Harvest for Rockwell et al Created 06 Apr 10:32

Stage: completed
Fetched: 06 Apr 10:32
Validated: 06 Apr 10:32
Deltas Created 06 Apr 10:32
Units Normalized: 06 Apr 10:32
Ancestry Built: 06 Apr 10:32
Nodes Matched: 06 Apr 10:32
Names Parsed: 06 Apr 10:32
New Models Stored: 06 Apr 10:32
Indexed: 06 Apr 10:32
Completed: 06 Apr 10:34
Time to Harvest: less than a minute
Harvesting Log

(138 lines)
# Logfile created on 2020-04-06 10:32:31 -0400 by logger.rb/56815
[START] [2020-04-06 10:32:31] logged process
[START] [2020-04-06 10:32:31] create_harvest_instance
[STOP] [2020-04-06 10:32:32] create_harvest_instance
[START] [2020-04-06 10:32:32] fetch_files
[STOP] [2020-04-06 10:32:32] fetch_files
[START] [2020-04-06 10:32:32] validate_each_file
[STOP] [2020-04-06 10:32:32] validate_each_file
[START] [2020-04-06 10:32:32] convert_to_csv
[CMD] [2020-04-06 10:32:32] /usr/bin/sort /app/public/converted_csv/rockwell_et_al_refs_20675.csv > /app/public/converted_csv/rockwell_et_al_refs_20675.csv_sorted
[CMD] [2020-04-06 10:32:32] /usr/bin/sort /app/public/converted_csv/rockwell_et_al_nodes_20676.csv > /app/public/converted_csv/rockwell_et_al_nodes_20676.csv_sorted
[CMD] [2020-04-06 10:32:32] /usr/bin/sort /app/public/converted_csv/rockwell_et_al_occurrences_20677.csv > /app/public/converted_csv/rockwell_et_al_occurrences_20677.csv_sorted
[CMD] [2020-04-06 10:32:32] /usr/bin/sort /app/public/converted_csv/rockwell_et_al_measurements_20678.csv > /app/public/converted_csv/rockwell_et_al_measurements_20678.csv_sorted
[STOP] [2020-04-06 10:32:32] convert_to_csv
[START] [2020-04-06 10:32:32] calculate_delta
[CMD] [2020-04-06 10:32:32] echo "0a" > /app/public/diff/rockwell_et_al_refs_20675.diff
[CMD] [2020-04-06 10:32:32] tail -n +1 /app/public/converted_csv/rockwell_et_al_refs_20675.csv >> /app/public/diff/rockwell_et_al_refs_20675.diff
[CMD] [2020-04-06 10:32:32] echo "." >> /app/public/diff/rockwell_et_al_refs_20675.diff
[CMD] [2020-04-06 10:32:32] echo "0a" > /app/public/diff/rockwell_et_al_nodes_20676.diff
[CMD] [2020-04-06 10:32:32] tail -n +1 /app/public/converted_csv/rockwell_et_al_nodes_20676.csv >> /app/public/diff/rockwell_et_al_nodes_20676.diff
[CMD] [2020-04-06 10:32:32] echo "." >> /app/public/diff/rockwell_et_al_nodes_20676.diff
[CMD] [2020-04-06 10:32:32] echo "0a" > /app/public/diff/rockwell_et_al_occurrences_20677.diff
[CMD] [2020-04-06 10:32:32] tail -n +1 /app/public/converted_csv/rockwell_et_al_occurrences_20677.csv >> /app/public/diff/rockwell_et_al_occurrences_20677.diff
[CMD] [2020-04-06 10:32:32] echo "." >> /app/public/diff/rockwell_et_al_occurrences_20677.diff
[CMD] [2020-04-06 10:32:32] echo "0a" > /app/public/diff/rockwell_et_al_measurements_20678.diff
[CMD] [2020-04-06 10:32:32] tail -n +1 /app/public/converted_csv/rockwell_et_al_measurements_20678.csv >> /app/public/diff/rockwell_et_al_measurements_20678.diff
[CMD] [2020-04-06 10:32:32] echo "." >> /app/public/diff/rockwell_et_al_measurements_20678.diff
[STOP] [2020-04-06 10:32:32] calculate_delta
[START] [2020-04-06 10:32:32] parse_diff_and_store
[INFO] [2020-04-06 10:32:32] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-06 10:32:32] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-06 10:32:32] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-04-06 10:32:32] Loading measurements diff file into memory (true lines)...
[INFO] [2020-04-06 10:32:34] Storing 1 References
[INFO] [2020-04-06 10:32:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.0
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[INFO] [2020-04-06 10:32:34] Storing 1 ScientificNames
[INFO] [2020-04-06 10:32:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.0
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[INFO] [2020-04-06 10:32:34] Storing 1 Nodes
[INFO] [2020-04-06 10:32:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.0
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[INFO] [2020-04-06 10:32:34] Storing 1 Occurrences
[INFO] [2020-04-06 10:32:34] Processing group of 1 in 1 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.0
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[INFO] [2020-04-06 10:32:34] Storing 2 TraitsReferences
[INFO] [2020-04-06 10:32:34] Processing group of 2 in 1 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.0
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[INFO] [2020-04-06 10:32:34] Storing 1324 Traits
[INFO] [2020-04-06 10:32:34] Processing group of 1324 in 2 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.18
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[INFO] [2020-04-06 10:32:34] Storing 4 MetaTraits
[INFO] [2020-04-06 10:32:34] Processing group of 4 in 1 groups of 1000
[INFO] [2020-04-06 10:32:34] Average Time: 0.0
[INFO] [2020-04-06 10:32:34] Total Time: 1s
[STOP] [2020-04-06 10:32:34] parse_diff_and_store
[START] [2020-04-06 10:32:34] resolve_keys
[INFO] [2020-04-06 10:32:39] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-06 10:32:39] traits to occurrences...
[INFO] [2020-04-06 10:32:39] traits to nodes (through occurrences)...
[INFO] [2020-04-06 10:32:39] Traits to sex term...
[INFO] [2020-04-06 10:32:39] Traits to lifestage term...
[INFO] [2020-04-06 10:32:39] MetaTraits to traits...
[INFO] [2020-04-06 10:32:39] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-06 10:32:39] Assocs to occurrences...
[INFO] [2020-04-06 10:32:39] Assocs to nodes...
[INFO] [2020-04-06 10:32:39] Assoc to sex term...
[INFO] [2020-04-06 10:32:39] Assoc to lifestage term...
[STOP] [2020-04-06 10:32:39] resolve_keys
[START] [2020-04-06 10:32:39] hold_for_later_1
[STOP] [2020-04-06 10:32:39] hold_for_later_1
[START] [2020-04-06 10:32:39] hold_for_later_2
[STOP] [2020-04-06 10:32:39] hold_for_later_2
[START] [2020-04-06 10:32:39] resolve_missing_parents
[STOP] [2020-04-06 10:32:39] resolve_missing_parents
[START] [2020-04-06 10:32:39] rebuild_nodes
[START] [2020-04-06 10:32:39] Flattener#flatten
[START] [2020-04-06 10:32:39] Flattener#study_resource
[START] [2020-04-06 10:32:39] Flattener#build_ancestry
[STOP] [2020-04-06 10:32:39] Flattener#build_ancestry
[INFO] [2020-04-06 10:32:39] 1 ancestry keys
[START] [2020-04-06 10:32:39] build_node_ancestors
[INFO] [2020-04-06 10:32:39] old ancestors deleted.
[STOP] [2020-04-06 10:32:39] build_node_ancestors
[WARN] [2020-04-06 10:32:39] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-06 10:32:39] Flattener#flatten
[STOP] [2020-04-06 10:32:39] rebuild_nodes
[START] [2020-04-06 10:32:39] resolve_missing_media_owners
[STOP] [2020-04-06 10:32:39] resolve_missing_media_owners
[START] [2020-04-06 10:32:39] sanitize_media_verbatims
[STOP] [2020-04-06 10:32:39] sanitize_media_verbatims
[START] [2020-04-06 10:32:39] queue_downloads
[STOP] [2020-04-06 10:32:39] queue_downloads
[START] [2020-04-06 10:32:39] parse_names
[WARN] [2020-04-06 10:32:39] I see 1 names which still need to be parsed.
[STOP] [2020-04-06 10:32:40] parse_names
[START] [2020-04-06 10:32:40] denormalize_canonical_names_to_nodes
[STOP] [2020-04-06 10:32:40] denormalize_canonical_names_to_nodes
[START] [2020-04-06 10:32:40] match_nodes
[START] [2020-04-06 10:32:40] map_all_nodes_to_pages
[STOP] [2020-04-06 10:32:40] map_all_nodes_to_pages
[INFO] [2020-04-06 10:32:40] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-04-06 10:32:40] update_nodes
[STOP] [2020-04-06 10:32:40] update_nodes
[STOP] [2020-04-06 10:32:40] match_nodes
[START] [2020-04-06 10:32:40] reindex_search
[STOP] [2020-04-06 10:32:40] reindex_search
[START] [2020-04-06 10:32:40] normalize_units
[STOP] [2020-04-06 10:32:40] normalize_units
[START] [2020-04-06 10:32:40] calculate_statistics
[2020-04-06 10:32:40] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-06 10:32:40] calculate_statistics
[START] [2020-04-06 10:32:40] complete_harvest_instance
[START] [2020-04-06 10:32:40] overall_tsv_creation
[INFO] [2020-04-06 10:32:40] Processing group of 1 in 1 batches of 10000
[INFO] [2020-04-06 10:33:29] 2 Traits (unfiltered)...
[INFO] [2020-04-06 10:33:41] 2 Traits (filtered)...
[INFO] [2020-04-06 10:33:41] 0 Associations (filtered)...
[INFO] [2020-04-06 10:34:15] 1328 metadata added.
[INFO] [2020-04-06 10:34:15] 0 metadata added.
[INFO] [2020-04-06 10:34:15] Average Time: 66.16
[INFO] [2020-04-06 10:34:15] Total Time: 1m35s
[STOP] [2020-04-06 10:34:15] overall_tsv_creation
[INFO] [2020-04-06 10:34:15] Done. Check your files:
[INFO] [2020-04-06 10:34:15] (1 lines) /app/public/data/rockwell_et_al/publish_nodes.tsv
[INFO] [2020-04-06 10:34:15] (1 lines) /app/public/data/rockwell_et_al/publish_scientific_names.tsv
[INFO] [2020-04-06 10:34:15] (3 lines) /app/public/data/rockwell_et_al/publish_traits.tsv
[INFO] [2020-04-06 10:34:15] (1329 lines) /app/public/data/rockwell_et_al/publish_metadata.tsv
[STOP] [2020-04-06 10:34:15] complete_harvest_instance
[START] [2020-04-06 10:34:15] completed
[STOP] [2020-04-06 10:34:15] completed
[STOP] [2020-04-06 10:34:15] logged process, took 103.96
Latest Process

06 Apr 10:32 EXITED currently processing 0