Harvest for Armchair Taxonomists Created 09 Apr 08:39

Stage: completed
Fetched: 09 Apr 08:39
Validated: 09 Apr 08:39
Deltas Created 09 Apr 08:39
Units Normalized: 09 Apr 08:40
Ancestry Built: 09 Apr 08:40
Nodes Matched: 09 Apr 08:40
Names Parsed: 09 Apr 08:40
New Models Stored: 09 Apr 08:39
Indexed: 09 Apr 08:40
Completed: 09 Apr 08:41
Time to Harvest: less than a minute
Harvesting Log

(141 lines)
# Logfile created on 2020-04-09 08:39:34 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-09 08:39:34] ## HARVEST: type = -harvest
[START] [2020-04-09 08:39:37] logged process
[START] [2020-04-09 08:39:37] create_harvest_instance
[STOP] [2020-04-09 08:39:42] create_harvest_instance
[START] [2020-04-09 08:39:42] fetch_files
[STOP] [2020-04-09 08:39:42] fetch_files
[START] [2020-04-09 08:39:42] validate_each_file
[STOP] [2020-04-09 08:39:42] validate_each_file
[START] [2020-04-09 08:39:42] convert_to_csv
[CMD] [2020-04-09 08:39:42] /usr/bin/sort /app/public/converted_csv/armchair_taxonom_agents_20694.csv > /app/public/converted_csv/armchair_taxonom_agents_20694.csv_sorted
[CMD] [2020-04-09 08:39:42] /usr/bin/sort /app/public/converted_csv/armchair_taxonom_refs_20695.csv > /app/public/converted_csv/armchair_taxonom_refs_20695.csv_sorted
[CMD] [2020-04-09 08:39:42] /usr/bin/sort /app/public/converted_csv/armchair_taxonom_nodes_20696.csv > /app/public/converted_csv/armchair_taxonom_nodes_20696.csv_sorted
[CMD] [2020-04-09 08:39:42] /usr/bin/sort /app/public/converted_csv/armchair_taxonom_media_20697.csv > /app/public/converted_csv/armchair_taxonom_media_20697.csv_sorted
[CMD] [2020-04-09 08:39:42] /usr/bin/sort /app/public/converted_csv/armchair_taxonom_vernaculars_20698.csv > /app/public/converted_csv/armchair_taxonom_vernaculars_20698.csv_sorted
[STOP] [2020-04-09 08:39:42] convert_to_csv
[START] [2020-04-09 08:39:42] calculate_delta
[CMD] [2020-04-09 08:39:42] echo "0a" > /app/public/diff/armchair_taxonom_agents_20694.diff
[CMD] [2020-04-09 08:39:42] tail -n +1 /app/public/converted_csv/armchair_taxonom_agents_20694.csv >> /app/public/diff/armchair_taxonom_agents_20694.diff
[CMD] [2020-04-09 08:39:42] echo "." >> /app/public/diff/armchair_taxonom_agents_20694.diff
[CMD] [2020-04-09 08:39:42] echo "0a" > /app/public/diff/armchair_taxonom_refs_20695.diff
[CMD] [2020-04-09 08:39:42] tail -n +1 /app/public/converted_csv/armchair_taxonom_refs_20695.csv >> /app/public/diff/armchair_taxonom_refs_20695.diff
[CMD] [2020-04-09 08:39:42] echo "." >> /app/public/diff/armchair_taxonom_refs_20695.diff
[CMD] [2020-04-09 08:39:42] echo "0a" > /app/public/diff/armchair_taxonom_nodes_20696.diff
[CMD] [2020-04-09 08:39:42] tail -n +1 /app/public/converted_csv/armchair_taxonom_nodes_20696.csv >> /app/public/diff/armchair_taxonom_nodes_20696.diff
[CMD] [2020-04-09 08:39:43] echo "." >> /app/public/diff/armchair_taxonom_nodes_20696.diff
[CMD] [2020-04-09 08:39:43] echo "0a" > /app/public/diff/armchair_taxonom_media_20697.diff
[CMD] [2020-04-09 08:39:43] tail -n +1 /app/public/converted_csv/armchair_taxonom_media_20697.csv >> /app/public/diff/armchair_taxonom_media_20697.diff
[CMD] [2020-04-09 08:39:43] echo "." >> /app/public/diff/armchair_taxonom_media_20697.diff
[CMD] [2020-04-09 08:39:43] echo "0a" > /app/public/diff/armchair_taxonom_vernaculars_20698.diff
[CMD] [2020-04-09 08:39:43] tail -n +1 /app/public/converted_csv/armchair_taxonom_vernaculars_20698.csv >> /app/public/diff/armchair_taxonom_vernaculars_20698.diff
[CMD] [2020-04-09 08:39:43] echo "." >> /app/public/diff/armchair_taxonom_vernaculars_20698.diff
[STOP] [2020-04-09 08:39:43] calculate_delta
[START] [2020-04-09 08:39:43] parse_diff_and_store
[INFO] [2020-04-09 08:39:43] Loading agents diff file into memory (true lines)...
[INFO] [2020-04-09 08:39:43] Loading refs diff file into memory (true lines)...
[INFO] [2020-04-09 08:39:43] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-09 08:39:43] Loading media diff file into memory (true lines)...
[INFO] [2020-04-09 08:39:43] Loading vernaculars diff file into memory (true lines)...
[INFO] [2020-04-09 08:39:43] Storing 2 Attributions
[INFO] [2020-04-09 08:39:43] Processing group of 2 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.0
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[INFO] [2020-04-09 08:39:43] Storing 75 References
[INFO] [2020-04-09 08:39:43] Processing group of 75 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.02
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[INFO] [2020-04-09 08:39:43] Storing 12 ScientificNames
[INFO] [2020-04-09 08:39:43] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.01
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[INFO] [2020-04-09 08:39:43] Storing 12 Nodes
[INFO] [2020-04-09 08:39:43] Processing group of 12 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.01
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[INFO] [2020-04-09 08:39:43] Storing 15 ContentAttributions
[INFO] [2020-04-09 08:39:43] Processing group of 15 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.0
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[INFO] [2020-04-09 08:39:43] Storing 9 ArticlesSections
[INFO] [2020-04-09 08:39:43] Processing group of 9 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.01
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[INFO] [2020-04-09 08:39:43] Storing 9 Articles
[INFO] [2020-04-09 08:39:43] Processing group of 9 in 1 groups of 1000
[INFO] [2020-04-09 08:39:43] Average Time: 0.01
[INFO] [2020-04-09 08:39:43] Total Time: 1s
[STOP] [2020-04-09 08:39:43] parse_diff_and_store
[START] [2020-04-09 08:39:43] resolve_keys
[INFO] [2020-04-09 08:40:44] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-09 08:40:44] traits to occurrences...
[INFO] [2020-04-09 08:40:44] traits to nodes (through occurrences)...
[INFO] [2020-04-09 08:40:44] Traits to sex term...
[INFO] [2020-04-09 08:40:44] Traits to lifestage term...
[INFO] [2020-04-09 08:40:44] MetaTraits to traits...
[INFO] [2020-04-09 08:40:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-09 08:40:44] Assocs to occurrences...
[INFO] [2020-04-09 08:40:44] Assocs to nodes...
[INFO] [2020-04-09 08:40:44] Assoc to sex term...
[INFO] [2020-04-09 08:40:44] Assoc to lifestage term...
[STOP] [2020-04-09 08:40:44] resolve_keys
[START] [2020-04-09 08:40:44] hold_for_later_1
[STOP] [2020-04-09 08:40:44] hold_for_later_1
[START] [2020-04-09 08:40:44] hold_for_later_2
[STOP] [2020-04-09 08:40:44] hold_for_later_2
[START] [2020-04-09 08:40:44] resolve_missing_parents
[STOP] [2020-04-09 08:40:44] resolve_missing_parents
[START] [2020-04-09 08:40:44] rebuild_nodes
[START] [2020-04-09 08:40:44] Flattener#flatten
[START] [2020-04-09 08:40:44] Flattener#study_resource
[START] [2020-04-09 08:40:44] Flattener#build_ancestry
[STOP] [2020-04-09 08:40:44] Flattener#build_ancestry
[INFO] [2020-04-09 08:40:44] 12 ancestry keys
[START] [2020-04-09 08:40:44] build_node_ancestors
[INFO] [2020-04-09 08:40:44] old ancestors deleted.
[STOP] [2020-04-09 08:40:44] build_node_ancestors
[START] [2020-04-09 08:40:44] Flattener#propagate_ancestor_ids
[STOP] [2020-04-09 08:40:44] Flattener#propagate_ancestor_ids
[STOP] [2020-04-09 08:40:44] Flattener#flatten
[STOP] [2020-04-09 08:40:44] rebuild_nodes
[START] [2020-04-09 08:40:44] resolve_missing_media_owners
[STOP] [2020-04-09 08:40:44] resolve_missing_media_owners
[START] [2020-04-09 08:40:44] sanitize_media_verbatims
[STOP] [2020-04-09 08:40:44] sanitize_media_verbatims
[START] [2020-04-09 08:40:44] queue_downloads
[STOP] [2020-04-09 08:40:44] queue_downloads
[START] [2020-04-09 08:40:44] parse_names
[WARN] [2020-04-09 08:40:44] I see 12 names which still need to be parsed.
[STOP] [2020-04-09 08:40:45] parse_names
[START] [2020-04-09 08:40:45] denormalize_canonical_names_to_nodes
[STOP] [2020-04-09 08:40:45] denormalize_canonical_names_to_nodes
[START] [2020-04-09 08:40:45] match_nodes
[START] [2020-04-09 08:40:45] map_all_nodes_to_pages
[STOP] [2020-04-09 08:40:46] map_all_nodes_to_pages
[INFO] [2020-04-09 08:40:46] Unmatched nodes (2 of 12): Tenrecinae (#68219754); Bacteria (#68219752)
[START] [2020-04-09 08:40:46] update_nodes
[STOP] [2020-04-09 08:40:46] update_nodes
[STOP] [2020-04-09 08:40:46] match_nodes
[START] [2020-04-09 08:40:46] reindex_search
[STOP] [2020-04-09 08:40:46] reindex_search
[START] [2020-04-09 08:40:46] normalize_units
[STOP] [2020-04-09 08:40:46] normalize_units
[START] [2020-04-09 08:40:46] calculate_statistics
[STOP] [2020-04-09 08:40:46] calculate_statistics
[START] [2020-04-09 08:40:46] complete_harvest_instance
[START] [2020-04-09 08:40:46] overall_tsv_creation
[INFO] [2020-04-09 08:40:46] Processing group of 12 in 1 batches of 10000
[INFO] [2020-04-09 08:41:35] Average Time: 11.37
[INFO] [2020-04-09 08:41:35] Total Time: 50s
[STOP] [2020-04-09 08:41:35] overall_tsv_creation
[INFO] [2020-04-09 08:41:35] Done. Check your files:
[INFO] [2020-04-09 08:41:35] (12 lines) /app/public/data/armchair_taxonom/publish_nodes.tsv
[INFO] [2020-04-09 08:41:35] (9 lines) /app/public/data/armchair_taxonom/publish_node_ancestors.tsv
[INFO] [2020-04-09 08:41:35] (12 lines) /app/public/data/armchair_taxonom/publish_scientific_names.tsv
[INFO] [2020-04-09 08:41:35] (9 lines) /app/public/data/armchair_taxonom/publish_articles.tsv
[INFO] [2020-04-09 08:41:35] (15 lines) /app/public/data/armchair_taxonom/publish_attributions.tsv
[INFO] [2020-04-09 08:41:35] (9 lines) /app/public/data/armchair_taxonom/publish_content_sections.tsv
[STOP] [2020-04-09 08:41:35] complete_harvest_instance
[START] [2020-04-09 08:41:35] completed
[STOP] [2020-04-09 08:41:35] completed
[STOP] [2020-04-09 08:41:35] logged process, took 118.24
Latest Process

09 Apr 08:39 EXITED currently processing 0