Harvest for
wikipedia ID
Created
30 Oct 12:25
Stage:
completed
Fetched:
30 Oct 12:25
Validated:
30 Oct 12:26
Deltas Created
30 Oct 12:26
Units Normalized:
30 Oct 15:53
Ancestry Built:
30 Oct 13:00
Nodes Matched:
30 Oct 15:45
Names Parsed:
30 Oct 13:02
New Models Stored:
30 Oct 12:47
Indexed:
30 Oct 15:53
Completed:
30 Oct 16:28
Time to Harvest:
4 minutes
Harvesting Log
(130 lines)
# Logfile created on 2019-10-30 12:25:43 -0400 by logger.rb/56815
[START] [2019-10-30 12:25:43] logged process
[START] [2019-10-30 12:25:43] create_harvest_instance
[STOP] [2019-10-30 12:25:44] create_harvest_instance
[START] [2019-10-30 12:25:44] fetch_files
[STOP] [2019-10-30 12:25:44] fetch_files
[START] [2019-10-30 12:25:44] validate_each_file
[STOP] [2019-10-30 12:26:12] validate_each_file
[START] [2019-10-30 12:26:12] convert_to_csv
[CMD] [2019-10-30 12:26:12] /usr/bin/sort /app/public/converted_csv/wiki_id_indonesi_nodes_17874.csv > /app/public/converted_csv/wiki_id_indonesi_nodes_17874.csv_sorted
[CMD] [2019-10-30 12:26:12] /usr/bin/sort /app/public/converted_csv/wiki_id_indonesi_media_17875.csv > /app/public/converted_csv/wiki_id_indonesi_media_17875.csv_sorted
[STOP] [2019-10-30 12:26:13] convert_to_csv
[START] [2019-10-30 12:26:13] calculate_delta
[CMD] [2019-10-30 12:26:13] echo "0a" > /app/public/diff/wiki_id_indonesi_nodes_17874.diff
[CMD] [2019-10-30 12:26:13] tail -n +1 /app/public/converted_csv/wiki_id_indonesi_nodes_17874.csv >> /app/public/diff/wiki_id_indonesi_nodes_17874.diff
[CMD] [2019-10-30 12:26:13] echo "." >> /app/public/diff/wiki_id_indonesi_nodes_17874.diff
[CMD] [2019-10-30 12:26:13] echo "0a" > /app/public/diff/wiki_id_indonesi_media_17875.diff
[CMD] [2019-10-30 12:26:13] tail -n +1 /app/public/converted_csv/wiki_id_indonesi_media_17875.csv >> /app/public/diff/wiki_id_indonesi_media_17875.diff
[CMD] [2019-10-30 12:26:14] echo "." >> /app/public/diff/wiki_id_indonesi_media_17875.diff
[STOP] [2019-10-30 12:26:14] calculate_delta
[START] [2019-10-30 12:26:14] parse_diff_and_store
[INFO] [2019-10-30 12:26:14] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-30 12:27:19] Loading media diff file into memory (true lines)...
[INFO] [2019-10-30 12:41:20] Storing 130506 ScientificNames
[INFO] [2019-10-30 12:41:20] Processing group of 130506 in 131 groups of 1000
[INFO] [2019-10-30 12:42:28] Average Time: 0.514
[INFO] [2019-10-30 12:42:28] Total Time: 1m8s
[INFO] [2019-10-30 12:42:28] last 3 / first 3: 0.65
[INFO] [2019-10-30 12:42:28] Std.Dev: 0.8360621986431392; Max: 5.36
[INFO] [2019-10-30 12:42:28] Storing 130506 Identifiers
[INFO] [2019-10-30 12:42:28] Processing group of 130506 in 131 groups of 1000
[INFO] [2019-10-30 12:42:51] Average Time: 0.168
[INFO] [2019-10-30 12:42:51] Total Time: 23s
[INFO] [2019-10-30 12:42:51] last 3 / first 3: 0.64
[INFO] [2019-10-30 12:42:51] Std.Dev: 0.6387487769068525; Max: 5.28
[INFO] [2019-10-30 12:42:51] Storing 130506 Nodes
[INFO] [2019-10-30 12:42:51] Processing group of 130506 in 131 groups of 1000
[INFO] [2019-10-30 12:43:57] Average Time: 0.504
[INFO] [2019-10-30 12:43:57] Total Time: 1m7s
[INFO] [2019-10-30 12:43:57] last 3 / first 3: 0.69
[INFO] [2019-10-30 12:43:57] Std.Dev: 0.9203260291874831; Max: 6.14
[INFO] [2019-10-30 12:43:57] Storing 244932 ArticlesSections
[INFO] [2019-10-30 12:43:57] Processing group of 244932 in 245 groups of 1000
[INFO] [2019-10-30 12:44:25] Average Time: 0.107
[INFO] [2019-10-30 12:44:25] Total Time: 28s
[INFO] [2019-10-30 12:44:25] last 3 / first 3: 0.94
[INFO] [2019-10-30 12:44:25] Std.Dev: 0.5431390245600107; Max: 6.11
[INFO] [2019-10-30 12:44:25] Storing 244932 Articles
[INFO] [2019-10-30 12:44:25] Processing group of 244932 in 245 groups of 1000
[INFO] [2019-10-30 12:47:34] Average Time: 0.767
[INFO] [2019-10-30 12:47:34] Total Time: 3m9s
[INFO] [2019-10-30 12:47:34] last 3 / first 3: 0.62
[INFO] [2019-10-30 12:47:34] Std.Dev: 1.4293355099485916; Max: 7.18
[STOP] [2019-10-30 12:47:34] parse_diff_and_store
[START] [2019-10-30 12:47:34] resolve_keys
[INFO] [2019-10-30 12:50:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-30 12:50:19] traits to occurrences...
[INFO] [2019-10-30 12:50:19] traits to nodes (through occurrences)...
[INFO] [2019-10-30 12:50:19] Traits to sex term...
[INFO] [2019-10-30 12:50:19] Traits to lifestage term...
[INFO] [2019-10-30 12:50:19] MetaTraits to traits...
[INFO] [2019-10-30 12:50:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-30 12:50:19] Assocs to occurrences...
[INFO] [2019-10-30 12:50:19] Assocs to nodes...
[INFO] [2019-10-30 12:50:19] Assoc to sex term...
[INFO] [2019-10-30 12:50:19] Assoc to lifestage term...
[STOP] [2019-10-30 12:50:19] resolve_keys
[START] [2019-10-30 12:50:19] hold_for_later_1
[STOP] [2019-10-30 12:50:19] hold_for_later_1
[START] [2019-10-30 12:50:19] hold_for_later_2
[STOP] [2019-10-30 12:50:19] hold_for_later_2
[START] [2019-10-30 12:50:19] resolve_missing_parents
[STOP] [2019-10-30 12:50:27] resolve_missing_parents
[START] [2019-10-30 12:50:28] rebuild_nodes
[START] [2019-10-30 12:50:28] Flattener#flatten
[START] [2019-10-30 12:50:28] Flattener#study_resource
[START] [2019-10-30 12:50:28] Flattener#build_ancestry
[STOP] [2019-10-30 12:51:04] Flattener#build_ancestry
[INFO] [2019-10-30 12:51:04] 130506 ancestry keys
[START] [2019-10-30 12:51:04] build_node_ancestors
[INFO] [2019-10-30 12:51:04] old ancestors deleted.
[STOP] [2019-10-30 12:57:52] build_node_ancestors
[START] [2019-10-30 12:57:53] Flattener#propagate_ancestor_ids
[STOP] [2019-10-30 13:00:22] Flattener#propagate_ancestor_ids
[STOP] [2019-10-30 13:00:22] Flattener#flatten
[STOP] [2019-10-30 13:00:22] rebuild_nodes
[START] [2019-10-30 13:00:22] resolve_missing_media_owners
[STOP] [2019-10-30 13:00:22] resolve_missing_media_owners
[START] [2019-10-30 13:00:22] sanitize_media_verbatims
[STOP] [2019-10-30 13:00:22] sanitize_media_verbatims
[START] [2019-10-30 13:00:22] queue_downloads
[STOP] [2019-10-30 13:00:22] queue_downloads
[START] [2019-10-30 13:00:22] parse_names
[WARN] [2019-10-30 13:00:22] I see 130506 names which still need to be parsed.
[WARN] [2019-10-30 13:02:02] I see 6 names which still need to be parsed.
[STOP] [2019-10-30 13:02:04] parse_names
[START] [2019-10-30 13:02:04] denormalize_canonical_names_to_nodes
[STOP] [2019-10-30 13:02:06] denormalize_canonical_names_to_nodes
[START] [2019-10-30 13:02:06] match_nodes
[START] [2019-10-30 13:02:06] map_all_nodes_to_pages
[STOP] [2019-10-30 15:44:48] map_all_nodes_to_pages
[INFO] [2019-10-30 15:44:48] 4555 Unmatched nodes (of 130506)! That's too many to output. First 10: Biota (#53912742); Bacteria (#53818713); Negibacteria (#53925567); Pseudomonas syringae (#53924567); Salmonella enterica (#53910155); Escherichia coli (#53916094); Ralstoniaceae (#53925879); Ralstonia eutropha (#53820419); Aquificae (#53935449); Aquificae (#53906895)
[START] [2019-10-30 15:44:48] update_nodes
[STOP] [2019-10-30 15:45:00] update_nodes
[STOP] [2019-10-30 15:45:00] match_nodes
[START] [2019-10-30 15:45:00] reindex_search
[STOP] [2019-10-30 15:53:14] reindex_search
[START] [2019-10-30 15:53:14] normalize_units
[STOP] [2019-10-30 15:53:14] normalize_units
[START] [2019-10-30 15:53:14] calculate_statistics
[STOP] [2019-10-30 15:53:15] calculate_statistics
[START] [2019-10-30 15:53:15] complete_harvest_instance
[START] [2019-10-30 15:53:15] overall_tsv_creation
[INFO] [2019-10-30 15:53:16] Processing group of 130506 in 14 batches of 10000
[INFO] [2019-10-30 16:28:28] Average Time: 98.058
[INFO] [2019-10-30 16:28:28] Total Time: 35m13s
[INFO] [2019-10-30 16:28:28] last 3 / first 3: 0.78
[INFO] [2019-10-30 16:28:28] Std.Dev: 25.50441138313135; Max: 113.01
[STOP] [2019-10-30 16:28:28] overall_tsv_creation
[INFO] [2019-10-30 16:28:28] Done. Check your files:
[INFO] [2019-10-30 16:28:29] (130506 lines) /app/public/data/wiki_id_indonesi/publish_nodes.tsv
[INFO] [2019-10-30 16:28:29] (130506 lines) /app/public/data/wiki_id_indonesi/publish_identifiers.tsv
[INFO] [2019-10-30 16:28:29] (2810770 lines) /app/public/data/wiki_id_indonesi/publish_node_ancestors.tsv
[INFO] [2019-10-30 16:28:29] (130506 lines) /app/public/data/wiki_id_indonesi/publish_scientific_names.tsv
[INFO] [2019-10-30 16:28:30] (696096 lines) /app/public/data/wiki_id_indonesi/publish_articles.tsv
[INFO] [2019-10-30 16:28:30] (244932 lines) /app/public/data/wiki_id_indonesi/publish_content_sections.tsv
[STOP] [2019-10-30 16:28:30] complete_harvest_instance
[START] [2019-10-30 16:28:30] completed
[STOP] [2019-10-30 16:28:30] completed
[STOP] [2019-10-30 16:28:30] logged process, took 14566.73
Latest Process