Harvest for Stanier and Cohen Bazire 1977 Created 03 Apr 15:19

Stage: completed
Fetched: 03 Apr 15:19
Validated: 03 Apr 15:19
Deltas Created 03 Apr 15:19
Units Normalized: 03 Apr 15:19
Ancestry Built: 03 Apr 15:19
Nodes Matched: 03 Apr 15:19
Names Parsed: 03 Apr 15:19
New Models Stored: 03 Apr 15:19
Indexed: 03 Apr 15:19
Completed: 03 Apr 15:20
Time to Harvest: less than a minute
Harvesting Log

(125 lines)
# Logfile created on 2020-04-03 15:19:16 -0400 by logger.rb/56815
[START] [2020-04-03 15:19:16] logged process
[START] [2020-04-03 15:19:16] create_harvest_instance
[STOP] [2020-04-03 15:19:16] create_harvest_instance
[START] [2020-04-03 15:19:16] fetch_files
[STOP] [2020-04-03 15:19:16] fetch_files
[START] [2020-04-03 15:19:16] validate_each_file
[STOP] [2020-04-03 15:19:16] validate_each_file
[START] [2020-04-03 15:19:16] convert_to_csv
[CMD] [2020-04-03 15:19:16] /usr/bin/sort /app/public/converted_csv/stanier_cohen_ba_nodes_20624.csv > /app/public/converted_csv/stanier_cohen_ba_nodes_20624.csv_sorted
[CMD] [2020-04-03 15:19:16] /usr/bin/sort /app/public/converted_csv/stanier_cohen_ba_occurrences_20625.csv > /app/public/converted_csv/stanier_cohen_ba_occurrences_20625.csv_sorted
[CMD] [2020-04-03 15:19:16] /usr/bin/sort /app/public/converted_csv/stanier_cohen_ba_measurements_20626.csv > /app/public/converted_csv/stanier_cohen_ba_measurements_20626.csv_sorted
[STOP] [2020-04-03 15:19:16] convert_to_csv
[START] [2020-04-03 15:19:16] calculate_delta
[CMD] [2020-04-03 15:19:16] echo "0a" > /app/public/diff/stanier_cohen_ba_nodes_20624.diff
[CMD] [2020-04-03 15:19:16] tail -n +1 /app/public/converted_csv/stanier_cohen_ba_nodes_20624.csv >> /app/public/diff/stanier_cohen_ba_nodes_20624.diff
[CMD] [2020-04-03 15:19:16] echo "." >> /app/public/diff/stanier_cohen_ba_nodes_20624.diff
[CMD] [2020-04-03 15:19:16] echo "0a" > /app/public/diff/stanier_cohen_ba_occurrences_20625.diff
[CMD] [2020-04-03 15:19:16] tail -n +1 /app/public/converted_csv/stanier_cohen_ba_occurrences_20625.csv >> /app/public/diff/stanier_cohen_ba_occurrences_20625.diff
[CMD] [2020-04-03 15:19:16] echo "." >> /app/public/diff/stanier_cohen_ba_occurrences_20625.diff
[CMD] [2020-04-03 15:19:16] echo "0a" > /app/public/diff/stanier_cohen_ba_measurements_20626.diff
[CMD] [2020-04-03 15:19:16] tail -n +1 /app/public/converted_csv/stanier_cohen_ba_measurements_20626.csv >> /app/public/diff/stanier_cohen_ba_measurements_20626.diff
[CMD] [2020-04-03 15:19:16] echo "." >> /app/public/diff/stanier_cohen_ba_measurements_20626.diff
[STOP] [2020-04-03 15:19:16] calculate_delta
[START] [2020-04-03 15:19:16] parse_diff_and_store
[INFO] [2020-04-03 15:19:16] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-03 15:19:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-03 15:19:16] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-03 15:19:16] Storing 1 ScientificNames
[INFO] [2020-04-03 15:19:16] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-03 15:19:16] Average Time: 0.0
[INFO] [2020-04-03 15:19:16] Total Time: 1s
[INFO] [2020-04-03 15:19:16] Storing 1 Nodes
[INFO] [2020-04-03 15:19:16] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-03 15:19:16] Average Time: 0.0
[INFO] [2020-04-03 15:19:16] Total Time: 1s
[INFO] [2020-04-03 15:19:16] Storing 1 Occurrences
[INFO] [2020-04-03 15:19:16] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-03 15:19:16] Average Time: 0.0
[INFO] [2020-04-03 15:19:16] Total Time: 1s
[INFO] [2020-04-03 15:19:16] Storing 4 Traits
[INFO] [2020-04-03 15:19:16] Processing group of 4 in 1 groups of 1000
[INFO] [2020-04-03 15:19:16] Average Time: 0.0
[INFO] [2020-04-03 15:19:16] Total Time: 1s
[INFO] [2020-04-03 15:19:16] Storing 4 MetaTraits
[INFO] [2020-04-03 15:19:16] Processing group of 4 in 1 groups of 1000
[INFO] [2020-04-03 15:19:16] Average Time: 0.0
[INFO] [2020-04-03 15:19:16] Total Time: 1s
[STOP] [2020-04-03 15:19:16] parse_diff_and_store
[START] [2020-04-03 15:19:16] resolve_keys
[INFO] [2020-04-03 15:19:22] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-03 15:19:22] traits to occurrences...
[INFO] [2020-04-03 15:19:22] traits to nodes (through occurrences)...
[INFO] [2020-04-03 15:19:22] Traits to sex term...
[INFO] [2020-04-03 15:19:22] Traits to lifestage term...
[INFO] [2020-04-03 15:19:22] MetaTraits to traits...
[INFO] [2020-04-03 15:19:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-03 15:19:22] Assocs to occurrences...
[INFO] [2020-04-03 15:19:22] Assocs to nodes...
[INFO] [2020-04-03 15:19:22] Assoc to sex term...
[INFO] [2020-04-03 15:19:22] Assoc to lifestage term...
[STOP] [2020-04-03 15:19:22] resolve_keys
[START] [2020-04-03 15:19:22] hold_for_later_1
[STOP] [2020-04-03 15:19:22] hold_for_later_1
[START] [2020-04-03 15:19:22] hold_for_later_2
[STOP] [2020-04-03 15:19:22] hold_for_later_2
[START] [2020-04-03 15:19:22] resolve_missing_parents
[STOP] [2020-04-03 15:19:22] resolve_missing_parents
[START] [2020-04-03 15:19:22] rebuild_nodes
[START] [2020-04-03 15:19:22] Flattener#flatten
[START] [2020-04-03 15:19:22] Flattener#study_resource
[START] [2020-04-03 15:19:22] Flattener#build_ancestry
[STOP] [2020-04-03 15:19:22] Flattener#build_ancestry
[INFO] [2020-04-03 15:19:22] 1 ancestry keys
[START] [2020-04-03 15:19:22] build_node_ancestors
[INFO] [2020-04-03 15:19:22] old ancestors deleted.
[STOP] [2020-04-03 15:19:22] build_node_ancestors
[WARN] [2020-04-03 15:19:22] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-03 15:19:22] Flattener#flatten
[STOP] [2020-04-03 15:19:22] rebuild_nodes
[START] [2020-04-03 15:19:22] resolve_missing_media_owners
[STOP] [2020-04-03 15:19:22] resolve_missing_media_owners
[START] [2020-04-03 15:19:22] sanitize_media_verbatims
[STOP] [2020-04-03 15:19:22] sanitize_media_verbatims
[START] [2020-04-03 15:19:22] queue_downloads
[STOP] [2020-04-03 15:19:22] queue_downloads
[START] [2020-04-03 15:19:22] parse_names
[WARN] [2020-04-03 15:19:22] I see 1 names which still need to be parsed.
[STOP] [2020-04-03 15:19:23] parse_names
[START] [2020-04-03 15:19:23] denormalize_canonical_names_to_nodes
[STOP] [2020-04-03 15:19:23] denormalize_canonical_names_to_nodes
[START] [2020-04-03 15:19:23] match_nodes
[START] [2020-04-03 15:19:23] map_all_nodes_to_pages
[STOP] [2020-04-03 15:19:23] map_all_nodes_to_pages
[INFO] [2020-04-03 15:19:23] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-04-03 15:19:23] update_nodes
[STOP] [2020-04-03 15:19:23] update_nodes
[STOP] [2020-04-03 15:19:23] match_nodes
[START] [2020-04-03 15:19:23] reindex_search
[STOP] [2020-04-03 15:19:23] reindex_search
[START] [2020-04-03 15:19:23] normalize_units
[STOP] [2020-04-03 15:19:23] normalize_units
[START] [2020-04-03 15:19:23] calculate_statistics
[2020-04-03 15:19:23] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-03 15:19:23] calculate_statistics
[START] [2020-04-03 15:19:23] complete_harvest_instance
[START] [2020-04-03 15:19:23] overall_tsv_creation
[INFO] [2020-04-03 15:19:23] Processing group of 1 in 1 batches of 10000
[INFO] [2020-04-03 15:20:12] 2 Traits (unfiltered)...
[INFO] [2020-04-03 15:20:23] 2 Traits (filtered)...
[INFO] [2020-04-03 15:20:23] 0 Associations (filtered)...
[INFO] [2020-04-03 15:20:57] 6 metadata added.
[INFO] [2020-04-03 15:20:57] 0 metadata added.
[INFO] [2020-04-03 15:20:57] Average Time: 66.1
[INFO] [2020-04-03 15:20:57] Total Time: 1m35s
[STOP] [2020-04-03 15:20:57] overall_tsv_creation
[INFO] [2020-04-03 15:20:57] Done. Check your files:
[INFO] [2020-04-03 15:20:57] (1 lines) /app/public/data/stanier_cohen_ba/publish_nodes.tsv
[INFO] [2020-04-03 15:20:57] (1 lines) /app/public/data/stanier_cohen_ba/publish_scientific_names.tsv
[INFO] [2020-04-03 15:20:57] (3 lines) /app/public/data/stanier_cohen_ba/publish_traits.tsv
[INFO] [2020-04-03 15:20:57] (7 lines) /app/public/data/stanier_cohen_ba/publish_metadata.tsv
[STOP] [2020-04-03 15:20:57] complete_harvest_instance
[START] [2020-04-03 15:20:57] completed
[STOP] [2020-04-03 15:20:57] completed
[STOP] [2020-04-03 15:20:57] logged process, took 101.62
Latest Process

03 Apr 15:19 EXITED currently processing 0