Harvest for wikipedia MS Created 18 Feb 16:10

Stage: completed
Fetched: 18 Feb 16:10
Validated: 18 Feb 16:10
Deltas Created 18 Feb 16:10
Units Normalized: 18 Feb 16:23
Ancestry Built: 18 Feb 16:12
Nodes Matched: 18 Feb 16:22
Names Parsed: 18 Feb 16:12
New Models Stored: 18 Feb 16:11
Indexed: 18 Feb 16:23
Completed: 18 Feb 16:24
Time to Harvest: less than a minute
Harvesting Log

(128 lines)
# Logfile created on 2020-02-18 16:10:20 -0500 by logger.rb/56815
[START] [2020-02-18 16:10:20] logged process
[START] [2020-02-18 16:10:20] create_harvest_instance
[STOP] [2020-02-18 16:10:20] create_harvest_instance
[START] [2020-02-18 16:10:20] fetch_files
[STOP] [2020-02-18 16:10:20] fetch_files
[START] [2020-02-18 16:10:20] validate_each_file
[STOP] [2020-02-18 16:10:22] validate_each_file
[START] [2020-02-18 16:10:22] convert_to_csv
[CMD] [2020-02-18 16:10:22] /usr/bin/sort /app/public/converted_csv/wiki_ms_malay_nodes_20205.csv > /app/public/converted_csv/wiki_ms_malay_nodes_20205.csv_sorted
[CMD] [2020-02-18 16:10:22] /usr/bin/sort /app/public/converted_csv/wiki_ms_malay_media_20206.csv > /app/public/converted_csv/wiki_ms_malay_media_20206.csv_sorted
[STOP] [2020-02-18 16:10:22] convert_to_csv
[START] [2020-02-18 16:10:22] calculate_delta
[CMD] [2020-02-18 16:10:22] echo "0a" > /app/public/diff/wiki_ms_malay_nodes_20205.diff
[CMD] [2020-02-18 16:10:22] tail -n +1 /app/public/converted_csv/wiki_ms_malay_nodes_20205.csv >> /app/public/diff/wiki_ms_malay_nodes_20205.diff
[CMD] [2020-02-18 16:10:22] echo "." >> /app/public/diff/wiki_ms_malay_nodes_20205.diff
[CMD] [2020-02-18 16:10:22] echo "0a" > /app/public/diff/wiki_ms_malay_media_20206.diff
[CMD] [2020-02-18 16:10:22] tail -n +1 /app/public/converted_csv/wiki_ms_malay_media_20206.csv >> /app/public/diff/wiki_ms_malay_media_20206.diff
[CMD] [2020-02-18 16:10:22] echo "." >> /app/public/diff/wiki_ms_malay_media_20206.diff
[STOP] [2020-02-18 16:10:22] calculate_delta
[START] [2020-02-18 16:10:22] parse_diff_and_store
[INFO] [2020-02-18 16:10:22] Loading nodes diff file into memory (true lines)...
[INFO] [2020-02-18 16:10:25] Loading media diff file into memory (true lines)...
[INFO] [2020-02-18 16:11:01] Storing 6862 ScientificNames
[INFO] [2020-02-18 16:11:01] Processing group of 6862 in 7 groups of 1000
[INFO] [2020-02-18 16:11:05] Average Time: 0.523
[INFO] [2020-02-18 16:11:05] Total Time: 4s
[INFO] [2020-02-18 16:11:05] last 3 / first 3: 0.8
[INFO] [2020-02-18 16:11:05] Std.Dev: 0.1224744871391589; Max: 0.71
[INFO] [2020-02-18 16:11:05] Storing 6862 Identifiers
[INFO] [2020-02-18 16:11:05] Processing group of 6862 in 7 groups of 1000
[INFO] [2020-02-18 16:11:06] Average Time: 0.136
[INFO] [2020-02-18 16:11:06] Total Time: 1s
[INFO] [2020-02-18 16:11:06] last 3 / first 3: 0.66
[INFO] [2020-02-18 16:11:06] Std.Dev: 0.05477225575051661; Max: 0.25
[INFO] [2020-02-18 16:11:06] Storing 6862 Nodes
[INFO] [2020-02-18 16:11:06] Processing group of 6862 in 7 groups of 1000
[INFO] [2020-02-18 16:11:09] Average Time: 0.44
[INFO] [2020-02-18 16:11:09] Total Time: 4s
[INFO] [2020-02-18 16:11:09] last 3 / first 3: 0.73
[INFO] [2020-02-18 16:11:09] Std.Dev: 0.09486832980505137; Max: 0.54
[INFO] [2020-02-18 16:11:09] Storing 7383 ArticlesSections
[INFO] [2020-02-18 16:11:09] Processing group of 7383 in 8 groups of 1000
[INFO] [2020-02-18 16:11:09] Average Time: 0.05
[INFO] [2020-02-18 16:11:09] Total Time: 1s
[INFO] [2020-02-18 16:11:09] last 3 / first 3: 0.75
[INFO] [2020-02-18 16:11:09] Std.Dev: 0.0; Max: 0.06
[INFO] [2020-02-18 16:11:09] Storing 7383 Articles
[INFO] [2020-02-18 16:11:09] Processing group of 7383 in 8 groups of 1000
[INFO] [2020-02-18 16:11:16] Average Time: 0.803
[INFO] [2020-02-18 16:11:16] Total Time: 7s
[INFO] [2020-02-18 16:11:16] last 3 / first 3: 0.64
[INFO] [2020-02-18 16:11:16] Std.Dev: 0.2588435821108957; Max: 1.11
[STOP] [2020-02-18 16:11:16] parse_diff_and_store
[START] [2020-02-18 16:11:16] resolve_keys
[INFO] [2020-02-18 16:12:05] Occurrences to nodes (through scientific_names)...
[INFO] [2020-02-18 16:12:05] traits to occurrences...
[INFO] [2020-02-18 16:12:05] traits to nodes (through occurrences)...
[INFO] [2020-02-18 16:12:05] Traits to sex term...
[INFO] [2020-02-18 16:12:05] Traits to lifestage term...
[INFO] [2020-02-18 16:12:05] MetaTraits to traits...
[INFO] [2020-02-18 16:12:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-02-18 16:12:05] Assocs to occurrences...
[INFO] [2020-02-18 16:12:05] Assocs to nodes...
[INFO] [2020-02-18 16:12:05] Assoc to sex term...
[INFO] [2020-02-18 16:12:05] Assoc to lifestage term...
[STOP] [2020-02-18 16:12:05] resolve_keys
[START] [2020-02-18 16:12:05] hold_for_later_1
[STOP] [2020-02-18 16:12:05] hold_for_later_1
[START] [2020-02-18 16:12:05] hold_for_later_2
[STOP] [2020-02-18 16:12:05] hold_for_later_2
[START] [2020-02-18 16:12:05] resolve_missing_parents
[STOP] [2020-02-18 16:12:08] resolve_missing_parents
[START] [2020-02-18 16:12:08] rebuild_nodes
[START] [2020-02-18 16:12:08] Flattener#flatten
[START] [2020-02-18 16:12:08] Flattener#study_resource
[START] [2020-02-18 16:12:08] Flattener#build_ancestry
[STOP] [2020-02-18 16:12:08] Flattener#build_ancestry
[INFO] [2020-02-18 16:12:08] 6862 ancestry keys
[START] [2020-02-18 16:12:08] build_node_ancestors
[INFO] [2020-02-18 16:12:08] old ancestors deleted.
[STOP] [2020-02-18 16:12:25] build_node_ancestors
[START] [2020-02-18 16:12:27] Flattener#propagate_ancestor_ids
[STOP] [2020-02-18 16:12:31] Flattener#propagate_ancestor_ids
[STOP] [2020-02-18 16:12:31] Flattener#flatten
[STOP] [2020-02-18 16:12:31] rebuild_nodes
[START] [2020-02-18 16:12:31] resolve_missing_media_owners
[STOP] [2020-02-18 16:12:31] resolve_missing_media_owners
[START] [2020-02-18 16:12:31] sanitize_media_verbatims
[STOP] [2020-02-18 16:12:31] sanitize_media_verbatims
[START] [2020-02-18 16:12:31] queue_downloads
[STOP] [2020-02-18 16:12:31] queue_downloads
[START] [2020-02-18 16:12:31] parse_names
[WARN] [2020-02-18 16:12:31] I see 6862 names which still need to be parsed.
[WARN] [2020-02-18 16:12:37] I see 15 names which still need to be parsed.
[STOP] [2020-02-18 16:12:38] parse_names
[START] [2020-02-18 16:12:38] denormalize_canonical_names_to_nodes
[STOP] [2020-02-18 16:12:38] denormalize_canonical_names_to_nodes
[START] [2020-02-18 16:12:38] match_nodes
[START] [2020-02-18 16:12:38] map_all_nodes_to_pages
[STOP] [2020-02-18 16:22:46] map_all_nodes_to_pages
[INFO] [2020-02-18 16:22:46] 976 Unmatched nodes (of 6862)! That's too many to output. First 10: Biota (#63421624); Prokaryota (#63420765); Bacteria (#63418574); Negibacteria (#63422765); Borrelia burgdorferi (#63422186); Escherichia coli (#63421804); Posibacteria (#63422810); Actinobacteria (#63419027); Actinobacteria (#63421921); Actinobacteridae (#63418418)
[START] [2020-02-18 16:22:46] update_nodes
[STOP] [2020-02-18 16:22:49] update_nodes
[STOP] [2020-02-18 16:22:49] match_nodes
[START] [2020-02-18 16:22:49] reindex_search
[STOP] [2020-02-18 16:23:09] reindex_search
[START] [2020-02-18 16:23:09] normalize_units
[STOP] [2020-02-18 16:23:09] normalize_units
[START] [2020-02-18 16:23:09] calculate_statistics
[STOP] [2020-02-18 16:23:09] calculate_statistics
[START] [2020-02-18 16:23:09] complete_harvest_instance
[START] [2020-02-18 16:23:09] overall_tsv_creation
[INFO] [2020-02-18 16:23:09] Processing group of 6862 in 1 batches of 10000
[INFO] [2020-02-18 16:24:31] Average Time: 46.95
[INFO] [2020-02-18 16:24:31] Total Time: 1m23s
[STOP] [2020-02-18 16:24:31] overall_tsv_creation
[INFO] [2020-02-18 16:24:31] Done. Check your files:
[INFO] [2020-02-18 16:24:31] (6862 lines) /app/public/data/wiki_ms_malay/publish_nodes.tsv
[INFO] [2020-02-18 16:24:31] (6862 lines) /app/public/data/wiki_ms_malay/publish_identifiers.tsv
[INFO] [2020-02-18 16:24:31] (136837 lines) /app/public/data/wiki_ms_malay/publish_node_ancestors.tsv
[INFO] [2020-02-18 16:24:32] (6862 lines) /app/public/data/wiki_ms_malay/publish_scientific_names.tsv
[INFO] [2020-02-18 16:24:32] (65760 lines) /app/public/data/wiki_ms_malay/publish_articles.tsv
[INFO] [2020-02-18 16:24:32] (7383 lines) /app/public/data/wiki_ms_malay/publish_content_sections.tsv
[STOP] [2020-02-18 16:24:32] complete_harvest_instance
[START] [2020-02-18 16:24:32] completed
[STOP] [2020-02-18 16:24:32] completed
[STOP] [2020-02-18 16:24:32] logged process, took 852.11
Latest Process

18 Feb 16:10 EXITED currently processing 0