Harvest for wikipedia LT Created 16 Jan 10:51

Stage: completed
Fetched: 16 Jan 10:51
Validated: 16 Jan 10:51
Deltas Created 16 Jan 10:52
Units Normalized: 16 Jan 11:53
Ancestry Built: 16 Jan 10:59
Nodes Matched: 16 Jan 11:52
Names Parsed: 16 Jan 10:59
New Models Stored: 16 Jan 10:54
Indexed: 16 Jan 11:53
Completed: 16 Jan 11:57
Time to Harvest: 1 minute
Harvesting Log

(128 lines)
# Logfile created on 2020-01-16 10:51:55 -0500 by logger.rb/56815
[START] [2020-01-16 10:51:55] logged process
[START] [2020-01-16 10:51:55] create_harvest_instance
[STOP] [2020-01-16 10:51:55] create_harvest_instance
[START] [2020-01-16 10:51:55] fetch_files
[STOP] [2020-01-16 10:51:55] fetch_files
[START] [2020-01-16 10:51:55] validate_each_file
[STOP] [2020-01-16 10:51:59] validate_each_file
[START] [2020-01-16 10:51:59] convert_to_csv
[CMD] [2020-01-16 10:51:59] /usr/bin/sort /app/public/converted_csv/wiki_lt_lithuani_nodes_19978.csv > /app/public/converted_csv/wiki_lt_lithuani_nodes_19978.csv_sorted
[CMD] [2020-01-16 10:51:59] /usr/bin/sort /app/public/converted_csv/wiki_lt_lithuani_media_19979.csv > /app/public/converted_csv/wiki_lt_lithuani_media_19979.csv_sorted
[STOP] [2020-01-16 10:52:00] convert_to_csv
[START] [2020-01-16 10:52:00] calculate_delta
[CMD] [2020-01-16 10:52:00] echo "0a" > /app/public/diff/wiki_lt_lithuani_nodes_19978.diff
[CMD] [2020-01-16 10:52:01] tail -n +1 /app/public/converted_csv/wiki_lt_lithuani_nodes_19978.csv >> /app/public/diff/wiki_lt_lithuani_nodes_19978.diff
[CMD] [2020-01-16 10:52:01] echo "." >> /app/public/diff/wiki_lt_lithuani_nodes_19978.diff
[CMD] [2020-01-16 10:52:02] echo "0a" > /app/public/diff/wiki_lt_lithuani_media_19979.diff
[CMD] [2020-01-16 10:52:03] tail -n +1 /app/public/converted_csv/wiki_lt_lithuani_media_19979.csv >> /app/public/diff/wiki_lt_lithuani_media_19979.diff
[CMD] [2020-01-16 10:52:03] echo "." >> /app/public/diff/wiki_lt_lithuani_media_19979.diff
[STOP] [2020-01-16 10:52:04] calculate_delta
[START] [2020-01-16 10:52:04] parse_diff_and_store
[INFO] [2020-01-16 10:52:05] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-16 10:52:12] Loading media diff file into memory (true lines)...
[INFO] [2020-01-16 10:53:09] Storing 12845 ScientificNames
[INFO] [2020-01-16 10:53:09] Processing group of 12845 in 13 groups of 1000
[INFO] [2020-01-16 10:53:14] Average Time: 0.383
[INFO] [2020-01-16 10:53:14] Total Time: 6s
[INFO] [2020-01-16 10:53:14] last 3 / first 3: 0.7
[INFO] [2020-01-16 10:53:14] Std.Dev: 0.07071067811865475; Max: 0.53
[INFO] [2020-01-16 10:53:14] Storing 12845 Identifiers
[INFO] [2020-01-16 10:53:14] Processing group of 12845 in 13 groups of 1000
[INFO] [2020-01-16 10:53:16] Average Time: 0.115
[INFO] [2020-01-16 10:53:16] Total Time: 2s
[INFO] [2020-01-16 10:53:16] last 3 / first 3: 0.91
[INFO] [2020-01-16 10:53:16] Std.Dev: 0.0; Max: 0.14
[INFO] [2020-01-16 10:53:16] Storing 12845 Nodes
[INFO] [2020-01-16 10:53:16] Processing group of 12845 in 13 groups of 1000
[INFO] [2020-01-16 10:53:20] Average Time: 0.328
[INFO] [2020-01-16 10:53:20] Total Time: 5s
[INFO] [2020-01-16 10:53:20] last 3 / first 3: 1.19
[INFO] [2020-01-16 10:53:20] Std.Dev: 0.07745966692414834; Max: 0.57
[INFO] [2020-01-16 10:53:20] Storing 15664 ArticlesSections
[INFO] [2020-01-16 10:53:20] Processing group of 15664 in 16 groups of 1000
[INFO] [2020-01-16 10:53:21] Average Time: 0.064
[INFO] [2020-01-16 10:53:21] Total Time: 2s
[INFO] [2020-01-16 10:53:21] last 3 / first 3: 0.47
[INFO] [2020-01-16 10:53:21] Std.Dev: 0.044721359549995794; Max: 0.24
[INFO] [2020-01-16 10:53:21] Storing 15664 Articles
[INFO] [2020-01-16 10:53:21] Processing group of 15664 in 16 groups of 1000
[INFO] [2020-01-16 10:54:36] Average Time: 4.696
[INFO] [2020-01-16 10:54:36] Total Time: 1m16s
[INFO] [2020-01-16 10:54:36] last 3 / first 3: 0.02
[INFO] [2020-01-16 10:54:36] Std.Dev: 17.12372623000029; Max: 68.91
[STOP] [2020-01-16 10:54:36] parse_diff_and_store
[START] [2020-01-16 10:54:36] resolve_keys
[INFO] [2020-01-16 10:58:48] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-16 10:58:48] traits to occurrences...
[INFO] [2020-01-16 10:58:48] traits to nodes (through occurrences)...
[INFO] [2020-01-16 10:58:48] Traits to sex term...
[INFO] [2020-01-16 10:58:48] Traits to lifestage term...
[INFO] [2020-01-16 10:58:48] MetaTraits to traits...
[INFO] [2020-01-16 10:58:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-16 10:58:48] Assocs to occurrences...
[INFO] [2020-01-16 10:58:48] Assocs to nodes...
[INFO] [2020-01-16 10:58:48] Assoc to sex term...
[INFO] [2020-01-16 10:58:48] Assoc to lifestage term...
[STOP] [2020-01-16 10:58:48] resolve_keys
[START] [2020-01-16 10:58:48] hold_for_later_1
[STOP] [2020-01-16 10:58:48] hold_for_later_1
[START] [2020-01-16 10:58:48] hold_for_later_2
[STOP] [2020-01-16 10:58:48] hold_for_later_2
[START] [2020-01-16 10:58:48] resolve_missing_parents
[STOP] [2020-01-16 10:58:52] resolve_missing_parents
[START] [2020-01-16 10:58:52] rebuild_nodes
[START] [2020-01-16 10:58:52] Flattener#flatten
[START] [2020-01-16 10:58:52] Flattener#study_resource
[START] [2020-01-16 10:58:52] Flattener#build_ancestry
[STOP] [2020-01-16 10:58:53] Flattener#build_ancestry
[INFO] [2020-01-16 10:58:53] 12845 ancestry keys
[START] [2020-01-16 10:58:53] build_node_ancestors
[INFO] [2020-01-16 10:58:53] old ancestors deleted.
[STOP] [2020-01-16 10:59:29] build_node_ancestors
[START] [2020-01-16 10:59:33] Flattener#propagate_ancestor_ids
[STOP] [2020-01-16 10:59:39] Flattener#propagate_ancestor_ids
[STOP] [2020-01-16 10:59:39] Flattener#flatten
[STOP] [2020-01-16 10:59:39] rebuild_nodes
[START] [2020-01-16 10:59:39] resolve_missing_media_owners
[STOP] [2020-01-16 10:59:39] resolve_missing_media_owners
[START] [2020-01-16 10:59:39] sanitize_media_verbatims
[STOP] [2020-01-16 10:59:39] sanitize_media_verbatims
[START] [2020-01-16 10:59:39] queue_downloads
[STOP] [2020-01-16 10:59:39] queue_downloads
[START] [2020-01-16 10:59:39] parse_names
[WARN] [2020-01-16 10:59:39] I see 12845 names which still need to be parsed.
[WARN] [2020-01-16 10:59:51] I see 21 names which still need to be parsed.
[STOP] [2020-01-16 10:59:53] parse_names
[START] [2020-01-16 10:59:53] denormalize_canonical_names_to_nodes
[STOP] [2020-01-16 10:59:53] denormalize_canonical_names_to_nodes
[START] [2020-01-16 10:59:53] match_nodes
[START] [2020-01-16 10:59:53] map_all_nodes_to_pages
[STOP] [2020-01-16 11:52:16] map_all_nodes_to_pages
[INFO] [2020-01-16 11:52:16] 1460 Unmatched nodes (of 12845)! That's too many to output. First 10: Biota (#62878808); Prokaryota (#62877365); Bacteria (#62872579); Negibacteria (#62880798); Deferribacteres (#62873138); Escherichia coli (#62879165); Ideonella (#62875046); Ideonella sakaiensis (#62878655); Aquificae (#62882572); Posibacteria (#62880873)
[START] [2020-01-16 11:52:16] update_nodes
[STOP] [2020-01-16 11:52:21] update_nodes
[STOP] [2020-01-16 11:52:21] match_nodes
[START] [2020-01-16 11:52:21] reindex_search
[STOP] [2020-01-16 11:53:33] reindex_search
[START] [2020-01-16 11:53:33] normalize_units
[STOP] [2020-01-16 11:53:33] normalize_units
[START] [2020-01-16 11:53:33] calculate_statistics
[STOP] [2020-01-16 11:53:34] calculate_statistics
[START] [2020-01-16 11:53:34] complete_harvest_instance
[START] [2020-01-16 11:53:34] overall_tsv_creation
[INFO] [2020-01-16 11:53:34] Processing group of 12845 in 2 batches of 10000
[INFO] [2020-01-16 11:57:11] Average Time: 56.65
[INFO] [2020-01-16 11:57:11] Total Time: 3m37s
[STOP] [2020-01-16 11:57:11] overall_tsv_creation
[INFO] [2020-01-16 11:57:11] Done. Check your files:
[INFO] [2020-01-16 11:57:12] (12845 lines) /app/public/data/wiki_lt_lithuani/publish_nodes.tsv
[INFO] [2020-01-16 11:57:12] (12845 lines) /app/public/data/wiki_lt_lithuani/publish_identifiers.tsv
[INFO] [2020-01-16 11:57:13] (240234 lines) /app/public/data/wiki_lt_lithuani/publish_node_ancestors.tsv
[INFO] [2020-01-16 11:57:14] (12845 lines) /app/public/data/wiki_lt_lithuani/publish_scientific_names.tsv
[INFO] [2020-01-16 11:57:14] (130012 lines) /app/public/data/wiki_lt_lithuani/publish_articles.tsv
[INFO] [2020-01-16 11:57:15] (15664 lines) /app/public/data/wiki_lt_lithuani/publish_content_sections.tsv
[STOP] [2020-01-16 11:57:15] complete_harvest_instance
[START] [2020-01-16 11:57:15] completed
[STOP] [2020-01-16 11:57:15] completed
[STOP] [2020-01-16 11:57:15] logged process, took 3920.63
Latest Process

16 Jan 10:51 EXITED currently processing 0