Harvest for Grabowsky 1994 Created 30 Jul 14:54

Stage: completed
Fetched: 30 Jul 14:54
Validated: 30 Jul 14:54
Deltas Created 30 Jul 14:54
Units Normalized: 30 Jul 14:54
Ancestry Built: 30 Jul 14:54
Nodes Matched: 30 Jul 14:54
Names Parsed: 30 Jul 14:54
New Models Stored: 30 Jul 14:54
Indexed: 30 Jul 14:54
Completed: 30 Jul 14:55
Time to Harvest: less than a minute
Harvesting Log

(137 lines)
# Logfile created on 2020-07-30 14:53:43 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 14:53:43] logged process
[START] [2020-07-30 14:53:43] Creating resource from OpenData
[START] [2020-07-30 14:53:43] logged process
[START] [2020-07-30 14:53:43] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:53:43] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:53:43] Creating resource from OpenData
[INFO] [2020-07-30 14:53:59] ## HARVEST: type = -harvest
[START] [2020-07-30 14:54:02] logged process
[START] [2020-07-30 14:54:03] create_harvest_instance
[STOP] [2020-07-30 14:54:04] create_harvest_instance
[START] [2020-07-30 14:54:04] fetch_files
[STOP] [2020-07-30 14:54:04] fetch_files
[START] [2020-07-30 14:54:04] validate_each_file
[STOP] [2020-07-30 14:54:04] validate_each_file
[START] [2020-07-30 14:54:04] convert_to_csv
[CMD] [2020-07-30 14:54:04] /usr/bin/sort /app/public/converted_csv/grabowsky_grabow_refs_22332.csv > /app/public/converted_csv/grabowsky_grabow_refs_22332.csv_sorted
[CMD] [2020-07-30 14:54:04] /usr/bin/sort /app/public/converted_csv/grabowsky_grabow_nodes_22333.csv > /app/public/converted_csv/grabowsky_grabow_nodes_22333.csv_sorted
[CMD] [2020-07-30 14:54:04] /usr/bin/sort /app/public/converted_csv/grabowsky_grabow_occurrences_22334.csv > /app/public/converted_csv/grabowsky_grabow_occurrences_22334.csv_sorted
[CMD] [2020-07-30 14:54:04] /usr/bin/sort /app/public/converted_csv/grabowsky_grabow_measurements_22335.csv > /app/public/converted_csv/grabowsky_grabow_measurements_22335.csv_sorted
[STOP] [2020-07-30 14:54:04] convert_to_csv
[START] [2020-07-30 14:54:04] calculate_delta
[CMD] [2020-07-30 14:54:04] echo "0a" > /app/public/diff/grabowsky_grabow_refs_22332.diff
[CMD] [2020-07-30 14:54:04] tail -n +1 /app/public/converted_csv/grabowsky_grabow_refs_22332.csv >> /app/public/diff/grabowsky_grabow_refs_22332.diff
[CMD] [2020-07-30 14:54:04] echo "." >> /app/public/diff/grabowsky_grabow_refs_22332.diff
[CMD] [2020-07-30 14:54:04] echo "0a" > /app/public/diff/grabowsky_grabow_nodes_22333.diff
[CMD] [2020-07-30 14:54:04] tail -n +1 /app/public/converted_csv/grabowsky_grabow_nodes_22333.csv >> /app/public/diff/grabowsky_grabow_nodes_22333.diff
[CMD] [2020-07-30 14:54:04] echo "." >> /app/public/diff/grabowsky_grabow_nodes_22333.diff
[CMD] [2020-07-30 14:54:04] echo "0a" > /app/public/diff/grabowsky_grabow_occurrences_22334.diff
[CMD] [2020-07-30 14:54:04] tail -n +1 /app/public/converted_csv/grabowsky_grabow_occurrences_22334.csv >> /app/public/diff/grabowsky_grabow_occurrences_22334.diff
[CMD] [2020-07-30 14:54:04] echo "." >> /app/public/diff/grabowsky_grabow_occurrences_22334.diff
[CMD] [2020-07-30 14:54:04] echo "0a" > /app/public/diff/grabowsky_grabow_measurements_22335.diff
[CMD] [2020-07-30 14:54:04] tail -n +1 /app/public/converted_csv/grabowsky_grabow_measurements_22335.csv >> /app/public/diff/grabowsky_grabow_measurements_22335.diff
[CMD] [2020-07-30 14:54:04] echo "." >> /app/public/diff/grabowsky_grabow_measurements_22335.diff
[STOP] [2020-07-30 14:54:04] calculate_delta
[START] [2020-07-30 14:54:04] parse_diff_and_store
[INFO] [2020-07-30 14:54:04] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:54:04] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:54:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:54:04] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:54:04] Storing 1 ScientificNames
[INFO] [2020-07-30 14:54:04] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:54:04] Average Time: 0.0
[INFO] [2020-07-30 14:54:04] Total Time: 1s
[INFO] [2020-07-30 14:54:04] Storing 1 Nodes
[INFO] [2020-07-30 14:54:04] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:54:04] Average Time: 0.0
[INFO] [2020-07-30 14:54:04] Total Time: 1s
[INFO] [2020-07-30 14:54:04] Storing 1 Occurrences
[INFO] [2020-07-30 14:54:04] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:54:04] Average Time: 0.0
[INFO] [2020-07-30 14:54:04] Total Time: 1s
[INFO] [2020-07-30 14:54:04] Storing 7 Traits
[INFO] [2020-07-30 14:54:04] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-30 14:54:04] Average Time: 0.0
[INFO] [2020-07-30 14:54:04] Total Time: 1s
[INFO] [2020-07-30 14:54:04] Storing 4 MetaTraits
[INFO] [2020-07-30 14:54:04] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:54:04] Average Time: 0.0
[INFO] [2020-07-30 14:54:04] Total Time: 1s
[STOP] [2020-07-30 14:54:04] parse_diff_and_store
[START] [2020-07-30 14:54:04] resolve_keys
[INFO] [2020-07-30 14:54:11] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:54:11] traits to occurrences...
[INFO] [2020-07-30 14:54:11] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:54:11] Traits to sex term...
[INFO] [2020-07-30 14:54:11] Traits to lifestage term...
[INFO] [2020-07-30 14:54:11] MetaTraits to traits...
[INFO] [2020-07-30 14:54:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:54:11] Assocs to occurrences...
[INFO] [2020-07-30 14:54:11] Assocs to nodes...
[INFO] [2020-07-30 14:54:11] Assoc to sex term...
[INFO] [2020-07-30 14:54:11] Assoc to lifestage term...
[STOP] [2020-07-30 14:54:11] resolve_keys
[START] [2020-07-30 14:54:11] hold_for_later_1
[STOP] [2020-07-30 14:54:11] hold_for_later_1
[START] [2020-07-30 14:54:11] hold_for_later_2
[STOP] [2020-07-30 14:54:11] hold_for_later_2
[START] [2020-07-30 14:54:11] resolve_missing_parents
[STOP] [2020-07-30 14:54:11] resolve_missing_parents
[START] [2020-07-30 14:54:11] rebuild_nodes
[START] [2020-07-30 14:54:11] Flattener#flatten
[START] [2020-07-30 14:54:11] Flattener#study_resource
[START] [2020-07-30 14:54:11] Flattener#build_ancestry
[STOP] [2020-07-30 14:54:11] Flattener#build_ancestry
[INFO] [2020-07-30 14:54:11] 1 ancestry keys
[START] [2020-07-30 14:54:11] build_node_ancestors
[INFO] [2020-07-30 14:54:11] old ancestors deleted.
[STOP] [2020-07-30 14:54:11] build_node_ancestors
[WARN] [2020-07-30 14:54:11] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:54:11] Flattener#flatten
[STOP] [2020-07-30 14:54:11] rebuild_nodes
[START] [2020-07-30 14:54:11] resolve_missing_media_owners
[STOP] [2020-07-30 14:54:11] resolve_missing_media_owners
[START] [2020-07-30 14:54:11] sanitize_media_verbatims
[STOP] [2020-07-30 14:54:11] sanitize_media_verbatims
[START] [2020-07-30 14:54:11] queue_downloads
[STOP] [2020-07-30 14:54:11] queue_downloads
[START] [2020-07-30 14:54:11] parse_names
[WARN] [2020-07-30 14:54:11] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 14:54:13] parse_names
[START] [2020-07-30 14:54:13] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:54:13] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:54:13] match_nodes
[START] [2020-07-30 14:54:13] map_all_nodes_to_pages
[STOP] [2020-07-30 14:54:13] map_all_nodes_to_pages
[INFO] [2020-07-30 14:54:13] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 14:54:13] update_nodes
[STOP] [2020-07-30 14:54:13] update_nodes
[STOP] [2020-07-30 14:54:13] match_nodes
[START] [2020-07-30 14:54:13] reindex_search
[STOP] [2020-07-30 14:54:13] reindex_search
[START] [2020-07-30 14:54:13] normalize_units
[STOP] [2020-07-30 14:54:13] normalize_units
[START] [2020-07-30 14:54:13] calculate_statistics
[2020-07-30 14:54:13] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:54:13] calculate_statistics
[START] [2020-07-30 14:54:13] complete_harvest_instance
[START] [2020-07-30 14:54:13] overall_tsv_creation
[INFO] [2020-07-30 14:54:13] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 14:55:01] 2 Traits (unfiltered)...
[INFO] [2020-07-30 14:55:36] 2 Traits (filtered)...
[INFO] [2020-07-30 14:55:36] 0 Associations (filtered)...
[INFO] [2020-07-30 14:55:36] 9 metadata added.
[INFO] [2020-07-30 14:55:36] 0 metadata added.
[INFO] [2020-07-30 14:55:36] Average Time: 56.55
[INFO] [2020-07-30 14:55:36] Total Time: 1m24s
[STOP] [2020-07-30 14:55:36] overall_tsv_creation
[INFO] [2020-07-30 14:55:36] Done. Check your files:
[INFO] [2020-07-30 14:55:36] (1 lines) /app/public/data/grabowsky_grabow/publish_nodes.tsv
[INFO] [2020-07-30 14:55:36] (1 lines) /app/public/data/grabowsky_grabow/publish_scientific_names.tsv
[INFO] [2020-07-30 14:55:36] (3 lines) /app/public/data/grabowsky_grabow/publish_traits.tsv
[INFO] [2020-07-30 14:55:36] (6 lines) /app/public/data/grabowsky_grabow/publish_metadata.tsv
[STOP] [2020-07-30 14:55:36] complete_harvest_instance
[START] [2020-07-30 14:55:36] completed
[STOP] [2020-07-30 14:55:36] completed
[STOP] [2020-07-30 14:55:36] logged process, took 93.73
Latest Process

30 Jul 14:54 EXITED currently processing 0