Harvest for Vatican City Species List Created 17 Oct 11:25

Stage: completed
Fetched: 17 Oct 11:25
Validated: 17 Oct 11:25
Deltas Created 17 Oct 11:25
Units Normalized: 17 Oct 11:25
Ancestry Built: 17 Oct 11:25
Nodes Matched: 17 Oct 11:25
Names Parsed: 17 Oct 11:25
New Models Stored: 17 Oct 11:25
Indexed: 17 Oct 11:25
Completed: 17 Oct 11:27
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-17 11:25:31 -0400 by logger.rb/56815
[START] [2019-10-17 11:25:31] logged process
[START] [2019-10-17 11:25:31] create_harvest_instance
[STOP] [2019-10-17 11:25:32] create_harvest_instance
[START] [2019-10-17 11:25:32] fetch_files
[STOP] [2019-10-17 11:25:32] fetch_files
[START] [2019-10-17 11:25:32] validate_each_file
[STOP] [2019-10-17 11:25:32] validate_each_file
[START] [2019-10-17 11:25:32] convert_to_csv
[CMD] [2019-10-17 11:25:32] /usr/bin/sort /app/public/converted_csv/vatican_city_sp__refs_17737.csv > /app/public/converted_csv/vatican_city_sp__refs_17737.csv_sorted
[CMD] [2019-10-17 11:25:32] /usr/bin/sort /app/public/converted_csv/vatican_city_sp__nodes_17738.csv > /app/public/converted_csv/vatican_city_sp__nodes_17738.csv_sorted
[CMD] [2019-10-17 11:25:32] /usr/bin/sort /app/public/converted_csv/vatican_city_sp__occurrences_17739.csv > /app/public/converted_csv/vatican_city_sp__occurrences_17739.csv_sorted
[CMD] [2019-10-17 11:25:32] /usr/bin/sort /app/public/converted_csv/vatican_city_sp__measurements_17740.csv > /app/public/converted_csv/vatican_city_sp__measurements_17740.csv_sorted
[STOP] [2019-10-17 11:25:32] convert_to_csv
[START] [2019-10-17 11:25:32] calculate_delta
[CMD] [2019-10-17 11:25:32] echo "0a" > /app/public/diff/vatican_city_sp__refs_17737.diff
[CMD] [2019-10-17 11:25:32] tail -n +1 /app/public/converted_csv/vatican_city_sp__refs_17737.csv >> /app/public/diff/vatican_city_sp__refs_17737.diff
[CMD] [2019-10-17 11:25:32] echo "." >> /app/public/diff/vatican_city_sp__refs_17737.diff
[CMD] [2019-10-17 11:25:32] echo "0a" > /app/public/diff/vatican_city_sp__nodes_17738.diff
[CMD] [2019-10-17 11:25:33] tail -n +1 /app/public/converted_csv/vatican_city_sp__nodes_17738.csv >> /app/public/diff/vatican_city_sp__nodes_17738.diff
[CMD] [2019-10-17 11:25:33] echo "." >> /app/public/diff/vatican_city_sp__nodes_17738.diff
[CMD] [2019-10-17 11:25:33] echo "0a" > /app/public/diff/vatican_city_sp__occurrences_17739.diff
[CMD] [2019-10-17 11:25:33] tail -n +1 /app/public/converted_csv/vatican_city_sp__occurrences_17739.csv >> /app/public/diff/vatican_city_sp__occurrences_17739.diff
[CMD] [2019-10-17 11:25:33] echo "." >> /app/public/diff/vatican_city_sp__occurrences_17739.diff
[CMD] [2019-10-17 11:25:33] echo "0a" > /app/public/diff/vatican_city_sp__measurements_17740.diff
[CMD] [2019-10-17 11:25:33] tail -n +1 /app/public/converted_csv/vatican_city_sp__measurements_17740.csv >> /app/public/diff/vatican_city_sp__measurements_17740.diff
[CMD] [2019-10-17 11:25:33] echo "." >> /app/public/diff/vatican_city_sp__measurements_17740.diff
[STOP] [2019-10-17 11:25:33] calculate_delta
[START] [2019-10-17 11:25:33] parse_diff_and_store
[INFO] [2019-10-17 11:25:33] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:25:33] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:25:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:25:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:25:34] Storing 2 References
[INFO] [2019-10-17 11:25:34] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.0
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[INFO] [2019-10-17 11:25:34] Storing 147 ScientificNames
[INFO] [2019-10-17 11:25:34] Processing group of 147 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.1
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[INFO] [2019-10-17 11:25:34] Storing 147 Nodes
[INFO] [2019-10-17 11:25:34] Processing group of 147 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.04
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[INFO] [2019-10-17 11:25:34] Storing 49 Occurrences
[INFO] [2019-10-17 11:25:34] Processing group of 49 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.01
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[INFO] [2019-10-17 11:25:34] Storing 98 TraitsReferences
[INFO] [2019-10-17 11:25:34] Processing group of 98 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.04
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[INFO] [2019-10-17 11:25:34] Storing 98 Traits
[INFO] [2019-10-17 11:25:34] Processing group of 98 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.06
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[INFO] [2019-10-17 11:25:34] Storing 98 MetaTraits
[INFO] [2019-10-17 11:25:34] Processing group of 98 in 1 groups of 1000
[INFO] [2019-10-17 11:25:34] Average Time: 0.03
[INFO] [2019-10-17 11:25:34] Total Time: 1s
[STOP] [2019-10-17 11:25:34] parse_diff_and_store
[START] [2019-10-17 11:25:34] resolve_keys
[INFO] [2019-10-17 11:25:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:25:38] traits to occurrences...
[INFO] [2019-10-17 11:25:38] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:25:38] Traits to sex term...
[INFO] [2019-10-17 11:25:38] Traits to lifestage term...
[INFO] [2019-10-17 11:25:38] MetaTraits to traits...
[INFO] [2019-10-17 11:25:39] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:25:39] Assocs to occurrences...
[INFO] [2019-10-17 11:25:39] Assocs to nodes...
[INFO] [2019-10-17 11:25:39] Assoc to sex term...
[INFO] [2019-10-17 11:25:39] Assoc to lifestage term...
[STOP] [2019-10-17 11:25:39] resolve_keys
[START] [2019-10-17 11:25:39] hold_for_later_1
[STOP] [2019-10-17 11:25:39] hold_for_later_1
[START] [2019-10-17 11:25:39] hold_for_later_2
[STOP] [2019-10-17 11:25:39] hold_for_later_2
[START] [2019-10-17 11:25:39] resolve_missing_parents
[STOP] [2019-10-17 11:25:39] resolve_missing_parents
[START] [2019-10-17 11:25:39] rebuild_nodes
[START] [2019-10-17 11:25:39] Flattener#flatten
[START] [2019-10-17 11:25:39] Flattener#study_resource
[START] [2019-10-17 11:25:39] Flattener#build_ancestry
[STOP] [2019-10-17 11:25:39] Flattener#build_ancestry
[INFO] [2019-10-17 11:25:39] 147 ancestry keys
[START] [2019-10-17 11:25:39] build_node_ancestors
[INFO] [2019-10-17 11:25:39] old ancestors deleted.
[STOP] [2019-10-17 11:25:39] build_node_ancestors
[START] [2019-10-17 11:25:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:25:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:25:39] Flattener#flatten
[STOP] [2019-10-17 11:25:39] rebuild_nodes
[START] [2019-10-17 11:25:39] resolve_missing_media_owners
[STOP] [2019-10-17 11:25:39] resolve_missing_media_owners
[START] [2019-10-17 11:25:39] sanitize_media_verbatims
[STOP] [2019-10-17 11:25:39] sanitize_media_verbatims
[START] [2019-10-17 11:25:39] queue_downloads
[STOP] [2019-10-17 11:25:39] queue_downloads
[START] [2019-10-17 11:25:39] parse_names
[WARN] [2019-10-17 11:25:39] I see 147 names which still need to be parsed.
[STOP] [2019-10-17 11:25:40] parse_names
[START] [2019-10-17 11:25:40] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:25:40] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:25:40] match_nodes
[START] [2019-10-17 11:25:40] map_all_nodes_to_pages
[STOP] [2019-10-17 11:25:49] map_all_nodes_to_pages
[INFO] [2019-10-17 11:25:49] Unmatched nodes (3 of 147): Magnoliophyta (#52722415); Magnoliopsida (#52722421); Pinophyta (#52722456)
[START] [2019-10-17 11:25:49] update_nodes
[STOP] [2019-10-17 11:25:49] update_nodes
[STOP] [2019-10-17 11:25:49] match_nodes
[START] [2019-10-17 11:25:49] reindex_search
[STOP] [2019-10-17 11:25:50] reindex_search
[START] [2019-10-17 11:25:50] normalize_units
[STOP] [2019-10-17 11:25:50] normalize_units
[START] [2019-10-17 11:25:50] calculate_statistics
[STOP] [2019-10-17 11:25:50] calculate_statistics
[START] [2019-10-17 11:25:50] complete_harvest_instance
[START] [2019-10-17 11:25:50] overall_tsv_creation
[INFO] [2019-10-17 11:25:50] Processing group of 147 in 1 batches of 10000
[INFO] [2019-10-17 11:26:32] 49 Traits (unfiltered)...
[INFO] [2019-10-17 11:26:45] 49 Traits (filtered)...
[INFO] [2019-10-17 11:26:45] 0 Associations (filtered)...
[INFO] [2019-10-17 11:27:22] 245 metadata added.
[INFO] [2019-10-17 11:27:22] 0 metadata added.
[INFO] [2019-10-17 11:27:22] Average Time: 71.34
[INFO] [2019-10-17 11:27:22] Total Time: 1m32s
[STOP] [2019-10-17 11:27:22] overall_tsv_creation
[INFO] [2019-10-17 11:27:22] Done. Check your files:
[INFO] [2019-10-17 11:27:22] (147 lines) /app/public/data/vatican_city_sp_/publish_nodes.tsv
[INFO] [2019-10-17 11:27:22] (682 lines) /app/public/data/vatican_city_sp_/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:27:22] (147 lines) /app/public/data/vatican_city_sp_/publish_scientific_names.tsv
[INFO] [2019-10-17 11:27:22] (50 lines) /app/public/data/vatican_city_sp_/publish_traits.tsv
[INFO] [2019-10-17 11:27:22] (246 lines) /app/public/data/vatican_city_sp_/publish_metadata.tsv
[STOP] [2019-10-17 11:27:22] complete_harvest_instance
[START] [2019-10-17 11:27:22] completed
[STOP] [2019-10-17 11:27:22] completed
[STOP] [2019-10-17 11:27:22] logged process, took 110.79
Latest Process

17 Oct 11:25 EXITED currently processing 0