Harvest for Taiwan Encyclopedia of Life Created 31 Dec 10:00

Stage: completed
Fetched: 31 Dec 10:00
Validated: 31 Dec 10:00
Deltas Created 31 Dec 10:00
Units Normalized: 31 Dec 10:04
Ancestry Built: 31 Dec 10:01
Nodes Matched: 31 Dec 10:04
Names Parsed: 31 Dec 10:01
New Models Stored: 31 Dec 10:01
Indexed: 31 Dec 10:04
Completed: 31 Dec 10:05
Time to Harvest: less than a minute
Harvesting Log

(138 lines)
# Logfile created on 2019-12-31 10:00:38 -0500 by logger.rb/56815
[START] [2019-12-31 10:00:38] logged process
[START] [2019-12-31 10:00:38] create_harvest_instance
[STOP] [2019-12-31 10:00:38] create_harvest_instance
[START] [2019-12-31 10:00:38] fetch_files
[STOP] [2019-12-31 10:00:38] fetch_files
[START] [2019-12-31 10:00:38] validate_each_file
[STOP] [2019-12-31 10:00:39] validate_each_file
[START] [2019-12-31 10:00:39] convert_to_csv
[CMD] [2019-12-31 10:00:39] /usr/bin/sort /app/public/converted_csv/teldt_agents_19797.csv > /app/public/converted_csv/teldt_agents_19797.csv_sorted
[CMD] [2019-12-31 10:00:39] /usr/bin/sort /app/public/converted_csv/teldt_nodes_19798.csv > /app/public/converted_csv/teldt_nodes_19798.csv_sorted
[CMD] [2019-12-31 10:00:40] /usr/bin/sort /app/public/converted_csv/teldt_media_19799.csv > /app/public/converted_csv/teldt_media_19799.csv_sorted
[CMD] [2019-12-31 10:00:41] /usr/bin/sort /app/public/converted_csv/teldt_vernaculars_19800.csv > /app/public/converted_csv/teldt_vernaculars_19800.csv_sorted
[STOP] [2019-12-31 10:00:41] convert_to_csv
[START] [2019-12-31 10:00:41] calculate_delta
[CMD] [2019-12-31 10:00:41] echo "0a" > /app/public/diff/teldt_agents_19797.diff
[CMD] [2019-12-31 10:00:42] tail -n +1 /app/public/converted_csv/teldt_agents_19797.csv >> /app/public/diff/teldt_agents_19797.diff
[CMD] [2019-12-31 10:00:43] echo "." >> /app/public/diff/teldt_agents_19797.diff
[CMD] [2019-12-31 10:00:43] echo "0a" > /app/public/diff/teldt_nodes_19798.diff
[CMD] [2019-12-31 10:00:44] tail -n +1 /app/public/converted_csv/teldt_nodes_19798.csv >> /app/public/diff/teldt_nodes_19798.diff
[CMD] [2019-12-31 10:00:44] echo "." >> /app/public/diff/teldt_nodes_19798.diff
[CMD] [2019-12-31 10:00:45] echo "0a" > /app/public/diff/teldt_media_19799.diff
[CMD] [2019-12-31 10:00:46] tail -n +1 /app/public/converted_csv/teldt_media_19799.csv >> /app/public/diff/teldt_media_19799.diff
[CMD] [2019-12-31 10:00:46] echo "." >> /app/public/diff/teldt_media_19799.diff
[CMD] [2019-12-31 10:00:47] echo "0a" > /app/public/diff/teldt_vernaculars_19800.diff
[CMD] [2019-12-31 10:00:48] tail -n +1 /app/public/converted_csv/teldt_vernaculars_19800.csv >> /app/public/diff/teldt_vernaculars_19800.diff
[CMD] [2019-12-31 10:00:48] echo "." >> /app/public/diff/teldt_vernaculars_19800.diff
[STOP] [2019-12-31 10:00:49] calculate_delta
[START] [2019-12-31 10:00:49] parse_diff_and_store
[INFO] [2019-12-31 10:00:49] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-31 10:00:50] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-31 10:00:51] Loading media diff file into memory (true lines)...
[INFO] [2019-12-31 10:00:59] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-12-31 10:00:59] Storing 10 Attributions
[INFO] [2019-12-31 10:00:59] Processing group of 10 in 1 groups of 1000
[INFO] [2019-12-31 10:00:59] Average Time: 0.0
[INFO] [2019-12-31 10:00:59] Total Time: 1s
[INFO] [2019-12-31 10:00:59] Storing 1353 ScientificNames
[INFO] [2019-12-31 10:00:59] Processing group of 1353 in 2 groups of 1000
[INFO] [2019-12-31 10:01:00] Average Time: 0.265
[INFO] [2019-12-31 10:01:00] Total Time: 1s
[INFO] [2019-12-31 10:01:00] Storing 1353 Nodes
[INFO] [2019-12-31 10:01:00] Processing group of 1353 in 2 groups of 1000
[INFO] [2019-12-31 10:01:00] Average Time: 0.23
[INFO] [2019-12-31 10:01:00] Total Time: 1s
[INFO] [2019-12-31 10:01:00] Storing 6818 ContentAttributions
[INFO] [2019-12-31 10:01:00] Processing group of 6818 in 7 groups of 1000
[INFO] [2019-12-31 10:01:01] Average Time: 0.129
[INFO] [2019-12-31 10:01:01] Total Time: 1s
[INFO] [2019-12-31 10:01:01] last 3 / first 3: 0.62
[INFO] [2019-12-31 10:01:01] Std.Dev: 0.044721359549995794; Max: 0.2
[INFO] [2019-12-31 10:01:01] Storing 3409 ArticlesSections
[INFO] [2019-12-31 10:01:01] Processing group of 3409 in 4 groups of 1000
[INFO] [2019-12-31 10:01:01] Average Time: 0.047
[INFO] [2019-12-31 10:01:01] Total Time: 1s
[INFO] [2019-12-31 10:01:01] Storing 3409 Articles
[INFO] [2019-12-31 10:01:01] Processing group of 3409 in 4 groups of 1000
[INFO] [2019-12-31 10:01:02] Average Time: 0.248
[INFO] [2019-12-31 10:01:02] Total Time: 2s
[INFO] [2019-12-31 10:01:02] Storing 807 Vernaculars
[INFO] [2019-12-31 10:01:02] Processing group of 807 in 1 groups of 1000
[INFO] [2019-12-31 10:01:03] Average Time: 0.16
[INFO] [2019-12-31 10:01:03] Total Time: 1s
[STOP] [2019-12-31 10:01:03] parse_diff_and_store
[START] [2019-12-31 10:01:03] resolve_keys
[INFO] [2019-12-31 10:01:13] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-31 10:01:13] traits to occurrences...
[INFO] [2019-12-31 10:01:13] traits to nodes (through occurrences)...
[INFO] [2019-12-31 10:01:13] Traits to sex term...
[INFO] [2019-12-31 10:01:13] Traits to lifestage term...
[INFO] [2019-12-31 10:01:13] MetaTraits to traits...
[INFO] [2019-12-31 10:01:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-31 10:01:13] Assocs to occurrences...
[INFO] [2019-12-31 10:01:13] Assocs to nodes...
[INFO] [2019-12-31 10:01:13] Assoc to sex term...
[INFO] [2019-12-31 10:01:13] Assoc to lifestage term...
[STOP] [2019-12-31 10:01:13] resolve_keys
[START] [2019-12-31 10:01:13] hold_for_later_1
[STOP] [2019-12-31 10:01:13] hold_for_later_1
[START] [2019-12-31 10:01:13] hold_for_later_2
[STOP] [2019-12-31 10:01:13] hold_for_later_2
[START] [2019-12-31 10:01:13] resolve_missing_parents
[STOP] [2019-12-31 10:01:13] resolve_missing_parents
[START] [2019-12-31 10:01:13] rebuild_nodes
[START] [2019-12-31 10:01:13] Flattener#flatten
[START] [2019-12-31 10:01:13] Flattener#study_resource
[START] [2019-12-31 10:01:13] Flattener#build_ancestry
[STOP] [2019-12-31 10:01:13] Flattener#build_ancestry
[INFO] [2019-12-31 10:01:13] 1353 ancestry keys
[START] [2019-12-31 10:01:13] build_node_ancestors
[INFO] [2019-12-31 10:01:13] old ancestors deleted.
[STOP] [2019-12-31 10:01:13] build_node_ancestors
[START] [2019-12-31 10:01:14] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:01:14] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:01:14] Flattener#flatten
[STOP] [2019-12-31 10:01:14] rebuild_nodes
[START] [2019-12-31 10:01:14] resolve_missing_media_owners
[STOP] [2019-12-31 10:01:14] resolve_missing_media_owners
[START] [2019-12-31 10:01:14] sanitize_media_verbatims
[STOP] [2019-12-31 10:01:14] sanitize_media_verbatims
[START] [2019-12-31 10:01:14] queue_downloads
[STOP] [2019-12-31 10:01:14] queue_downloads
[START] [2019-12-31 10:01:14] parse_names
[WARN] [2019-12-31 10:01:14] I see 1353 names which still need to be parsed.
[STOP] [2019-12-31 10:01:16] parse_names
[START] [2019-12-31 10:01:16] denormalize_canonical_names_to_nodes
[STOP] [2019-12-31 10:01:16] denormalize_canonical_names_to_nodes
[START] [2019-12-31 10:01:16] match_nodes
[START] [2019-12-31 10:01:16] map_all_nodes_to_pages
[STOP] [2019-12-31 10:04:05] map_all_nodes_to_pages
[INFO] [2019-12-31 10:04:05] 186 Unmatched nodes (of 1353)! That's too many to output. First 10: Cucujus mniszechi (#62740266); Dinoplatypus flectus (#62741165); Dicranopselaphus nantai (#62740276); Ectopria hsui (#62740277); Eubrianax niger (#62740280); Homoeogenus laurae (#62740284); Mataeopsephus esakii (#62740287); Mataeopsephus taiwanicus (#62740288); Arthromacra minuta (#62740296); Crypsis gebieni (#62740314)
[START] [2019-12-31 10:04:05] update_nodes
[STOP] [2019-12-31 10:04:05] update_nodes
[STOP] [2019-12-31 10:04:05] match_nodes
[START] [2019-12-31 10:04:05] reindex_search
[STOP] [2019-12-31 10:04:08] reindex_search
[START] [2019-12-31 10:04:08] normalize_units
[STOP] [2019-12-31 10:04:08] normalize_units
[START] [2019-12-31 10:04:08] calculate_statistics
[STOP] [2019-12-31 10:04:08] calculate_statistics
[START] [2019-12-31 10:04:08] complete_harvest_instance
[START] [2019-12-31 10:04:08] overall_tsv_creation
[INFO] [2019-12-31 10:04:08] Processing group of 1353 in 1 batches of 10000
[INFO] [2019-12-31 10:05:15] Average Time: 20.24
[INFO] [2019-12-31 10:05:15] Total Time: 1m7s
[STOP] [2019-12-31 10:05:15] overall_tsv_creation
[INFO] [2019-12-31 10:05:15] Done. Check your files:
[INFO] [2019-12-31 10:05:15] (1353 lines) /app/public/data/teldt/publish_nodes.tsv
[INFO] [2019-12-31 10:05:16] (3990 lines) /app/public/data/teldt/publish_node_ancestors.tsv
[INFO] [2019-12-31 10:05:16] (1353 lines) /app/public/data/teldt/publish_scientific_names.tsv
[INFO] [2019-12-31 10:05:17] (3409 lines) /app/public/data/teldt/publish_articles.tsv
[INFO] [2019-12-31 10:05:18] (807 lines) /app/public/data/teldt/publish_vernaculars.tsv
[INFO] [2019-12-31 10:05:18] (6818 lines) /app/public/data/teldt/publish_attributions.tsv
[INFO] [2019-12-31 10:05:19] (3409 lines) /app/public/data/teldt/publish_content_sections.tsv
[STOP] [2019-12-31 10:05:19] complete_harvest_instance
[START] [2019-12-31 10:05:19] completed
[STOP] [2019-12-31 10:05:19] completed
[STOP] [2019-12-31 10:05:19] logged process, took 281.27
Latest Process

31 Dec 10:00 EXITED currently processing 0