Harvest for Dragonflies of Taiwan Created 31 Dec 10:13

Stage: completed
Fetched: 31 Dec 10:13
Validated: 31 Dec 10:13
Deltas Created 31 Dec 10:13
Units Normalized: 31 Dec 10:13
Ancestry Built: 31 Dec 10:13
Nodes Matched: 31 Dec 10:13
Names Parsed: 31 Dec 10:13
New Models Stored: 31 Dec 10:13
Indexed: 31 Dec 10:13
Completed: 31 Dec 10:14
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2019-12-31 10:13:10 -0500 by logger.rb/56815
[START] [2019-12-31 10:13:10] logged process
[START] [2019-12-31 10:13:10] create_harvest_instance
[STOP] [2019-12-31 10:13:11] create_harvest_instance
[START] [2019-12-31 10:13:11] fetch_files
[STOP] [2019-12-31 10:13:11] fetch_files
[START] [2019-12-31 10:13:11] validate_each_file
[STOP] [2019-12-31 10:13:11] validate_each_file
[START] [2019-12-31 10:13:11] convert_to_csv
[CMD] [2019-12-31 10:13:11] /usr/bin/sort /app/public/converted_csv/dragonflies_taiw_agents_19845.csv > /app/public/converted_csv/dragonflies_taiw_agents_19845.csv_sorted
[CMD] [2019-12-31 10:13:12] /usr/bin/sort /app/public/converted_csv/dragonflies_taiw_nodes_19846.csv > /app/public/converted_csv/dragonflies_taiw_nodes_19846.csv_sorted
[CMD] [2019-12-31 10:13:12] /usr/bin/sort /app/public/converted_csv/dragonflies_taiw_media_19847.csv > /app/public/converted_csv/dragonflies_taiw_media_19847.csv_sorted
[CMD] [2019-12-31 10:13:12] /usr/bin/sort /app/public/converted_csv/dragonflies_taiw_vernaculars_19848.csv > /app/public/converted_csv/dragonflies_taiw_vernaculars_19848.csv_sorted
[STOP] [2019-12-31 10:13:12] convert_to_csv
[START] [2019-12-31 10:13:12] calculate_delta
[CMD] [2019-12-31 10:13:12] echo "0a" > /app/public/diff/dragonflies_taiw_agents_19845.diff
[CMD] [2019-12-31 10:13:12] tail -n +1 /app/public/converted_csv/dragonflies_taiw_agents_19845.csv >> /app/public/diff/dragonflies_taiw_agents_19845.diff
[CMD] [2019-12-31 10:13:12] echo "." >> /app/public/diff/dragonflies_taiw_agents_19845.diff
[CMD] [2019-12-31 10:13:13] echo "0a" > /app/public/diff/dragonflies_taiw_nodes_19846.diff
[CMD] [2019-12-31 10:13:13] tail -n +1 /app/public/converted_csv/dragonflies_taiw_nodes_19846.csv >> /app/public/diff/dragonflies_taiw_nodes_19846.diff
[CMD] [2019-12-31 10:13:13] echo "." >> /app/public/diff/dragonflies_taiw_nodes_19846.diff
[CMD] [2019-12-31 10:13:13] echo "0a" > /app/public/diff/dragonflies_taiw_media_19847.diff
[CMD] [2019-12-31 10:13:13] tail -n +1 /app/public/converted_csv/dragonflies_taiw_media_19847.csv >> /app/public/diff/dragonflies_taiw_media_19847.diff
[CMD] [2019-12-31 10:13:13] echo "." >> /app/public/diff/dragonflies_taiw_media_19847.diff
[CMD] [2019-12-31 10:13:14] echo "0a" > /app/public/diff/dragonflies_taiw_vernaculars_19848.diff
[CMD] [2019-12-31 10:13:14] tail -n +1 /app/public/converted_csv/dragonflies_taiw_vernaculars_19848.csv >> /app/public/diff/dragonflies_taiw_vernaculars_19848.diff
[CMD] [2019-12-31 10:13:14] echo "." >> /app/public/diff/dragonflies_taiw_vernaculars_19848.diff
[STOP] [2019-12-31 10:13:14] calculate_delta
[START] [2019-12-31 10:13:14] parse_diff_and_store
[INFO] [2019-12-31 10:13:14] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-31 10:13:14] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-31 10:13:15] Loading media diff file into memory (true lines)...
[INFO] [2019-12-31 10:13:16] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-12-31 10:13:16] Storing 10 Attributions
[INFO] [2019-12-31 10:13:16] Processing group of 10 in 1 groups of 1000
[INFO] [2019-12-31 10:13:16] Average Time: 0.01
[INFO] [2019-12-31 10:13:16] Total Time: 1s
[INFO] [2019-12-31 10:13:16] Storing 161 ScientificNames
[INFO] [2019-12-31 10:13:16] Processing group of 161 in 1 groups of 1000
[INFO] [2019-12-31 10:13:16] Average Time: 0.14
[INFO] [2019-12-31 10:13:16] Total Time: 1s
[INFO] [2019-12-31 10:13:16] Storing 161 Nodes
[INFO] [2019-12-31 10:13:16] Processing group of 161 in 1 groups of 1000
[INFO] [2019-12-31 10:13:16] Average Time: 0.1
[INFO] [2019-12-31 10:13:16] Total Time: 1s
[INFO] [2019-12-31 10:13:16] Storing 800 ContentAttributions
[INFO] [2019-12-31 10:13:16] Processing group of 800 in 1 groups of 1000
[INFO] [2019-12-31 10:13:16] Average Time: 0.15
[INFO] [2019-12-31 10:13:16] Total Time: 1s
[INFO] [2019-12-31 10:13:16] Storing 400 Media
[INFO] [2019-12-31 10:13:16] Processing group of 400 in 1 groups of 1000
[INFO] [2019-12-31 10:13:17] Average Time: 0.27
[INFO] [2019-12-31 10:13:17] Total Time: 1s
[INFO] [2019-12-31 10:13:17] Storing 146 Vernaculars
[INFO] [2019-12-31 10:13:17] Processing group of 146 in 1 groups of 1000
[INFO] [2019-12-31 10:13:17] Average Time: 0.06
[INFO] [2019-12-31 10:13:17] Total Time: 1s
[STOP] [2019-12-31 10:13:17] parse_diff_and_store
[START] [2019-12-31 10:13:17] resolve_keys
[INFO] [2019-12-31 10:13:21] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-31 10:13:21] traits to occurrences...
[INFO] [2019-12-31 10:13:21] traits to nodes (through occurrences)...
[INFO] [2019-12-31 10:13:21] Traits to sex term...
[INFO] [2019-12-31 10:13:21] Traits to lifestage term...
[INFO] [2019-12-31 10:13:21] MetaTraits to traits...
[INFO] [2019-12-31 10:13:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-31 10:13:21] Assocs to occurrences...
[INFO] [2019-12-31 10:13:21] Assocs to nodes...
[INFO] [2019-12-31 10:13:21] Assoc to sex term...
[INFO] [2019-12-31 10:13:21] Assoc to lifestage term...
[STOP] [2019-12-31 10:13:21] resolve_keys
[START] [2019-12-31 10:13:21] hold_for_later_1
[STOP] [2019-12-31 10:13:21] hold_for_later_1
[START] [2019-12-31 10:13:21] hold_for_later_2
[STOP] [2019-12-31 10:13:21] hold_for_later_2
[START] [2019-12-31 10:13:21] resolve_missing_parents
[STOP] [2019-12-31 10:13:21] resolve_missing_parents
[START] [2019-12-31 10:13:21] rebuild_nodes
[START] [2019-12-31 10:13:21] Flattener#flatten
[START] [2019-12-31 10:13:21] Flattener#study_resource
[START] [2019-12-31 10:13:21] Flattener#build_ancestry
[STOP] [2019-12-31 10:13:21] Flattener#build_ancestry
[INFO] [2019-12-31 10:13:21] 161 ancestry keys
[START] [2019-12-31 10:13:21] build_node_ancestors
[INFO] [2019-12-31 10:13:21] old ancestors deleted.
[STOP] [2019-12-31 10:13:21] build_node_ancestors
[START] [2019-12-31 10:13:22] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:13:22] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:13:22] Flattener#flatten
[STOP] [2019-12-31 10:13:22] rebuild_nodes
[START] [2019-12-31 10:13:22] resolve_missing_media_owners
[STOP] [2019-12-31 10:13:22] resolve_missing_media_owners
[START] [2019-12-31 10:13:22] sanitize_media_verbatims
[STOP] [2019-12-31 10:13:22] sanitize_media_verbatims
[START] [2019-12-31 10:13:22] queue_downloads
[STOP] [2019-12-31 10:13:22] queue_downloads
[START] [2019-12-31 10:13:22] parse_names
[WARN] [2019-12-31 10:13:22] I see 161 names which still need to be parsed.
[STOP] [2019-12-31 10:13:23] parse_names
[START] [2019-12-31 10:13:23] denormalize_canonical_names_to_nodes
[STOP] [2019-12-31 10:13:23] denormalize_canonical_names_to_nodes
[START] [2019-12-31 10:13:23] match_nodes
[START] [2019-12-31 10:13:23] map_all_nodes_to_pages
[STOP] [2019-12-31 10:13:57] map_all_nodes_to_pages
[INFO] [2019-12-31 10:13:57] 12 Unmatched nodes (of 161)! That's too many to output. First 10: Anax parthenope julius (#62745448); Heliocypha perforata perforata (#62745468); Pseudagrion pilidorsum pilidorsum (#62745485); Copera ciliata (#62745575); Brachydiplax chalybea flavovittata (#62745527); Crocothemis servilia servilia (#62745530); Neurothemis tullia tullia (#62745541); Orthetrum albistylum speciosum (#62745543); Orthetrum pruinosum clelia (#62745548); Orthetrum pruinosum neglectum (#62745549)
[START] [2019-12-31 10:13:57] update_nodes
[STOP] [2019-12-31 10:13:57] update_nodes
[STOP] [2019-12-31 10:13:57] match_nodes
[START] [2019-12-31 10:13:57] reindex_search
[STOP] [2019-12-31 10:13:58] reindex_search
[START] [2019-12-31 10:13:58] normalize_units
[STOP] [2019-12-31 10:13:58] normalize_units
[START] [2019-12-31 10:13:58] calculate_statistics
[STOP] [2019-12-31 10:13:58] calculate_statistics
[START] [2019-12-31 10:13:58] complete_harvest_instance
[START] [2019-12-31 10:13:58] overall_tsv_creation
[INFO] [2019-12-31 10:13:58] Processing group of 161 in 1 batches of 10000
[INFO] [2019-12-31 10:14:34] Average Time: 12.82
[INFO] [2019-12-31 10:14:34] Total Time: 36s
[STOP] [2019-12-31 10:14:34] overall_tsv_creation
[INFO] [2019-12-31 10:14:34] Done. Check your files:
[INFO] [2019-12-31 10:14:34] (161 lines) /app/public/data/dragonflies_taiw/publish_nodes.tsv
[INFO] [2019-12-31 10:14:34] (465 lines) /app/public/data/dragonflies_taiw/publish_node_ancestors.tsv
[INFO] [2019-12-31 10:14:34] (161 lines) /app/public/data/dragonflies_taiw/publish_scientific_names.tsv
[INFO] [2019-12-31 10:14:34] (400 lines) /app/public/data/dragonflies_taiw/publish_media.tsv
[INFO] [2019-12-31 10:14:35] (103 lines) /app/public/data/dragonflies_taiw/publish_image_info.tsv
[INFO] [2019-12-31 10:14:35] (146 lines) /app/public/data/dragonflies_taiw/publish_vernaculars.tsv
[INFO] [2019-12-31 10:14:35] (800 lines) /app/public/data/dragonflies_taiw/publish_attributions.tsv
[STOP] [2019-12-31 10:14:35] complete_harvest_instance
[START] [2019-12-31 10:14:35] completed
[STOP] [2019-12-31 10:14:35] completed
[STOP] [2019-12-31 10:14:35] logged process, took 84.74
Latest Process

31 Dec 10:13 EXITED currently processing 0