD] [2020-07-30 15:09:46] echo "0a" > /app/public/diff/lauga_lauga_2006_nodes_22381.diff
[CMD] [2020-07-30 15:09:46] tail -n +1 /app/public/converted_csv/lauga_lauga_2006_nodes_22381.csv >> /app/public/diff/lauga_lauga_2006_nodes_22381.diff
[CMD] [2020-07-30 15:09:46] echo "." >> /app/public/diff/lauga_lauga_2006_nodes_22381.diff
[CMD] [2020-07-30 15:09:46] echo "0a" > /app/public/diff/lauga_lauga_2006_occurrences_22382.diff
[CMD] [2020-07-30 15:09:46] tail -n +1 /app/public/converted_csv/lauga_lauga_2006_occurrences_22382.csv >> /app/public/diff/lauga_lauga_2006_occurrences_22382.diff
[CMD] [2020-07-30 15:09:46] echo "." >> /app/public/diff/lauga_lauga_2006_occurrences_22382.diff
[CMD] [2020-07-30 15:09:46] echo "0a" > /app/public/diff/lauga_lauga_2006_measurements_22383.diff
[CMD] [2020-07-30 15:09:46] tail -n +1 /app/public/converted_csv/lauga_lauga_2006_measurements_22383.csv >> /app/public/diff/lauga_lauga_2006_measurements_22383.diff
[CMD] [2020-07-30 15:09:46] echo "." >> /app/public/diff/lauga_lauga_2006_measurements_22383.diff
[STOP] [2020-07-30 15:09:46] calculate_delta
[START] [2020-07-30 15:09:46] parse_diff_and_store
[INFO] [2020-07-30 15:09:46] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:46] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:46] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:46] Storing 1 ScientificNames
[INFO] [2020-07-30 15:09:46] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:46] Average Time: 0.0
[INFO] [2020-07-30 15:09:46] Total Time: 1s
[INFO] [2020-07-30 15:09:46] Storing 1 Nodes
[INFO] [2020-07-30 15:09:46] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:46] Average Time: 0.0
[INFO] [2020-07-30 15:09:46] Total Time: 1s
[INFO] [2020-07-30 15:09:46] Storing 1 Occurrences
[INFO] [2020-07-30 15:09:46] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:46] Average Time: 0.0
[INFO] [2020-07-30 15:09:46] Total Time: 1s
[INFO] [2020-07-30 15:09:46] Storing 1 OccurrenceMetadata
[INFO] [2020-07-30 15:09:46] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:46] Average Time: 0.0
[INFO] [2020-07-30 15:09:46] Total Time: 1s
[INFO] [2020-07-30 15:09:46] Storing 8 Traits
[INFO] [2020-07-30 15:09:46] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 15:09:46] Average Time: 0.0
[INFO] [2020-07-30 15:09:46] Total Time: 1s
[INFO] [2020-07-30 15:09:46] Storing 2 MetaTraits
[INFO] [2020-07-30 15:09:46] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:09:46] Average Time: 0.0
[INFO] [2020-07-30 15:09:46] Total Time: 1s
[STOP] [2020-07-30 15:09:46] parse_diff_and_store
[START] [2020-07-30 15:09:46] resolve_keys
[INFO] [2020-07-30 15:09:53] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 15:09:53] traits to occurrences...
[INFO] [2020-07-30 15:09:53] traits to nodes (through occurrences)...
[INFO] [2020-07-30 15:09:53] Traits to sex term...
[INFO] [2020-07-30 15:09:53] Traits to lifestage term...
[INFO] [2020-07-30 15:09:53] MetaTraits to traits...
[INFO] [2020-07-30 15:09:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 15:09:53] Assocs to occurrences...
[INFO] [2020-07-30 15:09:53] Assocs to nodes...
[INFO] [2020-07-30 15:09:53] Assoc to sex term...
[INFO] [2020-07-30 15:09:53] Assoc to lifestage term...
[STOP] [2020-07-30 15:09:53] resolve_keys
[START] [2020-07-30 15:09:53] hold_for_later_1
[STOP] [2020-07-30 15:09:53] hold_for_later_1
[START] [2020-07-30 15:09:53] hold_for_later_2
[STOP] [2020-07-30 15:09:53] hold_for_later_2
[START] [2020-07-30 15:09:53] resolve_missing_parents
[STOP] [2020-07-30 15:09:53] resolve_missing_parents
[START] [2020-07-30 15:09:53] rebuild_nodes
[START] [2020-07-30 15:09:53] Flattener#flatten
[START] [2020-07-30 15:09:53] Flattener#study_resource
[START] [2020-07-30 15:09:53] Flattener#build_ancestry
[STOP] [2020-07-30 15:09:53] Flattener#build_ancestry
[INFO] [2020-07-30 15:09:53] 1 ancestry keys
[START] [2020-07-30 15:09:53] build_node_ancestors
[INFO] [2020-07-30 15:09:53] old ancestors deleted.
[STOP] [2020-07-30 15:09:53] build_node_ancestors
[WARN] [2020-07-30 15:09:53] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 15:09:53] Flattener#flatten
[STOP] [2020-07-30 15:09:53] rebuild_nodes
[START] [2020-07-30 15:09:53] resolve_missing_media_owners
[STOP] [2020-07-30 15:09:53] resolve_missing_media_owners
[START] [2020-07-30 15:09:53] sanitize_media_verbatims
[STOP] [2020-07-30 15:09:53] sanitize_media_verbatims
[START] [2020-07-30 15:09:53] queue_downloads
[STOP] [2020-07-30 15:09:53] queue_downloads
[START] [2020-07-30 15:09:53] parse_names
[WARN] [2020-07-30 15:09:53] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 15:09:54] parse_names
[START] [2020-07-30 15:09:54] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 15:09:54] denormalize_canonical_names_to_nodes
[START] [2020-07-30 15:09:54] match_nodes
[START] [2020-07-30 15:09:54] map_all_nodes_to_pages
[STOP] [2020-07-30 15:09:54] map_all_nodes_to_pages
[INFO] [2020-07-30 15:09:54] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 15:09:54] update_nodes
[STOP] [2020-07-30 15:09:54] update_nodes
[STOP] [2020-07-30 15:09:54] match_nodes
[START] [2020-07-30 15:09:54] reindex_search
[STOP] [2020-07-30 15:09:54] reindex_search
[START] [2020-07-30 15:09:54] normalize_units
[STOP] [2020-07-30 15:09:54] normalize_units
[START] [2020-07-30 15:09:54] calculate_statistics
[2020-07-30 15:09:54] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 15:09:54] calculate_statistics
[START] [2020-07-30 15:09:54] complete_harvest_instance
[START] [2020-07-30 15:09:54] overall_tsv_creation
[INFO] [2020-07-30 15:09:54] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 15:10:42] 1 Traits (unfiltered)...
[INFO] [2020-07-30 15:11:17] 1 Traits (filtered)...
[INFO] [2020-07-30 15:11:17] 0 Associations (filtered)...
[INFO] [2020-07-30 15:11:17] 10 metadata added.
[INFO] [2020-07-30 15:11:17] 0 metadata added.
[INFO] [2020-07-30 15:11:17] Average Time: 56.21
[INFO] [2020-07-30 15:11:17] Total Time: 1m24s
[STOP] [2020-07-30 15:11:17] overall_tsv_creation
[INFO] [2020-07-30 15:11:17] Done. Check your files:
[INFO] [2020-07-30 15:11:17] (1 lines) /app/public/data/lauga_lauga_2006/publish_nodes.tsv
[INFO] [2020-07-30 15:11:17] (1 lines) /app/public/data/lauga_lauga_2006/publish_scientific_names.tsv
[INFO] [2020-07-30 15:11:17] (2 lines) /app/public/data/lauga_lauga_2006/publish_traits.tsv
[INFO] [2020-07-30 15:11:17] (9 lines) /app/public/data/lauga_lauga_2006/publish_metadata.tsv
[STOP] [2020-07-30 15:11:17] complete_harvest_instance
[START] [2020-07-30 15:11:17] completed
[STOP] [2020-07-30 15:11:17] completed
[STOP] [2020-07-30 15:11:17] logged process, took 92.98
Latest Process

30 Jul 15:09 EXITED currently processing 0