Harvest for Vettikkat et al 2020 Created 16 Jun 09:48

Stage: completed
Fetched: 16 Jun 09:48
Validated: 16 Jun 09:48
Deltas Created 16 Jun 09:48
Units Normalized: 16 Jun 09:48
Ancestry Built: 16 Jun 09:48
Nodes Matched: 16 Jun 09:48
Names Parsed: 16 Jun 09:48
New Models Stored: 16 Jun 09:48
Indexed: 16 Jun 09:48
Completed: 16 Jun 09:50
Time to Harvest: less than a minute
Harvesting Log

(127 lines)
# Logfile created on 2020-06-16 09:48:19 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:48:19] ## HARVEST: type = -harvest
[START] [2020-06-16 09:48:21] logged process
[START] [2020-06-16 09:48:21] create_harvest_instance
[STOP] [2020-06-16 09:48:22] create_harvest_instance
[START] [2020-06-16 09:48:22] fetch_files
[STOP] [2020-06-16 09:48:22] fetch_files
[START] [2020-06-16 09:48:22] validate_each_file
[STOP] [2020-06-16 09:48:22] validate_each_file
[START] [2020-06-16 09:48:22] convert_to_csv
[CMD] [2020-06-16 09:48:22] /usr/bin/sort /app/public/converted_csv/vettikkat_et_al__nodes_21314.csv > /app/public/converted_csv/vettikkat_et_al__nodes_21314.csv_sorted
[CMD] [2020-06-16 09:48:22] /usr/bin/sort /app/public/converted_csv/vettikkat_et_al__occurrences_21315.csv > /app/public/converted_csv/vettikkat_et_al__occurrences_21315.csv_sorted
[CMD] [2020-06-16 09:48:22] /usr/bin/sort /app/public/converted_csv/vettikkat_et_al__measurements_21316.csv > /app/public/converted_csv/vettikkat_et_al__measurements_21316.csv_sorted
[STOP] [2020-06-16 09:48:22] convert_to_csv
[START] [2020-06-16 09:48:22] calculate_delta
[CMD] [2020-06-16 09:48:22] echo "0a" > /app/public/diff/vettikkat_et_al__nodes_21314.diff
[CMD] [2020-06-16 09:48:22] tail -n +1 /app/public/converted_csv/vettikkat_et_al__nodes_21314.csv >> /app/public/diff/vettikkat_et_al__nodes_21314.diff
[CMD] [2020-06-16 09:48:22] echo "." >> /app/public/diff/vettikkat_et_al__nodes_21314.diff
[CMD] [2020-06-16 09:48:22] echo "0a" > /app/public/diff/vettikkat_et_al__occurrences_21315.diff
[CMD] [2020-06-16 09:48:22] tail -n +1 /app/public/converted_csv/vettikkat_et_al__occurrences_21315.csv >> /app/public/diff/vettikkat_et_al__occurrences_21315.diff
[CMD] [2020-06-16 09:48:22] echo "." >> /app/public/diff/vettikkat_et_al__occurrences_21315.diff
[CMD] [2020-06-16 09:48:22] echo "0a" > /app/public/diff/vettikkat_et_al__measurements_21316.diff
[CMD] [2020-06-16 09:48:22] tail -n +1 /app/public/converted_csv/vettikkat_et_al__measurements_21316.csv >> /app/public/diff/vettikkat_et_al__measurements_21316.diff
[CMD] [2020-06-16 09:48:22] echo "." >> /app/public/diff/vettikkat_et_al__measurements_21316.diff
[STOP] [2020-06-16 09:48:22] calculate_delta
[START] [2020-06-16 09:48:22] parse_diff_and_store
[INFO] [2020-06-16 09:48:22] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:48:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:48:22] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:48:22] Storing 4 ScientificNames
[INFO] [2020-06-16 09:48:22] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-16 09:48:22] Average Time: 0.0
[INFO] [2020-06-16 09:48:22] Total Time: 1s
[INFO] [2020-06-16 09:48:22] Storing 4 Nodes
[INFO] [2020-06-16 09:48:22] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-16 09:48:22] Average Time: 0.0
[INFO] [2020-06-16 09:48:22] Total Time: 1s
[INFO] [2020-06-16 09:48:22] Storing 1 Occurrences
[INFO] [2020-06-16 09:48:22] Processing group of 1 in 1 groups of 1000
[INFO] [2020-06-16 09:48:22] Average Time: 0.0
[INFO] [2020-06-16 09:48:22] Total Time: 1s
[INFO] [2020-06-16 09:48:22] Storing 2 Traits
[INFO] [2020-06-16 09:48:22] Processing group of 2 in 1 groups of 1000
[INFO] [2020-06-16 09:48:22] Average Time: 0.0
[INFO] [2020-06-16 09:48:22] Total Time: 1s
[INFO] [2020-06-16 09:48:22] Storing 4 MetaTraits
[INFO] [2020-06-16 09:48:22] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-16 09:48:22] Average Time: 0.0
[INFO] [2020-06-16 09:48:22] Total Time: 1s
[STOP] [2020-06-16 09:48:22] parse_diff_and_store
[START] [2020-06-16 09:48:22] resolve_keys
[INFO] [2020-06-16 09:48:29] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:48:29] traits to occurrences...
[INFO] [2020-06-16 09:48:29] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:48:29] Traits to sex term...
[INFO] [2020-06-16 09:48:29] Traits to lifestage term...
[INFO] [2020-06-16 09:48:29] MetaTraits to traits...
[INFO] [2020-06-16 09:48:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:48:29] Assocs to occurrences...
[INFO] [2020-06-16 09:48:29] Assocs to nodes...
[INFO] [2020-06-16 09:48:29] Assoc to sex term...
[INFO] [2020-06-16 09:48:29] Assoc to lifestage term...
[STOP] [2020-06-16 09:48:29] resolve_keys
[START] [2020-06-16 09:48:29] hold_for_later_1
[STOP] [2020-06-16 09:48:29] hold_for_later_1
[START] [2020-06-16 09:48:29] hold_for_later_2
[STOP] [2020-06-16 09:48:29] hold_for_later_2
[START] [2020-06-16 09:48:29] resolve_missing_parents
[STOP] [2020-06-16 09:48:29] resolve_missing_parents
[START] [2020-06-16 09:48:29] rebuild_nodes
[START] [2020-06-16 09:48:29] Flattener#flatten
[START] [2020-06-16 09:48:29] Flattener#study_resource
[START] [2020-06-16 09:48:29] Flattener#build_ancestry
[STOP] [2020-06-16 09:48:29] Flattener#build_ancestry
[INFO] [2020-06-16 09:48:29] 4 ancestry keys
[START] [2020-06-16 09:48:29] build_node_ancestors
[INFO] [2020-06-16 09:48:29] old ancestors deleted.
[STOP] [2020-06-16 09:48:29] build_node_ancestors
[START] [2020-06-16 09:48:29] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:48:29] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:48:29] Flattener#flatten
[STOP] [2020-06-16 09:48:29] rebuild_nodes
[START] [2020-06-16 09:48:29] resolve_missing_media_owners
[STOP] [2020-06-16 09:48:29] resolve_missing_media_owners
[START] [2020-06-16 09:48:29] sanitize_media_verbatims
[STOP] [2020-06-16 09:48:29] sanitize_media_verbatims
[START] [2020-06-16 09:48:29] queue_downloads
[STOP] [2020-06-16 09:48:29] queue_downloads
[START] [2020-06-16 09:48:29] parse_names
[WARN] [2020-06-16 09:48:29] I see 4 names which still need to be parsed.
[STOP] [2020-06-16 09:48:31] parse_names
[START] [2020-06-16 09:48:31] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:48:31] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:48:31] match_nodes
[START] [2020-06-16 09:48:31] map_all_nodes_to_pages
[STOP] [2020-06-16 09:48:31] map_all_nodes_to_pages
[INFO] [2020-06-16 09:48:31] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-06-16 09:48:31] update_nodes
[STOP] [2020-06-16 09:48:31] update_nodes
[STOP] [2020-06-16 09:48:31] match_nodes
[START] [2020-06-16 09:48:31] reindex_search
[STOP] [2020-06-16 09:48:31] reindex_search
[START] [2020-06-16 09:48:31] normalize_units
[STOP] [2020-06-16 09:48:31] normalize_units
[START] [2020-06-16 09:48:31] calculate_statistics
[STOP] [2020-06-16 09:48:31] calculate_statistics
[START] [2020-06-16 09:48:31] complete_harvest_instance
[START] [2020-06-16 09:48:31] overall_tsv_creation
[INFO] [2020-06-16 09:48:31] Processing group of 4 in 1 batches of 10000
[INFO] [2020-06-16 09:49:22] 1 Traits (unfiltered)...
[INFO] [2020-06-16 09:49:35] 1 Traits (filtered)...
[INFO] [2020-06-16 09:49:35] 0 Associations (filtered)...
[INFO] [2020-06-16 09:50:11] 4 metadata added.
[INFO] [2020-06-16 09:50:11] 0 metadata added.
[INFO] [2020-06-16 09:50:11] Average Time: 72.07
[INFO] [2020-06-16 09:50:11] Total Time: 1m41s
[STOP] [2020-06-16 09:50:11] overall_tsv_creation
[INFO] [2020-06-16 09:50:11] Done. Check your files:
[INFO] [2020-06-16 09:50:11] (4 lines) /app/public/data/vettikkat_et_al_/publish_nodes.tsv
[INFO] [2020-06-16 09:50:11] (6 lines) /app/public/data/vettikkat_et_al_/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:50:11] (4 lines) /app/public/data/vettikkat_et_al_/publish_scientific_names.tsv
[INFO] [2020-06-16 09:50:11] (2 lines) /app/public/data/vettikkat_et_al_/publish_traits.tsv
[INFO] [2020-06-16 09:50:11] (5 lines) /app/public/data/vettikkat_et_al_/publish_metadata.tsv
[STOP] [2020-06-16 09:50:11] complete_harvest_instance
[START] [2020-06-16 09:50:11] completed
[STOP] [2020-06-16 09:50:11] completed
[STOP] [2020-06-16 09:50:11] logged process, took 110.5
Latest Process

16 Jun 09:48 EXITED currently processing 0