Harvest for Lovegrove 2004 Created 22 Jul 14:53

Stage: completed
Fetched: 22 Jul 14:53
Validated: 22 Jul 14:53
Deltas Created 22 Jul 14:53
Units Normalized: 22 Jul 14:53
Ancestry Built: 22 Jul 14:53
Nodes Matched: 22 Jul 14:53
Names Parsed: 22 Jul 14:53
New Models Stored: 22 Jul 14:53
Indexed: 22 Jul 14:53
Completed: 22 Jul 14:54
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:50:56 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:50:56] logged process
[START] [2020-07-22 14:50:56] Creating resource from OpenData
[START] [2020-07-22 14:50:56] logged process
[START] [2020-07-22 14:50:56] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:50:56] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:50:56] Creating resource from OpenData
[INFO] [2020-07-22 14:53:00] ## HARVEST: type = -harvest
[START] [2020-07-22 14:53:02] logged process
[START] [2020-07-22 14:53:02] create_harvest_instance
[STOP] [2020-07-22 14:53:03] create_harvest_instance
[START] [2020-07-22 14:53:03] fetch_files
[STOP] [2020-07-22 14:53:03] fetch_files
[START] [2020-07-22 14:53:03] validate_each_file
[STOP] [2020-07-22 14:53:03] validate_each_file
[START] [2020-07-22 14:53:03] convert_to_csv
[CMD] [2020-07-22 14:53:03] /usr/bin/sort /app/public/converted_csv/lovegrove_lovegr_nodes_22012.csv > /app/public/converted_csv/lovegrove_lovegr_nodes_22012.csv_sorted
[CMD] [2020-07-22 14:53:03] /usr/bin/sort /app/public/converted_csv/lovegrove_lovegr_occurrences_22013.csv > /app/public/converted_csv/lovegrove_lovegr_occurrences_22013.csv_sorted
[CMD] [2020-07-22 14:53:03] /usr/bin/sort /app/public/converted_csv/lovegrove_lovegr_measurements_22014.csv > /app/public/converted_csv/lovegrove_lovegr_measurements_22014.csv_sorted
[STOP] [2020-07-22 14:53:03] convert_to_csv
[START] [2020-07-22 14:53:03] calculate_delta
[CMD] [2020-07-22 14:53:03] echo "0a" > /app/public/diff/lovegrove_lovegr_nodes_22012.diff
[CMD] [2020-07-22 14:53:03] tail -n +1 /app/public/converted_csv/lovegrove_lovegr_nodes_22012.csv >> /app/public/diff/lovegrove_lovegr_nodes_22012.diff
[CMD] [2020-07-22 14:53:03] echo "." >> /app/public/diff/lovegrove_lovegr_nodes_22012.diff
[CMD] [2020-07-22 14:53:03] echo "0a" > /app/public/diff/lovegrove_lovegr_occurrences_22013.diff
[CMD] [2020-07-22 14:53:03] tail -n +1 /app/public/converted_csv/lovegrove_lovegr_occurrences_22013.csv >> /app/public/diff/lovegrove_lovegr_occurrences_22013.diff
[CMD] [2020-07-22 14:53:03] echo "." >> /app/public/diff/lovegrove_lovegr_occurrences_22013.diff
[CMD] [2020-07-22 14:53:03] echo "0a" > /app/public/diff/lovegrove_lovegr_measurements_22014.diff
[CMD] [2020-07-22 14:53:03] tail -n +1 /app/public/converted_csv/lovegrove_lovegr_measurements_22014.csv >> /app/public/diff/lovegrove_lovegr_measurements_22014.diff
[CMD] [2020-07-22 14:53:03] echo "." >> /app/public/diff/lovegrove_lovegr_measurements_22014.diff
[STOP] [2020-07-22 14:53:03] calculate_delta
[START] [2020-07-22 14:53:03] parse_diff_and_store
[INFO] [2020-07-22 14:53:03] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:53:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:53:03] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:53:03] Storing 7 ScientificNames
[INFO] [2020-07-22 14:53:03] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-22 14:53:03] Average Time: 0.01
[INFO] [2020-07-22 14:53:03] Total Time: 1s
[INFO] [2020-07-22 14:53:03] Storing 7 Nodes
[INFO] [2020-07-22 14:53:03] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-22 14:53:03] Average Time: 0.0
[INFO] [2020-07-22 14:53:03] Total Time: 1s
[INFO] [2020-07-22 14:53:03] Storing 7 Occurrences
[INFO] [2020-07-22 14:53:03] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-22 14:53:03] Average Time: 0.0
[INFO] [2020-07-22 14:53:03] Total Time: 1s
[INFO] [2020-07-22 14:53:03] Storing 15 Traits
[INFO] [2020-07-22 14:53:03] Processing group of 15 in 1 groups of 1000
[INFO] [2020-07-22 14:53:03] Average Time: 0.01
[INFO] [2020-07-22 14:53:03] Total Time: 1s
[INFO] [2020-07-22 14:53:03] Storing 16 MetaTraits
[INFO] [2020-07-22 14:53:03] Processing group of 16 in 1 groups of 1000
[INFO] [2020-07-22 14:53:03] Average Time: 0.0
[INFO] [2020-07-22 14:53:03] Total Time: 1s
[STOP] [2020-07-22 14:53:03] parse_diff_and_store
[START] [2020-07-22 14:53:03] resolve_keys
[INFO] [2020-07-22 14:53:10] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:53:10] traits to occurrences...
[INFO] [2020-07-22 14:53:10] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:53:10] Traits to sex term...
[INFO] [2020-07-22 14:53:10] Traits to lifestage term...
[INFO] [2020-07-22 14:53:10] MetaTraits to traits...
[INFO] [2020-07-22 14:53:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:53:10] Assocs to occurrences...
[INFO] [2020-07-22 14:53:10] Assocs to nodes...
[INFO] [2020-07-22 14:53:10] Assoc to sex term...
[INFO] [2020-07-22 14:53:10] Assoc to lifestage term...
[STOP] [2020-07-22 14:53:10] resolve_keys
[START] [2020-07-22 14:53:10] hold_for_later_1
[STOP] [2020-07-22 14:53:10] hold_for_later_1
[START] [2020-07-22 14:53:10] hold_for_later_2
[STOP] [2020-07-22 14:53:10] hold_for_later_2
[START] [2020-07-22 14:53:10] resolve_missing_parents
[STOP] [2020-07-22 14:53:10] resolve_missing_parents
[START] [2020-07-22 14:53:10] rebuild_nodes
[START] [2020-07-22 14:53:10] Flattener#flatten
[START] [2020-07-22 14:53:10] Flattener#study_resource
[START] [2020-07-22 14:53:10] Flattener#build_ancestry
[STOP] [2020-07-22 14:53:10] Flattener#build_ancestry
[INFO] [2020-07-22 14:53:10] 7 ancestry keys
[START] [2020-07-22 14:53:10] build_node_ancestors
[INFO] [2020-07-22 14:53:10] old ancestors deleted.
[STOP] [2020-07-22 14:53:10] build_node_ancestors
[WARN] [2020-07-22 14:53:10] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:53:10] Flattener#flatten
[STOP] [2020-07-22 14:53:10] rebuild_nodes
[START] [2020-07-22 14:53:10] resolve_missing_media_owners
[STOP] [2020-07-22 14:53:10] resolve_missing_media_owners
[START] [2020-07-22 14:53:10] sanitize_media_verbatims
[STOP] [2020-07-22 14:53:10] sanitize_media_verbatims
[START] [2020-07-22 14:53:10] queue_downloads
[STOP] [2020-07-22 14:53:10] queue_downloads
[START] [2020-07-22 14:53:10] parse_names
[WARN] [2020-07-22 14:53:10] I see 7 names which still need to be parsed.
[STOP] [2020-07-22 14:53:11] parse_names
[START] [2020-07-22 14:53:11] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:53:11] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:53:11] match_nodes
[START] [2020-07-22 14:53:11] map_all_nodes_to_pages
[STOP] [2020-07-22 14:53:11] map_all_nodes_to_pages
[INFO] [2020-07-22 14:53:11] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2020-07-22 14:53:11] update_nodes
[STOP] [2020-07-22 14:53:11] update_nodes
[STOP] [2020-07-22 14:53:11] match_nodes
[START] [2020-07-22 14:53:11] reindex_search
[STOP] [2020-07-22 14:53:11] reindex_search
[START] [2020-07-22 14:53:11] normalize_units
[STOP] [2020-07-22 14:53:11] normalize_units
[START] [2020-07-22 14:53:11] calculate_statistics
[2020-07-22 14:53:11] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:53:11] calculate_statistics
[START] [2020-07-22 14:53:11] complete_harvest_instance
[START] [2020-07-22 14:53:11] overall_tsv_creation
[INFO] [2020-07-22 14:53:11] Processing group of 7 in 1 batches of 10000
[INFO] [2020-07-22 14:54:01] 7 Traits (unfiltered)...
[INFO] [2020-07-22 14:54:36] 7 Traits (filtered)...
[INFO] [2020-07-22 14:54:36] 0 Associations (filtered)...
[INFO] [2020-07-22 14:54:36] 24 metadata added.
[INFO] [2020-07-22 14:54:36] 0 metadata added.
[INFO] [2020-07-22 14:54:36] Average Time: 57.93
[INFO] [2020-07-22 14:54:36] Total Time: 1m25s
[STOP] [2020-07-22 14:54:36] overall_tsv_creation
[INFO] [2020-07-22 14:54:36] Done. Check your files:
[INFO] [2020-07-22 14:54:36] (7 lines) /app/public/data/lovegrove_lovegr/publish_nodes.tsv
[INFO] [2020-07-22 14:54:36] (7 lines) /app/public/data/lovegrove_lovegr/publish_scientific_names.tsv
[INFO] [2020-07-22 14:54:36] (8 lines) /app/public/data/lovegrove_lovegr/publish_traits.tsv
[INFO] [2020-07-22 14:54:36] (9 lines) /app/public/data/lovegrove_lovegr/publish_metadata.tsv
[STOP] [2020-07-22 14:54:36] complete_harvest_instance
[START] [2020-07-22 14:54:36] completed
[STOP] [2020-07-22 14:54:36] completed
[STOP] [2020-07-22 14:54:36] logged process, took 94.76
Latest Process

22 Jul 14:53 EXITED currently processing 0