Harvest for Kuwait Species List Created 14 Oct 00:41

Stage: completed
Fetched: 14 Oct 00:41
Validated: 14 Oct 00:41
Deltas Created 14 Oct 00:41
Units Normalized: 14 Oct 00:44
Ancestry Built: 14 Oct 00:42
Nodes Matched: 14 Oct 00:43
Names Parsed: 14 Oct 00:42
New Models Stored: 14 Oct 00:41
Indexed: 14 Oct 00:44
Completed: 14 Oct 00:45
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 00:41:49 -0400 by logger.rb/56815
[START] [2019-10-14 00:41:49] logged process
[START] [2019-10-14 00:41:49] create_harvest_instance
[STOP] [2019-10-14 00:41:49] create_harvest_instance
[START] [2019-10-14 00:41:49] fetch_files
[STOP] [2019-10-14 00:41:49] fetch_files
[START] [2019-10-14 00:41:49] validate_each_file
[STOP] [2019-10-14 00:41:50] validate_each_file
[START] [2019-10-14 00:41:50] convert_to_csv
[CMD] [2019-10-14 00:41:50] /usr/bin/sort /app/public/converted_csv/kuwait_sp_list_refs_16323.csv > /app/public/converted_csv/kuwait_sp_list_refs_16323.csv_sorted
[CMD] [2019-10-14 00:41:50] /usr/bin/sort /app/public/converted_csv/kuwait_sp_list_nodes_16324.csv > /app/public/converted_csv/kuwait_sp_list_nodes_16324.csv_sorted
[CMD] [2019-10-14 00:41:50] /usr/bin/sort /app/public/converted_csv/kuwait_sp_list_occurrences_16325.csv > /app/public/converted_csv/kuwait_sp_list_occurrences_16325.csv_sorted
[CMD] [2019-10-14 00:41:50] /usr/bin/sort /app/public/converted_csv/kuwait_sp_list_measurements_16326.csv > /app/public/converted_csv/kuwait_sp_list_measurements_16326.csv_sorted
[STOP] [2019-10-14 00:41:50] convert_to_csv
[START] [2019-10-14 00:41:50] calculate_delta
[CMD] [2019-10-14 00:41:50] echo "0a" > /app/public/diff/kuwait_sp_list_refs_16323.diff
[CMD] [2019-10-14 00:41:50] tail -n +1 /app/public/converted_csv/kuwait_sp_list_refs_16323.csv >> /app/public/diff/kuwait_sp_list_refs_16323.diff
[CMD] [2019-10-14 00:41:50] echo "." >> /app/public/diff/kuwait_sp_list_refs_16323.diff
[CMD] [2019-10-14 00:41:50] echo "0a" > /app/public/diff/kuwait_sp_list_nodes_16324.diff
[CMD] [2019-10-14 00:41:50] tail -n +1 /app/public/converted_csv/kuwait_sp_list_nodes_16324.csv >> /app/public/diff/kuwait_sp_list_nodes_16324.diff
[CMD] [2019-10-14 00:41:51] echo "." >> /app/public/diff/kuwait_sp_list_nodes_16324.diff
[CMD] [2019-10-14 00:41:51] echo "0a" > /app/public/diff/kuwait_sp_list_occurrences_16325.diff
[CMD] [2019-10-14 00:41:51] tail -n +1 /app/public/converted_csv/kuwait_sp_list_occurrences_16325.csv >> /app/public/diff/kuwait_sp_list_occurrences_16325.diff
[CMD] [2019-10-14 00:41:51] echo "." >> /app/public/diff/kuwait_sp_list_occurrences_16325.diff
[CMD] [2019-10-14 00:41:51] echo "0a" > /app/public/diff/kuwait_sp_list_measurements_16326.diff
[CMD] [2019-10-14 00:41:51] tail -n +1 /app/public/converted_csv/kuwait_sp_list_measurements_16326.csv >> /app/public/diff/kuwait_sp_list_measurements_16326.diff
[CMD] [2019-10-14 00:41:51] echo "." >> /app/public/diff/kuwait_sp_list_measurements_16326.diff
[STOP] [2019-10-14 00:41:51] calculate_delta
[START] [2019-10-14 00:41:51] parse_diff_and_store
[INFO] [2019-10-14 00:41:51] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 00:41:51] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 00:41:52] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 00:41:52] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 00:41:57] Storing 2 References
[INFO] [2019-10-14 00:41:57] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 00:41:57] Average Time: 0.0
[INFO] [2019-10-14 00:41:57] Total Time: 1s
[INFO] [2019-10-14 00:41:57] Storing 1556 ScientificNames
[INFO] [2019-10-14 00:41:57] Processing group of 1556 in 2 groups of 1000
[INFO] [2019-10-14 00:41:58] Average Time: 0.375
[INFO] [2019-10-14 00:41:58] Total Time: 1s
[INFO] [2019-10-14 00:41:58] Storing 1556 Nodes
[INFO] [2019-10-14 00:41:58] Processing group of 1556 in 2 groups of 1000
[INFO] [2019-10-14 00:41:58] Average Time: 0.295
[INFO] [2019-10-14 00:41:58] Total Time: 1s
[INFO] [2019-10-14 00:41:58] Storing 482 Occurrences
[INFO] [2019-10-14 00:41:58] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-14 00:41:58] Average Time: 0.07
[INFO] [2019-10-14 00:41:58] Total Time: 1s
[INFO] [2019-10-14 00:41:58] Storing 1550 TraitsReferences
[INFO] [2019-10-14 00:41:58] Processing group of 1550 in 2 groups of 1000
[INFO] [2019-10-14 00:41:59] Average Time: 0.095
[INFO] [2019-10-14 00:41:59] Total Time: 1s
[INFO] [2019-10-14 00:41:59] Storing 1549 Traits
[INFO] [2019-10-14 00:41:59] Processing group of 1549 in 2 groups of 1000
[INFO] [2019-10-14 00:41:59] Average Time: 0.285
[INFO] [2019-10-14 00:41:59] Total Time: 1s
[INFO] [2019-10-14 00:41:59] Storing 1550 MetaTraits
[INFO] [2019-10-14 00:41:59] Processing group of 1550 in 2 groups of 1000
[INFO] [2019-10-14 00:41:59] Average Time: 0.1
[INFO] [2019-10-14 00:41:59] Total Time: 1s
[STOP] [2019-10-14 00:41:59] parse_diff_and_store
[START] [2019-10-14 00:41:59] resolve_keys
[INFO] [2019-10-14 00:42:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 00:42:08] traits to occurrences...
[INFO] [2019-10-14 00:42:09] traits to nodes (through occurrences)...
[INFO] [2019-10-14 00:42:09] Traits to sex term...
[INFO] [2019-10-14 00:42:09] Traits to lifestage term...
[INFO] [2019-10-14 00:42:09] MetaTraits to traits...
[INFO] [2019-10-14 00:42:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 00:42:10] Assocs to occurrences...
[INFO] [2019-10-14 00:42:10] Assocs to nodes...
[INFO] [2019-10-14 00:42:10] Assoc to sex term...
[INFO] [2019-10-14 00:42:10] Assoc to lifestage term...
[STOP] [2019-10-14 00:42:10] resolve_keys
[START] [2019-10-14 00:42:10] hold_for_later_1
[STOP] [2019-10-14 00:42:10] hold_for_later_1
[START] [2019-10-14 00:42:10] hold_for_later_2
[STOP] [2019-10-14 00:42:10] hold_for_later_2
[START] [2019-10-14 00:42:10] resolve_missing_parents
[STOP] [2019-10-14 00:42:11] resolve_missing_parents
[START] [2019-10-14 00:42:11] rebuild_nodes
[START] [2019-10-14 00:42:11] Flattener#flatten
[START] [2019-10-14 00:42:11] Flattener#study_resource
[START] [2019-10-14 00:42:11] Flattener#build_ancestry
[STOP] [2019-10-14 00:42:13] Flattener#build_ancestry
[INFO] [2019-10-14 00:42:13] 1556 ancestry keys
[START] [2019-10-14 00:42:13] build_node_ancestors
[INFO] [2019-10-14 00:42:13] old ancestors deleted.
[STOP] [2019-10-14 00:42:14] build_node_ancestors
[START] [2019-10-14 00:42:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:42:14] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:42:14] Flattener#flatten
[STOP] [2019-10-14 00:42:14] rebuild_nodes
[START] [2019-10-14 00:42:14] resolve_missing_media_owners
[STOP] [2019-10-14 00:42:14] resolve_missing_media_owners
[START] [2019-10-14 00:42:14] sanitize_media_verbatims
[STOP] [2019-10-14 00:42:14] sanitize_media_verbatims
[START] [2019-10-14 00:42:14] queue_downloads
[STOP] [2019-10-14 00:42:14] queue_downloads
[START] [2019-10-14 00:42:14] parse_names
[WARN] [2019-10-14 00:42:14] I see 1556 names which still need to be parsed.
[STOP] [2019-10-14 00:42:16] parse_names
[START] [2019-10-14 00:42:16] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 00:42:16] denormalize_canonical_names_to_nodes
[START] [2019-10-14 00:42:16] match_nodes
[START] [2019-10-14 00:42:16] map_all_nodes_to_pages
[STOP] [2019-10-14 00:43:58] map_all_nodes_to_pages
[INFO] [2019-10-14 00:43:58] 63 Unmatched nodes (of 1556)! That's too many to output. First 10: Calandrella rufescens (#50507826); Erythropygia (#50507636); Erythropygia galactotes (#50507635); Phylloscopus sibillatrix (#50508300); Petronia xanthocollis (#50508408); Acrocephalus caligata (#50508225); Turdoides huttoni (#50507945); Carduelis cannabina (#50508508); Carduelis spinus (#50508604); Temenuchus (#50508840)
[START] [2019-10-14 00:43:58] update_nodes
[STOP] [2019-10-14 00:43:59] update_nodes
[STOP] [2019-10-14 00:43:59] match_nodes
[START] [2019-10-14 00:43:59] reindex_search
[STOP] [2019-10-14 00:44:02] reindex_search
[START] [2019-10-14 00:44:02] normalize_units
[STOP] [2019-10-14 00:44:02] normalize_units
[START] [2019-10-14 00:44:02] calculate_statistics
[STOP] [2019-10-14 00:44:02] calculate_statistics
[START] [2019-10-14 00:44:02] complete_harvest_instance
[START] [2019-10-14 00:44:02] overall_tsv_creation
[INFO] [2019-10-14 00:44:03] Processing group of 1556 in 1 batches of 10000
[INFO] [2019-10-14 00:44:53] 482 Traits (unfiltered)...
[INFO] [2019-10-14 00:45:07] 482 Traits (filtered)...
[INFO] [2019-10-14 00:45:07] 0 Associations (filtered)...
[INFO] [2019-10-14 00:45:47] 2410 metadata added.
[INFO] [2019-10-14 00:45:47] 0 metadata added.
[INFO] [2019-10-14 00:45:47] Average Time: 83.08
[INFO] [2019-10-14 00:45:47] Total Time: 1m45s
[STOP] [2019-10-14 00:45:47] overall_tsv_creation
[INFO] [2019-10-14 00:45:47] Done. Check your files:
[INFO] [2019-10-14 00:45:47] (1556 lines) /app/public/data/kuwait_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 00:45:47] (3418 lines) /app/public/data/kuwait_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 00:45:47] (1556 lines) /app/public/data/kuwait_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 00:45:47] (483 lines) /app/public/data/kuwait_sp_list/publish_traits.tsv
[INFO] [2019-10-14 00:45:47] (2411 lines) /app/public/data/kuwait_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 00:45:47] complete_harvest_instance
[START] [2019-10-14 00:45:47] completed
[STOP] [2019-10-14 00:45:47] completed
[STOP] [2019-10-14 00:45:47] logged process, took 238.25
Latest Process

14 Oct 00:41 EXITED currently processing 0