Harvest for Tibet Species List Created 16 Oct 17:18

Stage: completed
Fetched: 16 Oct 17:18
Validated: 16 Oct 17:18
Deltas Created 16 Oct 17:18
Units Normalized: 16 Oct 17:28
Ancestry Built: 16 Oct 17:20
Nodes Matched: 16 Oct 17:27
Names Parsed: 16 Oct 17:20
New Models Stored: 16 Oct 17:19
Indexed: 16 Oct 17:28
Completed: 16 Oct 17:30
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-16 17:18:48 -0400 by logger.rb/56815
[START] [2019-10-16 17:18:48] logged process
[START] [2019-10-16 17:18:48] create_harvest_instance
[STOP] [2019-10-16 17:18:49] create_harvest_instance
[START] [2019-10-16 17:18:49] fetch_files
[STOP] [2019-10-16 17:18:49] fetch_files
[START] [2019-10-16 17:18:49] validate_each_file
[STOP] [2019-10-16 17:18:52] validate_each_file
[START] [2019-10-16 17:18:52] convert_to_csv
[CMD] [2019-10-16 17:18:52] /usr/bin/sort /app/public/converted_csv/tibet_sp_list_refs_17489.csv > /app/public/converted_csv/tibet_sp_list_refs_17489.csv_sorted
[CMD] [2019-10-16 17:18:52] /usr/bin/sort /app/public/converted_csv/tibet_sp_list_nodes_17490.csv > /app/public/converted_csv/tibet_sp_list_nodes_17490.csv_sorted
[CMD] [2019-10-16 17:18:52] /usr/bin/sort /app/public/converted_csv/tibet_sp_list_occurrences_17491.csv > /app/public/converted_csv/tibet_sp_list_occurrences_17491.csv_sorted
[CMD] [2019-10-16 17:18:52] /usr/bin/sort /app/public/converted_csv/tibet_sp_list_measurements_17492.csv > /app/public/converted_csv/tibet_sp_list_measurements_17492.csv_sorted
[STOP] [2019-10-16 17:18:52] convert_to_csv
[START] [2019-10-16 17:18:52] calculate_delta
[CMD] [2019-10-16 17:18:52] echo "0a" > /app/public/diff/tibet_sp_list_refs_17489.diff
[CMD] [2019-10-16 17:18:52] tail -n +1 /app/public/converted_csv/tibet_sp_list_refs_17489.csv >> /app/public/diff/tibet_sp_list_refs_17489.diff
[CMD] [2019-10-16 17:18:52] echo "." >> /app/public/diff/tibet_sp_list_refs_17489.diff
[CMD] [2019-10-16 17:18:52] echo "0a" > /app/public/diff/tibet_sp_list_nodes_17490.diff
[CMD] [2019-10-16 17:18:52] tail -n +1 /app/public/converted_csv/tibet_sp_list_nodes_17490.csv >> /app/public/diff/tibet_sp_list_nodes_17490.diff
[CMD] [2019-10-16 17:18:53] echo "." >> /app/public/diff/tibet_sp_list_nodes_17490.diff
[CMD] [2019-10-16 17:18:53] echo "0a" > /app/public/diff/tibet_sp_list_occurrences_17491.diff
[CMD] [2019-10-16 17:18:53] tail -n +1 /app/public/converted_csv/tibet_sp_list_occurrences_17491.csv >> /app/public/diff/tibet_sp_list_occurrences_17491.diff
[CMD] [2019-10-16 17:18:53] echo "." >> /app/public/diff/tibet_sp_list_occurrences_17491.diff
[CMD] [2019-10-16 17:18:53] echo "0a" > /app/public/diff/tibet_sp_list_measurements_17492.diff
[CMD] [2019-10-16 17:18:53] tail -n +1 /app/public/converted_csv/tibet_sp_list_measurements_17492.csv >> /app/public/diff/tibet_sp_list_measurements_17492.diff
[CMD] [2019-10-16 17:18:53] echo "." >> /app/public/diff/tibet_sp_list_measurements_17492.diff
[STOP] [2019-10-16 17:18:53] calculate_delta
[START] [2019-10-16 17:18:53] parse_diff_and_store
[INFO] [2019-10-16 17:18:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 17:18:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 17:18:55] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 17:18:56] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 17:19:22] Storing 2 References
[INFO] [2019-10-16 17:19:22] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 17:19:22] Average Time: 0.0
[INFO] [2019-10-16 17:19:22] Total Time: 1s
[INFO] [2019-10-16 17:19:22] Storing 6925 ScientificNames
[INFO] [2019-10-16 17:19:22] Processing group of 6925 in 7 groups of 1000
[INFO] [2019-10-16 17:19:24] Average Time: 0.344
[INFO] [2019-10-16 17:19:24] Total Time: 3s
[INFO] [2019-10-16 17:19:24] last 3 / first 3: 0.85
[INFO] [2019-10-16 17:19:24] Std.Dev: 0.05477225575051661; Max: 0.47
[INFO] [2019-10-16 17:19:24] Storing 6925 Nodes
[INFO] [2019-10-16 17:19:24] Processing group of 6925 in 7 groups of 1000
[INFO] [2019-10-16 17:19:26] Average Time: 0.284
[INFO] [2019-10-16 17:19:26] Total Time: 3s
[INFO] [2019-10-16 17:19:26] last 3 / first 3: 1.0
[INFO] [2019-10-16 17:19:26] Std.Dev: 0.0; Max: 0.3
[INFO] [2019-10-16 17:19:26] Storing 4338 Occurrences
[INFO] [2019-10-16 17:19:26] Processing group of 4338 in 5 groups of 1000
[INFO] [2019-10-16 17:19:27] Average Time: 0.09
[INFO] [2019-10-16 17:19:27] Total Time: 1s
[INFO] [2019-10-16 17:19:27] Storing 9516 TraitsReferences
[INFO] [2019-10-16 17:19:27] Processing group of 9516 in 10 groups of 1000
[INFO] [2019-10-16 17:19:28] Average Time: 0.069
[INFO] [2019-10-16 17:19:28] Total Time: 1s
[INFO] [2019-10-16 17:19:28] last 3 / first 3: 0.59
[INFO] [2019-10-16 17:19:28] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-16 17:19:28] Storing 9515 Traits
[INFO] [2019-10-16 17:19:28] Processing group of 9515 in 10 groups of 1000
[INFO] [2019-10-16 17:19:31] Average Time: 0.331
[INFO] [2019-10-16 17:19:31] Total Time: 4s
[INFO] [2019-10-16 17:19:31] last 3 / first 3: 0.88
[INFO] [2019-10-16 17:19:31] Std.Dev: 0.08944271909999159; Max: 0.44
[INFO] [2019-10-16 17:19:31] Storing 9510 MetaTraits
[INFO] [2019-10-16 17:19:31] Processing group of 9510 in 10 groups of 1000
[INFO] [2019-10-16 17:19:32] Average Time: 0.124
[INFO] [2019-10-16 17:19:32] Total Time: 2s
[INFO] [2019-10-16 17:19:32] last 3 / first 3: 0.8
[INFO] [2019-10-16 17:19:32] Std.Dev: 0.0; Max: 0.15
[STOP] [2019-10-16 17:19:32] parse_diff_and_store
[START] [2019-10-16 17:19:32] resolve_keys
[INFO] [2019-10-16 17:20:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 17:20:05] traits to occurrences...
[INFO] [2019-10-16 17:20:08] traits to nodes (through occurrences)...
[INFO] [2019-10-16 17:20:09] Traits to sex term...
[INFO] [2019-10-16 17:20:12] Traits to lifestage term...
[INFO] [2019-10-16 17:20:15] MetaTraits to traits...
[INFO] [2019-10-16 17:20:16] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 17:20:17] Assocs to occurrences...
[INFO] [2019-10-16 17:20:17] Assocs to nodes...
[INFO] [2019-10-16 17:20:17] Assoc to sex term...
[INFO] [2019-10-16 17:20:17] Assoc to lifestage term...
[STOP] [2019-10-16 17:20:17] resolve_keys
[START] [2019-10-16 17:20:17] hold_for_later_1
[STOP] [2019-10-16 17:20:17] hold_for_later_1
[START] [2019-10-16 17:20:17] hold_for_later_2
[STOP] [2019-10-16 17:20:17] hold_for_later_2
[START] [2019-10-16 17:20:17] resolve_missing_parents
[STOP] [2019-10-16 17:20:32] resolve_missing_parents
[START] [2019-10-16 17:20:32] rebuild_nodes
[START] [2019-10-16 17:20:32] Flattener#flatten
[START] [2019-10-16 17:20:32] Flattener#study_resource
[START] [2019-10-16 17:20:32] Flattener#build_ancestry
[STOP] [2019-10-16 17:20:32] Flattener#build_ancestry
[INFO] [2019-10-16 17:20:32] 6925 ancestry keys
[START] [2019-10-16 17:20:32] build_node_ancestors
[INFO] [2019-10-16 17:20:32] old ancestors deleted.
[STOP] [2019-10-16 17:20:33] build_node_ancestors
[START] [2019-10-16 17:20:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 17:20:36] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 17:20:36] Flattener#flatten
[STOP] [2019-10-16 17:20:36] rebuild_nodes
[START] [2019-10-16 17:20:36] resolve_missing_media_owners
[STOP] [2019-10-16 17:20:36] resolve_missing_media_owners
[START] [2019-10-16 17:20:36] sanitize_media_verbatims
[STOP] [2019-10-16 17:20:36] sanitize_media_verbatims
[START] [2019-10-16 17:20:36] queue_downloads
[STOP] [2019-10-16 17:20:36] queue_downloads
[START] [2019-10-16 17:20:36] parse_names
[WARN] [2019-10-16 17:20:36] I see 6925 names which still need to be parsed.
[STOP] [2019-10-16 17:20:42] parse_names
[START] [2019-10-16 17:20:42] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 17:20:42] denormalize_canonical_names_to_nodes
[START] [2019-10-16 17:20:42] match_nodes
[START] [2019-10-16 17:20:42] map_all_nodes_to_pages
[STOP] [2019-10-16 17:27:53] map_all_nodes_to_pages
[INFO] [2019-10-16 17:27:53] 419 Unmatched nodes (of 6925)! That's too many to output. First 10: Magnoliopsida (#52473178); Prunus vulgaris (#52476223); Potentilla sino-nivea (#52473357); Potentilla leuconota (#52475438); Potentilla cuneata (#52476478); Potentilla parviflora (#52479401); Cotoneaster obovata (#52473535); Cotoneaster prostrata (#52474148); Cotoneaster microphylla (#52474536); Coluria (#52475116)
[START] [2019-10-16 17:27:53] update_nodes
[STOP] [2019-10-16 17:27:55] update_nodes
[STOP] [2019-10-16 17:27:55] match_nodes
[START] [2019-10-16 17:27:55] reindex_search
[STOP] [2019-10-16 17:28:17] reindex_search
[START] [2019-10-16 17:28:17] normalize_units
[STOP] [2019-10-16 17:28:17] normalize_units
[START] [2019-10-16 17:28:17] calculate_statistics
[STOP] [2019-10-16 17:28:17] calculate_statistics
[START] [2019-10-16 17:28:17] complete_harvest_instance
[START] [2019-10-16 17:28:17] overall_tsv_creation
[INFO] [2019-10-16 17:28:17] Processing group of 6925 in 1 batches of 10000
[INFO] [2019-10-16 17:29:29] 4338 Traits (unfiltered)...
[INFO] [2019-10-16 17:29:42] 4338 Traits (filtered)...
[INFO] [2019-10-16 17:29:42] 0 Associations (filtered)...
[INFO] [2019-10-16 17:30:27] 21687 metadata added.
[INFO] [2019-10-16 17:30:27] 0 metadata added.
[INFO] [2019-10-16 17:30:28] Average Time: 105.23
[INFO] [2019-10-16 17:30:28] Total Time: 2m11s
[STOP] [2019-10-16 17:30:28] overall_tsv_creation
[INFO] [2019-10-16 17:30:28] Done. Check your files:
[INFO] [2019-10-16 17:30:28] (6925 lines) /app/public/data/tibet_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 17:30:28] (23675 lines) /app/public/data/tibet_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 17:30:28] (6925 lines) /app/public/data/tibet_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 17:30:28] (4339 lines) /app/public/data/tibet_sp_list/publish_traits.tsv
[INFO] [2019-10-16 17:30:28] (21688 lines) /app/public/data/tibet_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 17:30:28] complete_harvest_instance
[START] [2019-10-16 17:30:28] completed
[STOP] [2019-10-16 17:30:28] completed
[STOP] [2019-10-16 17:30:28] logged process, took 699.77
Latest Process

16 Oct 17:18 EXITED currently processing 0