Harvest for Moldova Species List Created 14 Oct 08:56

Stage: completed
Fetched: 14 Oct 08:56
Validated: 14 Oct 08:56
Deltas Created 14 Oct 08:56
Units Normalized: 14 Oct 08:57
Ancestry Built: 14 Oct 08:56
Nodes Matched: 14 Oct 08:57
Names Parsed: 14 Oct 08:56
New Models Stored: 14 Oct 08:56
Indexed: 14 Oct 08:57
Completed: 14 Oct 08:59
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 08:56:14 -0400 by logger.rb/56815
[START] [2019-10-14 08:56:14] logged process
[START] [2019-10-14 08:56:14] create_harvest_instance
[STOP] [2019-10-14 08:56:14] create_harvest_instance
[START] [2019-10-14 08:56:14] fetch_files
[STOP] [2019-10-14 08:56:14] fetch_files
[START] [2019-10-14 08:56:14] validate_each_file
[STOP] [2019-10-14 08:56:14] validate_each_file
[START] [2019-10-14 08:56:14] convert_to_csv
[CMD] [2019-10-14 08:56:14] /usr/bin/sort /app/public/converted_csv/moldova_sp_list_refs_16587.csv > /app/public/converted_csv/moldova_sp_list_refs_16587.csv_sorted
[CMD] [2019-10-14 08:56:14] /usr/bin/sort /app/public/converted_csv/moldova_sp_list_nodes_16588.csv > /app/public/converted_csv/moldova_sp_list_nodes_16588.csv_sorted
[CMD] [2019-10-14 08:56:14] /usr/bin/sort /app/public/converted_csv/moldova_sp_list_occurrences_16589.csv > /app/public/converted_csv/moldova_sp_list_occurrences_16589.csv_sorted
[CMD] [2019-10-14 08:56:15] /usr/bin/sort /app/public/converted_csv/moldova_sp_list_measurements_16590.csv > /app/public/converted_csv/moldova_sp_list_measurements_16590.csv_sorted
[STOP] [2019-10-14 08:56:15] convert_to_csv
[START] [2019-10-14 08:56:15] calculate_delta
[CMD] [2019-10-14 08:56:15] echo "0a" > /app/public/diff/moldova_sp_list_refs_16587.diff
[CMD] [2019-10-14 08:56:15] tail -n +1 /app/public/converted_csv/moldova_sp_list_refs_16587.csv >> /app/public/diff/moldova_sp_list_refs_16587.diff
[CMD] [2019-10-14 08:56:15] echo "." >> /app/public/diff/moldova_sp_list_refs_16587.diff
[CMD] [2019-10-14 08:56:15] echo "0a" > /app/public/diff/moldova_sp_list_nodes_16588.diff
[CMD] [2019-10-14 08:56:15] tail -n +1 /app/public/converted_csv/moldova_sp_list_nodes_16588.csv >> /app/public/diff/moldova_sp_list_nodes_16588.diff
[CMD] [2019-10-14 08:56:15] echo "." >> /app/public/diff/moldova_sp_list_nodes_16588.diff
[CMD] [2019-10-14 08:56:15] echo "0a" > /app/public/diff/moldova_sp_list_occurrences_16589.diff
[CMD] [2019-10-14 08:56:15] tail -n +1 /app/public/converted_csv/moldova_sp_list_occurrences_16589.csv >> /app/public/diff/moldova_sp_list_occurrences_16589.diff
[CMD] [2019-10-14 08:56:15] echo "." >> /app/public/diff/moldova_sp_list_occurrences_16589.diff
[CMD] [2019-10-14 08:56:15] echo "0a" > /app/public/diff/moldova_sp_list_measurements_16590.diff
[CMD] [2019-10-14 08:56:16] tail -n +1 /app/public/converted_csv/moldova_sp_list_measurements_16590.csv >> /app/public/diff/moldova_sp_list_measurements_16590.diff
[CMD] [2019-10-14 08:56:16] echo "." >> /app/public/diff/moldova_sp_list_measurements_16590.diff
[STOP] [2019-10-14 08:56:16] calculate_delta
[START] [2019-10-14 08:56:16] parse_diff_and_store
[INFO] [2019-10-14 08:56:16] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 08:56:16] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 08:56:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 08:56:17] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 08:56:19] Storing 2 References
[INFO] [2019-10-14 08:56:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 08:56:19] Average Time: 0.0
[INFO] [2019-10-14 08:56:19] Total Time: 1s
[INFO] [2019-10-14 08:56:19] Storing 854 ScientificNames
[INFO] [2019-10-14 08:56:19] Processing group of 854 in 1 groups of 1000
[INFO] [2019-10-14 08:56:19] Average Time: 0.41
[INFO] [2019-10-14 08:56:19] Total Time: 1s
[INFO] [2019-10-14 08:56:19] Storing 854 Nodes
[INFO] [2019-10-14 08:56:19] Processing group of 854 in 1 groups of 1000
[INFO] [2019-10-14 08:56:19] Average Time: 0.29
[INFO] [2019-10-14 08:56:19] Total Time: 1s
[INFO] [2019-10-14 08:56:19] Storing 355 Occurrences
[INFO] [2019-10-14 08:56:19] Processing group of 355 in 1 groups of 1000
[INFO] [2019-10-14 08:56:20] Average Time: 0.07
[INFO] [2019-10-14 08:56:20] Total Time: 1s
[INFO] [2019-10-14 08:56:20] Storing 710 TraitsReferences
[INFO] [2019-10-14 08:56:20] Processing group of 710 in 1 groups of 1000
[INFO] [2019-10-14 08:56:20] Average Time: 0.12
[INFO] [2019-10-14 08:56:20] Total Time: 1s
[INFO] [2019-10-14 08:56:20] Storing 710 Traits
[INFO] [2019-10-14 08:56:20] Processing group of 710 in 1 groups of 1000
[INFO] [2019-10-14 08:56:20] Average Time: 0.33
[INFO] [2019-10-14 08:56:20] Total Time: 1s
[INFO] [2019-10-14 08:56:20] Storing 710 MetaTraits
[INFO] [2019-10-14 08:56:20] Processing group of 710 in 1 groups of 1000
[INFO] [2019-10-14 08:56:20] Average Time: 0.11
[INFO] [2019-10-14 08:56:20] Total Time: 1s
[STOP] [2019-10-14 08:56:20] parse_diff_and_store
[START] [2019-10-14 08:56:20] resolve_keys
[INFO] [2019-10-14 08:56:26] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 08:56:26] traits to occurrences...
[INFO] [2019-10-14 08:56:26] traits to nodes (through occurrences)...
[INFO] [2019-10-14 08:56:26] Traits to sex term...
[INFO] [2019-10-14 08:56:26] Traits to lifestage term...
[INFO] [2019-10-14 08:56:26] MetaTraits to traits...
[INFO] [2019-10-14 08:56:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 08:56:26] Assocs to occurrences...
[INFO] [2019-10-14 08:56:26] Assocs to nodes...
[INFO] [2019-10-14 08:56:26] Assoc to sex term...
[INFO] [2019-10-14 08:56:27] Assoc to lifestage term...
[STOP] [2019-10-14 08:56:27] resolve_keys
[START] [2019-10-14 08:56:27] hold_for_later_1
[STOP] [2019-10-14 08:56:27] hold_for_later_1
[START] [2019-10-14 08:56:27] hold_for_later_2
[STOP] [2019-10-14 08:56:27] hold_for_later_2
[START] [2019-10-14 08:56:27] resolve_missing_parents
[STOP] [2019-10-14 08:56:27] resolve_missing_parents
[START] [2019-10-14 08:56:27] rebuild_nodes
[START] [2019-10-14 08:56:27] Flattener#flatten
[START] [2019-10-14 08:56:27] Flattener#study_resource
[START] [2019-10-14 08:56:27] Flattener#build_ancestry
[STOP] [2019-10-14 08:56:27] Flattener#build_ancestry
[INFO] [2019-10-14 08:56:27] 854 ancestry keys
[START] [2019-10-14 08:56:27] build_node_ancestors
[INFO] [2019-10-14 08:56:27] old ancestors deleted.
[STOP] [2019-10-14 08:56:27] build_node_ancestors
[START] [2019-10-14 08:56:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 08:56:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 08:56:28] Flattener#flatten
[STOP] [2019-10-14 08:56:28] rebuild_nodes
[START] [2019-10-14 08:56:28] resolve_missing_media_owners
[STOP] [2019-10-14 08:56:28] resolve_missing_media_owners
[START] [2019-10-14 08:56:28] sanitize_media_verbatims
[STOP] [2019-10-14 08:56:28] sanitize_media_verbatims
[START] [2019-10-14 08:56:28] queue_downloads
[STOP] [2019-10-14 08:56:28] queue_downloads
[START] [2019-10-14 08:56:28] parse_names
[WARN] [2019-10-14 08:56:28] I see 854 names which still need to be parsed.
[STOP] [2019-10-14 08:56:29] parse_names
[START] [2019-10-14 08:56:29] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 08:56:29] denormalize_canonical_names_to_nodes
[START] [2019-10-14 08:56:29] match_nodes
[START] [2019-10-14 08:56:29] map_all_nodes_to_pages
[STOP] [2019-10-14 08:57:52] map_all_nodes_to_pages
[INFO] [2019-10-14 08:57:52] 42 Unmatched nodes (of 854)! That's too many to output. First 10: Magnoliopsida (#50777960); Solanum esculentum (#50778271); Chenopodiaceae (#50778555); Euphorbia villosa (#50778769); Magnoliophyta (#50777963); Pelophylax esculentus (#50778346); Phylloscopus sibillatrix (#50778217); Carduelis cannabina (#50778453); Carduelis chloris (#50778530); Anas querquedula (#50778436)
[START] [2019-10-14 08:57:52] update_nodes
[STOP] [2019-10-14 08:57:53] update_nodes
[STOP] [2019-10-14 08:57:53] match_nodes
[START] [2019-10-14 08:57:53] reindex_search
[STOP] [2019-10-14 08:57:54] reindex_search
[START] [2019-10-14 08:57:54] normalize_units
[STOP] [2019-10-14 08:57:54] normalize_units
[START] [2019-10-14 08:57:54] calculate_statistics
[STOP] [2019-10-14 08:57:54] calculate_statistics
[START] [2019-10-14 08:57:54] complete_harvest_instance
[START] [2019-10-14 08:57:54] overall_tsv_creation
[INFO] [2019-10-14 08:57:54] Processing group of 854 in 1 batches of 10000
[INFO] [2019-10-14 08:58:43] 355 Traits (unfiltered)...
[INFO] [2019-10-14 08:58:56] 355 Traits (filtered)...
[INFO] [2019-10-14 08:58:56] 0 Associations (filtered)...
[INFO] [2019-10-14 08:59:34] 1775 metadata added.
[INFO] [2019-10-14 08:59:34] 0 metadata added.
[INFO] [2019-10-14 08:59:34] Average Time: 77.88
[INFO] [2019-10-14 08:59:34] Total Time: 1m40s
[STOP] [2019-10-14 08:59:34] overall_tsv_creation
[INFO] [2019-10-14 08:59:34] Done. Check your files:
[INFO] [2019-10-14 08:59:34] (854 lines) /app/public/data/moldova_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 08:59:34] (4167 lines) /app/public/data/moldova_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 08:59:34] (854 lines) /app/public/data/moldova_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 08:59:34] (356 lines) /app/public/data/moldova_sp_list/publish_traits.tsv
[INFO] [2019-10-14 08:59:34] (1776 lines) /app/public/data/moldova_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 08:59:34] complete_harvest_instance
[START] [2019-10-14 08:59:34] completed
[STOP] [2019-10-14 08:59:34] completed
[STOP] [2019-10-14 08:59:34] logged process, took 200.47
Latest Process

14 Oct 08:56 EXITED currently processing 0