Harvest for Nepal Species List Created 14 Oct 11:33

Stage: completed
Fetched: 14 Oct 11:33
Validated: 14 Oct 11:33
Deltas Created 14 Oct 11:33
Units Normalized: 14 Oct 11:47
Ancestry Built: 14 Oct 11:35
Nodes Matched: 14 Oct 11:47
Names Parsed: 14 Oct 11:36
New Models Stored: 14 Oct 11:34
Indexed: 14 Oct 11:47
Completed: 14 Oct 11:50
Time to Harvest: less than a minute
Harvesting Log

(151 lines)
# Logfile created on 2019-10-14 11:33:22 -0400 by logger.rb/56815
[START] [2019-10-14 11:33:22] logged process
[START] [2019-10-14 11:33:22] create_harvest_instance
[STOP] [2019-10-14 11:33:23] create_harvest_instance
[START] [2019-10-14 11:33:23] fetch_files
[STOP] [2019-10-14 11:33:23] fetch_files
[START] [2019-10-14 11:33:23] validate_each_file
[STOP] [2019-10-14 11:33:24] validate_each_file
[START] [2019-10-14 11:33:24] convert_to_csv
[CMD] [2019-10-14 11:33:24] /usr/bin/sort /app/public/converted_csv/nepal_sp_list_refs_16683.csv > /app/public/converted_csv/nepal_sp_list_refs_16683.csv_sorted
[CMD] [2019-10-14 11:33:24] /usr/bin/sort /app/public/converted_csv/nepal_sp_list_nodes_16684.csv > /app/public/converted_csv/nepal_sp_list_nodes_16684.csv_sorted
[CMD] [2019-10-14 11:33:24] /usr/bin/sort /app/public/converted_csv/nepal_sp_list_occurrences_16685.csv > /app/public/converted_csv/nepal_sp_list_occurrences_16685.csv_sorted
[CMD] [2019-10-14 11:33:24] /usr/bin/sort /app/public/converted_csv/nepal_sp_list_measurements_16686.csv > /app/public/converted_csv/nepal_sp_list_measurements_16686.csv_sorted
[STOP] [2019-10-14 11:33:25] convert_to_csv
[START] [2019-10-14 11:33:25] calculate_delta
[CMD] [2019-10-14 11:33:25] echo "0a" > /app/public/diff/nepal_sp_list_refs_16683.diff
[CMD] [2019-10-14 11:33:25] tail -n +1 /app/public/converted_csv/nepal_sp_list_refs_16683.csv >> /app/public/diff/nepal_sp_list_refs_16683.diff
[CMD] [2019-10-14 11:33:25] echo "." >> /app/public/diff/nepal_sp_list_refs_16683.diff
[CMD] [2019-10-14 11:33:25] echo "0a" > /app/public/diff/nepal_sp_list_nodes_16684.diff
[CMD] [2019-10-14 11:33:25] tail -n +1 /app/public/converted_csv/nepal_sp_list_nodes_16684.csv >> /app/public/diff/nepal_sp_list_nodes_16684.diff
[CMD] [2019-10-14 11:33:25] echo "." >> /app/public/diff/nepal_sp_list_nodes_16684.diff
[CMD] [2019-10-14 11:33:25] echo "0a" > /app/public/diff/nepal_sp_list_occurrences_16685.diff
[CMD] [2019-10-14 11:33:25] tail -n +1 /app/public/converted_csv/nepal_sp_list_occurrences_16685.csv >> /app/public/diff/nepal_sp_list_occurrences_16685.diff
[CMD] [2019-10-14 11:33:25] echo "." >> /app/public/diff/nepal_sp_list_occurrences_16685.diff
[CMD] [2019-10-14 11:33:25] echo "0a" > /app/public/diff/nepal_sp_list_measurements_16686.diff
[CMD] [2019-10-14 11:33:26] tail -n +1 /app/public/converted_csv/nepal_sp_list_measurements_16686.csv >> /app/public/diff/nepal_sp_list_measurements_16686.diff
[CMD] [2019-10-14 11:33:26] echo "." >> /app/public/diff/nepal_sp_list_measurements_16686.diff
[STOP] [2019-10-14 11:33:26] calculate_delta
[START] [2019-10-14 11:33:26] parse_diff_and_store
[INFO] [2019-10-14 11:33:26] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 11:33:26] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 11:33:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 11:33:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 11:34:12] Storing 2 References
[INFO] [2019-10-14 11:34:12] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 11:34:12] Average Time: 0.0
[INFO] [2019-10-14 11:34:12] Total Time: 1s
[INFO] [2019-10-14 11:34:12] Storing 10263 ScientificNames
[INFO] [2019-10-14 11:34:12] Processing group of 10263 in 11 groups of 1000
[INFO] [2019-10-14 11:34:16] Average Time: 0.358
[INFO] [2019-10-14 11:34:16] Total Time: 4s
[INFO] [2019-10-14 11:34:16] last 3 / first 3: 0.74
[INFO] [2019-10-14 11:34:16] Std.Dev: 0.09486832980505137; Max: 0.48
[INFO] [2019-10-14 11:34:16] Storing 10263 Nodes
[INFO] [2019-10-14 11:34:16] Processing group of 10263 in 11 groups of 1000
[INFO] [2019-10-14 11:34:19] Average Time: 0.291
[INFO] [2019-10-14 11:34:19] Total Time: 4s
[INFO] [2019-10-14 11:34:19] last 3 / first 3: 0.73
[INFO] [2019-10-14 11:34:19] Std.Dev: 0.07071067811865475; Max: 0.34
[INFO] [2019-10-14 11:34:19] Storing 6748 Occurrences
[INFO] [2019-10-14 11:34:19] Processing group of 6748 in 7 groups of 1000
[INFO] [2019-10-14 11:34:20] Average Time: 0.101
[INFO] [2019-10-14 11:34:20] Total Time: 1s
[INFO] [2019-10-14 11:34:20] last 3 / first 3: 0.79
[INFO] [2019-10-14 11:34:20] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-14 11:34:20] Storing 13950 TraitsReferences
[INFO] [2019-10-14 11:34:20] Processing group of 13950 in 14 groups of 1000
[INFO] [2019-10-14 11:34:21] Average Time: 0.073
[INFO] [2019-10-14 11:34:21] Total Time: 2s
[INFO] [2019-10-14 11:34:21] last 3 / first 3: 0.66
[INFO] [2019-10-14 11:34:21] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-14 11:34:21] Storing 13949 Traits
[INFO] [2019-10-14 11:34:21] Processing group of 13949 in 14 groups of 1000
[INFO] [2019-10-14 11:34:25] Average Time: 0.303
[INFO] [2019-10-14 11:34:25] Total Time: 5s
[INFO] [2019-10-14 11:34:25] last 3 / first 3: 0.75
[INFO] [2019-10-14 11:34:25] Std.Dev: 0.07071067811865475; Max: 0.55
[INFO] [2019-10-14 11:34:25] Storing 13942 MetaTraits
[INFO] [2019-10-14 11:34:25] Processing group of 13942 in 14 groups of 1000
[INFO] [2019-10-14 11:34:27] Average Time: 0.121
[INFO] [2019-10-14 11:34:27] Total Time: 2s
[INFO] [2019-10-14 11:34:27] last 3 / first 3: 1.03
[INFO] [2019-10-14 11:34:27] Std.Dev: 0.03162277660168379; Max: 0.19
[STOP] [2019-10-14 11:34:27] parse_diff_and_store
[START] [2019-10-14 11:34:27] resolve_keys
[INFO] [2019-10-14 11:35:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 11:35:14] traits to occurrences...
[INFO] [2019-10-14 11:35:19] traits to nodes (through occurrences)...
[INFO] [2019-10-14 11:35:19] Traits to sex term...
[INFO] [2019-10-14 11:35:24] Traits to lifestage term...
[INFO] [2019-10-14 11:35:28] MetaTraits to traits...
[INFO] [2019-10-14 11:35:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 11:35:31] Assocs to occurrences...
[INFO] [2019-10-14 11:35:31] Assocs to nodes...
[INFO] [2019-10-14 11:35:31] Assoc to sex term...
[INFO] [2019-10-14 11:35:31] Assoc to lifestage term...
[STOP] [2019-10-14 11:35:31] resolve_keys
[START] [2019-10-14 11:35:31] hold_for_later_1
[STOP] [2019-10-14 11:35:31] hold_for_later_1
[START] [2019-10-14 11:35:31] hold_for_later_2
[STOP] [2019-10-14 11:35:31] hold_for_later_2
[START] [2019-10-14 11:35:31] resolve_missing_parents
[STOP] [2019-10-14 11:35:52] resolve_missing_parents
[START] [2019-10-14 11:35:52] rebuild_nodes
[START] [2019-10-14 11:35:52] Flattener#flatten
[START] [2019-10-14 11:35:52] Flattener#study_resource
[START] [2019-10-14 11:35:52] Flattener#build_ancestry
[STOP] [2019-10-14 11:35:54] Flattener#build_ancestry
[INFO] [2019-10-14 11:35:54] 10263 ancestry keys
[START] [2019-10-14 11:35:54] build_node_ancestors
[INFO] [2019-10-14 11:35:54] old ancestors deleted.
[STOP] [2019-10-14 11:35:56] build_node_ancestors
[START] [2019-10-14 11:35:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:35:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 11:35:58] Flattener#flatten
[STOP] [2019-10-14 11:35:58] rebuild_nodes
[START] [2019-10-14 11:35:58] resolve_missing_media_owners
[STOP] [2019-10-14 11:35:58] resolve_missing_media_owners
[START] [2019-10-14 11:35:58] sanitize_media_verbatims
[STOP] [2019-10-14 11:35:58] sanitize_media_verbatims
[START] [2019-10-14 11:35:58] queue_downloads
[STOP] [2019-10-14 11:35:58] queue_downloads
[START] [2019-10-14 11:35:58] parse_names
[WARN] [2019-10-14 11:35:58] I see 10263 names which still need to be parsed.
[STOP] [2019-10-14 11:36:07] parse_names
[START] [2019-10-14 11:36:07] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 11:36:07] denormalize_canonical_names_to_nodes
[START] [2019-10-14 11:36:07] match_nodes
[START] [2019-10-14 11:36:07] map_all_nodes_to_pages
[STOP] [2019-10-14 11:47:02] map_all_nodes_to_pages
[INFO] [2019-10-14 11:47:02] 795 Unmatched nodes (of 10263)! That's too many to output. First 10: Tenaxia schneideri (#50867196); Elymus nepalense (#50870582); Calamagrostis pulchella (#50864250); Calamagrostis triaristata (#50868324); Agrostis filiformis (#50870790); Leymus thomsonii (#50862205); Koeleria cristata (#50862436); Poa albertii (#50870628); Pennisetum glauca (#50870919); Oryzopsis gracile (#50863686)
[START] [2019-10-14 11:47:02] update_nodes
[STOP] [2019-10-14 11:47:06] update_nodes
[STOP] [2019-10-14 11:47:06] match_nodes
[START] [2019-10-14 11:47:06] reindex_search
[STOP] [2019-10-14 11:47:36] reindex_search
[START] [2019-10-14 11:47:36] normalize_units
[STOP] [2019-10-14 11:47:36] normalize_units
[START] [2019-10-14 11:47:36] calculate_statistics
[STOP] [2019-10-14 11:47:36] calculate_statistics
[START] [2019-10-14 11:47:36] complete_harvest_instance
[START] [2019-10-14 11:47:36] overall_tsv_creation
[INFO] [2019-10-14 11:47:36] Processing group of 10263 in 2 batches of 10000
[INFO] [2019-10-14 11:49:04] 6748 Traits (unfiltered)...
[INFO] [2019-10-14 11:49:17] 6748 Traits (filtered)...
[INFO] [2019-10-14 11:49:18] 0 Associations (filtered)...
[INFO] [2019-10-14 11:50:09] 33733 metadata added.
[INFO] [2019-10-14 11:50:09] 0 metadata added.
[INFO] [2019-10-14 11:50:42] Average Time: 69.43
[INFO] [2019-10-14 11:50:42] Total Time: 3m6s
[STOP] [2019-10-14 11:50:42] overall_tsv_creation
[INFO] [2019-10-14 11:50:42] Done. Check your files:
[INFO] [2019-10-14 11:50:42] (10263 lines) /app/public/data/nepal_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 11:50:42] (25163 lines) /app/public/data/nepal_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 11:50:42] (10263 lines) /app/public/data/nepal_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 11:50:42] (6749 lines) /app/public/data/nepal_sp_list/publish_traits.tsv
[INFO] [2019-10-14 11:50:42] (33734 lines) /app/public/data/nepal_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 11:50:43] complete_harvest_instance
[START] [2019-10-14 11:50:43] completed
[STOP] [2019-10-14 11:50:43] completed
[STOP] [2019-10-14 11:50:43] logged process, took 1040.63
Latest Process

14 Oct 11:33 EXITED currently processing 0