Harvest for wikipedia IS Created 20 Feb 11:12

Stage: completed
Fetched: 20 Feb 11:12
Validated: 20 Feb 11:12
Deltas Created 20 Feb 11:12
Units Normalized: 20 Feb 11:24
Ancestry Built: 20 Feb 11:14
Nodes Matched: 20 Feb 11:24
Names Parsed: 20 Feb 11:14
New Models Stored: 20 Feb 11:13
Indexed: 20 Feb 11:24
Completed: 20 Feb 11:26
Time to Harvest: less than a minute
Harvesting Log

(130 lines)
# Logfile created on 2020-02-20 11:12:29 -0500 by logger.rb/56815
[START] [2020-02-20 11:12:29] logged process
[START] [2020-02-20 11:12:29] create_harvest_instance
[STOP] [2020-02-20 11:12:29] create_harvest_instance
[START] [2020-02-20 11:12:29] fetch_files
[STOP] [2020-02-20 11:12:29] fetch_files
[START] [2020-02-20 11:12:29] validate_each_file
[STOP] [2020-02-20 11:12:31] validate_each_file
[START] [2020-02-20 11:12:31] convert_to_csv
[CMD] [2020-02-20 11:12:31] /usr/bin/sort /app/public/converted_csv/wiki_icelandic_nodes_20235.csv > /app/public/converted_csv/wiki_icelandic_nodes_20235.csv_sorted
[CMD] [2020-02-20 11:12:31] /usr/bin/sort /app/public/converted_csv/wiki_icelandic_media_20236.csv > /app/public/converted_csv/wiki_icelandic_media_20236.csv_sorted
[STOP] [2020-02-20 11:12:31] convert_to_csv
[START] [2020-02-20 11:12:31] calculate_delta
[CMD] [2020-02-20 11:12:31] echo "0a" > /app/public/diff/wiki_icelandic_nodes_20235.diff
[CMD] [2020-02-20 11:12:31] tail -n +1 /app/public/converted_csv/wiki_icelandic_nodes_20235.csv >> /app/public/diff/wiki_icelandic_nodes_20235.diff
[CMD] [2020-02-20 11:12:31] echo "." >> /app/public/diff/wiki_icelandic_nodes_20235.diff
[CMD] [2020-02-20 11:12:31] echo "0a" > /app/public/diff/wiki_icelandic_media_20236.diff
[CMD] [2020-02-20 11:12:31] tail -n +1 /app/public/converted_csv/wiki_icelandic_media_20236.csv >> /app/public/diff/wiki_icelandic_media_20236.diff
[CMD] [2020-02-20 11:12:31] echo "." >> /app/public/diff/wiki_icelandic_media_20236.diff
[STOP] [2020-02-20 11:12:31] calculate_delta
[START] [2020-02-20 11:12:31] parse_diff_and_store
[INFO] [2020-02-20 11:12:31] Loading nodes diff file into memory (true lines)...
[WARN] [2020-02-20 11:12:32] Filtered Scientific Name `Visna/maedi virus` to `Visnamaedi virus`
[WARN] [2020-02-20 11:12:33] Filtered Scientific Name `Ambystoma  hakié jas jas` to `Ambystoma hakié jas jas`
[INFO] [2020-02-20 11:12:34] Loading media diff file into memory (true lines)...
[INFO] [2020-02-20 11:13:02] Storing 6525 ScientificNames
[INFO] [2020-02-20 11:13:02] Processing group of 6525 in 7 groups of 1000
[INFO] [2020-02-20 11:13:04] Average Time: 0.33
[INFO] [2020-02-20 11:13:04] Total Time: 3s
[INFO] [2020-02-20 11:13:04] last 3 / first 3: 0.8
[INFO] [2020-02-20 11:13:04] Std.Dev: 0.07071067811865475; Max: 0.41
[INFO] [2020-02-20 11:13:04] Storing 6525 Identifiers
[INFO] [2020-02-20 11:13:04] Processing group of 6525 in 7 groups of 1000
[INFO] [2020-02-20 11:13:05] Average Time: 0.093
[INFO] [2020-02-20 11:13:05] Total Time: 1s
[INFO] [2020-02-20 11:13:05] last 3 / first 3: 0.81
[INFO] [2020-02-20 11:13:05] Std.Dev: 0.0; Max: 0.11
[INFO] [2020-02-20 11:13:05] Storing 6525 Nodes
[INFO] [2020-02-20 11:13:05] Processing group of 6525 in 7 groups of 1000
[INFO] [2020-02-20 11:13:07] Average Time: 0.286
[INFO] [2020-02-20 11:13:07] Total Time: 3s
[INFO] [2020-02-20 11:13:07] last 3 / first 3: 0.74
[INFO] [2020-02-20 11:13:07] Std.Dev: 0.07071067811865475; Max: 0.35
[INFO] [2020-02-20 11:13:07] Storing 7556 ArticlesSections
[INFO] [2020-02-20 11:13:07] Processing group of 7556 in 8 groups of 1000
[INFO] [2020-02-20 11:13:07] Average Time: 0.051
[INFO] [2020-02-20 11:13:07] Total Time: 1s
[INFO] [2020-02-20 11:13:07] last 3 / first 3: 0.72
[INFO] [2020-02-20 11:13:07] Std.Dev: 0.0; Max: 0.06
[INFO] [2020-02-20 11:13:07] Storing 7556 Articles
[INFO] [2020-02-20 11:13:07] Processing group of 7556 in 8 groups of 1000
[INFO] [2020-02-20 11:13:11] Average Time: 0.485
[INFO] [2020-02-20 11:13:11] Total Time: 4s
[INFO] [2020-02-20 11:13:11] last 3 / first 3: 0.79
[INFO] [2020-02-20 11:13:11] Std.Dev: 0.16431676725154984; Max: 0.74
[STOP] [2020-02-20 11:13:11] parse_diff_and_store
[START] [2020-02-20 11:13:11] resolve_keys
[INFO] [2020-02-20 11:13:44] Occurrences to nodes (through scientific_names)...
[INFO] [2020-02-20 11:13:44] traits to occurrences...
[INFO] [2020-02-20 11:13:44] traits to nodes (through occurrences)...
[INFO] [2020-02-20 11:13:44] Traits to sex term...
[INFO] [2020-02-20 11:13:44] Traits to lifestage term...
[INFO] [2020-02-20 11:13:44] MetaTraits to traits...
[INFO] [2020-02-20 11:13:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-02-20 11:13:44] Assocs to occurrences...
[INFO] [2020-02-20 11:13:44] Assocs to nodes...
[INFO] [2020-02-20 11:13:44] Assoc to sex term...
[INFO] [2020-02-20 11:13:44] Assoc to lifestage term...
[STOP] [2020-02-20 11:13:44] resolve_keys
[START] [2020-02-20 11:13:44] hold_for_later_1
[STOP] [2020-02-20 11:13:44] hold_for_later_1
[START] [2020-02-20 11:13:44] hold_for_later_2
[STOP] [2020-02-20 11:13:44] hold_for_later_2
[START] [2020-02-20 11:13:44] resolve_missing_parents
[STOP] [2020-02-20 11:13:46] resolve_missing_parents
[START] [2020-02-20 11:13:46] rebuild_nodes
[START] [2020-02-20 11:13:46] Flattener#flatten
[START] [2020-02-20 11:13:46] Flattener#study_resource
[START] [2020-02-20 11:13:46] Flattener#build_ancestry
[STOP] [2020-02-20 11:13:46] Flattener#build_ancestry
[INFO] [2020-02-20 11:13:46] 6525 ancestry keys
[START] [2020-02-20 11:13:46] build_node_ancestors
[INFO] [2020-02-20 11:13:46] old ancestors deleted.
[STOP] [2020-02-20 11:14:01] build_node_ancestors
[START] [2020-02-20 11:14:01] Flattener#propagate_ancestor_ids
[STOP] [2020-02-20 11:14:04] Flattener#propagate_ancestor_ids
[STOP] [2020-02-20 11:14:04] Flattener#flatten
[STOP] [2020-02-20 11:14:04] rebuild_nodes
[START] [2020-02-20 11:14:04] resolve_missing_media_owners
[STOP] [2020-02-20 11:14:04] resolve_missing_media_owners
[START] [2020-02-20 11:14:04] sanitize_media_verbatims
[STOP] [2020-02-20 11:14:04] sanitize_media_verbatims
[START] [2020-02-20 11:14:04] queue_downloads
[STOP] [2020-02-20 11:14:04] queue_downloads
[START] [2020-02-20 11:14:04] parse_names
[WARN] [2020-02-20 11:14:04] I see 6525 names which still need to be parsed.
[WARN] [2020-02-20 11:14:09] I see 6 names which still need to be parsed.
[STOP] [2020-02-20 11:14:10] parse_names
[START] [2020-02-20 11:14:10] denormalize_canonical_names_to_nodes
[STOP] [2020-02-20 11:14:10] denormalize_canonical_names_to_nodes
[START] [2020-02-20 11:14:10] match_nodes
[START] [2020-02-20 11:14:10] map_all_nodes_to_pages
[STOP] [2020-02-20 11:24:27] map_all_nodes_to_pages
[INFO] [2020-02-20 11:24:27] 852 Unmatched nodes (of 6525)! That's too many to output. First 10: Biota (#63436870); Prokaryota (#63436206); Bacteria (#63433378); Negibacteria (#63437791); Escherichia coli (#63437016); Ralstoniaceae (#63437849); Posibacteria (#63437839); Actinobacteria (#63433789); Actinobacteria (#63437128); Actinobacteridae (#63433226)
[START] [2020-02-20 11:24:27] update_nodes
[STOP] [2020-02-20 11:24:29] update_nodes
[STOP] [2020-02-20 11:24:29] match_nodes
[START] [2020-02-20 11:24:29] reindex_search
[STOP] [2020-02-20 11:24:47] reindex_search
[START] [2020-02-20 11:24:47] normalize_units
[STOP] [2020-02-20 11:24:47] normalize_units
[START] [2020-02-20 11:24:47] calculate_statistics
[STOP] [2020-02-20 11:24:47] calculate_statistics
[START] [2020-02-20 11:24:47] complete_harvest_instance
[START] [2020-02-20 11:24:47] overall_tsv_creation
[INFO] [2020-02-20 11:24:47] Processing group of 6525 in 1 batches of 10000
[INFO] [2020-02-20 11:26:06] Average Time: 44.37
[INFO] [2020-02-20 11:26:06] Total Time: 1m19s
[STOP] [2020-02-20 11:26:06] overall_tsv_creation
[INFO] [2020-02-20 11:26:06] Done. Check your files:
[INFO] [2020-02-20 11:26:06] (6525 lines) /app/public/data/wiki_icelandic/publish_nodes.tsv
[INFO] [2020-02-20 11:26:06] (6525 lines) /app/public/data/wiki_icelandic/publish_identifiers.tsv
[INFO] [2020-02-20 11:26:06] (104789 lines) /app/public/data/wiki_icelandic/publish_node_ancestors.tsv
[INFO] [2020-02-20 11:26:06] (6525 lines) /app/public/data/wiki_icelandic/publish_scientific_names.tsv
[INFO] [2020-02-20 11:26:06] (93990 lines) /app/public/data/wiki_icelandic/publish_articles.tsv
[INFO] [2020-02-20 11:26:06] (7556 lines) /app/public/data/wiki_icelandic/publish_content_sections.tsv
[STOP] [2020-02-20 11:26:07] complete_harvest_instance
[START] [2020-02-20 11:26:07] completed
[STOP] [2020-02-20 11:26:07] completed
[STOP] [2020-02-20 11:26:07] logged process, took 817.77
Latest Process

20 Feb 11:12 EXITED currently processing 0