Harvest for Ashley Ross 1994 Created 22 Jul 14:38

Stage: completed
Fetched: 22 Jul 14:38
Validated: 22 Jul 14:38
Deltas Created 22 Jul 14:38
Units Normalized: 22 Jul 14:38
Ancestry Built: 22 Jul 14:38
Nodes Matched: 22 Jul 14:38
Names Parsed: 22 Jul 14:38
New Models Stored: 22 Jul 14:38
Indexed: 22 Jul 14:38
Completed: 22 Jul 14:40
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-07-22 14:38:20 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:38:20] logged process
[START] [2020-07-22 14:38:20] Creating resource from OpenData
[START] [2020-07-22 14:38:21] logged process
[START] [2020-07-22 14:38:21] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:38:21] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:38:21] Creating resource from OpenData
[INFO] [2020-07-22 14:38:34] ## HARVEST: type = -harvest
[START] [2020-07-22 14:38:38] logged process
[START] [2020-07-22 14:38:38] create_harvest_instance
[STOP] [2020-07-22 14:38:39] create_harvest_instance
[START] [2020-07-22 14:38:39] fetch_files
[STOP] [2020-07-22 14:38:39] fetch_files
[START] [2020-07-22 14:38:39] validate_each_file
[STOP] [2020-07-22 14:38:39] validate_each_file
[START] [2020-07-22 14:38:39] convert_to_csv
[CMD] [2020-07-22 14:38:39] /usr/bin/sort /app/public/converted_csv/ashley_ross_ashl_refs_21984.csv > /app/public/converted_csv/ashley_ross_ashl_refs_21984.csv_sorted
[CMD] [2020-07-22 14:38:39] /usr/bin/sort /app/public/converted_csv/ashley_ross_ashl_nodes_21985.csv > /app/public/converted_csv/ashley_ross_ashl_nodes_21985.csv_sorted
[CMD] [2020-07-22 14:38:39] /usr/bin/sort /app/public/converted_csv/ashley_ross_ashl_occurrences_21986.csv > /app/public/converted_csv/ashley_ross_ashl_occurrences_21986.csv_sorted
[CMD] [2020-07-22 14:38:39] /usr/bin/sort /app/public/converted_csv/ashley_ross_ashl_measurements_21987.csv > /app/public/converted_csv/ashley_ross_ashl_measurements_21987.csv_sorted
[STOP] [2020-07-22 14:38:39] convert_to_csv
[START] [2020-07-22 14:38:39] calculate_delta
[CMD] [2020-07-22 14:38:39] echo "0a" > /app/public/diff/ashley_ross_ashl_refs_21984.diff
[CMD] [2020-07-22 14:38:39] tail -n +1 /app/public/converted_csv/ashley_ross_ashl_refs_21984.csv >> /app/public/diff/ashley_ross_ashl_refs_21984.diff
[CMD] [2020-07-22 14:38:39] echo "." >> /app/public/diff/ashley_ross_ashl_refs_21984.diff
[CMD] [2020-07-22 14:38:39] echo "0a" > /app/public/diff/ashley_ross_ashl_nodes_21985.diff
[CMD] [2020-07-22 14:38:39] tail -n +1 /app/public/converted_csv/ashley_ross_ashl_nodes_21985.csv >> /app/public/diff/ashley_ross_ashl_nodes_21985.diff
[CMD] [2020-07-22 14:38:39] echo "." >> /app/public/diff/ashley_ross_ashl_nodes_21985.diff
[CMD] [2020-07-22 14:38:39] echo "0a" > /app/public/diff/ashley_ross_ashl_occurrences_21986.diff
[CMD] [2020-07-22 14:38:39] tail -n +1 /app/public/converted_csv/ashley_ross_ashl_occurrences_21986.csv >> /app/public/diff/ashley_ross_ashl_occurrences_21986.diff
[CMD] [2020-07-22 14:38:39] echo "." >> /app/public/diff/ashley_ross_ashl_occurrences_21986.diff
[CMD] [2020-07-22 14:38:39] echo "0a" > /app/public/diff/ashley_ross_ashl_measurements_21987.diff
[CMD] [2020-07-22 14:38:39] tail -n +1 /app/public/converted_csv/ashley_ross_ashl_measurements_21987.csv >> /app/public/diff/ashley_ross_ashl_measurements_21987.diff
[CMD] [2020-07-22 14:38:39] echo "." >> /app/public/diff/ashley_ross_ashl_measurements_21987.diff
[STOP] [2020-07-22 14:38:39] calculate_delta
[START] [2020-07-22 14:38:39] parse_diff_and_store
[INFO] [2020-07-22 14:38:39] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-22 14:38:39] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:38:39] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:38:39] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:38:39] Storing 1 References
[INFO] [2020-07-22 14:38:39] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 14:38:39] Average Time: 0.0
[INFO] [2020-07-22 14:38:39] Total Time: 1s
[INFO] [2020-07-22 14:38:39] Storing 2 ScientificNames
[INFO] [2020-07-22 14:38:39] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[INFO] [2020-07-22 14:38:40] Storing 2 Nodes
[INFO] [2020-07-22 14:38:40] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[INFO] [2020-07-22 14:38:40] Storing 2 Occurrences
[INFO] [2020-07-22 14:38:40] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[INFO] [2020-07-22 14:38:40] Storing 2 OccurrenceMetadata
[INFO] [2020-07-22 14:38:40] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[INFO] [2020-07-22 14:38:40] Storing 2 TraitsReferences
[INFO] [2020-07-22 14:38:40] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[INFO] [2020-07-22 14:38:40] Storing 4 Traits
[INFO] [2020-07-22 14:38:40] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[INFO] [2020-07-22 14:38:40] Storing 5 MetaTraits
[INFO] [2020-07-22 14:38:40] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 14:38:40] Average Time: 0.0
[INFO] [2020-07-22 14:38:40] Total Time: 1s
[STOP] [2020-07-22 14:38:40] parse_diff_and_store
[START] [2020-07-22 14:38:40] resolve_keys
[INFO] [2020-07-22 14:38:46] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:38:46] traits to occurrences...
[INFO] [2020-07-22 14:38:46] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:38:46] Traits to sex term...
[INFO] [2020-07-22 14:38:46] Traits to lifestage term...
[INFO] [2020-07-22 14:38:46] MetaTraits to traits...
[INFO] [2020-07-22 14:38:46] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:38:46] Assocs to occurrences...
[INFO] [2020-07-22 14:38:46] Assocs to nodes...
[INFO] [2020-07-22 14:38:46] Assoc to sex term...
[INFO] [2020-07-22 14:38:46] Assoc to lifestage term...
[STOP] [2020-07-22 14:38:46] resolve_keys
[START] [2020-07-22 14:38:46] hold_for_later_1
[STOP] [2020-07-22 14:38:46] hold_for_later_1
[START] [2020-07-22 14:38:46] hold_for_later_2
[STOP] [2020-07-22 14:38:46] hold_for_later_2
[START] [2020-07-22 14:38:46] resolve_missing_parents
[STOP] [2020-07-22 14:38:46] resolve_missing_parents
[START] [2020-07-22 14:38:46] rebuild_nodes
[START] [2020-07-22 14:38:46] Flattener#flatten
[START] [2020-07-22 14:38:47] Flattener#study_resource
[START] [2020-07-22 14:38:47] Flattener#build_ancestry
[STOP] [2020-07-22 14:38:47] Flattener#build_ancestry
[INFO] [2020-07-22 14:38:47] 2 ancestry keys
[START] [2020-07-22 14:38:47] build_node_ancestors
[INFO] [2020-07-22 14:38:47] old ancestors deleted.
[STOP] [2020-07-22 14:38:47] build_node_ancestors
[WARN] [2020-07-22 14:38:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:38:47] Flattener#flatten
[STOP] [2020-07-22 14:38:47] rebuild_nodes
[START] [2020-07-22 14:38:47] resolve_missing_media_owners
[STOP] [2020-07-22 14:38:47] resolve_missing_media_owners
[START] [2020-07-22 14:38:47] sanitize_media_verbatims
[STOP] [2020-07-22 14:38:47] sanitize_media_verbatims
[START] [2020-07-22 14:38:47] queue_downloads
[STOP] [2020-07-22 14:38:47] queue_downloads
[START] [2020-07-22 14:38:47] parse_names
[WARN] [2020-07-22 14:38:47] I see 2 names which still need to be parsed.
[STOP] [2020-07-22 14:38:48] parse_names
[START] [2020-07-22 14:38:48] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:38:48] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:38:48] match_nodes
[START] [2020-07-22 14:38:48] map_all_nodes_to_pages
[STOP] [2020-07-22 14:38:48] map_all_nodes_to_pages
[INFO] [2020-07-22 14:38:48] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-07-22 14:38:48] update_nodes
[STOP] [2020-07-22 14:38:48] update_nodes
[STOP] [2020-07-22 14:38:48] match_nodes
[START] [2020-07-22 14:38:48] reindex_search
[STOP] [2020-07-22 14:38:48] reindex_search
[START] [2020-07-22 14:38:48] normalize_units
[STOP] [2020-07-22 14:38:48] normalize_units
[START] [2020-07-22 14:38:48] calculate_statistics
[2020-07-22 14:38:48] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:38:48] calculate_statistics
[START] [2020-07-22 14:38:48] complete_harvest_instance
[START] [2020-07-22 14:38:48] overall_tsv_creation
[INFO] [2020-07-22 14:38:48] Processing group of 2 in 1 batches of 10000
[INFO] [2020-07-22 14:39:38] 2 Traits (unfiltered)...
[INFO] [2020-07-22 14:40:14] 2 Traits (filtered)...
[INFO] [2020-07-22 14:40:14] 0 Associations (filtered)...
[INFO] [2020-07-22 14:40:14] 11 metadata added.
[INFO] [2020-07-22 14:40:14] 0 metadata added.
[INFO] [2020-07-22 14:40:14] Average Time: 57.17
[INFO] [2020-07-22 14:40:14] Total Time: 1m26s
[STOP] [2020-07-22 14:40:14] overall_tsv_creation
[INFO] [2020-07-22 14:40:14] Done. Check your files:
[INFO] [2020-07-22 14:40:14] (2 lines) /app/public/data/ashley_ross_ashl/publish_nodes.tsv
[INFO] [2020-07-22 14:40:14] (2 lines) /app/public/data/ashley_ross_ashl/publish_scientific_names.tsv
[INFO] [2020-07-22 14:40:14] (3 lines) /app/public/data/ashley_ross_ashl/publish_traits.tsv
[INFO] [2020-07-22 14:40:14] (7 lines) /app/public/data/ashley_ross_ashl/publish_metadata.tsv
[STOP] [2020-07-22 14:40:14] complete_harvest_instance
[START] [2020-07-22 14:40:14] completed
[STOP] [2020-07-22 14:40:14] completed
[STOP] [2020-07-22 14:40:14] logged process, took 95.94

Latest Process