Harvest for wikipedia NN Created 24 Feb 18:02

Stage: completed
Fetched: 24 Feb 18:02
Validated: 24 Feb 18:02
Deltas Created 24 Feb 18:02
Units Normalized: 24 Feb 18:16
Ancestry Built: 24 Feb 18:03
Nodes Matched: 24 Feb 18:16
Names Parsed: 24 Feb 18:04
New Models Stored: 24 Feb 18:02
Indexed: 24 Feb 18:16
Completed: 24 Feb 18:18
Time to Harvest: less than a minute
Harvesting Log

(122 lines)
# Logfile created on 2020-02-24 18:02:12 -0500 by logger.rb/56815
[START] [2020-02-24 18:02:12] logged process
[START] [2020-02-24 18:02:12] create_harvest_instance
[STOP] [2020-02-24 18:02:12] create_harvest_instance
[START] [2020-02-24 18:02:12] fetch_files
[STOP] [2020-02-24 18:02:12] fetch_files
[START] [2020-02-24 18:02:12] validate_each_file
[STOP] [2020-02-24 18:02:14] validate_each_file
[START] [2020-02-24 18:02:14] convert_to_csv
[CMD] [2020-02-24 18:02:14] /usr/bin/sort /app/public/converted_csv/wiki_nn_norwegia_nodes_20255.csv > /app/public/converted_csv/wiki_nn_norwegia_nodes_20255.csv_sorted
[CMD] [2020-02-24 18:02:14] /usr/bin/sort /app/public/converted_csv/wiki_nn_norwegia_media_20256.csv > /app/public/converted_csv/wiki_nn_norwegia_media_20256.csv_sorted
[STOP] [2020-02-24 18:02:14] convert_to_csv
[START] [2020-02-24 18:02:14] calculate_delta
[CMD] [2020-02-24 18:02:14] echo "0a" > /app/public/diff/wiki_nn_norwegia_nodes_20255.diff
[CMD] [2020-02-24 18:02:14] tail -n +1 /app/public/converted_csv/wiki_nn_norwegia_nodes_20255.csv >> /app/public/diff/wiki_nn_norwegia_nodes_20255.diff
[CMD] [2020-02-24 18:02:14] echo "." >> /app/public/diff/wiki_nn_norwegia_nodes_20255.diff
[CMD] [2020-02-24 18:02:14] echo "0a" > /app/public/diff/wiki_nn_norwegia_media_20256.diff
[CMD] [2020-02-24 18:02:14] tail -n +1 /app/public/converted_csv/wiki_nn_norwegia_media_20256.csv >> /app/public/diff/wiki_nn_norwegia_media_20256.diff
[CMD] [2020-02-24 18:02:14] echo "." >> /app/public/diff/wiki_nn_norwegia_media_20256.diff
[STOP] [2020-02-24 18:02:14] calculate_delta
[START] [2020-02-24 18:02:14] parse_diff_and_store
[INFO] [2020-02-24 18:02:14] Loading nodes diff file into memory (true lines)...
[INFO] [2020-02-24 18:02:17] Loading media diff file into memory (true lines)...
[INFO] [2020-02-24 18:02:44] Storing 5674 ScientificNames
[INFO] [2020-02-24 18:02:44] Processing group of 5674 in 6 groups of 1000
[INFO] [2020-02-24 18:02:46] Average Time: 0.345
[INFO] [2020-02-24 18:02:46] Total Time: 3s
[INFO] [2020-02-24 18:02:46] Storing 5675 Identifiers
[INFO] [2020-02-24 18:02:46] Processing group of 5675 in 6 groups of 1000
[INFO] [2020-02-24 18:02:47] Average Time: 0.147
[INFO] [2020-02-24 18:02:47] Total Time: 1s
[INFO] [2020-02-24 18:02:47] Storing 5674 Nodes
[INFO] [2020-02-24 18:02:47] Processing group of 5674 in 6 groups of 1000
[INFO] [2020-02-24 18:02:49] Average Time: 0.29
[INFO] [2020-02-24 18:02:49] Total Time: 2s
[INFO] [2020-02-24 18:02:49] Storing 6438 ArticlesSections
[INFO] [2020-02-24 18:02:49] Processing group of 6438 in 7 groups of 1000
[INFO] [2020-02-24 18:02:49] Average Time: 0.046
[INFO] [2020-02-24 18:02:49] Total Time: 1s
[INFO] [2020-02-24 18:02:49] last 3 / first 3: 0.8
[INFO] [2020-02-24 18:02:49] Std.Dev: 0.0; Max: 0.05
[INFO] [2020-02-24 18:02:49] Storing 6438 Articles
[INFO] [2020-02-24 18:02:49] Processing group of 6438 in 7 groups of 1000
[INFO] [2020-02-24 18:02:54] Average Time: 0.74
[INFO] [2020-02-24 18:02:54] Total Time: 6s
[INFO] [2020-02-24 18:02:54] last 3 / first 3: 0.85
[INFO] [2020-02-24 18:02:54] Std.Dev: 0.27568097504180444; Max: 1.12
[STOP] [2020-02-24 18:02:54] parse_diff_and_store
[START] [2020-02-24 18:02:54] resolve_keys
[INFO] [2020-02-24 18:03:35] Occurrences to nodes (through scientific_names)...
[INFO] [2020-02-24 18:03:35] traits to occurrences...
[INFO] [2020-02-24 18:03:35] traits to nodes (through occurrences)...
[INFO] [2020-02-24 18:03:35] Traits to sex term...
[INFO] [2020-02-24 18:03:35] Traits to lifestage term...
[INFO] [2020-02-24 18:03:35] MetaTraits to traits...
[INFO] [2020-02-24 18:03:35] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-02-24 18:03:35] Assocs to occurrences...
[INFO] [2020-02-24 18:03:35] Assocs to nodes...
[INFO] [2020-02-24 18:03:35] Assoc to sex term...
[INFO] [2020-02-24 18:03:35] Assoc to lifestage term...
[STOP] [2020-02-24 18:03:35] resolve_keys
[START] [2020-02-24 18:03:35] hold_for_later_1
[STOP] [2020-02-24 18:03:35] hold_for_later_1
[START] [2020-02-24 18:03:35] hold_for_later_2
[STOP] [2020-02-24 18:03:35] hold_for_later_2
[START] [2020-02-24 18:03:35] resolve_missing_parents
[STOP] [2020-02-24 18:03:38] resolve_missing_parents
[START] [2020-02-24 18:03:38] rebuild_nodes
[START] [2020-02-24 18:03:38] Flattener#flatten
[START] [2020-02-24 18:03:38] Flattener#study_resource
[START] [2020-02-24 18:03:38] Flattener#build_ancestry
[STOP] [2020-02-24 18:03:38] Flattener#build_ancestry
[INFO] [2020-02-24 18:03:38] 5674 ancestry keys
[START] [2020-02-24 18:03:38] build_node_ancestors
[INFO] [2020-02-24 18:03:38] old ancestors deleted.
[STOP] [2020-02-24 18:03:52] build_node_ancestors
[START] [2020-02-24 18:03:53] Flattener#propagate_ancestor_ids
[STOP] [2020-02-24 18:03:55] Flattener#propagate_ancestor_ids
[STOP] [2020-02-24 18:03:55] Flattener#flatten
[STOP] [2020-02-24 18:03:55] rebuild_nodes
[START] [2020-02-24 18:03:55] resolve_missing_media_owners
[STOP] [2020-02-24 18:03:55] resolve_missing_media_owners
[START] [2020-02-24 18:03:55] sanitize_media_verbatims
[STOP] [2020-02-24 18:03:55] sanitize_media_verbatims
[START] [2020-02-24 18:03:55] queue_downloads
[STOP] [2020-02-24 18:03:55] queue_downloads
[START] [2020-02-24 18:03:55] parse_names
[WARN] [2020-02-24 18:03:55] I see 5674 names which still need to be parsed.
[WARN] [2020-02-24 18:04:00] I see 13 names which still need to be parsed.
[STOP] [2020-02-24 18:04:01] parse_names
[START] [2020-02-24 18:04:01] denormalize_canonical_names_to_nodes
[STOP] [2020-02-24 18:04:01] denormalize_canonical_names_to_nodes
[START] [2020-02-24 18:04:01] match_nodes
[START] [2020-02-24 18:04:01] map_all_nodes_to_pages
[STOP] [2020-02-24 18:16:31] map_all_nodes_to_pages
[INFO] [2020-02-24 18:16:31] 868 Unmatched nodes (of 5674)! That's too many to output. First 10: Biota (#63448833); Prokaryota (#63448121); Bacteria (#63446165); Negibacteria (#63449759); Escherichia coli (#63448987); Ideonella (#63447175); Ideonella sakaiensis (#63448780); Posibacteria (#63449797); Actinobacteria (#63446536); Actinobacteria (#63449111)
[START] [2020-02-24 18:16:31] update_nodes
[STOP] [2020-02-24 18:16:33] update_nodes
[STOP] [2020-02-24 18:16:33] match_nodes
[START] [2020-02-24 18:16:33] reindex_search
[STOP] [2020-02-24 18:16:49] reindex_search
[START] [2020-02-24 18:16:49] normalize_units
[STOP] [2020-02-24 18:16:49] normalize_units
[START] [2020-02-24 18:16:49] calculate_statistics
[STOP] [2020-02-24 18:16:50] calculate_statistics
[START] [2020-02-24 18:16:50] complete_harvest_instance
[START] [2020-02-24 18:16:50] overall_tsv_creation
[INFO] [2020-02-24 18:16:50] Processing group of 5674 in 1 batches of 10000
[INFO] [2020-02-24 18:18:06] Average Time: 40.62
[INFO] [2020-02-24 18:18:06] Total Time: 1m17s
[STOP] [2020-02-24 18:18:06] overall_tsv_creation
[INFO] [2020-02-24 18:18:06] Done. Check your files:
[INFO] [2020-02-24 18:18:06] (5674 lines) /app/public/data/wiki_nn_norwegia/publish_nodes.tsv
[INFO] [2020-02-24 18:18:06] (5675 lines) /app/public/data/wiki_nn_norwegia/publish_identifiers.tsv
[INFO] [2020-02-24 18:18:06] (106661 lines) /app/public/data/wiki_nn_norwegia/publish_node_ancestors.tsv
[INFO] [2020-02-24 18:18:06] (5674 lines) /app/public/data/wiki_nn_norwegia/publish_scientific_names.tsv
[INFO] [2020-02-24 18:18:06] (84985 lines) /app/public/data/wiki_nn_norwegia/publish_articles.tsv
[INFO] [2020-02-24 18:18:06] (6438 lines) /app/public/data/wiki_nn_norwegia/publish_content_sections.tsv
[STOP] [2020-02-24 18:18:07] complete_harvest_instance
[START] [2020-02-24 18:18:07] completed
[STOP] [2020-02-24 18:18:07] completed
[STOP] [2020-02-24 18:18:07] logged process, took 954.83
Latest Process

24 Feb 18:02 EXITED currently processing 0