Harvest for wikipedia ET Created 16 Jan 11:57

Stage: completed
Fetched: 16 Jan 11:57
Validated: 16 Jan 11:57
Deltas Created 16 Jan 11:57
Units Normalized: 16 Jan 12:38
Ancestry Built: 16 Jan 12:00
Nodes Matched: 16 Jan 12:37
Names Parsed: 16 Jan 12:00
New Models Stored: 16 Jan 11:58
Indexed: 16 Jan 12:38
Completed: 16 Jan 12:40
Time to Harvest: 1 minute
Harvesting Log

(128 lines)
# Logfile created on 2020-01-16 11:57:15 -0500 by logger.rb/56815
[START] [2020-01-16 11:57:15] logged process
[START] [2020-01-16 11:57:15] create_harvest_instance
[STOP] [2020-01-16 11:57:16] create_harvest_instance
[START] [2020-01-16 11:57:16] fetch_files
[STOP] [2020-01-16 11:57:16] fetch_files
[START] [2020-01-16 11:57:16] validate_each_file
[STOP] [2020-01-16 11:57:22] validate_each_file
[START] [2020-01-16 11:57:22] convert_to_csv
[CMD] [2020-01-16 11:57:22] /usr/bin/sort /app/public/converted_csv/wiki_et_estonian_nodes_19982.csv > /app/public/converted_csv/wiki_et_estonian_nodes_19982.csv_sorted
[CMD] [2020-01-16 11:57:23] /usr/bin/sort /app/public/converted_csv/wiki_et_estonian_media_19983.csv > /app/public/converted_csv/wiki_et_estonian_media_19983.csv_sorted
[STOP] [2020-01-16 11:57:24] convert_to_csv
[START] [2020-01-16 11:57:24] calculate_delta
[CMD] [2020-01-16 11:57:24] echo "0a" > /app/public/diff/wiki_et_estonian_nodes_19982.diff
[CMD] [2020-01-16 11:57:24] tail -n +1 /app/public/converted_csv/wiki_et_estonian_nodes_19982.csv >> /app/public/diff/wiki_et_estonian_nodes_19982.diff
[CMD] [2020-01-16 11:57:25] echo "." >> /app/public/diff/wiki_et_estonian_nodes_19982.diff
[CMD] [2020-01-16 11:57:26] echo "0a" > /app/public/diff/wiki_et_estonian_media_19983.diff
[CMD] [2020-01-16 11:57:26] tail -n +1 /app/public/converted_csv/wiki_et_estonian_media_19983.csv >> /app/public/diff/wiki_et_estonian_media_19983.diff
[CMD] [2020-01-16 11:57:27] echo "." >> /app/public/diff/wiki_et_estonian_media_19983.diff
[STOP] [2020-01-16 11:57:28] calculate_delta
[START] [2020-01-16 11:57:28] parse_diff_and_store
[INFO] [2020-01-16 11:57:29] Loading nodes diff file into memory (true lines)...
[INFO] [2020-01-16 11:57:36] Loading media diff file into memory (true lines)...
[INFO] [2020-01-16 11:58:38] Storing 11499 ScientificNames
[INFO] [2020-01-16 11:58:38] Processing group of 11499 in 12 groups of 1000
[INFO] [2020-01-16 11:58:43] Average Time: 0.414
[INFO] [2020-01-16 11:58:43] Total Time: 6s
[INFO] [2020-01-16 11:58:43] last 3 / first 3: 0.6
[INFO] [2020-01-16 11:58:43] Std.Dev: 0.12649110640673517; Max: 0.67
[INFO] [2020-01-16 11:58:43] Storing 11499 Identifiers
[INFO] [2020-01-16 11:58:43] Processing group of 11499 in 12 groups of 1000
[INFO] [2020-01-16 11:58:45] Average Time: 0.111
[INFO] [2020-01-16 11:58:45] Total Time: 2s
[INFO] [2020-01-16 11:58:45] last 3 / first 3: 0.76
[INFO] [2020-01-16 11:58:45] Std.Dev: 0.0; Max: 0.13
[INFO] [2020-01-16 11:58:45] Storing 11499 Nodes
[INFO] [2020-01-16 11:58:45] Processing group of 11499 in 12 groups of 1000
[INFO] [2020-01-16 11:58:49] Average Time: 0.312
[INFO] [2020-01-16 11:58:49] Total Time: 4s
[INFO] [2020-01-16 11:58:49] last 3 / first 3: 0.83
[INFO] [2020-01-16 11:58:49] Std.Dev: 0.05477225575051661; Max: 0.36
[INFO] [2020-01-16 11:58:49] Storing 14231 ArticlesSections
[INFO] [2020-01-16 11:58:49] Processing group of 14231 in 15 groups of 1000
[INFO] [2020-01-16 11:58:50] Average Time: 0.062
[INFO] [2020-01-16 11:58:50] Total Time: 1s
[INFO] [2020-01-16 11:58:50] last 3 / first 3: 0.83
[INFO] [2020-01-16 11:58:50] Std.Dev: 0.0; Max: 0.1
[INFO] [2020-01-16 11:58:50] Storing 14231 Articles
[INFO] [2020-01-16 11:58:50] Processing group of 14231 in 15 groups of 1000
[INFO] [2020-01-16 11:58:57] Average Time: 0.514
[INFO] [2020-01-16 11:58:57] Total Time: 8s
[INFO] [2020-01-16 11:58:57] last 3 / first 3: 0.71
[INFO] [2020-01-16 11:58:57] Std.Dev: 0.2449489742783178; Max: 1.09
[STOP] [2020-01-16 11:58:57] parse_diff_and_store
[START] [2020-01-16 11:58:57] resolve_keys
[INFO] [2020-01-16 11:59:39] Occurrences to nodes (through scientific_names)...
[INFO] [2020-01-16 11:59:39] traits to occurrences...
[INFO] [2020-01-16 11:59:39] traits to nodes (through occurrences)...
[INFO] [2020-01-16 11:59:39] Traits to sex term...
[INFO] [2020-01-16 11:59:39] Traits to lifestage term...
[INFO] [2020-01-16 11:59:39] MetaTraits to traits...
[INFO] [2020-01-16 11:59:39] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-01-16 11:59:39] Assocs to occurrences...
[INFO] [2020-01-16 11:59:39] Assocs to nodes...
[INFO] [2020-01-16 11:59:39] Assoc to sex term...
[INFO] [2020-01-16 11:59:39] Assoc to lifestage term...
[STOP] [2020-01-16 11:59:39] resolve_keys
[START] [2020-01-16 11:59:40] hold_for_later_1
[STOP] [2020-01-16 11:59:40] hold_for_later_1
[START] [2020-01-16 11:59:40] hold_for_later_2
[STOP] [2020-01-16 11:59:40] hold_for_later_2
[START] [2020-01-16 11:59:40] resolve_missing_parents
[STOP] [2020-01-16 11:59:44] resolve_missing_parents
[START] [2020-01-16 11:59:44] rebuild_nodes
[START] [2020-01-16 11:59:44] Flattener#flatten
[START] [2020-01-16 11:59:44] Flattener#study_resource
[START] [2020-01-16 11:59:44] Flattener#build_ancestry
[STOP] [2020-01-16 11:59:45] Flattener#build_ancestry
[INFO] [2020-01-16 11:59:45] 11499 ancestry keys
[START] [2020-01-16 11:59:45] build_node_ancestors
[INFO] [2020-01-16 11:59:45] old ancestors deleted.
[STOP] [2020-01-16 12:00:15] build_node_ancestors
[START] [2020-01-16 12:00:15] Flattener#propagate_ancestor_ids
[STOP] [2020-01-16 12:00:21] Flattener#propagate_ancestor_ids
[STOP] [2020-01-16 12:00:21] Flattener#flatten
[STOP] [2020-01-16 12:00:21] rebuild_nodes
[START] [2020-01-16 12:00:21] resolve_missing_media_owners
[STOP] [2020-01-16 12:00:21] resolve_missing_media_owners
[START] [2020-01-16 12:00:21] sanitize_media_verbatims
[STOP] [2020-01-16 12:00:21] sanitize_media_verbatims
[START] [2020-01-16 12:00:21] queue_downloads
[STOP] [2020-01-16 12:00:21] queue_downloads
[START] [2020-01-16 12:00:21] parse_names
[WARN] [2020-01-16 12:00:21] I see 11499 names which still need to be parsed.
[WARN] [2020-01-16 12:00:31] I see 21 names which still need to be parsed.
[STOP] [2020-01-16 12:00:32] parse_names
[START] [2020-01-16 12:00:32] denormalize_canonical_names_to_nodes
[STOP] [2020-01-16 12:00:32] denormalize_canonical_names_to_nodes
[START] [2020-01-16 12:00:32] match_nodes
[START] [2020-01-16 12:00:32] map_all_nodes_to_pages
[STOP] [2020-01-16 12:37:13] map_all_nodes_to_pages
[INFO] [2020-01-16 12:37:13] 1526 Unmatched nodes (of 11499)! That's too many to output. First 10: Biota (#62891315); Prokaryota (#62890011); Bacteria (#62885556); Eubacteria (#62891482); Ferrobacteria (#62885534); Negibacteria (#62893085); Thermotogae (#62885746); Gemmatimonadetes (#62885749); Gemmatimonales (#62890225); Gemmatimonaceae (#62890224)
[START] [2020-01-16 12:37:13] update_nodes
[STOP] [2020-01-16 12:37:17] update_nodes
[STOP] [2020-01-16 12:37:17] match_nodes
[START] [2020-01-16 12:37:17] reindex_search
[STOP] [2020-01-16 12:38:12] reindex_search
[START] [2020-01-16 12:38:12] normalize_units
[STOP] [2020-01-16 12:38:12] normalize_units
[START] [2020-01-16 12:38:12] calculate_statistics
[STOP] [2020-01-16 12:38:12] calculate_statistics
[START] [2020-01-16 12:38:12] complete_harvest_instance
[START] [2020-01-16 12:38:12] overall_tsv_creation
[INFO] [2020-01-16 12:38:12] Processing group of 11499 in 2 batches of 10000
[INFO] [2020-01-16 12:40:52] Average Time: 46.285
[INFO] [2020-01-16 12:40:52] Total Time: 2m41s
[STOP] [2020-01-16 12:40:52] overall_tsv_creation
[INFO] [2020-01-16 12:40:52] Done. Check your files:
[INFO] [2020-01-16 12:40:53] (11499 lines) /app/public/data/wiki_et_estonian/publish_nodes.tsv
[INFO] [2020-01-16 12:40:54] (11499 lines) /app/public/data/wiki_et_estonian/publish_identifiers.tsv
[INFO] [2020-01-16 12:40:54] (210685 lines) /app/public/data/wiki_et_estonian/publish_node_ancestors.tsv
[INFO] [2020-01-16 12:40:55] (11499 lines) /app/public/data/wiki_et_estonian/publish_scientific_names.tsv
[INFO] [2020-01-16 12:40:56] (150375 lines) /app/public/data/wiki_et_estonian/publish_articles.tsv
[INFO] [2020-01-16 12:40:56] (14231 lines) /app/public/data/wiki_et_estonian/publish_content_sections.tsv
[STOP] [2020-01-16 12:40:56] complete_harvest_instance
[START] [2020-01-16 12:40:56] completed
[STOP] [2020-01-16 12:40:56] completed
[STOP] [2020-01-16 12:40:56] logged process, took 2621.06
Latest Process

16 Jan 11:57 EXITED currently processing 0