Harvest for Slovakia Species List Created 15 Oct 19:15

Stage: completed
Fetched: 15 Oct 19:15
Validated: 15 Oct 19:15
Deltas Created 15 Oct 19:15
Units Normalized: 15 Oct 19:34
Ancestry Built: 15 Oct 19:18
Nodes Matched: 15 Oct 19:34
Names Parsed: 15 Oct 19:18
New Models Stored: 15 Oct 19:16
Indexed: 15 Oct 19:34
Completed: 15 Oct 19:39
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-15 19:15:25 -0400 by logger.rb/56815
[START] [2019-10-15 19:15:25] logged process
[START] [2019-10-15 19:15:25] create_harvest_instance
[STOP] [2019-10-15 19:15:25] create_harvest_instance
[START] [2019-10-15 19:15:25] fetch_files
[STOP] [2019-10-15 19:15:25] fetch_files
[START] [2019-10-15 19:15:25] validate_each_file
[STOP] [2019-10-15 19:15:27] validate_each_file
[START] [2019-10-15 19:15:27] convert_to_csv
[CMD] [2019-10-15 19:15:27] /usr/bin/sort /app/public/converted_csv/slovakia_sp_list_refs_17221.csv > /app/public/converted_csv/slovakia_sp_list_refs_17221.csv_sorted
[CMD] [2019-10-15 19:15:27] /usr/bin/sort /app/public/converted_csv/slovakia_sp_list_nodes_17222.csv > /app/public/converted_csv/slovakia_sp_list_nodes_17222.csv_sorted
[CMD] [2019-10-15 19:15:27] /usr/bin/sort /app/public/converted_csv/slovakia_sp_list_occurrences_17223.csv > /app/public/converted_csv/slovakia_sp_list_occurrences_17223.csv_sorted
[CMD] [2019-10-15 19:15:28] /usr/bin/sort /app/public/converted_csv/slovakia_sp_list_measurements_17224.csv > /app/public/converted_csv/slovakia_sp_list_measurements_17224.csv_sorted
[STOP] [2019-10-15 19:15:28] convert_to_csv
[START] [2019-10-15 19:15:28] calculate_delta
[CMD] [2019-10-15 19:15:28] echo "0a" > /app/public/diff/slovakia_sp_list_refs_17221.diff
[CMD] [2019-10-15 19:15:28] tail -n +1 /app/public/converted_csv/slovakia_sp_list_refs_17221.csv >> /app/public/diff/slovakia_sp_list_refs_17221.diff
[CMD] [2019-10-15 19:15:29] echo "." >> /app/public/diff/slovakia_sp_list_refs_17221.diff
[CMD] [2019-10-15 19:15:29] echo "0a" > /app/public/diff/slovakia_sp_list_nodes_17222.diff
[CMD] [2019-10-15 19:15:29] tail -n +1 /app/public/converted_csv/slovakia_sp_list_nodes_17222.csv >> /app/public/diff/slovakia_sp_list_nodes_17222.diff
[CMD] [2019-10-15 19:15:29] echo "." >> /app/public/diff/slovakia_sp_list_nodes_17222.diff
[CMD] [2019-10-15 19:15:30] echo "0a" > /app/public/diff/slovakia_sp_list_occurrences_17223.diff
[CMD] [2019-10-15 19:15:30] tail -n +1 /app/public/converted_csv/slovakia_sp_list_occurrences_17223.csv >> /app/public/diff/slovakia_sp_list_occurrences_17223.diff
[CMD] [2019-10-15 19:15:30] echo "." >> /app/public/diff/slovakia_sp_list_occurrences_17223.diff
[CMD] [2019-10-15 19:15:31] echo "0a" > /app/public/diff/slovakia_sp_list_measurements_17224.diff
[CMD] [2019-10-15 19:15:31] tail -n +1 /app/public/converted_csv/slovakia_sp_list_measurements_17224.csv >> /app/public/diff/slovakia_sp_list_measurements_17224.diff
[CMD] [2019-10-15 19:15:31] echo "." >> /app/public/diff/slovakia_sp_list_measurements_17224.diff
[STOP] [2019-10-15 19:15:31] calculate_delta
[START] [2019-10-15 19:15:31] parse_diff_and_store
[INFO] [2019-10-15 19:15:32] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 19:15:32] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 19:15:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 19:15:38] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 19:16:24] Storing 2 References
[INFO] [2019-10-15 19:16:24] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 19:16:24] Average Time: 0.0
[INFO] [2019-10-15 19:16:24] Total Time: 1s
[INFO] [2019-10-15 19:16:24] Storing 12346 ScientificNames
[INFO] [2019-10-15 19:16:24] Processing group of 12346 in 13 groups of 1000
[INFO] [2019-10-15 19:16:29] Average Time: 0.375
[INFO] [2019-10-15 19:16:29] Total Time: 5s
[INFO] [2019-10-15 19:16:29] last 3 / first 3: 0.52
[INFO] [2019-10-15 19:16:29] Std.Dev: 0.1341640786499874; Max: 0.73
[INFO] [2019-10-15 19:16:29] Storing 12346 Nodes
[INFO] [2019-10-15 19:16:29] Processing group of 12346 in 13 groups of 1000
[INFO] [2019-10-15 19:16:32] Average Time: 0.283
[INFO] [2019-10-15 19:16:32] Total Time: 4s
[INFO] [2019-10-15 19:16:32] last 3 / first 3: 0.78
[INFO] [2019-10-15 19:16:32] Std.Dev: 0.05477225575051661; Max: 0.32
[INFO] [2019-10-15 19:16:32] Storing 7712 Occurrences
[INFO] [2019-10-15 19:16:32] Processing group of 7712 in 8 groups of 1000
[INFO] [2019-10-15 19:16:33] Average Time: 0.103
[INFO] [2019-10-15 19:16:33] Total Time: 1s
[INFO] [2019-10-15 19:16:33] last 3 / first 3: 0.84
[INFO] [2019-10-15 19:16:33] Std.Dev: 0.0; Max: 0.13
[INFO] [2019-10-15 19:16:33] Storing 15630 TraitsReferences
[INFO] [2019-10-15 19:16:33] Processing group of 15630 in 16 groups of 1000
[INFO] [2019-10-15 19:16:35] Average Time: 0.076
[INFO] [2019-10-15 19:16:35] Total Time: 2s
[INFO] [2019-10-15 19:16:35] last 3 / first 3: 0.6
[INFO] [2019-10-15 19:16:35] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-15 19:16:35] Storing 15629 Traits
[INFO] [2019-10-15 19:16:35] Processing group of 15629 in 16 groups of 1000
[INFO] [2019-10-15 19:16:40] Average Time: 0.336
[INFO] [2019-10-15 19:16:40] Total Time: 6s
[INFO] [2019-10-15 19:16:40] last 3 / first 3: 0.81
[INFO] [2019-10-15 19:16:40] Std.Dev: 0.11832159566199232; Max: 0.71
[INFO] [2019-10-15 19:16:40] Storing 15618 MetaTraits
[INFO] [2019-10-15 19:16:40] Processing group of 15618 in 16 groups of 1000
[INFO] [2019-10-15 19:16:42] Average Time: 0.103
[INFO] [2019-10-15 19:16:42] Total Time: 2s
[INFO] [2019-10-15 19:16:42] last 3 / first 3: 0.8
[INFO] [2019-10-15 19:16:42] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-10-15 19:16:42] parse_diff_and_store
[START] [2019-10-15 19:16:42] resolve_keys
[INFO] [2019-10-15 19:17:30] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 19:17:34] traits to occurrences...
[INFO] [2019-10-15 19:17:40] traits to nodes (through occurrences)...
[INFO] [2019-10-15 19:17:40] Traits to sex term...
[INFO] [2019-10-15 19:17:45] Traits to lifestage term...
[INFO] [2019-10-15 19:17:49] MetaTraits to traits...
[INFO] [2019-10-15 19:17:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 19:17:53] Assocs to occurrences...
[INFO] [2019-10-15 19:17:53] Assocs to nodes...
[INFO] [2019-10-15 19:17:53] Assoc to sex term...
[INFO] [2019-10-15 19:17:53] Assoc to lifestage term...
[STOP] [2019-10-15 19:17:53] resolve_keys
[START] [2019-10-15 19:17:53] hold_for_later_1
[STOP] [2019-10-15 19:17:53] hold_for_later_1
[START] [2019-10-15 19:17:53] hold_for_later_2
[STOP] [2019-10-15 19:17:53] hold_for_later_2
[START] [2019-10-15 19:17:53] resolve_missing_parents
[STOP] [2019-10-15 19:18:16] resolve_missing_parents
[START] [2019-10-15 19:18:16] rebuild_nodes
[START] [2019-10-15 19:18:16] Flattener#flatten
[START] [2019-10-15 19:18:16] Flattener#study_resource
[START] [2019-10-15 19:18:16] Flattener#build_ancestry
[STOP] [2019-10-15 19:18:17] Flattener#build_ancestry
[INFO] [2019-10-15 19:18:17] 12346 ancestry keys
[START] [2019-10-15 19:18:17] build_node_ancestors
[INFO] [2019-10-15 19:18:17] old ancestors deleted.
[STOP] [2019-10-15 19:18:19] build_node_ancestors
[START] [2019-10-15 19:18:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 19:18:22] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 19:18:22] Flattener#flatten
[STOP] [2019-10-15 19:18:22] rebuild_nodes
[START] [2019-10-15 19:18:22] resolve_missing_media_owners
[STOP] [2019-10-15 19:18:22] resolve_missing_media_owners
[START] [2019-10-15 19:18:22] sanitize_media_verbatims
[STOP] [2019-10-15 19:18:22] sanitize_media_verbatims
[START] [2019-10-15 19:18:22] queue_downloads
[STOP] [2019-10-15 19:18:22] queue_downloads
[START] [2019-10-15 19:18:22] parse_names
[WARN] [2019-10-15 19:18:22] I see 12346 names which still need to be parsed.
[STOP] [2019-10-15 19:18:32] parse_names
[START] [2019-10-15 19:18:32] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 19:18:32] denormalize_canonical_names_to_nodes
[START] [2019-10-15 19:18:32] match_nodes
[START] [2019-10-15 19:18:32] map_all_nodes_to_pages
[STOP] [2019-10-15 19:34:08] map_all_nodes_to_pages
[INFO] [2019-10-15 19:34:08] 1699 Unmatched nodes (of 12346)! That's too many to output. First 10: Silene alba (#51835437); Silene album (#51835522); Silene pratense (#51836886); Silene baccifer (#51837847); Dianthus hungaricus (#51835681); Cerastium viscidum (#51828708); Cerastium tatrae (#51836638); Lychnis (#51827687); Heliosperma pusilla (#51835661); Chenopodiaceae (#51826622)
[START] [2019-10-15 19:34:08] update_nodes
[STOP] [2019-10-15 19:34:12] update_nodes
[STOP] [2019-10-15 19:34:12] match_nodes
[START] [2019-10-15 19:34:12] reindex_search
[STOP] [2019-10-15 19:34:51] reindex_search
[START] [2019-10-15 19:34:51] normalize_units
[STOP] [2019-10-15 19:34:51] normalize_units
[START] [2019-10-15 19:34:51] calculate_statistics
[STOP] [2019-10-15 19:34:51] calculate_statistics
[START] [2019-10-15 19:34:51] complete_harvest_instance
[START] [2019-10-15 19:34:51] overall_tsv_creation
[INFO] [2019-10-15 19:34:51] Processing group of 12346 in 2 batches of 10000
[INFO] [2019-10-15 19:36:20] 6176 Traits (unfiltered)...
[INFO] [2019-10-15 19:36:34] 6176 Traits (filtered)...
[INFO] [2019-10-15 19:36:34] 0 Associations (filtered)...
[INFO] [2019-10-15 19:37:25] 30873 metadata added.
[INFO] [2019-10-15 19:37:25] 0 metadata added.
[INFO] [2019-10-15 19:38:18] 1536 Traits (unfiltered)...
[INFO] [2019-10-15 19:38:32] 1536 Traits (filtered)...
[INFO] [2019-10-15 19:38:32] 0 Associations (filtered)...
[INFO] [2019-10-15 19:39:12] 7675 metadata added.
[INFO] [2019-10-15 19:39:12] 0 metadata added.
[INFO] [2019-10-15 19:39:13] Average Time: 106.315
[INFO] [2019-10-15 19:39:13] Total Time: 4m22s
[STOP] [2019-10-15 19:39:13] overall_tsv_creation
[INFO] [2019-10-15 19:39:13] Done. Check your files:
[INFO] [2019-10-15 19:39:13] (12346 lines) /app/public/data/slovakia_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 19:39:13] (30489 lines) /app/public/data/slovakia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 19:39:13] (12346 lines) /app/public/data/slovakia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 19:39:14] (7713 lines) /app/public/data/slovakia_sp_list/publish_traits.tsv
[INFO] [2019-10-15 19:39:14] (38549 lines) /app/public/data/slovakia_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 19:39:14] complete_harvest_instance
[START] [2019-10-15 19:39:14] completed
[STOP] [2019-10-15 19:39:14] completed
[STOP] [2019-10-15 19:39:14] logged process, took 1429.52
Latest Process

15 Oct 19:15 EXITED currently processing 0