Harvest for wikipedia BR Created 21 Jan 14:43

Stage: completed
Fetched: 21 Jan 14:43
Validated: 21 Jan 14:43
Deltas Created 21 Jan 14:43
Units Normalized: 21 Jan 15:52
Ancestry Built: 21 Jan 14:45
Nodes Matched: 21 Jan 15:50
Names Parsed: 21 Jan 14:46
New Models Stored: 21 Jan 14:44
Indexed: 21 Jan 15:52
Completed: 21 Jan 15:54
Time to Harvest: 1 minute

Harvesting Log

(128 lines)
# Logfile created on 2020-01-21 14:43:04 -0500 by logger.rb/56815
[START] [2020-01-21 14:43:04] logged process
[START] [2020-01-21 14:43:04] create_harvest_instance
[STOP] [2020-01-21 14:43:05] create_harvest_instance
[START] [2020-01-21 14:43:05] fetch_files
[STOP] [2020-01-21 14:43:05] fetch_files
[START] [2020-01-21 14:43:05] validate_each_file
[STOP] [2020-01-21 14:43:07] validate_each_file
[START] [2020-01-21 14:43:07] convert_to_csv
[CMD] [2020-01-21 14:43:07] /usr/bin/sort /app/public/converted_csv/wiki_br_breton_nodes_20110.csv > /app/public/converted_csv/wiki_br_breton_nodes_20110.csv_sorted
[CMD] [2020-01-21 14:43:07] /usr/bin/sort /app/public/converted_csv/wiki_br_breton_media_20111.csv > /app/public/converted_csv/wiki_br_breton_media_20111.csv_sorted
[STOP] [2020-01-21 14:43:08] convert_to_csv
[START] [2020-01-21 14:43:08] calculate_delta
[CMD] [2020-01-21 14:43:08] echo "0a" > /app/public/diff/wiki_br_breton_nodes_20110.diff
[CMD] [2020-01-21 14:43:08] tail -n +1 /app/public/converted_csv/wiki_br_breton_nodes_20110.csv >> /app/public/diff/wiki_br_breton_nodes_20110.diff
[CMD] [2020-01-21 14:43:08] echo "." >> /app/public/diff/wiki_br_breton_nodes_20110.diff
[CMD] [2020-01-21 14:43:08] echo "0a" > /app/public/diff/wiki_br_breton_media_20111.diff
[CMD] [2020-01-21 14:43:08] tail -n +1 /app/public/converted_csv/wiki_br_breton_media_20111.csv >> /app/public/diff/wiki_br_breton_media_20111.diff
[CMD] [2020-01-21 14:43:08] echo "." >> /app/public/diff/wiki_br_breton_media_20111.diff
[STOP] [2020-01-21 14:43:09] calculate_delta
[START] [2020-01-21 14:43:09] parse_diff_and_store
[INFO] [2020-01-21 14:43:09] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-21 14:43:15] Loading media diff file into memory (true lines)...
[INFO] [2020-01-21 14:43:59] Storing 9382 ScientificNames
[INFO] [2020-01-21 14:43:59] Processing group of 9382 in 10 groups of 1000
[INFO] [2020-01-21 14:44:03] Average Time: 0.343
[INFO] [2020-01-21 14:44:03] Total Time: 4s
[INFO] [2020-01-21 14:44:03] last 3 / first 3: 0.8
[INFO] [2020-01-21 14:44:03] Std.Dev: 0.10488088481701516; Max: 0.54
[INFO] [2020-01-21 14:44:03] Storing 9382 Identifiers
[INFO] [2020-01-21 14:44:03] Processing group of 9382 in 10 groups of 1000
[INFO] [2020-01-21 14:44:04] Average Time: 0.133
[INFO] [2020-01-21 14:44:04] Total Time: 2s
[INFO] [2020-01-21 14:44:04] last 3 / first 3: 0.58
[INFO] [2020-01-21 14:44:04] Std.Dev: 0.05477225575051661; Max: 0.26
[INFO] [2020-01-21 14:44:04] Storing 9382 Nodes
[INFO] [2020-01-21 14:44:04] Processing group of 9382 in 10 groups of 1000
[INFO] [2020-01-21 14:44:07] Average Time: 0.274
[INFO] [2020-01-21 14:44:07] Total Time: 3s
[INFO] [2020-01-21 14:44:07] last 3 / first 3: 0.68
[INFO] [2020-01-21 14:44:07] Std.Dev: 0.07071067811865475; Max: 0.39
[INFO] [2020-01-21 14:44:07] Storing 12758 ArticlesSections
[INFO] [2020-01-21 14:44:07] Processing group of 12758 in 13 groups of 1000
[INFO] [2020-01-21 14:44:08] Average Time: 0.062
[INFO] [2020-01-21 14:44:08] Total Time: 1s
[INFO] [2020-01-21 14:44:08] last 3 / first 3: 1.0
[INFO] [2020-01-21 14:44:08] Std.Dev: 0.0; Max: 0.13
[INFO] [2020-01-21 14:44:08] Storing 12758 Articles
[INFO] [2020-01-21 14:44:08] Processing group of 12758 in 13 groups of 1000
[INFO] [2020-01-21 14:44:15] Average Time: 0.536
[INFO] [2020-01-21 14:44:15] Total Time: 8s
[INFO] [2020-01-21 14:44:15] last 3 / first 3: 0.78
[INFO] [2020-01-21 14:44:15] Std.Dev: 0.216794833886788; Max: 1.03
[STOP] [2020-01-21 14:44:15] parse_diff_and_store
[START] [2020-01-21 14:44:15] resolve_keys
[INFO] [2020-01-21 14:44:58] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-21 14:44:58] traits to occurrences...
[INFO] [2020-01-21 14:44:58] traits to nodes (through occurrences)...
[INFO] [2020-01-21 14:44:58] Traits to sex term...
[INFO] [2020-01-21 14:44:58] Traits to lifestage term...
[INFO] [2020-01-21 14:44:58] MetaTraits to traits...
[INFO] [2020-01-21 14:44:58] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-21 14:44:58] Assocs to occurrences...
[INFO] [2020-01-21 14:44:58] Assocs to nodes...
[INFO] [2020-01-21 14:44:58] Assoc to sex term...
[INFO] [2020-01-21 14:44:58] Assoc to lifestage term...
[STOP] [2020-01-21 14:44:58] resolve_keys
[START] [2020-01-21 14:44:58] hold_for_later_1
[STOP] [2020-01-21 14:44:58] hold_for_later_1
[START] [2020-01-21 14:44:58] hold_for_later_2
[STOP] [2020-01-21 14:44:58] hold_for_later_2
[START] [2020-01-21 14:44:58] resolve_missing_parents
[STOP] [2020-01-21 14:45:02] resolve_missing_parents
[START] [2020-01-21 14:45:02] rebuild_nodes
[START] [2020-01-21 14:45:02] Flattener#flatten
[START] [2020-01-21 14:45:02] Flattener#study_resource
[START] [2020-01-21 14:45:02] Flattener#build_ancestry
[STOP] [2020-01-21 14:45:03] Flattener#build_ancestry
[INFO] [2020-01-21 14:45:03] 9382 ancestry keys
[START] [2020-01-21 14:45:03] build_node_ancestors
[INFO] [2020-01-21 14:45:03] old ancestors deleted.
[STOP] [2020-01-21 14:45:35] build_node_ancestors
[START] [2020-01-21 14:45:43] Flattener#propagate_ancestor_ids
[STOP] [2020-01-21 14:45:56] Flattener#propagate_ancestor_ids
[STOP] [2020-01-21 14:45:56] Flattener#flatten
[STOP] [2020-01-21 14:45:56] rebuild_nodes
[START] [2020-01-21 14:45:56] resolve_missing_media_owners
[STOP] [2020-01-21 14:45:56] resolve_missing_media_owners
[START] [2020-01-21 14:45:56] sanitize_media_verbatims
[STOP] [2020-01-21 14:45:56] sanitize_media_verbatims
[START] [2020-01-21 14:45:56] queue_downloads
[STOP] [2020-01-21 14:45:56] queue_downloads
[START] [2020-01-21 14:45:56] parse_names
[WARN] [2020-01-21 14:45:56] I see 9382 names which still need to be parsed.
[WARN] [2020-01-21 14:46:04] I see 24 names which still need to be parsed.
[STOP] [2020-01-21 14:46:05] parse_names
[START] [2020-01-21 14:46:05] denormalize_canonical_names_to_nodes
[STOP] [2020-01-21 14:46:05] denormalize_canonical_names_to_nodes
[START] [2020-01-21 14:46:05] match_nodes
[START] [2020-01-21 14:46:05] map_all_nodes_to_pages
[STOP] [2020-01-21 15:50:36] map_all_nodes_to_pages
[INFO] [2020-01-21 15:50:36] 674 Unmatched nodes (of 9382)! That's too many to output. First 10: Biota (#62916746); Prokaryota (#62915749); Bacteria (#62913266); Negibacteria (#62918238); Posibacteria (#62918299); Diaphoretickes (#62915353); Sar (#62914478); Phaeista (#62918265); Limnista (#62915645); Fucistia (#62918030)
[START] [2020-01-21 15:50:36] update_nodes
[STOP] [2020-01-21 15:50:40] update_nodes
[STOP] [2020-01-21 15:50:40] match_nodes
[START] [2020-01-21 15:50:40] reindex_search
[STOP] [2020-01-21 15:52:06] reindex_search
[START] [2020-01-21 15:52:06] normalize_units
[STOP] [2020-01-21 15:52:06] normalize_units
[START] [2020-01-21 15:52:06] calculate_statistics
[STOP] [2020-01-21 15:52:07] calculate_statistics
[START] [2020-01-21 15:52:07] complete_harvest_instance
[START] [2020-01-21 15:52:07] overall_tsv_creation
[INFO] [2020-01-21 15:52:07] Processing group of 9382 in 1 batches of 10000
[INFO] [2020-01-21 15:54:10] Average Time: 79.33
[INFO] [2020-01-21 15:54:10] Total Time: 2m4s
[STOP] [2020-01-21 15:54:10] overall_tsv_creation
[INFO] [2020-01-21 15:54:10] Done. Check your files:
[INFO] [2020-01-21 15:54:10] (9382 lines) /app/public/data/wiki_br_breton/publish_nodes.tsv
[INFO] [2020-01-21 15:54:11] (9382 lines) /app/public/data/wiki_br_breton/publish_identifiers.tsv
[INFO] [2020-01-21 15:54:11] (246919 lines) /app/public/data/wiki_br_breton/publish_node_ancestors.tsv
[INFO] [2020-01-21 15:54:11] (9382 lines) /app/public/data/wiki_br_breton/publish_scientific_names.tsv
[INFO] [2020-01-21 15:54:11] (129653 lines) /app/public/data/wiki_br_breton/publish_articles.tsv
[INFO] [2020-01-21 15:54:11] (12758 lines) /app/public/data/wiki_br_breton/publish_content_sections.tsv
[STOP] [2020-01-21 15:54:12] complete_harvest_instance
[START] [2020-01-21 15:54:12] completed
[STOP] [2020-01-21 15:54:12] completed
[STOP] [2020-01-21 15:54:12] logged process, took 4267.29

Latest Process