Harvest for Phytokeys Created 05 Jul 20:41

Stage: completed
Fetched: 05 Jul 20:41
Validated: 05 Jul 20:41
Deltas Created 05 Jul 20:41
Units Normalized: 05 Jul 20:42
Ancestry Built: 05 Jul 20:41
Nodes Matched: 05 Jul 20:42
Names Parsed: 05 Jul 20:41
New Models Stored: 05 Jul 20:41
Indexed: 05 Jul 20:42
Completed: 05 Jul 20:43
Time to Harvest: less than a minute
Harvesting Log

(152 lines)
# Logfile created on 2019-07-05 20:41:33 -0400 by logger.rb/56815
[START] [2019-07-05 20:41:33] logged process
[START] [2019-07-05 20:41:33] create_harvest_instance
[STOP] [2019-07-05 20:41:34] create_harvest_instance
[START] [2019-07-05 20:41:34] fetch_files
[STOP] [2019-07-05 20:41:34] fetch_files
[START] [2019-07-05 20:41:34] validate_each_file
[STOP] [2019-07-05 20:41:35] validate_each_file
[START] [2019-07-05 20:41:35] convert_to_csv
[CMD] [2019-07-05 20:41:35] /usr/bin/sort /app/public/converted_csv/phytokeys_agents_14084.csv > /app/public/converted_csv/phytokeys_agents_14084.csv_sorted
[CMD] [2019-07-05 20:41:35] /usr/bin/sort /app/public/converted_csv/phytokeys_refs_14085.csv > /app/public/converted_csv/phytokeys_refs_14085.csv_sorted
[CMD] [2019-07-05 20:41:35] /usr/bin/sort /app/public/converted_csv/phytokeys_nodes_14086.csv > /app/public/converted_csv/phytokeys_nodes_14086.csv_sorted
[CMD] [2019-07-05 20:41:35] /usr/bin/sort /app/public/converted_csv/phytokeys_media_14087.csv > /app/public/converted_csv/phytokeys_media_14087.csv_sorted
[STOP] [2019-07-05 20:41:35] convert_to_csv
[START] [2019-07-05 20:41:35] calculate_delta
[CMD] [2019-07-05 20:41:35] echo "0a" > /app/public/diff/phytokeys_agents_14084.diff
[CMD] [2019-07-05 20:41:35] tail -n +1 /app/public/converted_csv/phytokeys_agents_14084.csv >> /app/public/diff/phytokeys_agents_14084.diff
[CMD] [2019-07-05 20:41:35] echo "." >> /app/public/diff/phytokeys_agents_14084.diff
[CMD] [2019-07-05 20:41:35] echo "0a" > /app/public/diff/phytokeys_refs_14085.diff
[CMD] [2019-07-05 20:41:35] tail -n +1 /app/public/converted_csv/phytokeys_refs_14085.csv >> /app/public/diff/phytokeys_refs_14085.diff
[CMD] [2019-07-05 20:41:35] echo "." >> /app/public/diff/phytokeys_refs_14085.diff
[CMD] [2019-07-05 20:41:35] echo "0a" > /app/public/diff/phytokeys_nodes_14086.diff
[CMD] [2019-07-05 20:41:35] tail -n +1 /app/public/converted_csv/phytokeys_nodes_14086.csv >> /app/public/diff/phytokeys_nodes_14086.diff
[CMD] [2019-07-05 20:41:35] echo "." >> /app/public/diff/phytokeys_nodes_14086.diff
[CMD] [2019-07-05 20:41:35] echo "0a" > /app/public/diff/phytokeys_media_14087.diff
[CMD] [2019-07-05 20:41:35] tail -n +1 /app/public/converted_csv/phytokeys_media_14087.csv >> /app/public/diff/phytokeys_media_14087.diff
[CMD] [2019-07-05 20:41:35] echo "." >> /app/public/diff/phytokeys_media_14087.diff
[STOP] [2019-07-05 20:41:35] calculate_delta
[START] [2019-07-05 20:41:35] parse_diff_and_store
[INFO] [2019-07-05 20:41:35] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-05 20:41:35] Loading refs diff file into memory (true lines)...
[INFO] [2019-07-05 20:41:35] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-05 20:41:36] Loading media diff file into memory (true lines)...
[INFO] [2019-07-05 20:41:37] Storing 171 Attributions
[INFO] [2019-07-05 20:41:37] Processing group of 171 in 1 groups of 1000
[INFO] [2019-07-05 20:41:38] Average Time: 0.06
[INFO] [2019-07-05 20:41:38] Total Time: 1s
[INFO] [2019-07-05 20:41:38] Storing 66 References
[INFO] [2019-07-05 20:41:38] Processing group of 66 in 1 groups of 1000
[INFO] [2019-07-05 20:41:38] Average Time: 0.01
[INFO] [2019-07-05 20:41:38] Total Time: 1s
[INFO] [2019-07-05 20:41:38] Storing 425 ScientificNames
[INFO] [2019-07-05 20:41:38] Processing group of 425 in 1 groups of 1000
[INFO] [2019-07-05 20:41:38] Average Time: 0.25
[INFO] [2019-07-05 20:41:38] Total Time: 1s
[INFO] [2019-07-05 20:41:38] Storing 425 Nodes
[INFO] [2019-07-05 20:41:38] Processing group of 425 in 1 groups of 1000
[INFO] [2019-07-05 20:41:38] Average Time: 0.14
[INFO] [2019-07-05 20:41:38] Total Time: 1s
[INFO] [2019-07-05 20:41:38] Storing 383 NodesReferences
[INFO] [2019-07-05 20:41:38] Processing group of 383 in 1 groups of 1000
[INFO] [2019-07-05 20:41:38] Average Time: 0.15
[INFO] [2019-07-05 20:41:38] Total Time: 1s
[INFO] [2019-07-05 20:41:38] Storing 1186 BibliographicCitations
[INFO] [2019-07-05 20:41:38] Processing group of 1186 in 2 groups of 1000
[INFO] [2019-07-05 20:41:38] Average Time: 0.125
[INFO] [2019-07-05 20:41:38] Total Time: 1s
[INFO] [2019-07-05 20:41:38] Storing 1641 ContentAttributions
[INFO] [2019-07-05 20:41:38] Processing group of 1641 in 2 groups of 1000
[INFO] [2019-07-05 20:41:39] Average Time: 0.175
[INFO] [2019-07-05 20:41:39] Total Time: 1s
[INFO] [2019-07-05 20:41:39] Storing 527 ArticlesSections
[INFO] [2019-07-05 20:41:39] Processing group of 527 in 1 groups of 1000
[INFO] [2019-07-05 20:41:39] Average Time: 0.05
[INFO] [2019-07-05 20:41:39] Total Time: 1s
[INFO] [2019-07-05 20:41:39] Storing 527 Articles
[INFO] [2019-07-05 20:41:39] Processing group of 527 in 1 groups of 1000
[INFO] [2019-07-05 20:41:39] Average Time: 0.23
[INFO] [2019-07-05 20:41:39] Total Time: 1s
[INFO] [2019-07-05 20:41:39] Storing 659 Media
[INFO] [2019-07-05 20:41:39] Processing group of 659 in 1 groups of 1000
[INFO] [2019-07-05 20:41:39] Average Time: 0.35
[INFO] [2019-07-05 20:41:39] Total Time: 1s
[STOP] [2019-07-05 20:41:39] parse_diff_and_store
[START] [2019-07-05 20:41:39] resolve_keys
[INFO] [2019-07-05 20:41:48] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-05 20:41:48] traits to occurrences...
[INFO] [2019-07-05 20:41:48] traits to nodes (through occurrences)...
[INFO] [2019-07-05 20:41:48] Traits to sex term...
[INFO] [2019-07-05 20:41:48] Traits to lifestage term...
[INFO] [2019-07-05 20:41:48] MetaTraits to traits...
[INFO] [2019-07-05 20:41:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-05 20:41:48] Assocs to occurrences...
[INFO] [2019-07-05 20:41:48] Assocs to nodes...
[INFO] [2019-07-05 20:41:48] Assoc to sex term...
[INFO] [2019-07-05 20:41:48] Assoc to lifestage term...
[STOP] [2019-07-05 20:41:48] resolve_keys
[START] [2019-07-05 20:41:48] hold_for_later_1
[STOP] [2019-07-05 20:41:48] hold_for_later_1
[START] [2019-07-05 20:41:48] hold_for_later_2
[STOP] [2019-07-05 20:41:48] hold_for_later_2
[START] [2019-07-05 20:41:48] resolve_missing_parents
[STOP] [2019-07-05 20:41:48] resolve_missing_parents
[START] [2019-07-05 20:41:48] rebuild_nodes
[START] [2019-07-05 20:41:48] Flattener#flatten
[START] [2019-07-05 20:41:48] Flattener#study_resource
[START] [2019-07-05 20:41:48] Flattener#build_ancestry
[STOP] [2019-07-05 20:41:48] Flattener#build_ancestry
[INFO] [2019-07-05 20:41:48] 425 ancestry keys
[START] [2019-07-05 20:41:48] build_node_ancestors
[INFO] [2019-07-05 20:41:48] old ancestors deleted.
[STOP] [2019-07-05 20:41:49] build_node_ancestors
[START] [2019-07-05 20:41:49] Flattener#propagate_ancestor_ids
[STOP] [2019-07-05 20:41:49] Flattener#propagate_ancestor_ids
[STOP] [2019-07-05 20:41:49] Flattener#flatten
[STOP] [2019-07-05 20:41:49] rebuild_nodes
[START] [2019-07-05 20:41:49] resolve_missing_media_owners
[STOP] [2019-07-05 20:41:49] resolve_missing_media_owners
[START] [2019-07-05 20:41:49] sanitize_media_verbatims
[STOP] [2019-07-05 20:41:49] sanitize_media_verbatims
[START] [2019-07-05 20:41:49] queue_downloads
[STOP] [2019-07-05 20:41:49] queue_downloads
[START] [2019-07-05 20:41:49] parse_names
[WARN] [2019-07-05 20:41:49] I see 425 names which still need to be parsed.
[STOP] [2019-07-05 20:41:50] parse_names
[START] [2019-07-05 20:41:50] denormalize_canonical_names_to_nodes
[STOP] [2019-07-05 20:41:50] denormalize_canonical_names_to_nodes
[START] [2019-07-05 20:41:50] match_nodes
[START] [2019-07-05 20:41:50] map_all_nodes_to_pages
[STOP] [2019-07-05 20:42:11] map_all_nodes_to_pages
[INFO] [2019-07-05 20:42:11] 88 Unmatched nodes (of 425)! That's too many to output. First 10: Begonia yenyeniae (#44063690); Acropogon horarius (#44063693); Eriolaena rulkensii (#44063705); Hedychium viridibracteatum (#44063695); Hedychium ziroense (#44063884); Haplophyllum ermenekense (#44063697); Raphia gabonica (#44063699); Raphia zamiana (#44063700); Chrysosplenium ramosissimum (#44063702); Solanum kollastrum (#44063704)
[START] [2019-07-05 20:42:11] update_nodes
[STOP] [2019-07-05 20:42:11] update_nodes
[STOP] [2019-07-05 20:42:11] match_nodes
[START] [2019-07-05 20:42:11] reindex_search
[STOP] [2019-07-05 20:42:13] reindex_search
[START] [2019-07-05 20:42:13] normalize_units
[STOP] [2019-07-05 20:42:13] normalize_units
[START] [2019-07-05 20:42:13] calculate_statistics
[STOP] [2019-07-05 20:42:13] calculate_statistics
[START] [2019-07-05 20:42:13] complete_harvest_instance
[START] [2019-07-05 20:42:13] overall_tsv_creation
[INFO] [2019-07-05 20:42:13] Processing group of 425 in 1 batches of 10000
[INFO] [2019-07-05 20:43:09] Average Time: 16.92
[INFO] [2019-07-05 20:43:09] Total Time: 57s
[STOP] [2019-07-05 20:43:09] overall_tsv_creation
[INFO] [2019-07-05 20:43:09] Done. Check your files:
[INFO] [2019-07-05 20:43:09] (1186 lines) /app/public/data/phytokeys/publish_bibliographic_citations.tsv
[INFO] [2019-07-05 20:43:09] (425 lines) /app/public/data/phytokeys/publish_nodes.tsv
[INFO] [2019-07-05 20:43:09] (806 lines) /app/public/data/phytokeys/publish_node_ancestors.tsv
[INFO] [2019-07-05 20:43:09] (425 lines) /app/public/data/phytokeys/publish_scientific_names.tsv
[INFO] [2019-07-05 20:43:09] (659 lines) /app/public/data/phytokeys/publish_media.tsv
[INFO] [2019-07-05 20:43:09] (527 lines) /app/public/data/phytokeys/publish_articles.tsv
[INFO] [2019-07-05 20:43:09] (196 lines) /app/public/data/phytokeys/publish_image_info.tsv
[INFO] [2019-07-05 20:43:09] (66 lines) /app/public/data/phytokeys/publish_references.tsv
[INFO] [2019-07-05 20:43:09] (1641 lines) /app/public/data/phytokeys/publish_attributions.tsv
[INFO] [2019-07-05 20:43:09] (527 lines) /app/public/data/phytokeys/publish_content_sections.tsv
[INFO] [2019-07-05 20:43:09] (66 lines) /app/public/data/phytokeys/publish_referents.tsv
[STOP] [2019-07-05 20:43:09] complete_harvest_instance
[START] [2019-07-05 20:43:09] completed
[STOP] [2019-07-05 20:43:09] completed
[STOP] [2019-07-05 20:43:09] logged process, took 96.18
Latest Process

05 Jul 20:41 EXITED currently processing 0