Harvest for wikipedia LV Created 20 Feb 10:59

Stage: completed
Fetched: 20 Feb 10:59
Validated: 20 Feb 10:59
Deltas Created 20 Feb 10:59
Units Normalized: 20 Feb 11:10
Ancestry Built: 20 Feb 11:00
Nodes Matched: 20 Feb 11:10
Names Parsed: 20 Feb 11:01
New Models Stored: 20 Feb 10:59
Indexed: 20 Feb 11:10
Completed: 20 Feb 11:11
Time to Harvest: less than a minute
Harvesting Log

(123 lines)
# Logfile created on 2020-02-20 10:59:01 -0500 by logger.rb/56815
[START] [2020-02-20 10:59:01] logged process
[START] [2020-02-20 10:59:01] create_harvest_instance
[STOP] [2020-02-20 10:59:01] create_harvest_instance
[START] [2020-02-20 10:59:01] fetch_files
[STOP] [2020-02-20 10:59:01] fetch_files
[START] [2020-02-20 10:59:01] validate_each_file
[STOP] [2020-02-20 10:59:03] validate_each_file
[START] [2020-02-20 10:59:03] convert_to_csv
[CMD] [2020-02-20 10:59:03] /usr/bin/sort /app/public/converted_csv/wiki_lv_latvian_nodes_20227.csv > /app/public/converted_csv/wiki_lv_latvian_nodes_20227.csv_sorted
[CMD] [2020-02-20 10:59:03] /usr/bin/sort /app/public/converted_csv/wiki_lv_latvian_media_20228.csv > /app/public/converted_csv/wiki_lv_latvian_media_20228.csv_sorted
[STOP] [2020-02-20 10:59:03] convert_to_csv
[START] [2020-02-20 10:59:03] calculate_delta
[CMD] [2020-02-20 10:59:03] echo "0a" > /app/public/diff/wiki_lv_latvian_nodes_20227.diff
[CMD] [2020-02-20 10:59:03] tail -n +1 /app/public/converted_csv/wiki_lv_latvian_nodes_20227.csv >> /app/public/diff/wiki_lv_latvian_nodes_20227.diff
[CMD] [2020-02-20 10:59:03] echo "." >> /app/public/diff/wiki_lv_latvian_nodes_20227.diff
[CMD] [2020-02-20 10:59:03] echo "0a" > /app/public/diff/wiki_lv_latvian_media_20228.diff
[CMD] [2020-02-20 10:59:03] tail -n +1 /app/public/converted_csv/wiki_lv_latvian_media_20228.csv >> /app/public/diff/wiki_lv_latvian_media_20228.diff
[CMD] [2020-02-20 10:59:03] echo "." >> /app/public/diff/wiki_lv_latvian_media_20228.diff
[STOP] [2020-02-20 10:59:03] calculate_delta
[START] [2020-02-20 10:59:03] parse_diff_and_store
[INFO] [2020-02-20 10:59:03] Loading nodes diff file into memory (true lines)...
[WARN] [2020-02-20 10:59:05] Filtered Scientific Name `Ambystoma  hakié jas jas` to `Ambystoma hakié jas jas`
[INFO] [2020-02-20 10:59:06] Loading media diff file into memory (true lines)...
[INFO] [2020-02-20 10:59:45] Storing 5371 ScientificNames
[INFO] [2020-02-20 10:59:45] Processing group of 5371 in 6 groups of 1000
[INFO] [2020-02-20 10:59:47] Average Time: 0.36
[INFO] [2020-02-20 10:59:47] Total Time: 3s
[INFO] [2020-02-20 10:59:47] Storing 5371 Identifiers
[INFO] [2020-02-20 10:59:47] Processing group of 5371 in 6 groups of 1000
[INFO] [2020-02-20 10:59:48] Average Time: 0.093
[INFO] [2020-02-20 10:59:48] Total Time: 1s
[INFO] [2020-02-20 10:59:48] Storing 5371 Nodes
[INFO] [2020-02-20 10:59:48] Processing group of 5371 in 6 groups of 1000
[INFO] [2020-02-20 10:59:50] Average Time: 0.402
[INFO] [2020-02-20 10:59:50] Total Time: 3s
[INFO] [2020-02-20 10:59:50] Storing 6742 ArticlesSections
[INFO] [2020-02-20 10:59:50] Processing group of 6742 in 7 groups of 1000
[INFO] [2020-02-20 10:59:50] Average Time: 0.057
[INFO] [2020-02-20 10:59:50] Total Time: 1s
[INFO] [2020-02-20 10:59:50] last 3 / first 3: 0.79
[INFO] [2020-02-20 10:59:50] Std.Dev: 0.0; Max: 0.07
[INFO] [2020-02-20 10:59:50] Storing 6742 Articles
[INFO] [2020-02-20 10:59:50] Processing group of 6742 in 7 groups of 1000
[INFO] [2020-02-20 10:59:55] Average Time: 0.693
[INFO] [2020-02-20 10:59:55] Total Time: 5s
[INFO] [2020-02-20 10:59:55] last 3 / first 3: 0.81
[INFO] [2020-02-20 10:59:55] Std.Dev: 0.09486832980505137; Max: 0.85
[STOP] [2020-02-20 10:59:55] parse_diff_and_store
[START] [2020-02-20 10:59:55] resolve_keys
[INFO] [2020-02-20 11:00:36] Occurrences to nodes (through scientific_names)...
[INFO] [2020-02-20 11:00:36] traits to occurrences...
[INFO] [2020-02-20 11:00:36] traits to nodes (through occurrences)...
[INFO] [2020-02-20 11:00:36] Traits to sex term...
[INFO] [2020-02-20 11:00:36] Traits to lifestage term...
[INFO] [2020-02-20 11:00:36] MetaTraits to traits...
[INFO] [2020-02-20 11:00:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-02-20 11:00:36] Assocs to occurrences...
[INFO] [2020-02-20 11:00:36] Assocs to nodes...
[INFO] [2020-02-20 11:00:36] Assoc to sex term...
[INFO] [2020-02-20 11:00:36] Assoc to lifestage term...
[STOP] [2020-02-20 11:00:36] resolve_keys
[START] [2020-02-20 11:00:36] hold_for_later_1
[STOP] [2020-02-20 11:00:36] hold_for_later_1
[START] [2020-02-20 11:00:36] hold_for_later_2
[STOP] [2020-02-20 11:00:36] hold_for_later_2
[START] [2020-02-20 11:00:36] resolve_missing_parents
[STOP] [2020-02-20 11:00:38] resolve_missing_parents
[START] [2020-02-20 11:00:38] rebuild_nodes
[START] [2020-02-20 11:00:38] Flattener#flatten
[START] [2020-02-20 11:00:38] Flattener#study_resource
[START] [2020-02-20 11:00:38] Flattener#build_ancestry
[STOP] [2020-02-20 11:00:38] Flattener#build_ancestry
[INFO] [2020-02-20 11:00:38] 5371 ancestry keys
[START] [2020-02-20 11:00:38] build_node_ancestors
[INFO] [2020-02-20 11:00:38] old ancestors deleted.
[STOP] [2020-02-20 11:00:52] build_node_ancestors
[START] [2020-02-20 11:00:53] Flattener#propagate_ancestor_ids
[STOP] [2020-02-20 11:00:55] Flattener#propagate_ancestor_ids
[STOP] [2020-02-20 11:00:55] Flattener#flatten
[STOP] [2020-02-20 11:00:55] rebuild_nodes
[START] [2020-02-20 11:00:55] resolve_missing_media_owners
[STOP] [2020-02-20 11:00:55] resolve_missing_media_owners
[START] [2020-02-20 11:00:55] sanitize_media_verbatims
[STOP] [2020-02-20 11:00:55] sanitize_media_verbatims
[START] [2020-02-20 11:00:55] queue_downloads
[STOP] [2020-02-20 11:00:55] queue_downloads
[START] [2020-02-20 11:00:55] parse_names
[WARN] [2020-02-20 11:00:55] I see 5371 names which still need to be parsed.
[WARN] [2020-02-20 11:01:00] I see 9 names which still need to be parsed.
[STOP] [2020-02-20 11:01:01] parse_names
[START] [2020-02-20 11:01:01] denormalize_canonical_names_to_nodes
[STOP] [2020-02-20 11:01:01] denormalize_canonical_names_to_nodes
[START] [2020-02-20 11:01:01] match_nodes
[START] [2020-02-20 11:01:01] map_all_nodes_to_pages
[STOP] [2020-02-20 11:10:26] map_all_nodes_to_pages
[INFO] [2020-02-20 11:10:26] 943 Unmatched nodes (of 5371)! That's too many to output. First 10: Biota (#63430511); Prokaryota (#63429804); Bacteria (#63427934); Negibacteria (#63431413); Haemophilus ducreyi (#63427970); Salmonella enterica (#63430413); Escherichia coli (#63430685); Posibacteria (#63431447); Actinobacteria (#63428229); Actinobacteria (#63430819)
[START] [2020-02-20 11:10:26] update_nodes
[STOP] [2020-02-20 11:10:28] update_nodes
[STOP] [2020-02-20 11:10:28] match_nodes
[START] [2020-02-20 11:10:28] reindex_search
[STOP] [2020-02-20 11:10:42] reindex_search
[START] [2020-02-20 11:10:42] normalize_units
[STOP] [2020-02-20 11:10:42] normalize_units
[START] [2020-02-20 11:10:42] calculate_statistics
[STOP] [2020-02-20 11:10:43] calculate_statistics
[START] [2020-02-20 11:10:43] complete_harvest_instance
[START] [2020-02-20 11:10:43] overall_tsv_creation
[INFO] [2020-02-20 11:10:43] Processing group of 5371 in 1 batches of 10000
[INFO] [2020-02-20 11:11:58] Average Time: 39.94
[INFO] [2020-02-20 11:11:58] Total Time: 1m16s
[STOP] [2020-02-20 11:11:58] overall_tsv_creation
[INFO] [2020-02-20 11:11:58] Done. Check your files:
[INFO] [2020-02-20 11:11:58] (5371 lines) /app/public/data/wiki_lv_latvian/publish_nodes.tsv
[INFO] [2020-02-20 11:11:58] (5371 lines) /app/public/data/wiki_lv_latvian/publish_identifiers.tsv
[INFO] [2020-02-20 11:11:58] (103257 lines) /app/public/data/wiki_lv_latvian/publish_node_ancestors.tsv
[INFO] [2020-02-20 11:11:58] (5371 lines) /app/public/data/wiki_lv_latvian/publish_scientific_names.tsv
[INFO] [2020-02-20 11:11:58] (127835 lines) /app/public/data/wiki_lv_latvian/publish_articles.tsv
[INFO] [2020-02-20 11:11:58] (6742 lines) /app/public/data/wiki_lv_latvian/publish_content_sections.tsv
[STOP] [2020-02-20 11:11:58] complete_harvest_instance
[START] [2020-02-20 11:11:58] completed
[STOP] [2020-02-20 11:11:58] completed
[STOP] [2020-02-20 11:11:58] logged process, took 777.62
Latest Process

20 Feb 10:59 EXITED currently processing 0