Harvest for Celtic Sea Species List Created 22 Dec 23:40

Stage: completed
Fetched: 22 Dec 23:40
Validated: 22 Dec 23:40
Deltas Created 22 Dec 23:40
Units Normalized: 23 Dec 00:06
Ancestry Built: 22 Dec 23:41
Nodes Matched: 23 Dec 00:06
Names Parsed: 22 Dec 23:41
New Models Stored: 22 Dec 23:40
Indexed: 23 Dec 00:06
Completed: 23 Dec 00:09
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-22 23:40:01 -0500 by logger.rb/56815
[START] [2019-12-22 23:40:01] logged process
[START] [2019-12-22 23:40:01] create_harvest_instance
[STOP] [2019-12-22 23:40:02] create_harvest_instance
[START] [2019-12-22 23:40:02] fetch_files
[STOP] [2019-12-22 23:40:02] fetch_files
[START] [2019-12-22 23:40:02] validate_each_file
[STOP] [2019-12-22 23:40:03] validate_each_file
[START] [2019-12-22 23:40:03] convert_to_csv
[CMD] [2019-12-22 23:40:03] /usr/bin/sort /app/public/converted_csv/celtic_sea_sp_li_refs_19170.csv > /app/public/converted_csv/celtic_sea_sp_li_refs_19170.csv_sorted
[CMD] [2019-12-22 23:40:03] /usr/bin/sort /app/public/converted_csv/celtic_sea_sp_li_nodes_19171.csv > /app/public/converted_csv/celtic_sea_sp_li_nodes_19171.csv_sorted
[CMD] [2019-12-22 23:40:03] /usr/bin/sort /app/public/converted_csv/celtic_sea_sp_li_occurrences_19172.csv > /app/public/converted_csv/celtic_sea_sp_li_occurrences_19172.csv_sorted
[CMD] [2019-12-22 23:40:03] /usr/bin/sort /app/public/converted_csv/celtic_sea_sp_li_measurements_19173.csv > /app/public/converted_csv/celtic_sea_sp_li_measurements_19173.csv_sorted
[STOP] [2019-12-22 23:40:03] convert_to_csv
[START] [2019-12-22 23:40:03] calculate_delta
[CMD] [2019-12-22 23:40:03] echo "0a" > /app/public/diff/celtic_sea_sp_li_refs_19170.diff
[CMD] [2019-12-22 23:40:03] tail -n +1 /app/public/converted_csv/celtic_sea_sp_li_refs_19170.csv >> /app/public/diff/celtic_sea_sp_li_refs_19170.diff
[CMD] [2019-12-22 23:40:03] echo "." >> /app/public/diff/celtic_sea_sp_li_refs_19170.diff
[CMD] [2019-12-22 23:40:03] echo "0a" > /app/public/diff/celtic_sea_sp_li_nodes_19171.diff
[CMD] [2019-12-22 23:40:03] tail -n +1 /app/public/converted_csv/celtic_sea_sp_li_nodes_19171.csv >> /app/public/diff/celtic_sea_sp_li_nodes_19171.diff
[CMD] [2019-12-22 23:40:03] echo "." >> /app/public/diff/celtic_sea_sp_li_nodes_19171.diff
[CMD] [2019-12-22 23:40:03] echo "0a" > /app/public/diff/celtic_sea_sp_li_occurrences_19172.diff
[CMD] [2019-12-22 23:40:03] tail -n +1 /app/public/converted_csv/celtic_sea_sp_li_occurrences_19172.csv >> /app/public/diff/celtic_sea_sp_li_occurrences_19172.diff
[CMD] [2019-12-22 23:40:03] echo "." >> /app/public/diff/celtic_sea_sp_li_occurrences_19172.diff
[CMD] [2019-12-22 23:40:03] echo "0a" > /app/public/diff/celtic_sea_sp_li_measurements_19173.diff
[CMD] [2019-12-22 23:40:04] tail -n +1 /app/public/converted_csv/celtic_sea_sp_li_measurements_19173.csv >> /app/public/diff/celtic_sea_sp_li_measurements_19173.diff
[CMD] [2019-12-22 23:40:04] echo "." >> /app/public/diff/celtic_sea_sp_li_measurements_19173.diff
[STOP] [2019-12-22 23:40:04] calculate_delta
[START] [2019-12-22 23:40:04] parse_diff_and_store
[INFO] [2019-12-22 23:40:04] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 23:40:04] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 23:40:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 23:40:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 23:40:29] Storing 2 References
[INFO] [2019-12-22 23:40:29] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 23:40:29] Average Time: 0.0
[INFO] [2019-12-22 23:40:29] Total Time: 1s
[INFO] [2019-12-22 23:40:29] Storing 7402 ScientificNames
[INFO] [2019-12-22 23:40:29] Processing group of 7402 in 8 groups of 1000
[INFO] [2019-12-22 23:40:32] Average Time: 0.386
[INFO] [2019-12-22 23:40:32] Total Time: 4s
[INFO] [2019-12-22 23:40:32] last 3 / first 3: 0.73
[INFO] [2019-12-22 23:40:32] Std.Dev: 0.10488088481701516; Max: 0.53
[INFO] [2019-12-22 23:40:32] Storing 7402 Nodes
[INFO] [2019-12-22 23:40:32] Processing group of 7402 in 8 groups of 1000
[INFO] [2019-12-22 23:40:35] Average Time: 0.355
[INFO] [2019-12-22 23:40:35] Total Time: 3s
[INFO] [2019-12-22 23:40:35] last 3 / first 3: 0.74
[INFO] [2019-12-22 23:40:35] Std.Dev: 0.12649110640673517; Max: 0.6
[INFO] [2019-12-22 23:40:35] Storing 3768 Occurrences
[INFO] [2019-12-22 23:40:35] Processing group of 3768 in 4 groups of 1000
[INFO] [2019-12-22 23:40:36] Average Time: 0.11
[INFO] [2019-12-22 23:40:36] Total Time: 1s
[INFO] [2019-12-22 23:40:36] Storing 7536 TraitsReferences
[INFO] [2019-12-22 23:40:36] Processing group of 7536 in 8 groups of 1000
[INFO] [2019-12-22 23:40:36] Average Time: 0.089
[INFO] [2019-12-22 23:40:36] Total Time: 1s
[INFO] [2019-12-22 23:40:36] last 3 / first 3: 0.67
[INFO] [2019-12-22 23:40:36] Std.Dev: 0.03162277660168379; Max: 0.17
[INFO] [2019-12-22 23:40:36] Storing 7536 Traits
[INFO] [2019-12-22 23:40:36] Processing group of 7536 in 8 groups of 1000
[INFO] [2019-12-22 23:40:39] Average Time: 0.351
[INFO] [2019-12-22 23:40:39] Total Time: 3s
[INFO] [2019-12-22 23:40:39] last 3 / first 3: 0.77
[INFO] [2019-12-22 23:40:39] Std.Dev: 0.07745966692414834; Max: 0.48
[INFO] [2019-12-22 23:40:39] Storing 7534 MetaTraits
[INFO] [2019-12-22 23:40:39] Processing group of 7534 in 8 groups of 1000
[INFO] [2019-12-22 23:40:40] Average Time: 0.163
[INFO] [2019-12-22 23:40:40] Total Time: 2s
[INFO] [2019-12-22 23:40:40] last 3 / first 3: 0.76
[INFO] [2019-12-22 23:40:40] Std.Dev: 0.044721359549995794; Max: 0.22
[STOP] [2019-12-22 23:40:40] parse_diff_and_store
[START] [2019-12-22 23:40:40] resolve_keys
[INFO] [2019-12-22 23:41:10] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 23:41:13] traits to occurrences...
[INFO] [2019-12-22 23:41:15] traits to nodes (through occurrences)...
[INFO] [2019-12-22 23:41:15] Traits to sex term...
[INFO] [2019-12-22 23:41:16] Traits to lifestage term...
[INFO] [2019-12-22 23:41:18] MetaTraits to traits...
[INFO] [2019-12-22 23:41:18] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 23:41:19] Assocs to occurrences...
[INFO] [2019-12-22 23:41:19] Assocs to nodes...
[INFO] [2019-12-22 23:41:19] Assoc to sex term...
[INFO] [2019-12-22 23:41:19] Assoc to lifestage term...
[STOP] [2019-12-22 23:41:19] resolve_keys
[START] [2019-12-22 23:41:19] hold_for_later_1
[STOP] [2019-12-22 23:41:19] hold_for_later_1
[START] [2019-12-22 23:41:19] hold_for_later_2
[STOP] [2019-12-22 23:41:19] hold_for_later_2
[START] [2019-12-22 23:41:19] resolve_missing_parents
[STOP] [2019-12-22 23:41:37] resolve_missing_parents
[START] [2019-12-22 23:41:37] rebuild_nodes
[START] [2019-12-22 23:41:37] Flattener#flatten
[START] [2019-12-22 23:41:37] Flattener#study_resource
[START] [2019-12-22 23:41:37] Flattener#build_ancestry
[STOP] [2019-12-22 23:41:38] Flattener#build_ancestry
[INFO] [2019-12-22 23:41:38] 7402 ancestry keys
[START] [2019-12-22 23:41:38] build_node_ancestors
[INFO] [2019-12-22 23:41:38] old ancestors deleted.
[STOP] [2019-12-22 23:41:41] build_node_ancestors
[START] [2019-12-22 23:41:44] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:41:44] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 23:41:44] Flattener#flatten
[STOP] [2019-12-22 23:41:44] rebuild_nodes
[START] [2019-12-22 23:41:44] resolve_missing_media_owners
[STOP] [2019-12-22 23:41:44] resolve_missing_media_owners
[START] [2019-12-22 23:41:44] sanitize_media_verbatims
[STOP] [2019-12-22 23:41:44] sanitize_media_verbatims
[START] [2019-12-22 23:41:44] queue_downloads
[STOP] [2019-12-22 23:41:44] queue_downloads
[START] [2019-12-22 23:41:44] parse_names
[WARN] [2019-12-22 23:41:44] I see 7402 names which still need to be parsed.
[STOP] [2019-12-22 23:41:52] parse_names
[START] [2019-12-22 23:41:52] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 23:41:52] denormalize_canonical_names_to_nodes
[START] [2019-12-22 23:41:52] match_nodes
[START] [2019-12-22 23:41:52] map_all_nodes_to_pages
[STOP] [2019-12-23 00:06:20] map_all_nodes_to_pages
[INFO] [2019-12-23 00:06:20] 375 Unmatched nodes (of 7402)! That's too many to output. First 10: Puffinus griseus (#61808233); Larus melanocephalus (#61810641); Arenaria serpyllifolia (#61808749); Philomachus (#61811361); Philomachus pugnax (#61811360); Limnodromus (#61812500); Anas penelope (#61808537); Anas strepera (#61808684); Anas clypeata (#61809048); Anas americana (#61810984)
[START] [2019-12-23 00:06:20] update_nodes
[STOP] [2019-12-23 00:06:22] update_nodes
[STOP] [2019-12-23 00:06:22] match_nodes
[START] [2019-12-23 00:06:22] reindex_search
[STOP] [2019-12-23 00:06:40] reindex_search
[START] [2019-12-23 00:06:40] normalize_units
[STOP] [2019-12-23 00:06:40] normalize_units
[START] [2019-12-23 00:06:40] calculate_statistics
[STOP] [2019-12-23 00:06:40] calculate_statistics
[START] [2019-12-23 00:06:40] complete_harvest_instance
[START] [2019-12-23 00:06:40] overall_tsv_creation
[INFO] [2019-12-23 00:06:41] Processing group of 7402 in 1 batches of 10000
[INFO] [2019-12-23 00:08:01] 3768 Traits (unfiltered)...
[INFO] [2019-12-23 00:08:15] 3768 Traits (filtered)...
[INFO] [2019-12-23 00:08:15] 0 Associations (filtered)...
[INFO] [2019-12-23 00:09:01] 18838 metadata added.
[INFO] [2019-12-23 00:09:01] 0 metadata added.
[INFO] [2019-12-23 00:09:01] Average Time: 112.12
[INFO] [2019-12-23 00:09:01] Total Time: 2m21s
[STOP] [2019-12-23 00:09:01] overall_tsv_creation
[INFO] [2019-12-23 00:09:01] Done. Check your files:
[INFO] [2019-12-23 00:09:01] (7402 lines) /app/public/data/celtic_sea_sp_li/publish_nodes.tsv
[INFO] [2019-12-23 00:09:01] (36958 lines) /app/public/data/celtic_sea_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-23 00:09:01] (7402 lines) /app/public/data/celtic_sea_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-23 00:09:01] (3769 lines) /app/public/data/celtic_sea_sp_li/publish_traits.tsv
[INFO] [2019-12-23 00:09:01] (18839 lines) /app/public/data/celtic_sea_sp_li/publish_metadata.tsv
[STOP] [2019-12-23 00:09:01] complete_harvest_instance
[START] [2019-12-23 00:09:01] completed
[STOP] [2019-12-23 00:09:01] completed
[STOP] [2019-12-23 00:09:01] logged process, took 1739.63
Latest Process

22 Dec 23:40 EXITED currently processing 0