Harvest for Webb 1984 Created 22 Jul 14:55

Stage: completed
Fetched: 22 Jul 14:55
Validated: 22 Jul 14:55
Deltas Created 22 Jul 14:55
Units Normalized: 22 Jul 14:55
Ancestry Built: 22 Jul 14:55
Nodes Matched: 22 Jul 14:55
Names Parsed: 22 Jul 14:55
New Models Stored: 22 Jul 14:55
Indexed: 22 Jul 14:55
Completed: 22 Jul 14:56
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:52:37 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:52:38] logged process
[START] [2020-07-22 14:52:38] Creating resource from OpenData
[START] [2020-07-22 14:52:38] logged process
[START] [2020-07-22 14:52:38] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:52:38] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:52:38] Creating resource from OpenData
[INFO] [2020-07-22 14:55:19] ## HARVEST: type = -harvest
[START] [2020-07-22 14:55:22] logged process
[START] [2020-07-22 14:55:22] create_harvest_instance
[STOP] [2020-07-22 14:55:23] create_harvest_instance
[START] [2020-07-22 14:55:23] fetch_files
[STOP] [2020-07-22 14:55:23] fetch_files
[START] [2020-07-22 14:55:24] validate_each_file
[STOP] [2020-07-22 14:55:24] validate_each_file
[START] [2020-07-22 14:55:24] convert_to_csv
[CMD] [2020-07-22 14:55:24] /usr/bin/sort /app/public/converted_csv/webb_webb_1984_nodes_22018.csv > /app/public/converted_csv/webb_webb_1984_nodes_22018.csv_sorted
[CMD] [2020-07-22 14:55:24] /usr/bin/sort /app/public/converted_csv/webb_webb_1984_occurrences_22019.csv > /app/public/converted_csv/webb_webb_1984_occurrences_22019.csv_sorted
[CMD] [2020-07-22 14:55:24] /usr/bin/sort /app/public/converted_csv/webb_webb_1984_measurements_22020.csv > /app/public/converted_csv/webb_webb_1984_measurements_22020.csv_sorted
[STOP] [2020-07-22 14:55:24] convert_to_csv
[START] [2020-07-22 14:55:24] calculate_delta
[CMD] [2020-07-22 14:55:24] echo "0a" > /app/public/diff/webb_webb_1984_nodes_22018.diff
[CMD] [2020-07-22 14:55:24] tail -n +1 /app/public/converted_csv/webb_webb_1984_nodes_22018.csv >> /app/public/diff/webb_webb_1984_nodes_22018.diff
[CMD] [2020-07-22 14:55:24] echo "." >> /app/public/diff/webb_webb_1984_nodes_22018.diff
[CMD] [2020-07-22 14:55:24] echo "0a" > /app/public/diff/webb_webb_1984_occurrences_22019.diff
[CMD] [2020-07-22 14:55:24] tail -n +1 /app/public/converted_csv/webb_webb_1984_occurrences_22019.csv >> /app/public/diff/webb_webb_1984_occurrences_22019.diff
[CMD] [2020-07-22 14:55:24] echo "." >> /app/public/diff/webb_webb_1984_occurrences_22019.diff
[CMD] [2020-07-22 14:55:24] echo "0a" > /app/public/diff/webb_webb_1984_measurements_22020.diff
[CMD] [2020-07-22 14:55:24] tail -n +1 /app/public/converted_csv/webb_webb_1984_measurements_22020.csv >> /app/public/diff/webb_webb_1984_measurements_22020.diff
[CMD] [2020-07-22 14:55:24] echo "." >> /app/public/diff/webb_webb_1984_measurements_22020.diff
[STOP] [2020-07-22 14:55:24] calculate_delta
[START] [2020-07-22 14:55:24] parse_diff_and_store
[INFO] [2020-07-22 14:55:24] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:55:24] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:55:24] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:55:24] Storing 3 ScientificNames
[INFO] [2020-07-22 14:55:24] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-22 14:55:24] Average Time: 0.0
[INFO] [2020-07-22 14:55:24] Total Time: 1s
[INFO] [2020-07-22 14:55:24] Storing 3 Nodes
[INFO] [2020-07-22 14:55:24] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-22 14:55:24] Average Time: 0.0
[INFO] [2020-07-22 14:55:24] Total Time: 1s
[INFO] [2020-07-22 14:55:24] Storing 3 Occurrences
[INFO] [2020-07-22 14:55:24] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-22 14:55:24] Average Time: 0.0
[INFO] [2020-07-22 14:55:24] Total Time: 1s
[INFO] [2020-07-22 14:55:24] Storing 6 Traits
[INFO] [2020-07-22 14:55:24] Processing group of 6 in 1 groups of 1000
[INFO] [2020-07-22 14:55:24] Average Time: 0.0
[INFO] [2020-07-22 14:55:24] Total Time: 1s
[INFO] [2020-07-22 14:55:24] Storing 8 MetaTraits
[INFO] [2020-07-22 14:55:24] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-22 14:55:24] Average Time: 0.0
[INFO] [2020-07-22 14:55:24] Total Time: 1s
[STOP] [2020-07-22 14:55:24] parse_diff_and_store
[START] [2020-07-22 14:55:24] resolve_keys
[INFO] [2020-07-22 14:55:31] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:55:31] traits to occurrences...
[INFO] [2020-07-22 14:55:31] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:55:31] Traits to sex term...
[INFO] [2020-07-22 14:55:31] Traits to lifestage term...
[INFO] [2020-07-22 14:55:31] MetaTraits to traits...
[INFO] [2020-07-22 14:55:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:55:31] Assocs to occurrences...
[INFO] [2020-07-22 14:55:31] Assocs to nodes...
[INFO] [2020-07-22 14:55:31] Assoc to sex term...
[INFO] [2020-07-22 14:55:31] Assoc to lifestage term...
[STOP] [2020-07-22 14:55:31] resolve_keys
[START] [2020-07-22 14:55:31] hold_for_later_1
[STOP] [2020-07-22 14:55:31] hold_for_later_1
[START] [2020-07-22 14:55:31] hold_for_later_2
[STOP] [2020-07-22 14:55:31] hold_for_later_2
[START] [2020-07-22 14:55:31] resolve_missing_parents
[STOP] [2020-07-22 14:55:31] resolve_missing_parents
[START] [2020-07-22 14:55:31] rebuild_nodes
[START] [2020-07-22 14:55:31] Flattener#flatten
[START] [2020-07-22 14:55:31] Flattener#study_resource
[START] [2020-07-22 14:55:31] Flattener#build_ancestry
[STOP] [2020-07-22 14:55:31] Flattener#build_ancestry
[INFO] [2020-07-22 14:55:31] 3 ancestry keys
[START] [2020-07-22 14:55:31] build_node_ancestors
[INFO] [2020-07-22 14:55:31] old ancestors deleted.
[STOP] [2020-07-22 14:55:31] build_node_ancestors
[WARN] [2020-07-22 14:55:31] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:55:31] Flattener#flatten
[STOP] [2020-07-22 14:55:31] rebuild_nodes
[START] [2020-07-22 14:55:31] resolve_missing_media_owners
[STOP] [2020-07-22 14:55:31] resolve_missing_media_owners
[START] [2020-07-22 14:55:31] sanitize_media_verbatims
[STOP] [2020-07-22 14:55:31] sanitize_media_verbatims
[START] [2020-07-22 14:55:31] queue_downloads
[STOP] [2020-07-22 14:55:31] queue_downloads
[START] [2020-07-22 14:55:31] parse_names
[WARN] [2020-07-22 14:55:31] I see 3 names which still need to be parsed.
[STOP] [2020-07-22 14:55:32] parse_names
[START] [2020-07-22 14:55:32] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:55:32] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:55:32] match_nodes
[START] [2020-07-22 14:55:32] map_all_nodes_to_pages
[STOP] [2020-07-22 14:55:32] map_all_nodes_to_pages
[INFO] [2020-07-22 14:55:32] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-07-22 14:55:32] update_nodes
[STOP] [2020-07-22 14:55:32] update_nodes
[STOP] [2020-07-22 14:55:32] match_nodes
[START] [2020-07-22 14:55:32] reindex_search
[STOP] [2020-07-22 14:55:32] reindex_search
[START] [2020-07-22 14:55:32] normalize_units
[STOP] [2020-07-22 14:55:32] normalize_units
[START] [2020-07-22 14:55:32] calculate_statistics
[2020-07-22 14:55:32] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:55:32] calculate_statistics
[START] [2020-07-22 14:55:32] complete_harvest_instance
[START] [2020-07-22 14:55:32] overall_tsv_creation
[INFO] [2020-07-22 14:55:32] Processing group of 3 in 1 batches of 10000
[INFO] [2020-07-22 14:56:21] 3 Traits (unfiltered)...
[INFO] [2020-07-22 14:56:57] 3 Traits (filtered)...
[INFO] [2020-07-22 14:56:57] 0 Associations (filtered)...
[INFO] [2020-07-22 14:56:57] 11 metadata added.
[INFO] [2020-07-22 14:56:57] 0 metadata added.
[INFO] [2020-07-22 14:56:57] Average Time: 57.5
[INFO] [2020-07-22 14:56:57] Total Time: 1m25s
[STOP] [2020-07-22 14:56:57] overall_tsv_creation
[INFO] [2020-07-22 14:56:57] Done. Check your files:
[INFO] [2020-07-22 14:56:57] (3 lines) /app/public/data/webb_webb_1984/publish_nodes.tsv
[INFO] [2020-07-22 14:56:57] (3 lines) /app/public/data/webb_webb_1984/publish_scientific_names.tsv
[INFO] [2020-07-22 14:56:57] (4 lines) /app/public/data/webb_webb_1984/publish_traits.tsv
[INFO] [2020-07-22 14:56:57] (4 lines) /app/public/data/webb_webb_1984/publish_metadata.tsv
[STOP] [2020-07-22 14:56:57] complete_harvest_instance
[START] [2020-07-22 14:56:57] completed
[STOP] [2020-07-22 14:56:57] completed
[STOP] [2020-07-22 14:56:57] logged process, took 94.27
Latest Process

22 Jul 14:55 EXITED currently processing 0