Harvest for wikipedia SL Created 27 Feb 17:21

Stage: completed
Fetched: 27 Feb 17:21
Validated: 27 Feb 17:21
Deltas Created 27 Feb 17:21
Units Normalized: 27 Feb 17:39
Ancestry Built: 27 Feb 17:29
Nodes Matched: 27 Feb 17:39
Names Parsed: 27 Feb 17:29
New Models Stored: 27 Feb 17:21
Indexed: 27 Feb 17:39
Completed: 27 Feb 17:41
Time to Harvest: less than a minute
Harvesting Log

(118 lines)
# Logfile created on 2020-02-27 17:21:12 -0500 by logger.rb/56815
[START] [2020-02-27 17:21:12] logged process
[START] [2020-02-27 17:21:12] create_harvest_instance
[STOP] [2020-02-27 17:21:12] create_harvest_instance
[START] [2020-02-27 17:21:12] fetch_files
[STOP] [2020-02-27 17:21:12] fetch_files
[START] [2020-02-27 17:21:12] validate_each_file
[STOP] [2020-02-27 17:21:14] validate_each_file
[START] [2020-02-27 17:21:14] convert_to_csv
[CMD] [2020-02-27 17:21:14] /usr/bin/sort /app/public/converted_csv/wiki_sl_slovenia_nodes_20273.csv > /app/public/converted_csv/wiki_sl_slovenia_nodes_20273.csv_sorted
[CMD] [2020-02-27 17:21:14] /usr/bin/sort /app/public/converted_csv/wiki_sl_slovenia_media_20274.csv > /app/public/converted_csv/wiki_sl_slovenia_media_20274.csv_sorted
[STOP] [2020-02-27 17:21:14] convert_to_csv
[START] [2020-02-27 17:21:14] calculate_delta
[CMD] [2020-02-27 17:21:14] echo "0a" > /app/public/diff/wiki_sl_slovenia_nodes_20273.diff
[CMD] [2020-02-27 17:21:14] tail -n +1 /app/public/converted_csv/wiki_sl_slovenia_nodes_20273.csv >> /app/public/diff/wiki_sl_slovenia_nodes_20273.diff
[CMD] [2020-02-27 17:21:14] echo "." >> /app/public/diff/wiki_sl_slovenia_nodes_20273.diff
[CMD] [2020-02-27 17:21:14] echo "0a" > /app/public/diff/wiki_sl_slovenia_media_20274.diff
[CMD] [2020-02-27 17:21:14] tail -n +1 /app/public/converted_csv/wiki_sl_slovenia_media_20274.csv >> /app/public/diff/wiki_sl_slovenia_media_20274.diff
[CMD] [2020-02-27 17:21:14] echo "." >> /app/public/diff/wiki_sl_slovenia_media_20274.diff
[STOP] [2020-02-27 17:21:15] calculate_delta
[START] [2020-02-27 17:21:15] parse_diff_and_store
[INFO] [2020-02-27 17:21:15] Loading nodes diff file into memory (true lines)...
[INFO] [2020-02-27 17:21:18] Loading media diff file into memory (true lines)...
[INFO] [2020-02-27 17:21:44] Storing 5769 ScientificNames
[INFO] [2020-02-27 17:21:44] Processing group of 5769 in 6 groups of 1000
[INFO] [2020-02-27 17:21:47] Average Time: 0.388
[INFO] [2020-02-27 17:21:47] Total Time: 3s
[INFO] [2020-02-27 17:21:47] Storing 5769 Identifiers
[INFO] [2020-02-27 17:21:47] Processing group of 5769 in 6 groups of 1000
[INFO] [2020-02-27 17:21:48] Average Time: 0.172
[INFO] [2020-02-27 17:21:48] Total Time: 2s
[INFO] [2020-02-27 17:21:48] Storing 5769 Nodes
[INFO] [2020-02-27 17:21:48] Processing group of 5769 in 6 groups of 1000
[INFO] [2020-02-27 17:21:50] Average Time: 0.307
[INFO] [2020-02-27 17:21:50] Total Time: 2s
[INFO] [2020-02-27 17:21:50] Storing 4976 ArticlesSections
[INFO] [2020-02-27 17:21:50] Processing group of 4976 in 5 groups of 1000
[INFO] [2020-02-27 17:21:50] Average Time: 0.064
[INFO] [2020-02-27 17:21:50] Total Time: 1s
[INFO] [2020-02-27 17:21:50] Storing 4976 Articles
[INFO] [2020-02-27 17:21:50] Processing group of 4976 in 5 groups of 1000
[INFO] [2020-02-27 17:21:54] Average Time: 0.862
[INFO] [2020-02-27 17:21:54] Total Time: 5s
[STOP] [2020-02-27 17:21:54] parse_diff_and_store
[START] [2020-02-27 17:21:54] resolve_keys
[INFO] [2020-02-27 17:29:06] Occurrences to nodes (through scientific_names)...
[INFO] [2020-02-27 17:29:06] traits to occurrences...
[INFO] [2020-02-27 17:29:06] traits to nodes (through occurrences)...
[INFO] [2020-02-27 17:29:06] Traits to sex term...
[INFO] [2020-02-27 17:29:06] Traits to lifestage term...
[INFO] [2020-02-27 17:29:06] MetaTraits to traits...
[INFO] [2020-02-27 17:29:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-02-27 17:29:06] Assocs to occurrences...
[INFO] [2020-02-27 17:29:06] Assocs to nodes...
[INFO] [2020-02-27 17:29:06] Assoc to sex term...
[INFO] [2020-02-27 17:29:06] Assoc to lifestage term...
[STOP] [2020-02-27 17:29:06] resolve_keys
[START] [2020-02-27 17:29:06] hold_for_later_1
[STOP] [2020-02-27 17:29:06] hold_for_later_1
[START] [2020-02-27 17:29:06] hold_for_later_2
[STOP] [2020-02-27 17:29:06] hold_for_later_2
[START] [2020-02-27 17:29:06] resolve_missing_parents
[STOP] [2020-02-27 17:29:08] resolve_missing_parents
[START] [2020-02-27 17:29:08] rebuild_nodes
[START] [2020-02-27 17:29:08] Flattener#flatten
[START] [2020-02-27 17:29:08] Flattener#study_resource
[START] [2020-02-27 17:29:08] Flattener#build_ancestry
[STOP] [2020-02-27 17:29:08] Flattener#build_ancestry
[INFO] [2020-02-27 17:29:08] 5769 ancestry keys
[START] [2020-02-27 17:29:08] build_node_ancestors
[INFO] [2020-02-27 17:29:09] old ancestors deleted.
[STOP] [2020-02-27 17:29:24] build_node_ancestors
[START] [2020-02-27 17:29:24] Flattener#propagate_ancestor_ids
[STOP] [2020-02-27 17:29:27] Flattener#propagate_ancestor_ids
[STOP] [2020-02-27 17:29:27] Flattener#flatten
[STOP] [2020-02-27 17:29:27] rebuild_nodes
[START] [2020-02-27 17:29:27] resolve_missing_media_owners
[STOP] [2020-02-27 17:29:27] resolve_missing_media_owners
[START] [2020-02-27 17:29:27] sanitize_media_verbatims
[STOP] [2020-02-27 17:29:27] sanitize_media_verbatims
[START] [2020-02-27 17:29:27] queue_downloads
[STOP] [2020-02-27 17:29:27] queue_downloads
[START] [2020-02-27 17:29:27] parse_names
[WARN] [2020-02-27 17:29:27] I see 5769 names which still need to be parsed.
[WARN] [2020-02-27 17:29:32] I see 14 names which still need to be parsed.
[STOP] [2020-02-27 17:29:33] parse_names
[START] [2020-02-27 17:29:33] denormalize_canonical_names_to_nodes
[STOP] [2020-02-27 17:29:33] denormalize_canonical_names_to_nodes
[START] [2020-02-27 17:29:33] match_nodes
[START] [2020-02-27 17:29:33] map_all_nodes_to_pages
[STOP] [2020-02-27 17:39:27] map_all_nodes_to_pages
[INFO] [2020-02-27 17:39:27] 1032 Unmatched nodes (of 5769)! That's too many to output. First 10: Biota (#64303923); Prokaryota (#64303192); Bacteria (#64301089); Negibacteria (#64304834); Borrelia burgdorferi (#64304361); Escherichia coli (#64304087); Synechococcophycideae (#64303124); Pseudanabaenales (#64303123); Spirulinoideae (#64303121); Posibacteria (#64304881)
[START] [2020-02-27 17:39:27] update_nodes
[STOP] [2020-02-27 17:39:29] update_nodes
[STOP] [2020-02-27 17:39:29] match_nodes
[START] [2020-02-27 17:39:29] reindex_search
[STOP] [2020-02-27 17:39:47] reindex_search
[START] [2020-02-27 17:39:47] normalize_units
[STOP] [2020-02-27 17:39:47] normalize_units
[START] [2020-02-27 17:39:47] calculate_statistics
[STOP] [2020-02-27 17:39:47] calculate_statistics
[START] [2020-02-27 17:39:47] complete_harvest_instance
[START] [2020-02-27 17:39:47] overall_tsv_creation
[INFO] [2020-02-27 17:39:47] Processing group of 5769 in 1 batches of 10000
[INFO] [2020-02-27 17:41:41] Average Time: 53.45
[INFO] [2020-02-27 17:41:41] Total Time: 1m54s
[STOP] [2020-02-27 17:41:41] overall_tsv_creation
[INFO] [2020-02-27 17:41:41] Done. Check your files:
[INFO] [2020-02-27 17:41:41] (5769 lines) /app/public/data/wiki_sl_slovenia/publish_nodes.tsv
[INFO] [2020-02-27 17:41:41] (5769 lines) /app/public/data/wiki_sl_slovenia/publish_identifiers.tsv
[INFO] [2020-02-27 17:41:41] (106868 lines) /app/public/data/wiki_sl_slovenia/publish_node_ancestors.tsv
[INFO] [2020-02-27 17:41:41] (5769 lines) /app/public/data/wiki_sl_slovenia/publish_scientific_names.tsv
[INFO] [2020-02-27 17:41:41] (50001 lines) /app/public/data/wiki_sl_slovenia/publish_articles.tsv
[INFO] [2020-02-27 17:41:41] (4976 lines) /app/public/data/wiki_sl_slovenia/publish_content_sections.tsv
[STOP] [2020-02-27 17:41:41] complete_harvest_instance
[START] [2020-02-27 17:41:41] completed
[STOP] [2020-02-27 17:41:41] completed
[STOP] [2020-02-27 17:41:41] logged process, took 1229.39
Latest Process

27 Feb 17:21 EXITED currently processing 0