Harvest for Albania Species List Created 01 Oct 16:12

Stage: completed
Fetched: 01 Oct 16:12
Validated: 01 Oct 16:12
Deltas Created 01 Oct 16:13
Units Normalized: 01 Oct 16:15
Ancestry Built: 01 Oct 16:13
Nodes Matched: 01 Oct 16:15
Names Parsed: 01 Oct 16:13
New Models Stored: 01 Oct 16:13
Indexed: 01 Oct 16:15
Completed: 01 Oct 16:17
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-01 16:12:49 -0400 by logger.rb/56815
[START] [2019-10-01 16:12:49] logged process
[START] [2019-10-01 16:12:49] create_harvest_instance
[STOP] [2019-10-01 16:12:49] create_harvest_instance
[START] [2019-10-01 16:12:49] fetch_files
[STOP] [2019-10-01 16:12:49] fetch_files
[START] [2019-10-01 16:12:49] validate_each_file
[STOP] [2019-10-01 16:12:50] validate_each_file
[START] [2019-10-01 16:12:50] convert_to_csv
[CMD] [2019-10-01 16:12:50] /usr/bin/sort /app/public/converted_csv/albania_sp_list_refs_14742.csv > /app/public/converted_csv/albania_sp_list_refs_14742.csv_sorted
[CMD] [2019-10-01 16:12:51] /usr/bin/sort /app/public/converted_csv/albania_sp_list_nodes_14743.csv > /app/public/converted_csv/albania_sp_list_nodes_14743.csv_sorted
[CMD] [2019-10-01 16:12:53] /usr/bin/sort /app/public/converted_csv/albania_sp_list_occurrences_14744.csv > /app/public/converted_csv/albania_sp_list_occurrences_14744.csv_sorted
[CMD] [2019-10-01 16:12:54] /usr/bin/sort /app/public/converted_csv/albania_sp_list_measurements_14745.csv > /app/public/converted_csv/albania_sp_list_measurements_14745.csv_sorted
[STOP] [2019-10-01 16:12:55] convert_to_csv
[START] [2019-10-01 16:12:56] calculate_delta
[CMD] [2019-10-01 16:12:56] echo "0a" > /app/public/diff/albania_sp_list_refs_14742.diff
[CMD] [2019-10-01 16:12:57] tail -n +1 /app/public/converted_csv/albania_sp_list_refs_14742.csv >> /app/public/diff/albania_sp_list_refs_14742.diff
[CMD] [2019-10-01 16:12:58] echo "." >> /app/public/diff/albania_sp_list_refs_14742.diff
[CMD] [2019-10-01 16:13:00] echo "0a" > /app/public/diff/albania_sp_list_nodes_14743.diff
[CMD] [2019-10-01 16:13:01] tail -n +1 /app/public/converted_csv/albania_sp_list_nodes_14743.csv >> /app/public/diff/albania_sp_list_nodes_14743.diff
[CMD] [2019-10-01 16:13:03] echo "." >> /app/public/diff/albania_sp_list_nodes_14743.diff
[CMD] [2019-10-01 16:13:04] echo "0a" > /app/public/diff/albania_sp_list_occurrences_14744.diff
[CMD] [2019-10-01 16:13:06] tail -n +1 /app/public/converted_csv/albania_sp_list_occurrences_14744.csv >> /app/public/diff/albania_sp_list_occurrences_14744.diff
[CMD] [2019-10-01 16:13:07] echo "." >> /app/public/diff/albania_sp_list_occurrences_14744.diff
[CMD] [2019-10-01 16:13:09] echo "0a" > /app/public/diff/albania_sp_list_measurements_14745.diff
[CMD] [2019-10-01 16:13:10] tail -n +1 /app/public/converted_csv/albania_sp_list_measurements_14745.csv >> /app/public/diff/albania_sp_list_measurements_14745.diff
[CMD] [2019-10-01 16:13:12] echo "." >> /app/public/diff/albania_sp_list_measurements_14745.diff
[STOP] [2019-10-01 16:13:13] calculate_delta
[START] [2019-10-01 16:13:13] parse_diff_and_store
[INFO] [2019-10-01 16:13:15] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-01 16:13:16] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-01 16:13:19] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-01 16:13:20] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-01 16:13:27] Storing 2 References
[INFO] [2019-10-01 16:13:27] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-01 16:13:27] Average Time: 0.0
[INFO] [2019-10-01 16:13:27] Total Time: 1s
[INFO] [2019-10-01 16:13:27] Storing 2395 ScientificNames
[INFO] [2019-10-01 16:13:27] Processing group of 2395 in 3 groups of 1000
[INFO] [2019-10-01 16:13:30] Average Time: 0.773
[INFO] [2019-10-01 16:13:30] Total Time: 3s
[INFO] [2019-10-01 16:13:30] Storing 2395 Nodes
[INFO] [2019-10-01 16:13:30] Processing group of 2395 in 3 groups of 1000
[INFO] [2019-10-01 16:13:31] Average Time: 0.26
[INFO] [2019-10-01 16:13:31] Total Time: 1s
[INFO] [2019-10-01 16:13:31] Storing 964 Occurrences
[INFO] [2019-10-01 16:13:31] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-01 16:13:31] Average Time: 0.11
[INFO] [2019-10-01 16:13:31] Total Time: 1s
[INFO] [2019-10-01 16:13:31] Storing 2700 TraitsReferences
[INFO] [2019-10-01 16:13:31] Processing group of 2700 in 3 groups of 1000
[INFO] [2019-10-01 16:13:31] Average Time: 0.083
[INFO] [2019-10-01 16:13:31] Total Time: 1s
[INFO] [2019-10-01 16:13:31] Storing 2699 Traits
[INFO] [2019-10-01 16:13:31] Processing group of 2699 in 3 groups of 1000
[INFO] [2019-10-01 16:13:32] Average Time: 0.313
[INFO] [2019-10-01 16:13:32] Total Time: 1s
[INFO] [2019-10-01 16:13:32] Storing 2696 MetaTraits
[INFO] [2019-10-01 16:13:32] Processing group of 2696 in 3 groups of 1000
[INFO] [2019-10-01 16:13:32] Average Time: 0.147
[INFO] [2019-10-01 16:13:32] Total Time: 1s
[STOP] [2019-10-01 16:13:32] parse_diff_and_store
[START] [2019-10-01 16:13:32] resolve_keys
[INFO] [2019-10-01 16:13:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-01 16:13:46] traits to occurrences...
[INFO] [2019-10-01 16:13:47] traits to nodes (through occurrences)...
[INFO] [2019-10-01 16:13:47] Traits to sex term...
[INFO] [2019-10-01 16:13:48] Traits to lifestage term...
[INFO] [2019-10-01 16:13:49] MetaTraits to traits...
[INFO] [2019-10-01 16:13:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-01 16:13:50] Assocs to occurrences...
[INFO] [2019-10-01 16:13:50] Assocs to nodes...
[INFO] [2019-10-01 16:13:50] Assoc to sex term...
[INFO] [2019-10-01 16:13:50] Assoc to lifestage term...
[STOP] [2019-10-01 16:13:50] resolve_keys
[START] [2019-10-01 16:13:50] hold_for_later_1
[STOP] [2019-10-01 16:13:50] hold_for_later_1
[START] [2019-10-01 16:13:50] hold_for_later_2
[STOP] [2019-10-01 16:13:50] hold_for_later_2
[START] [2019-10-01 16:13:50] resolve_missing_parents
[STOP] [2019-10-01 16:13:53] resolve_missing_parents
[START] [2019-10-01 16:13:53] rebuild_nodes
[START] [2019-10-01 16:13:53] Flattener#flatten
[START] [2019-10-01 16:13:53] Flattener#study_resource
[START] [2019-10-01 16:13:53] Flattener#build_ancestry
[STOP] [2019-10-01 16:13:54] Flattener#build_ancestry
[INFO] [2019-10-01 16:13:54] 2395 ancestry keys
[START] [2019-10-01 16:13:54] build_node_ancestors
[INFO] [2019-10-01 16:13:54] old ancestors deleted.
[STOP] [2019-10-01 16:13:54] build_node_ancestors
[START] [2019-10-01 16:13:54] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 16:13:54] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 16:13:54] Flattener#flatten
[STOP] [2019-10-01 16:13:54] rebuild_nodes
[START] [2019-10-01 16:13:54] resolve_missing_media_owners
[STOP] [2019-10-01 16:13:54] resolve_missing_media_owners
[START] [2019-10-01 16:13:54] sanitize_media_verbatims
[STOP] [2019-10-01 16:13:54] sanitize_media_verbatims
[START] [2019-10-01 16:13:54] queue_downloads
[STOP] [2019-10-01 16:13:54] queue_downloads
[START] [2019-10-01 16:13:54] parse_names
[WARN] [2019-10-01 16:13:54] I see 2395 names which still need to be parsed.
[STOP] [2019-10-01 16:13:57] parse_names
[START] [2019-10-01 16:13:57] denormalize_canonical_names_to_nodes
[STOP] [2019-10-01 16:13:57] denormalize_canonical_names_to_nodes
[START] [2019-10-01 16:13:57] match_nodes
[START] [2019-10-01 16:13:57] map_all_nodes_to_pages
[STOP] [2019-10-01 16:15:28] map_all_nodes_to_pages
[INFO] [2019-10-01 16:15:28] 105 Unmatched nodes (of 2395)! That's too many to output. First 10: Corvus monedula (#47343276); Hirundo rupestris (#47344516); Carduelis cannabina (#47343490); Carduelis chloris (#47344765); Carduelis spinus (#47345538); Monticola (#47343612); Astragalus cicera (#47345418); Solanum esculentum (#47343294); Larus melanocephalus (#47345360); Thalaseus (#47344420)
[START] [2019-10-01 16:15:28] update_nodes
[STOP] [2019-10-01 16:15:29] update_nodes
[STOP] [2019-10-01 16:15:29] match_nodes
[START] [2019-10-01 16:15:29] reindex_search
[STOP] [2019-10-01 16:15:33] reindex_search
[START] [2019-10-01 16:15:33] normalize_units
[STOP] [2019-10-01 16:15:33] normalize_units
[START] [2019-10-01 16:15:33] calculate_statistics
[STOP] [2019-10-01 16:15:33] calculate_statistics
[START] [2019-10-01 16:15:33] complete_harvest_instance
[START] [2019-10-01 16:15:33] overall_tsv_creation
[INFO] [2019-10-01 16:15:33] Processing group of 2395 in 1 batches of 10000
[INFO] [2019-10-01 16:16:28] 964 Traits (unfiltered)...
[INFO] [2019-10-01 16:16:40] 964 Traits (filtered)...
[INFO] [2019-10-01 16:16:40] 0 Associations (filtered)...
[INFO] [2019-10-01 16:17:19] 4818 metadata added.
[INFO] [2019-10-01 16:17:19] 0 metadata added.
[INFO] [2019-10-01 16:17:19] Average Time: 81.87
[INFO] [2019-10-01 16:17:19] Total Time: 1m46s
[STOP] [2019-10-01 16:17:19] overall_tsv_creation
[INFO] [2019-10-01 16:17:19] Done. Check your files:
[INFO] [2019-10-01 16:17:20] (2395 lines) /app/public/data/albania_sp_list/publish_nodes.tsv
[INFO] [2019-10-01 16:17:22] (3318 lines) /app/public/data/albania_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-01 16:17:23] (2395 lines) /app/public/data/albania_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-01 16:17:25] (965 lines) /app/public/data/albania_sp_list/publish_traits.tsv
[INFO] [2019-10-01 16:17:26] (4819 lines) /app/public/data/albania_sp_list/publish_metadata.tsv
[STOP] [2019-10-01 16:17:26] complete_harvest_instance
[START] [2019-10-01 16:17:26] completed
[STOP] [2019-10-01 16:17:26] completed
[STOP] [2019-10-01 16:17:26] logged process, took 277.76
Latest Process

01 Oct 16:12 EXITED currently processing 0