Harvest for Bay of Bengal Species List Created 22 Dec 21:26

Stage: completed
Fetched: 22 Dec 21:26
Validated: 22 Dec 21:26
Deltas Created 22 Dec 21:27
Units Normalized: 22 Dec 21:54
Ancestry Built: 22 Dec 21:29
Nodes Matched: 22 Dec 21:53
Names Parsed: 22 Dec 21:29
New Models Stored: 22 Dec 21:27
Indexed: 22 Dec 21:54
Completed: 22 Dec 21:58
Time to Harvest: 1 minute
Harvesting Log

(156 lines)
# Logfile created on 2019-12-22 21:26:57 -0500 by logger.rb/56815
[START] [2019-12-22 21:26:57] logged process
[START] [2019-12-22 21:26:57] create_harvest_instance
[STOP] [2019-12-22 21:26:58] create_harvest_instance
[START] [2019-12-22 21:26:58] fetch_files
[STOP] [2019-12-22 21:26:58] fetch_files
[START] [2019-12-22 21:26:58] validate_each_file
[STOP] [2019-12-22 21:26:59] validate_each_file
[START] [2019-12-22 21:26:59] convert_to_csv
[CMD] [2019-12-22 21:26:59] /usr/bin/sort /app/public/converted_csv/bay_bengal_sp_li_refs_19082.csv > /app/public/converted_csv/bay_bengal_sp_li_refs_19082.csv_sorted
[CMD] [2019-12-22 21:26:59] /usr/bin/sort /app/public/converted_csv/bay_bengal_sp_li_nodes_19083.csv > /app/public/converted_csv/bay_bengal_sp_li_nodes_19083.csv_sorted
[CMD] [2019-12-22 21:26:59] /usr/bin/sort /app/public/converted_csv/bay_bengal_sp_li_occurrences_19084.csv > /app/public/converted_csv/bay_bengal_sp_li_occurrences_19084.csv_sorted
[CMD] [2019-12-22 21:26:59] /usr/bin/sort /app/public/converted_csv/bay_bengal_sp_li_measurements_19085.csv > /app/public/converted_csv/bay_bengal_sp_li_measurements_19085.csv_sorted
[STOP] [2019-12-22 21:26:59] convert_to_csv
[START] [2019-12-22 21:26:59] calculate_delta
[CMD] [2019-12-22 21:26:59] echo "0a" > /app/public/diff/bay_bengal_sp_li_refs_19082.diff
[CMD] [2019-12-22 21:26:59] tail -n +1 /app/public/converted_csv/bay_bengal_sp_li_refs_19082.csv >> /app/public/diff/bay_bengal_sp_li_refs_19082.diff
[CMD] [2019-12-22 21:26:59] echo "." >> /app/public/diff/bay_bengal_sp_li_refs_19082.diff
[CMD] [2019-12-22 21:26:59] echo "0a" > /app/public/diff/bay_bengal_sp_li_nodes_19083.diff
[CMD] [2019-12-22 21:26:59] tail -n +1 /app/public/converted_csv/bay_bengal_sp_li_nodes_19083.csv >> /app/public/diff/bay_bengal_sp_li_nodes_19083.diff
[CMD] [2019-12-22 21:27:00] echo "." >> /app/public/diff/bay_bengal_sp_li_nodes_19083.diff
[CMD] [2019-12-22 21:27:00] echo "0a" > /app/public/diff/bay_bengal_sp_li_occurrences_19084.diff
[CMD] [2019-12-22 21:27:00] tail -n +1 /app/public/converted_csv/bay_bengal_sp_li_occurrences_19084.csv >> /app/public/diff/bay_bengal_sp_li_occurrences_19084.diff
[CMD] [2019-12-22 21:27:00] echo "." >> /app/public/diff/bay_bengal_sp_li_occurrences_19084.diff
[CMD] [2019-12-22 21:27:00] echo "0a" > /app/public/diff/bay_bengal_sp_li_measurements_19085.diff
[CMD] [2019-12-22 21:27:00] tail -n +1 /app/public/converted_csv/bay_bengal_sp_li_measurements_19085.csv >> /app/public/diff/bay_bengal_sp_li_measurements_19085.diff
[CMD] [2019-12-22 21:27:00] echo "." >> /app/public/diff/bay_bengal_sp_li_measurements_19085.diff
[STOP] [2019-12-22 21:27:00] calculate_delta
[START] [2019-12-22 21:27:00] parse_diff_and_store
[INFO] [2019-12-22 21:27:00] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 21:27:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 21:27:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 21:27:05] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 21:27:40] Storing 2 References
[INFO] [2019-12-22 21:27:40] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 21:27:40] Average Time: 0.0
[INFO] [2019-12-22 21:27:40] Total Time: 1s
[INFO] [2019-12-22 21:27:40] Storing 11516 ScientificNames
[INFO] [2019-12-22 21:27:40] Processing group of 11516 in 12 groups of 1000
[INFO] [2019-12-22 21:27:45] Average Time: 0.375
[INFO] [2019-12-22 21:27:45] Total Time: 5s
[INFO] [2019-12-22 21:27:45] last 3 / first 3: 1.08
[INFO] [2019-12-22 21:27:45] Std.Dev: 0.09486832980505137; Max: 0.64
[INFO] [2019-12-22 21:27:45] Storing 11516 Nodes
[INFO] [2019-12-22 21:27:45] Processing group of 11516 in 12 groups of 1000
[INFO] [2019-12-22 21:27:48] Average Time: 0.277
[INFO] [2019-12-22 21:27:48] Total Time: 4s
[INFO] [2019-12-22 21:27:48] last 3 / first 3: 0.93
[INFO] [2019-12-22 21:27:48] Std.Dev: 0.044721359549995794; Max: 0.32
[INFO] [2019-12-22 21:27:48] Storing 6608 Occurrences
[INFO] [2019-12-22 21:27:48] Processing group of 6608 in 7 groups of 1000
[INFO] [2019-12-22 21:27:49] Average Time: 0.097
[INFO] [2019-12-22 21:27:49] Total Time: 1s
[INFO] [2019-12-22 21:27:49] last 3 / first 3: 0.81
[INFO] [2019-12-22 21:27:49] Std.Dev: 0.0; Max: 0.11
[INFO] [2019-12-22 21:27:49] Storing 13216 TraitsReferences
[INFO] [2019-12-22 21:27:49] Processing group of 13216 in 14 groups of 1000
[INFO] [2019-12-22 21:27:50] Average Time: 0.076
[INFO] [2019-12-22 21:27:50] Total Time: 2s
[INFO] [2019-12-22 21:27:50] last 3 / first 3: 0.74
[INFO] [2019-12-22 21:27:50] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-12-22 21:27:50] Storing 13216 Traits
[INFO] [2019-12-22 21:27:50] Processing group of 13216 in 14 groups of 1000
[INFO] [2019-12-22 21:27:55] Average Time: 0.345
[INFO] [2019-12-22 21:27:55] Total Time: 5s
[INFO] [2019-12-22 21:27:55] last 3 / first 3: 0.58
[INFO] [2019-12-22 21:27:55] Std.Dev: 0.1414213562373095; Max: 0.68
[INFO] [2019-12-22 21:27:55] Storing 13215 MetaTraits
[INFO] [2019-12-22 21:27:55] Processing group of 13215 in 14 groups of 1000
[INFO] [2019-12-22 21:27:57] Average Time: 0.126
[INFO] [2019-12-22 21:27:57] Total Time: 2s
[INFO] [2019-12-22 21:27:57] last 3 / first 3: 0.68
[INFO] [2019-12-22 21:27:57] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-12-22 21:27:57] parse_diff_and_store
[START] [2019-12-22 21:27:57] resolve_keys
[INFO] [2019-12-22 21:28:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 21:28:44] traits to occurrences...
[INFO] [2019-12-22 21:28:49] traits to nodes (through occurrences)...
[INFO] [2019-12-22 21:28:49] Traits to sex term...
[INFO] [2019-12-22 21:28:53] Traits to lifestage term...
[INFO] [2019-12-22 21:28:58] MetaTraits to traits...
[INFO] [2019-12-22 21:28:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 21:29:01] Assocs to occurrences...
[INFO] [2019-12-22 21:29:01] Assocs to nodes...
[INFO] [2019-12-22 21:29:01] Assoc to sex term...
[INFO] [2019-12-22 21:29:01] Assoc to lifestage term...
[STOP] [2019-12-22 21:29:01] resolve_keys
[START] [2019-12-22 21:29:01] hold_for_later_1
[STOP] [2019-12-22 21:29:01] hold_for_later_1
[START] [2019-12-22 21:29:01] hold_for_later_2
[STOP] [2019-12-22 21:29:01] hold_for_later_2
[START] [2019-12-22 21:29:01] resolve_missing_parents
[STOP] [2019-12-22 21:29:22] resolve_missing_parents
[START] [2019-12-22 21:29:22] rebuild_nodes
[START] [2019-12-22 21:29:22] Flattener#flatten
[START] [2019-12-22 21:29:22] Flattener#study_resource
[START] [2019-12-22 21:29:23] Flattener#build_ancestry
[STOP] [2019-12-22 21:29:23] Flattener#build_ancestry
[INFO] [2019-12-22 21:29:23] 11516 ancestry keys
[START] [2019-12-22 21:29:23] build_node_ancestors
[INFO] [2019-12-22 21:29:23] old ancestors deleted.
[STOP] [2019-12-22 21:29:27] build_node_ancestors
[START] [2019-12-22 21:29:31] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:29:33] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:29:33] Flattener#flatten
[STOP] [2019-12-22 21:29:33] rebuild_nodes
[START] [2019-12-22 21:29:33] resolve_missing_media_owners
[STOP] [2019-12-22 21:29:33] resolve_missing_media_owners
[START] [2019-12-22 21:29:33] sanitize_media_verbatims
[STOP] [2019-12-22 21:29:33] sanitize_media_verbatims
[START] [2019-12-22 21:29:33] queue_downloads
[STOP] [2019-12-22 21:29:33] queue_downloads
[START] [2019-12-22 21:29:33] parse_names
[WARN] [2019-12-22 21:29:33] I see 11516 names which still need to be parsed.
[STOP] [2019-12-22 21:29:43] parse_names
[START] [2019-12-22 21:29:43] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 21:29:43] denormalize_canonical_names_to_nodes
[START] [2019-12-22 21:29:43] match_nodes
[START] [2019-12-22 21:29:43] map_all_nodes_to_pages
[STOP] [2019-12-22 21:53:48] map_all_nodes_to_pages
[INFO] [2019-12-22 21:53:48] 576 Unmatched nodes (of 11516)! That's too many to output. First 10: Egretta intermedia (#61725609); Philomachus (#61725730); Philomachus pugnax (#61725729); Limicola (#61725945); Limicola falcinellus (#61725944); Limnodromus (#61736313); Ceyx erithacus (#61733466); Megalaima (#61725843); Megalaima haemacephala (#61725842); Anas querquedula (#61725704)
[START] [2019-12-22 21:53:48] update_nodes
[STOP] [2019-12-22 21:53:51] update_nodes
[STOP] [2019-12-22 21:53:51] match_nodes
[START] [2019-12-22 21:53:51] reindex_search
[STOP] [2019-12-22 21:54:10] reindex_search
[START] [2019-12-22 21:54:10] normalize_units
[STOP] [2019-12-22 21:54:10] normalize_units
[START] [2019-12-22 21:54:10] calculate_statistics
[STOP] [2019-12-22 21:54:11] calculate_statistics
[START] [2019-12-22 21:54:11] complete_harvest_instance
[START] [2019-12-22 21:54:11] overall_tsv_creation
[INFO] [2019-12-22 21:54:11] Processing group of 11516 in 2 batches of 10000
[INFO] [2019-12-22 21:55:54] 5586 Traits (unfiltered)...
[INFO] [2019-12-22 21:56:10] 5586 Traits (filtered)...
[INFO] [2019-12-22 21:56:10] 0 Associations (filtered)...
[INFO] [2019-12-22 21:57:03] 27929 metadata added.
[INFO] [2019-12-22 21:57:03] 0 metadata added.
[INFO] [2019-12-22 21:57:56] 1022 Traits (unfiltered)...
[INFO] [2019-12-22 21:58:09] 1022 Traits (filtered)...
[INFO] [2019-12-22 21:58:09] 0 Associations (filtered)...
[INFO] [2019-12-22 21:58:48] 5110 metadata added.
[INFO] [2019-12-22 21:58:48] 0 metadata added.
[INFO] [2019-12-22 21:58:48] Average Time: 112.12
[INFO] [2019-12-22 21:58:48] Total Time: 4m38s
[STOP] [2019-12-22 21:58:48] overall_tsv_creation
[INFO] [2019-12-22 21:58:48] Done. Check your files:
[INFO] [2019-12-22 21:58:48] (11516 lines) /app/public/data/bay_bengal_sp_li/publish_nodes.tsv
[INFO] [2019-12-22 21:58:48] (60428 lines) /app/public/data/bay_bengal_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-22 21:58:48] (11516 lines) /app/public/data/bay_bengal_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-22 21:58:48] (6609 lines) /app/public/data/bay_bengal_sp_li/publish_traits.tsv
[INFO] [2019-12-22 21:58:48] (33040 lines) /app/public/data/bay_bengal_sp_li/publish_metadata.tsv
[STOP] [2019-12-22 21:58:48] complete_harvest_instance
[START] [2019-12-22 21:58:48] completed
[STOP] [2019-12-22 21:58:48] completed
[STOP] [2019-12-22 21:58:48] logged process, took 1911.34
Latest Process

22 Dec 21:26 EXITED currently processing 0