Harvest for Biewener 1989 Created 22 Jul 14:41

Stage: completed
Fetched: 22 Jul 14:41
Validated: 22 Jul 14:41
Deltas Created 22 Jul 14:41
Units Normalized: 22 Jul 14:41
Ancestry Built: 22 Jul 14:41
Nodes Matched: 22 Jul 14:41
Names Parsed: 22 Jul 14:41
New Models Stored: 22 Jul 14:41
Indexed: 22 Jul 14:41
Completed: 22 Jul 14:43
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:40:49 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:40:49] logged process
[START] [2020-07-22 14:40:49] Creating resource from OpenData
[START] [2020-07-22 14:40:49] logged process
[START] [2020-07-22 14:40:49] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:40:49] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:40:49] Creating resource from OpenData
[INFO] [2020-07-22 14:41:30] ## HARVEST: type = -harvest
[START] [2020-07-22 14:41:34] logged process
[START] [2020-07-22 14:41:34] create_harvest_instance
[STOP] [2020-07-22 14:41:35] create_harvest_instance
[START] [2020-07-22 14:41:35] fetch_files
[STOP] [2020-07-22 14:41:35] fetch_files
[START] [2020-07-22 14:41:35] validate_each_file
[STOP] [2020-07-22 14:41:35] validate_each_file
[START] [2020-07-22 14:41:35] convert_to_csv
[CMD] [2020-07-22 14:41:35] /usr/bin/sort /app/public/converted_csv/biewener_biewen2_nodes_21991.csv > /app/public/converted_csv/biewener_biewen2_nodes_21991.csv_sorted
[CMD] [2020-07-22 14:41:35] /usr/bin/sort /app/public/converted_csv/biewener_biewen2_occurrences_21992.csv > /app/public/converted_csv/biewener_biewen2_occurrences_21992.csv_sorted
[CMD] [2020-07-22 14:41:35] /usr/bin/sort /app/public/converted_csv/biewener_biewen2_measurements_21993.csv > /app/public/converted_csv/biewener_biewen2_measurements_21993.csv_sorted
[STOP] [2020-07-22 14:41:35] convert_to_csv
[START] [2020-07-22 14:41:35] calculate_delta
[CMD] [2020-07-22 14:41:35] echo "0a" > /app/public/diff/biewener_biewen2_nodes_21991.diff
[CMD] [2020-07-22 14:41:35] tail -n +1 /app/public/converted_csv/biewener_biewen2_nodes_21991.csv >> /app/public/diff/biewener_biewen2_nodes_21991.diff
[CMD] [2020-07-22 14:41:35] echo "." >> /app/public/diff/biewener_biewen2_nodes_21991.diff
[CMD] [2020-07-22 14:41:35] echo "0a" > /app/public/diff/biewener_biewen2_occurrences_21992.diff
[CMD] [2020-07-22 14:41:35] tail -n +1 /app/public/converted_csv/biewener_biewen2_occurrences_21992.csv >> /app/public/diff/biewener_biewen2_occurrences_21992.diff
[CMD] [2020-07-22 14:41:35] echo "." >> /app/public/diff/biewener_biewen2_occurrences_21992.diff
[CMD] [2020-07-22 14:41:35] echo "0a" > /app/public/diff/biewener_biewen2_measurements_21993.diff
[CMD] [2020-07-22 14:41:35] tail -n +1 /app/public/converted_csv/biewener_biewen2_measurements_21993.csv >> /app/public/diff/biewener_biewen2_measurements_21993.diff
[CMD] [2020-07-22 14:41:35] echo "." >> /app/public/diff/biewener_biewen2_measurements_21993.diff
[STOP] [2020-07-22 14:41:35] calculate_delta
[START] [2020-07-22 14:41:35] parse_diff_and_store
[INFO] [2020-07-22 14:41:35] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:41:35] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:41:35] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:41:35] Storing 1 ScientificNames
[INFO] [2020-07-22 14:41:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:41:35] Average Time: 0.0
[INFO] [2020-07-22 14:41:35] Total Time: 1s
[INFO] [2020-07-22 14:41:35] Storing 1 Nodes
[INFO] [2020-07-22 14:41:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:41:35] Average Time: 0.0
[INFO] [2020-07-22 14:41:35] Total Time: 1s
[INFO] [2020-07-22 14:41:35] Storing 1 Occurrences
[INFO] [2020-07-22 14:41:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:41:35] Average Time: 0.0
[INFO] [2020-07-22 14:41:35] Total Time: 1s
[INFO] [2020-07-22 14:41:35] Storing 6 Traits
[INFO] [2020-07-22 14:41:35] Processing group of 6 in 1 groups of 1000
[INFO] [2020-07-22 14:41:35] Average Time: 0.0
[INFO] [2020-07-22 14:41:35] Total Time: 1s
[INFO] [2020-07-22 14:41:35] Storing 2 MetaTraits
[INFO] [2020-07-22 14:41:35] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:41:35] Average Time: 0.0
[INFO] [2020-07-22 14:41:35] Total Time: 1s
[STOP] [2020-07-22 14:41:35] parse_diff_and_store
[START] [2020-07-22 14:41:35] resolve_keys
[INFO] [2020-07-22 14:41:42] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:41:42] traits to occurrences...
[INFO] [2020-07-22 14:41:42] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:41:42] Traits to sex term...
[INFO] [2020-07-22 14:41:42] Traits to lifestage term...
[INFO] [2020-07-22 14:41:42] MetaTraits to traits...
[INFO] [2020-07-22 14:41:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:41:42] Assocs to occurrences...
[INFO] [2020-07-22 14:41:42] Assocs to nodes...
[INFO] [2020-07-22 14:41:42] Assoc to sex term...
[INFO] [2020-07-22 14:41:42] Assoc to lifestage term...
[STOP] [2020-07-22 14:41:42] resolve_keys
[START] [2020-07-22 14:41:42] hold_for_later_1
[STOP] [2020-07-22 14:41:42] hold_for_later_1
[START] [2020-07-22 14:41:42] hold_for_later_2
[STOP] [2020-07-22 14:41:42] hold_for_later_2
[START] [2020-07-22 14:41:42] resolve_missing_parents
[STOP] [2020-07-22 14:41:42] resolve_missing_parents
[START] [2020-07-22 14:41:42] rebuild_nodes
[START] [2020-07-22 14:41:42] Flattener#flatten
[START] [2020-07-22 14:41:42] Flattener#study_resource
[START] [2020-07-22 14:41:42] Flattener#build_ancestry
[STOP] [2020-07-22 14:41:42] Flattener#build_ancestry
[INFO] [2020-07-22 14:41:42] 1 ancestry keys
[START] [2020-07-22 14:41:42] build_node_ancestors
[INFO] [2020-07-22 14:41:42] old ancestors deleted.
[STOP] [2020-07-22 14:41:42] build_node_ancestors
[WARN] [2020-07-22 14:41:42] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:41:42] Flattener#flatten
[STOP] [2020-07-22 14:41:42] rebuild_nodes
[START] [2020-07-22 14:41:42] resolve_missing_media_owners
[STOP] [2020-07-22 14:41:42] resolve_missing_media_owners
[START] [2020-07-22 14:41:42] sanitize_media_verbatims
[STOP] [2020-07-22 14:41:42] sanitize_media_verbatims
[START] [2020-07-22 14:41:42] queue_downloads
[STOP] [2020-07-22 14:41:42] queue_downloads
[START] [2020-07-22 14:41:42] parse_names
[WARN] [2020-07-22 14:41:42] I see 1 names which still need to be parsed.
[STOP] [2020-07-22 14:41:43] parse_names
[START] [2020-07-22 14:41:43] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:41:43] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:41:43] match_nodes
[START] [2020-07-22 14:41:43] map_all_nodes_to_pages
[STOP] [2020-07-22 14:41:43] map_all_nodes_to_pages
[INFO] [2020-07-22 14:41:43] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-22 14:41:43] update_nodes
[STOP] [2020-07-22 14:41:43] update_nodes
[STOP] [2020-07-22 14:41:43] match_nodes
[START] [2020-07-22 14:41:43] reindex_search
[STOP] [2020-07-22 14:41:43] reindex_search
[START] [2020-07-22 14:41:43] normalize_units
[STOP] [2020-07-22 14:41:43] normalize_units
[START] [2020-07-22 14:41:43] calculate_statistics
[2020-07-22 14:41:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:41:43] calculate_statistics
[START] [2020-07-22 14:41:43] complete_harvest_instance
[START] [2020-07-22 14:41:43] overall_tsv_creation
[INFO] [2020-07-22 14:41:43] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-22 14:42:32] 1 Traits (unfiltered)...
[INFO] [2020-07-22 14:43:06] 1 Traits (filtered)...
[INFO] [2020-07-22 14:43:06] 0 Associations (filtered)...
[INFO] [2020-07-22 14:43:06] 7 metadata added.
[INFO] [2020-07-22 14:43:06] 0 metadata added.
[INFO] [2020-07-22 14:43:06] Average Time: 55.74
[INFO] [2020-07-22 14:43:06] Total Time: 1m23s
[STOP] [2020-07-22 14:43:06] overall_tsv_creation
[INFO] [2020-07-22 14:43:06] Done. Check your files:
[INFO] [2020-07-22 14:43:06] (1 lines) /app/public/data/biewener_biewen2/publish_nodes.tsv
[INFO] [2020-07-22 14:43:06] (1 lines) /app/public/data/biewener_biewen2/publish_scientific_names.tsv
[INFO] [2020-07-22 14:43:06] (2 lines) /app/public/data/biewener_biewen2/publish_traits.tsv
[INFO] [2020-07-22 14:43:06] (6 lines) /app/public/data/biewener_biewen2/publish_metadata.tsv
[STOP] [2020-07-22 14:43:06] complete_harvest_instance
[START] [2020-07-22 14:43:06] completed
[STOP] [2020-07-22 14:43:06] completed
[STOP] [2020-07-22 14:43:06] logged process, took 92.51
Latest Process

22 Jul 14:41 EXITED currently processing 0