Harvest for Steinke et al 2018 Created 16 Jun 09:54

Stage: completed
Fetched: 16 Jun 09:54
Validated: 16 Jun 09:54
Deltas Created 16 Jun 09:54
Units Normalized: 16 Jun 09:54
Ancestry Built: 16 Jun 09:54
Nodes Matched: 16 Jun 09:54
Names Parsed: 16 Jun 09:54
New Models Stored: 16 Jun 09:54
Indexed: 16 Jun 09:54
Completed: 16 Jun 09:56
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2020-06-16 09:54:24 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:54:24] ## HARVEST: type = -harvest
[START] [2020-06-16 09:54:28] logged process
[START] [2020-06-16 09:54:28] create_harvest_instance
[STOP] [2020-06-16 09:54:29] create_harvest_instance
[START] [2020-06-16 09:54:29] fetch_files
[STOP] [2020-06-16 09:54:29] fetch_files
[START] [2020-06-16 09:54:29] validate_each_file
[STOP] [2020-06-16 09:54:29] validate_each_file
[START] [2020-06-16 09:54:29] convert_to_csv
[CMD] [2020-06-16 09:54:29] /usr/bin/sort /app/public/converted_csv/steinke_et_al_st_nodes_21326.csv > /app/public/converted_csv/steinke_et_al_st_nodes_21326.csv_sorted
[CMD] [2020-06-16 09:54:29] /usr/bin/sort /app/public/converted_csv/steinke_et_al_st_occurrences_21327.csv > /app/public/converted_csv/steinke_et_al_st_occurrences_21327.csv_sorted
[CMD] [2020-06-16 09:54:29] /usr/bin/sort /app/public/converted_csv/steinke_et_al_st_measurements_21328.csv > /app/public/converted_csv/steinke_et_al_st_measurements_21328.csv_sorted
[STOP] [2020-06-16 09:54:29] convert_to_csv
[START] [2020-06-16 09:54:29] calculate_delta
[CMD] [2020-06-16 09:54:29] echo "0a" > /app/public/diff/steinke_et_al_st_nodes_21326.diff
[CMD] [2020-06-16 09:54:29] tail -n +1 /app/public/converted_csv/steinke_et_al_st_nodes_21326.csv >> /app/public/diff/steinke_et_al_st_nodes_21326.diff
[CMD] [2020-06-16 09:54:29] echo "." >> /app/public/diff/steinke_et_al_st_nodes_21326.diff
[CMD] [2020-06-16 09:54:29] echo "0a" > /app/public/diff/steinke_et_al_st_occurrences_21327.diff
[CMD] [2020-06-16 09:54:29] tail -n +1 /app/public/converted_csv/steinke_et_al_st_occurrences_21327.csv >> /app/public/diff/steinke_et_al_st_occurrences_21327.diff
[CMD] [2020-06-16 09:54:29] echo "." >> /app/public/diff/steinke_et_al_st_occurrences_21327.diff
[CMD] [2020-06-16 09:54:29] echo "0a" > /app/public/diff/steinke_et_al_st_measurements_21328.diff
[CMD] [2020-06-16 09:54:29] tail -n +1 /app/public/converted_csv/steinke_et_al_st_measurements_21328.csv >> /app/public/diff/steinke_et_al_st_measurements_21328.diff
[CMD] [2020-06-16 09:54:29] echo "." >> /app/public/diff/steinke_et_al_st_measurements_21328.diff
[STOP] [2020-06-16 09:54:29] calculate_delta
[START] [2020-06-16 09:54:29] parse_diff_and_store
[INFO] [2020-06-16 09:54:29] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:54:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:54:29] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:54:29] Storing 10 ScientificNames
[INFO] [2020-06-16 09:54:29] Processing group of 10 in 1 groups of 1000
[INFO] [2020-06-16 09:54:29] Average Time: 0.01
[INFO] [2020-06-16 09:54:29] Total Time: 1s
[INFO] [2020-06-16 09:54:29] Storing 10 Nodes
[INFO] [2020-06-16 09:54:29] Processing group of 10 in 1 groups of 1000
[INFO] [2020-06-16 09:54:29] Average Time: 0.0
[INFO] [2020-06-16 09:54:29] Total Time: 1s
[INFO] [2020-06-16 09:54:29] Storing 3 Occurrences
[INFO] [2020-06-16 09:54:29] Processing group of 3 in 1 groups of 1000
[INFO] [2020-06-16 09:54:29] Average Time: 0.0
[INFO] [2020-06-16 09:54:29] Total Time: 1s
[INFO] [2020-06-16 09:54:29] Storing 6 Traits
[INFO] [2020-06-16 09:54:29] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-16 09:54:29] Average Time: 0.0
[INFO] [2020-06-16 09:54:29] Total Time: 1s
[INFO] [2020-06-16 09:54:29] Storing 12 MetaTraits
[INFO] [2020-06-16 09:54:29] Processing group of 12 in 1 groups of 1000
[INFO] [2020-06-16 09:54:29] Average Time: 0.0
[INFO] [2020-06-16 09:54:29] Total Time: 1s
[STOP] [2020-06-16 09:54:29] parse_diff_and_store
[START] [2020-06-16 09:54:29] resolve_keys
[INFO] [2020-06-16 09:54:36] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:54:36] traits to occurrences...
[INFO] [2020-06-16 09:54:36] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:54:36] Traits to sex term...
[INFO] [2020-06-16 09:54:36] Traits to lifestage term...
[INFO] [2020-06-16 09:54:36] MetaTraits to traits...
[INFO] [2020-06-16 09:54:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:54:36] Assocs to occurrences...
[INFO] [2020-06-16 09:54:36] Assocs to nodes...
[INFO] [2020-06-16 09:54:36] Assoc to sex term...
[INFO] [2020-06-16 09:54:36] Assoc to lifestage term...
[STOP] [2020-06-16 09:54:36] resolve_keys
[START] [2020-06-16 09:54:36] hold_for_later_1
[STOP] [2020-06-16 09:54:36] hold_for_later_1
[START] [2020-06-16 09:54:36] hold_for_later_2
[STOP] [2020-06-16 09:54:36] hold_for_later_2
[START] [2020-06-16 09:54:36] resolve_missing_parents
[STOP] [2020-06-16 09:54:36] resolve_missing_parents
[START] [2020-06-16 09:54:36] rebuild_nodes
[START] [2020-06-16 09:54:36] Flattener#flatten
[START] [2020-06-16 09:54:36] Flattener#study_resource
[START] [2020-06-16 09:54:36] Flattener#build_ancestry
[STOP] [2020-06-16 09:54:36] Flattener#build_ancestry
[INFO] [2020-06-16 09:54:36] 10 ancestry keys
[START] [2020-06-16 09:54:36] build_node_ancestors
[INFO] [2020-06-16 09:54:36] old ancestors deleted.
[STOP] [2020-06-16 09:54:36] build_node_ancestors
[START] [2020-06-16 09:54:36] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:54:36] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:54:36] Flattener#flatten
[STOP] [2020-06-16 09:54:36] rebuild_nodes
[START] [2020-06-16 09:54:36] resolve_missing_media_owners
[STOP] [2020-06-16 09:54:36] resolve_missing_media_owners
[START] [2020-06-16 09:54:36] sanitize_media_verbatims
[STOP] [2020-06-16 09:54:36] sanitize_media_verbatims
[START] [2020-06-16 09:54:36] queue_downloads
[STOP] [2020-06-16 09:54:36] queue_downloads
[START] [2020-06-16 09:54:36] parse_names
[WARN] [2020-06-16 09:54:36] I see 10 names which still need to be parsed.
[STOP] [2020-06-16 09:54:37] parse_names
[START] [2020-06-16 09:54:37] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:54:37] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:54:37] match_nodes
[START] [2020-06-16 09:54:37] map_all_nodes_to_pages
[STOP] [2020-06-16 09:54:38] map_all_nodes_to_pages
[INFO] [2020-06-16 09:54:38] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2020-06-16 09:54:38] update_nodes
[STOP] [2020-06-16 09:54:38] update_nodes
[STOP] [2020-06-16 09:54:38] match_nodes
[START] [2020-06-16 09:54:38] reindex_search
[STOP] [2020-06-16 09:54:38] reindex_search
[START] [2020-06-16 09:54:38] normalize_units
[STOP] [2020-06-16 09:54:38] normalize_units
[START] [2020-06-16 09:54:38] calculate_statistics
[STOP] [2020-06-16 09:54:38] calculate_statistics
[START] [2020-06-16 09:54:38] complete_harvest_instance
[START] [2020-06-16 09:54:38] overall_tsv_creation
[INFO] [2020-06-16 09:54:38] Processing group of 10 in 1 batches of 10000
[INFO] [2020-06-16 09:55:28] 3 Traits (unfiltered)...
[INFO] [2020-06-16 09:55:41] 3 Traits (filtered)...
[INFO] [2020-06-16 09:55:41] 0 Associations (filtered)...
[INFO] [2020-06-16 09:56:18] 12 metadata added.
[INFO] [2020-06-16 09:56:18] 0 metadata added.
[INFO] [2020-06-16 09:56:18] Average Time: 71.86
[INFO] [2020-06-16 09:56:18] Total Time: 1m40s
[STOP] [2020-06-16 09:56:18] overall_tsv_creation
[INFO] [2020-06-16 09:56:18] Done. Check your files:
[INFO] [2020-06-16 09:56:18] (10 lines) /app/public/data/steinke_et_al_st/publish_nodes.tsv
[INFO] [2020-06-16 09:56:18] (17 lines) /app/public/data/steinke_et_al_st/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:56:18] (10 lines) /app/public/data/steinke_et_al_st/publish_scientific_names.tsv
[INFO] [2020-06-16 09:56:18] (4 lines) /app/public/data/steinke_et_al_st/publish_traits.tsv
[INFO] [2020-06-16 09:56:18] (13 lines) /app/public/data/steinke_et_al_st/publish_metadata.tsv
[STOP] [2020-06-16 09:56:18] complete_harvest_instance
[START] [2020-06-16 09:56:18] completed
[STOP] [2020-06-16 09:56:18] completed
[STOP] [2020-06-16 09:56:18] logged process, took 109.98

Latest Process