Harvest for Butterflies of Taiwan Created 31 Dec 10:08

Stage: completed
Fetched: 31 Dec 10:08
Validated: 31 Dec 10:08
Deltas Created 31 Dec 10:08
Units Normalized: 31 Dec 10:10
Ancestry Built: 31 Dec 10:09
Nodes Matched: 31 Dec 10:10
Names Parsed: 31 Dec 10:09
New Models Stored: 31 Dec 10:08
Indexed: 31 Dec 10:10
Completed: 31 Dec 10:10
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2019-12-31 10:08:50 -0500 by logger.rb/56815
[START] [2019-12-31 10:08:50] logged process
[START] [2019-12-31 10:08:50] create_harvest_instance
[STOP] [2019-12-31 10:08:51] create_harvest_instance
[START] [2019-12-31 10:08:51] fetch_files
[STOP] [2019-12-31 10:08:51] fetch_files
[START] [2019-12-31 10:08:51] validate_each_file
[STOP] [2019-12-31 10:08:51] validate_each_file
[START] [2019-12-31 10:08:51] convert_to_csv
[CMD] [2019-12-31 10:08:51] /usr/bin/sort /app/public/converted_csv/butterflies_taiw_agents_19821.csv > /app/public/converted_csv/butterflies_taiw_agents_19821.csv_sorted
[CMD] [2019-12-31 10:08:51] /usr/bin/sort /app/public/converted_csv/butterflies_taiw_nodes_19822.csv > /app/public/converted_csv/butterflies_taiw_nodes_19822.csv_sorted
[CMD] [2019-12-31 10:08:52] /usr/bin/sort /app/public/converted_csv/butterflies_taiw_media_19823.csv > /app/public/converted_csv/butterflies_taiw_media_19823.csv_sorted
[CMD] [2019-12-31 10:08:52] /usr/bin/sort /app/public/converted_csv/butterflies_taiw_vernaculars_19824.csv > /app/public/converted_csv/butterflies_taiw_vernaculars_19824.csv_sorted
[STOP] [2019-12-31 10:08:52] convert_to_csv
[START] [2019-12-31 10:08:52] calculate_delta
[CMD] [2019-12-31 10:08:52] echo "0a" > /app/public/diff/butterflies_taiw_agents_19821.diff
[CMD] [2019-12-31 10:08:52] tail -n +1 /app/public/converted_csv/butterflies_taiw_agents_19821.csv >> /app/public/diff/butterflies_taiw_agents_19821.diff
[CMD] [2019-12-31 10:08:52] echo "." >> /app/public/diff/butterflies_taiw_agents_19821.diff
[CMD] [2019-12-31 10:08:52] echo "0a" > /app/public/diff/butterflies_taiw_nodes_19822.diff
[CMD] [2019-12-31 10:08:53] tail -n +1 /app/public/converted_csv/butterflies_taiw_nodes_19822.csv >> /app/public/diff/butterflies_taiw_nodes_19822.diff
[CMD] [2019-12-31 10:08:53] echo "." >> /app/public/diff/butterflies_taiw_nodes_19822.diff
[CMD] [2019-12-31 10:08:53] echo "0a" > /app/public/diff/butterflies_taiw_media_19823.diff
[CMD] [2019-12-31 10:08:53] tail -n +1 /app/public/converted_csv/butterflies_taiw_media_19823.csv >> /app/public/diff/butterflies_taiw_media_19823.diff
[CMD] [2019-12-31 10:08:53] echo "." >> /app/public/diff/butterflies_taiw_media_19823.diff
[CMD] [2019-12-31 10:08:53] echo "0a" > /app/public/diff/butterflies_taiw_vernaculars_19824.diff
[CMD] [2019-12-31 10:08:54] tail -n +1 /app/public/converted_csv/butterflies_taiw_vernaculars_19824.csv >> /app/public/diff/butterflies_taiw_vernaculars_19824.diff
[CMD] [2019-12-31 10:08:54] echo "." >> /app/public/diff/butterflies_taiw_vernaculars_19824.diff
[STOP] [2019-12-31 10:08:54] calculate_delta
[START] [2019-12-31 10:08:54] parse_diff_and_store
[INFO] [2019-12-31 10:08:54] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-31 10:08:54] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-31 10:08:55] Loading media diff file into memory (true lines)...
[INFO] [2019-12-31 10:08:55] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-12-31 10:08:55] Storing 1 Attributions
[INFO] [2019-12-31 10:08:55] Processing group of 1 in 1 groups of 1000
[INFO] [2019-12-31 10:08:55] Average Time: 0.01
[INFO] [2019-12-31 10:08:55] Total Time: 1s
[INFO] [2019-12-31 10:08:55] Storing 372 ScientificNames
[INFO] [2019-12-31 10:08:55] Processing group of 372 in 1 groups of 1000
[INFO] [2019-12-31 10:08:56] Average Time: 0.18
[INFO] [2019-12-31 10:08:56] Total Time: 1s
[INFO] [2019-12-31 10:08:56] Storing 372 Nodes
[INFO] [2019-12-31 10:08:56] Processing group of 372 in 1 groups of 1000
[INFO] [2019-12-31 10:08:56] Average Time: 0.12
[INFO] [2019-12-31 10:08:56] Total Time: 1s
[INFO] [2019-12-31 10:08:56] Storing 629 ContentAttributions
[INFO] [2019-12-31 10:08:56] Processing group of 629 in 1 groups of 1000
[INFO] [2019-12-31 10:08:56] Average Time: 0.13
[INFO] [2019-12-31 10:08:56] Total Time: 1s
[INFO] [2019-12-31 10:08:56] Storing 629 Media
[INFO] [2019-12-31 10:08:56] Processing group of 629 in 1 groups of 1000
[INFO] [2019-12-31 10:08:56] Average Time: 0.38
[INFO] [2019-12-31 10:08:56] Total Time: 1s
[INFO] [2019-12-31 10:08:56] Storing 364 Vernaculars
[INFO] [2019-12-31 10:08:56] Processing group of 364 in 1 groups of 1000
[INFO] [2019-12-31 10:08:56] Average Time: 0.08
[INFO] [2019-12-31 10:08:56] Total Time: 1s
[STOP] [2019-12-31 10:08:56] parse_diff_and_store
[START] [2019-12-31 10:08:56] resolve_keys
[INFO] [2019-12-31 10:09:01] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-31 10:09:01] traits to occurrences...
[INFO] [2019-12-31 10:09:01] traits to nodes (through occurrences)...
[INFO] [2019-12-31 10:09:01] Traits to sex term...
[INFO] [2019-12-31 10:09:01] Traits to lifestage term...
[INFO] [2019-12-31 10:09:01] MetaTraits to traits...
[INFO] [2019-12-31 10:09:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-31 10:09:01] Assocs to occurrences...
[INFO] [2019-12-31 10:09:01] Assocs to nodes...
[INFO] [2019-12-31 10:09:01] Assoc to sex term...
[INFO] [2019-12-31 10:09:01] Assoc to lifestage term...
[STOP] [2019-12-31 10:09:01] resolve_keys
[START] [2019-12-31 10:09:01] hold_for_later_1
[STOP] [2019-12-31 10:09:01] hold_for_later_1
[START] [2019-12-31 10:09:01] hold_for_later_2
[STOP] [2019-12-31 10:09:01] hold_for_later_2
[START] [2019-12-31 10:09:01] resolve_missing_parents
[STOP] [2019-12-31 10:09:01] resolve_missing_parents
[START] [2019-12-31 10:09:01] rebuild_nodes
[START] [2019-12-31 10:09:01] Flattener#flatten
[START] [2019-12-31 10:09:01] Flattener#study_resource
[START] [2019-12-31 10:09:01] Flattener#build_ancestry
[STOP] [2019-12-31 10:09:01] Flattener#build_ancestry
[INFO] [2019-12-31 10:09:01] 372 ancestry keys
[START] [2019-12-31 10:09:01] build_node_ancestors
[INFO] [2019-12-31 10:09:01] old ancestors deleted.
[STOP] [2019-12-31 10:09:01] build_node_ancestors
[START] [2019-12-31 10:09:01] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:09:01] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:09:01] Flattener#flatten
[STOP] [2019-12-31 10:09:01] rebuild_nodes
[START] [2019-12-31 10:09:01] resolve_missing_media_owners
[STOP] [2019-12-31 10:09:01] resolve_missing_media_owners
[START] [2019-12-31 10:09:01] sanitize_media_verbatims
[STOP] [2019-12-31 10:09:01] sanitize_media_verbatims
[START] [2019-12-31 10:09:01] queue_downloads
[STOP] [2019-12-31 10:09:01] queue_downloads
[START] [2019-12-31 10:09:01] parse_names
[WARN] [2019-12-31 10:09:01] I see 372 names which still need to be parsed.
[STOP] [2019-12-31 10:09:03] parse_names
[START] [2019-12-31 10:09:03] denormalize_canonical_names_to_nodes
[STOP] [2019-12-31 10:09:03] denormalize_canonical_names_to_nodes
[START] [2019-12-31 10:09:03] match_nodes
[START] [2019-12-31 10:09:03] map_all_nodes_to_pages
[STOP] [2019-12-31 10:10:02] map_all_nodes_to_pages
[INFO] [2019-12-31 10:10:02] 69 Unmatched nodes (of 372)! That's too many to output. First 10: Aeromachus bandaishanus (#62741612); Celaenorrhinus major (#62741624); Ochlodes niitakanus (#62741640); Parnara bada (#62741642); Parnara guttata (#62741643); Polytremis kiraizana (#62741649); Potanthus motzui (#62741653); Satarupa majasra (#62741657); Telicota bambusae horisha (#62741662); Thoressa horishana (#62741665)
[START] [2019-12-31 10:10:02] update_nodes
[STOP] [2019-12-31 10:10:03] update_nodes
[STOP] [2019-12-31 10:10:03] match_nodes
[START] [2019-12-31 10:10:03] reindex_search
[STOP] [2019-12-31 10:10:03] reindex_search
[START] [2019-12-31 10:10:03] normalize_units
[STOP] [2019-12-31 10:10:03] normalize_units
[START] [2019-12-31 10:10:03] calculate_statistics
[STOP] [2019-12-31 10:10:03] calculate_statistics
[START] [2019-12-31 10:10:03] complete_harvest_instance
[START] [2019-12-31 10:10:03] overall_tsv_creation
[INFO] [2019-12-31 10:10:03] Processing group of 372 in 1 batches of 10000
[INFO] [2019-12-31 10:10:45] Average Time: 14.82
[INFO] [2019-12-31 10:10:45] Total Time: 42s
[STOP] [2019-12-31 10:10:45] overall_tsv_creation
[INFO] [2019-12-31 10:10:45] Done. Check your files:
[INFO] [2019-12-31 10:10:45] (372 lines) /app/public/data/butterflies_taiw/publish_nodes.tsv
[INFO] [2019-12-31 10:10:45] (1106 lines) /app/public/data/butterflies_taiw/publish_node_ancestors.tsv
[INFO] [2019-12-31 10:10:45] (372 lines) /app/public/data/butterflies_taiw/publish_scientific_names.tsv
[INFO] [2019-12-31 10:10:46] (629 lines) /app/public/data/butterflies_taiw/publish_media.tsv
[INFO] [2019-12-31 10:10:46] (629 lines) /app/public/data/butterflies_taiw/publish_image_info.tsv
[INFO] [2019-12-31 10:10:46] (364 lines) /app/public/data/butterflies_taiw/publish_vernaculars.tsv
[INFO] [2019-12-31 10:10:46] (629 lines) /app/public/data/butterflies_taiw/publish_attributions.tsv
[STOP] [2019-12-31 10:10:46] complete_harvest_instance
[START] [2019-12-31 10:10:46] completed
[STOP] [2019-12-31 10:10:46] completed
[STOP] [2019-12-31 10:10:46] logged process, took 115.82
Latest Process

31 Dec 10:08 EXITED currently processing 0