Harvest for Spain 2002 Created 30 Jul 14:49

Stage: completed
Fetched: 30 Jul 14:49
Validated: 30 Jul 14:49
Deltas Created 30 Jul 14:49
Units Normalized: 30 Jul 14:49
Ancestry Built: 30 Jul 14:49
Nodes Matched: 30 Jul 14:49
Names Parsed: 30 Jul 14:49
New Models Stored: 30 Jul 14:49
Indexed: 30 Jul 14:49
Completed: 30 Jul 14:51
Time to Harvest: less than a minute
Harvesting Log

(137 lines)
# Logfile created on 2020-07-30 14:49:26 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 14:49:26] logged process
[START] [2020-07-30 14:49:26] Creating resource from OpenData
[START] [2020-07-30 14:49:26] logged process
[START] [2020-07-30 14:49:26] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:49:26] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:49:26] Creating resource from OpenData
[INFO] [2020-07-30 14:49:40] ## HARVEST: type = -harvest
[START] [2020-07-30 14:49:41] logged process
[START] [2020-07-30 14:49:41] create_harvest_instance
[STOP] [2020-07-30 14:49:43] create_harvest_instance
[START] [2020-07-30 14:49:43] fetch_files
[STOP] [2020-07-30 14:49:43] fetch_files
[START] [2020-07-30 14:49:43] validate_each_file
[STOP] [2020-07-30 14:49:43] validate_each_file
[START] [2020-07-30 14:49:43] convert_to_csv
[CMD] [2020-07-30 14:49:43] /usr/bin/sort /app/public/converted_csv/spain_spain_2002_refs_22316.csv > /app/public/converted_csv/spain_spain_2002_refs_22316.csv_sorted
[CMD] [2020-07-30 14:49:43] /usr/bin/sort /app/public/converted_csv/spain_spain_2002_nodes_22317.csv > /app/public/converted_csv/spain_spain_2002_nodes_22317.csv_sorted
[CMD] [2020-07-30 14:49:43] /usr/bin/sort /app/public/converted_csv/spain_spain_2002_occurrences_22318.csv > /app/public/converted_csv/spain_spain_2002_occurrences_22318.csv_sorted
[CMD] [2020-07-30 14:49:43] /usr/bin/sort /app/public/converted_csv/spain_spain_2002_measurements_22319.csv > /app/public/converted_csv/spain_spain_2002_measurements_22319.csv_sorted
[STOP] [2020-07-30 14:49:43] convert_to_csv
[START] [2020-07-30 14:49:43] calculate_delta
[CMD] [2020-07-30 14:49:43] echo "0a" > /app/public/diff/spain_spain_2002_refs_22316.diff
[CMD] [2020-07-30 14:49:43] tail -n +1 /app/public/converted_csv/spain_spain_2002_refs_22316.csv >> /app/public/diff/spain_spain_2002_refs_22316.diff
[CMD] [2020-07-30 14:49:43] echo "." >> /app/public/diff/spain_spain_2002_refs_22316.diff
[CMD] [2020-07-30 14:49:43] echo "0a" > /app/public/diff/spain_spain_2002_nodes_22317.diff
[CMD] [2020-07-30 14:49:43] tail -n +1 /app/public/converted_csv/spain_spain_2002_nodes_22317.csv >> /app/public/diff/spain_spain_2002_nodes_22317.diff
[CMD] [2020-07-30 14:49:43] echo "." >> /app/public/diff/spain_spain_2002_nodes_22317.diff
[CMD] [2020-07-30 14:49:43] echo "0a" > /app/public/diff/spain_spain_2002_occurrences_22318.diff
[CMD] [2020-07-30 14:49:43] tail -n +1 /app/public/converted_csv/spain_spain_2002_occurrences_22318.csv >> /app/public/diff/spain_spain_2002_occurrences_22318.diff
[CMD] [2020-07-30 14:49:43] echo "." >> /app/public/diff/spain_spain_2002_occurrences_22318.diff
[CMD] [2020-07-30 14:49:43] echo "0a" > /app/public/diff/spain_spain_2002_measurements_22319.diff
[CMD] [2020-07-30 14:49:43] tail -n +1 /app/public/converted_csv/spain_spain_2002_measurements_22319.csv >> /app/public/diff/spain_spain_2002_measurements_22319.diff
[CMD] [2020-07-30 14:49:43] echo "." >> /app/public/diff/spain_spain_2002_measurements_22319.diff
[STOP] [2020-07-30 14:49:43] calculate_delta
[START] [2020-07-30 14:49:43] parse_diff_and_store
[INFO] [2020-07-30 14:49:43] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:49:43] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:49:43] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:49:43] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:49:43] Storing 2 ScientificNames
[INFO] [2020-07-30 14:49:43] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 14:49:43] Average Time: 0.0
[INFO] [2020-07-30 14:49:43] Total Time: 1s
[INFO] [2020-07-30 14:49:43] Storing 2 Nodes
[INFO] [2020-07-30 14:49:43] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 14:49:43] Average Time: 0.0
[INFO] [2020-07-30 14:49:43] Total Time: 1s
[INFO] [2020-07-30 14:49:43] Storing 2 Occurrences
[INFO] [2020-07-30 14:49:43] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 14:49:43] Average Time: 0.0
[INFO] [2020-07-30 14:49:43] Total Time: 1s
[INFO] [2020-07-30 14:49:43] Storing 4 Traits
[INFO] [2020-07-30 14:49:43] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:49:43] Average Time: 0.0
[INFO] [2020-07-30 14:49:43] Total Time: 1s
[INFO] [2020-07-30 14:49:43] Storing 8 MetaTraits
[INFO] [2020-07-30 14:49:43] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 14:49:43] Average Time: 0.0
[INFO] [2020-07-30 14:49:43] Total Time: 1s
[STOP] [2020-07-30 14:49:43] parse_diff_and_store
[START] [2020-07-30 14:49:43] resolve_keys
[INFO] [2020-07-30 14:49:50] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:49:50] traits to occurrences...
[INFO] [2020-07-30 14:49:50] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:49:50] Traits to sex term...
[INFO] [2020-07-30 14:49:50] Traits to lifestage term...
[INFO] [2020-07-30 14:49:50] MetaTraits to traits...
[INFO] [2020-07-30 14:49:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:49:50] Assocs to occurrences...
[INFO] [2020-07-30 14:49:50] Assocs to nodes...
[INFO] [2020-07-30 14:49:50] Assoc to sex term...
[INFO] [2020-07-30 14:49:50] Assoc to lifestage term...
[STOP] [2020-07-30 14:49:50] resolve_keys
[START] [2020-07-30 14:49:50] hold_for_later_1
[STOP] [2020-07-30 14:49:50] hold_for_later_1
[START] [2020-07-30 14:49:50] hold_for_later_2
[STOP] [2020-07-30 14:49:50] hold_for_later_2
[START] [2020-07-30 14:49:50] resolve_missing_parents
[STOP] [2020-07-30 14:49:50] resolve_missing_parents
[START] [2020-07-30 14:49:50] rebuild_nodes
[START] [2020-07-30 14:49:50] Flattener#flatten
[START] [2020-07-30 14:49:50] Flattener#study_resource
[START] [2020-07-30 14:49:50] Flattener#build_ancestry
[STOP] [2020-07-30 14:49:50] Flattener#build_ancestry
[INFO] [2020-07-30 14:49:50] 2 ancestry keys
[START] [2020-07-30 14:49:50] build_node_ancestors
[INFO] [2020-07-30 14:49:50] old ancestors deleted.
[STOP] [2020-07-30 14:49:50] build_node_ancestors
[WARN] [2020-07-30 14:49:50] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:49:50] Flattener#flatten
[STOP] [2020-07-30 14:49:50] rebuild_nodes
[START] [2020-07-30 14:49:50] resolve_missing_media_owners
[STOP] [2020-07-30 14:49:50] resolve_missing_media_owners
[START] [2020-07-30 14:49:50] sanitize_media_verbatims
[STOP] [2020-07-30 14:49:50] sanitize_media_verbatims
[START] [2020-07-30 14:49:50] queue_downloads
[STOP] [2020-07-30 14:49:50] queue_downloads
[START] [2020-07-30 14:49:50] parse_names
[WARN] [2020-07-30 14:49:50] I see 2 names which still need to be parsed.
[STOP] [2020-07-30 14:49:51] parse_names
[START] [2020-07-30 14:49:51] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:49:51] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:49:51] match_nodes
[START] [2020-07-30 14:49:51] map_all_nodes_to_pages
[STOP] [2020-07-30 14:49:51] map_all_nodes_to_pages
[INFO] [2020-07-30 14:49:51] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-07-30 14:49:51] update_nodes
[STOP] [2020-07-30 14:49:51] update_nodes
[STOP] [2020-07-30 14:49:51] match_nodes
[START] [2020-07-30 14:49:51] reindex_search
[STOP] [2020-07-30 14:49:51] reindex_search
[START] [2020-07-30 14:49:51] normalize_units
[STOP] [2020-07-30 14:49:51] normalize_units
[START] [2020-07-30 14:49:51] calculate_statistics
[2020-07-30 14:49:51] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:49:51] calculate_statistics
[START] [2020-07-30 14:49:51] complete_harvest_instance
[START] [2020-07-30 14:49:51] overall_tsv_creation
[INFO] [2020-07-30 14:49:51] Processing group of 2 in 1 batches of 10000
[INFO] [2020-07-30 14:50:40] 2 Traits (unfiltered)...
[INFO] [2020-07-30 14:51:17] 2 Traits (filtered)...
[INFO] [2020-07-30 14:51:17] 0 Associations (filtered)...
[INFO] [2020-07-30 14:51:17] 10 metadata added.
[INFO] [2020-07-30 14:51:17] 0 metadata added.
[INFO] [2020-07-30 14:51:17] Average Time: 58.18
[INFO] [2020-07-30 14:51:17] Total Time: 1m26s
[STOP] [2020-07-30 14:51:17] overall_tsv_creation
[INFO] [2020-07-30 14:51:17] Done. Check your files:
[INFO] [2020-07-30 14:51:17] (2 lines) /app/public/data/spain_spain_2002/publish_nodes.tsv
[INFO] [2020-07-30 14:51:17] (2 lines) /app/public/data/spain_spain_2002/publish_scientific_names.tsv
[INFO] [2020-07-30 14:51:17] (3 lines) /app/public/data/spain_spain_2002/publish_traits.tsv
[INFO] [2020-07-30 14:51:17] (3 lines) /app/public/data/spain_spain_2002/publish_metadata.tsv
[STOP] [2020-07-30 14:51:17] complete_harvest_instance
[START] [2020-07-30 14:51:17] completed
[STOP] [2020-07-30 14:51:17] completed
[STOP] [2020-07-30 14:51:17] logged process, took 95.3
Latest Process

30 Jul 14:49 EXITED currently processing 0