Harvest for Hatt 1932 Created 22 Jul 14:50

Stage: completed
Fetched: 22 Jul 14:50
Validated: 22 Jul 14:50
Deltas Created 22 Jul 14:50
Units Normalized: 22 Jul 14:50
Ancestry Built: 22 Jul 14:50
Nodes Matched: 22 Jul 14:50
Names Parsed: 22 Jul 14:50
New Models Stored: 22 Jul 14:50
Indexed: 22 Jul 14:50
Completed: 22 Jul 14:52
Time to Harvest: less than a minute

Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:43:51 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:43:51] logged process
[START] [2020-07-22 14:43:51] Creating resource from OpenData
[START] [2020-07-22 14:43:51] logged process
[START] [2020-07-22 14:43:51] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:43:51] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:43:51] Creating resource from OpenData
[INFO] [2020-07-22 14:50:42] ## HARVEST: type = -harvest
[START] [2020-07-22 14:50:46] logged process
[START] [2020-07-22 14:50:46] create_harvest_instance
[STOP] [2020-07-22 14:50:47] create_harvest_instance
[START] [2020-07-22 14:50:47] fetch_files
[STOP] [2020-07-22 14:50:47] fetch_files
[START] [2020-07-22 14:50:47] validate_each_file
[STOP] [2020-07-22 14:50:47] validate_each_file
[START] [2020-07-22 14:50:47] convert_to_csv
[CMD] [2020-07-22 14:50:47] /usr/bin/sort /app/public/converted_csv/hatt_hatt_1932_nodes_22003.csv > /app/public/converted_csv/hatt_hatt_1932_nodes_22003.csv_sorted
[CMD] [2020-07-22 14:50:47] /usr/bin/sort /app/public/converted_csv/hatt_hatt_1932_occurrences_22004.csv > /app/public/converted_csv/hatt_hatt_1932_occurrences_22004.csv_sorted
[CMD] [2020-07-22 14:50:47] /usr/bin/sort /app/public/converted_csv/hatt_hatt_1932_measurements_22005.csv > /app/public/converted_csv/hatt_hatt_1932_measurements_22005.csv_sorted
[STOP] [2020-07-22 14:50:47] convert_to_csv
[START] [2020-07-22 14:50:47] calculate_delta
[CMD] [2020-07-22 14:50:47] echo "0a" > /app/public/diff/hatt_hatt_1932_nodes_22003.diff
[CMD] [2020-07-22 14:50:47] tail -n +1 /app/public/converted_csv/hatt_hatt_1932_nodes_22003.csv >> /app/public/diff/hatt_hatt_1932_nodes_22003.diff
[CMD] [2020-07-22 14:50:47] echo "." >> /app/public/diff/hatt_hatt_1932_nodes_22003.diff
[CMD] [2020-07-22 14:50:47] echo "0a" > /app/public/diff/hatt_hatt_1932_occurrences_22004.diff
[CMD] [2020-07-22 14:50:47] tail -n +1 /app/public/converted_csv/hatt_hatt_1932_occurrences_22004.csv >> /app/public/diff/hatt_hatt_1932_occurrences_22004.diff
[CMD] [2020-07-22 14:50:47] echo "." >> /app/public/diff/hatt_hatt_1932_occurrences_22004.diff
[CMD] [2020-07-22 14:50:47] echo "0a" > /app/public/diff/hatt_hatt_1932_measurements_22005.diff
[CMD] [2020-07-22 14:50:47] tail -n +1 /app/public/converted_csv/hatt_hatt_1932_measurements_22005.csv >> /app/public/diff/hatt_hatt_1932_measurements_22005.diff
[CMD] [2020-07-22 14:50:47] echo "." >> /app/public/diff/hatt_hatt_1932_measurements_22005.diff
[STOP] [2020-07-22 14:50:47] calculate_delta
[START] [2020-07-22 14:50:47] parse_diff_and_store
[INFO] [2020-07-22 14:50:47] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:50:47] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:50:47] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:50:47] Storing 8 ScientificNames
[INFO] [2020-07-22 14:50:47] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-22 14:50:47] Average Time: 0.01
[INFO] [2020-07-22 14:50:47] Total Time: 1s
[INFO] [2020-07-22 14:50:47] Storing 8 Nodes
[INFO] [2020-07-22 14:50:47] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-22 14:50:47] Average Time: 0.0
[INFO] [2020-07-22 14:50:47] Total Time: 1s
[INFO] [2020-07-22 14:50:47] Storing 8 Occurrences
[INFO] [2020-07-22 14:50:47] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-22 14:50:47] Average Time: 0.0
[INFO] [2020-07-22 14:50:47] Total Time: 1s
[INFO] [2020-07-22 14:50:47] Storing 16 Traits
[INFO] [2020-07-22 14:50:47] Processing group of 16 in 1 groups of 1000
[INFO] [2020-07-22 14:50:47] Average Time: 0.01
[INFO] [2020-07-22 14:50:47] Total Time: 1s
[INFO] [2020-07-22 14:50:47] Storing 16 MetaTraits
[INFO] [2020-07-22 14:50:47] Processing group of 16 in 1 groups of 1000
[INFO] [2020-07-22 14:50:47] Average Time: 0.0
[INFO] [2020-07-22 14:50:47] Total Time: 1s
[STOP] [2020-07-22 14:50:47] parse_diff_and_store
[START] [2020-07-22 14:50:47] resolve_keys
[INFO] [2020-07-22 14:50:54] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:50:54] traits to occurrences...
[INFO] [2020-07-22 14:50:54] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:50:54] Traits to sex term...
[INFO] [2020-07-22 14:50:54] Traits to lifestage term...
[INFO] [2020-07-22 14:50:54] MetaTraits to traits...
[INFO] [2020-07-22 14:50:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:50:54] Assocs to occurrences...
[INFO] [2020-07-22 14:50:54] Assocs to nodes...
[INFO] [2020-07-22 14:50:54] Assoc to sex term...
[INFO] [2020-07-22 14:50:54] Assoc to lifestage term...
[STOP] [2020-07-22 14:50:54] resolve_keys
[START] [2020-07-22 14:50:54] hold_for_later_1
[STOP] [2020-07-22 14:50:54] hold_for_later_1
[START] [2020-07-22 14:50:54] hold_for_later_2
[STOP] [2020-07-22 14:50:54] hold_for_later_2
[START] [2020-07-22 14:50:54] resolve_missing_parents
[STOP] [2020-07-22 14:50:54] resolve_missing_parents
[START] [2020-07-22 14:50:54] rebuild_nodes
[START] [2020-07-22 14:50:54] Flattener#flatten
[START] [2020-07-22 14:50:54] Flattener#study_resource
[START] [2020-07-22 14:50:54] Flattener#build_ancestry
[STOP] [2020-07-22 14:50:54] Flattener#build_ancestry
[INFO] [2020-07-22 14:50:54] 8 ancestry keys
[START] [2020-07-22 14:50:54] build_node_ancestors
[INFO] [2020-07-22 14:50:54] old ancestors deleted.
[STOP] [2020-07-22 14:50:54] build_node_ancestors
[WARN] [2020-07-22 14:50:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:50:54] Flattener#flatten
[STOP] [2020-07-22 14:50:54] rebuild_nodes
[START] [2020-07-22 14:50:54] resolve_missing_media_owners
[STOP] [2020-07-22 14:50:54] resolve_missing_media_owners
[START] [2020-07-22 14:50:54] sanitize_media_verbatims
[STOP] [2020-07-22 14:50:54] sanitize_media_verbatims
[START] [2020-07-22 14:50:54] queue_downloads
[STOP] [2020-07-22 14:50:54] queue_downloads
[START] [2020-07-22 14:50:54] parse_names
[WARN] [2020-07-22 14:50:54] I see 8 names which still need to be parsed.
[STOP] [2020-07-22 14:50:55] parse_names
[START] [2020-07-22 14:50:55] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:50:55] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:50:55] match_nodes
[START] [2020-07-22 14:50:55] map_all_nodes_to_pages
[STOP] [2020-07-22 14:50:55] map_all_nodes_to_pages
[INFO] [2020-07-22 14:50:55] ZERO unmatched nodes (of 8)! Nicely done.
[START] [2020-07-22 14:50:55] update_nodes
[STOP] [2020-07-22 14:50:55] update_nodes
[STOP] [2020-07-22 14:50:55] match_nodes
[START] [2020-07-22 14:50:55] reindex_search
[STOP] [2020-07-22 14:50:55] reindex_search
[START] [2020-07-22 14:50:55] normalize_units
[STOP] [2020-07-22 14:50:55] normalize_units
[START] [2020-07-22 14:50:55] calculate_statistics
[2020-07-22 14:50:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:50:55] calculate_statistics
[START] [2020-07-22 14:50:55] complete_harvest_instance
[START] [2020-07-22 14:50:55] overall_tsv_creation
[INFO] [2020-07-22 14:50:56] Processing group of 8 in 1 batches of 10000
[INFO] [2020-07-22 14:51:44] 8 Traits (unfiltered)...
[INFO] [2020-07-22 14:52:20] 8 Traits (filtered)...
[INFO] [2020-07-22 14:52:20] 0 Associations (filtered)...
[INFO] [2020-07-22 14:52:20] 24 metadata added.
[INFO] [2020-07-22 14:52:20] 0 metadata added.
[INFO] [2020-07-22 14:52:20] Average Time: 57.97
[INFO] [2020-07-22 14:52:20] Total Time: 1m25s
[STOP] [2020-07-22 14:52:20] overall_tsv_creation
[INFO] [2020-07-22 14:52:20] Done. Check your files:
[INFO] [2020-07-22 14:52:20] (8 lines) /app/public/data/hatt_hatt_1932/publish_nodes.tsv
[INFO] [2020-07-22 14:52:20] (8 lines) /app/public/data/hatt_hatt_1932/publish_scientific_names.tsv
[INFO] [2020-07-22 14:52:20] (9 lines) /app/public/data/hatt_hatt_1932/publish_traits.tsv
[INFO] [2020-07-22 14:52:20] (9 lines) /app/public/data/hatt_hatt_1932/publish_metadata.tsv
[STOP] [2020-07-22 14:52:20] complete_harvest_instance
[START] [2020-07-22 14:52:20] completed
[STOP] [2020-07-22 14:52:20] completed
[STOP] [2020-07-22 14:52:20] logged process, took 94.74

Latest Process