Harvest for Bay of Biscay Species List Created 22 Dec 21:32

Stage: completed
Fetched: 22 Dec 21:32
Validated: 22 Dec 21:32
Deltas Created 22 Dec 21:33
Units Normalized: 22 Dec 21:48
Ancestry Built: 22 Dec 21:34
Nodes Matched: 22 Dec 21:48
Names Parsed: 22 Dec 21:34
New Models Stored: 22 Dec 21:33
Indexed: 22 Dec 21:48
Completed: 22 Dec 21:50
Time to Harvest: less than a minute
Harvesting Log

(143 lines)
# Logfile created on 2019-12-22 21:32:50 -0500 by logger.rb/56815
[START] [2019-12-22 21:32:50] logged process
[START] [2019-12-22 21:32:50] create_harvest_instance
[STOP] [2019-12-22 21:32:50] create_harvest_instance
[START] [2019-12-22 21:32:50] fetch_files
[STOP] [2019-12-22 21:32:50] fetch_files
[START] [2019-12-22 21:32:50] validate_each_file
[STOP] [2019-12-22 21:32:51] validate_each_file
[START] [2019-12-22 21:32:51] convert_to_csv
[CMD] [2019-12-22 21:32:51] /usr/bin/sort /app/public/converted_csv/bay_biscay_sp_li_refs_19090.csv > /app/public/converted_csv/bay_biscay_sp_li_refs_19090.csv_sorted
[CMD] [2019-12-22 21:32:52] /usr/bin/sort /app/public/converted_csv/bay_biscay_sp_li_nodes_19091.csv > /app/public/converted_csv/bay_biscay_sp_li_nodes_19091.csv_sorted
[CMD] [2019-12-22 21:32:52] /usr/bin/sort /app/public/converted_csv/bay_biscay_sp_li_occurrences_19092.csv > /app/public/converted_csv/bay_biscay_sp_li_occurrences_19092.csv_sorted
[CMD] [2019-12-22 21:32:53] /usr/bin/sort /app/public/converted_csv/bay_biscay_sp_li_measurements_19093.csv > /app/public/converted_csv/bay_biscay_sp_li_measurements_19093.csv_sorted
[STOP] [2019-12-22 21:32:54] convert_to_csv
[START] [2019-12-22 21:32:54] calculate_delta
[CMD] [2019-12-22 21:32:54] echo "0a" > /app/public/diff/bay_biscay_sp_li_refs_19090.diff
[CMD] [2019-12-22 21:32:54] tail -n +1 /app/public/converted_csv/bay_biscay_sp_li_refs_19090.csv >> /app/public/diff/bay_biscay_sp_li_refs_19090.diff
[CMD] [2019-12-22 21:32:55] echo "." >> /app/public/diff/bay_biscay_sp_li_refs_19090.diff
[CMD] [2019-12-22 21:32:56] echo "0a" > /app/public/diff/bay_biscay_sp_li_nodes_19091.diff
[CMD] [2019-12-22 21:32:57] tail -n +1 /app/public/converted_csv/bay_biscay_sp_li_nodes_19091.csv >> /app/public/diff/bay_biscay_sp_li_nodes_19091.diff
[CMD] [2019-12-22 21:32:57] echo "." >> /app/public/diff/bay_biscay_sp_li_nodes_19091.diff
[CMD] [2019-12-22 21:32:58] echo "0a" > /app/public/diff/bay_biscay_sp_li_occurrences_19092.diff
[CMD] [2019-12-22 21:32:59] tail -n +1 /app/public/converted_csv/bay_biscay_sp_li_occurrences_19092.csv >> /app/public/diff/bay_biscay_sp_li_occurrences_19092.diff
[CMD] [2019-12-22 21:32:59] echo "." >> /app/public/diff/bay_biscay_sp_li_occurrences_19092.diff
[CMD] [2019-12-22 21:33:00] echo "0a" > /app/public/diff/bay_biscay_sp_li_measurements_19093.diff
[CMD] [2019-12-22 21:33:01] tail -n +1 /app/public/converted_csv/bay_biscay_sp_li_measurements_19093.csv >> /app/public/diff/bay_biscay_sp_li_measurements_19093.diff
[CMD] [2019-12-22 21:33:01] echo "." >> /app/public/diff/bay_biscay_sp_li_measurements_19093.diff
[STOP] [2019-12-22 21:33:02] calculate_delta
[START] [2019-12-22 21:33:02] parse_diff_and_store
[INFO] [2019-12-22 21:33:03] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-22 21:33:03] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-22 21:33:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-22 21:33:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-22 21:33:25] Storing 2 References
[INFO] [2019-12-22 21:33:25] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-22 21:33:25] Average Time: 0.0
[INFO] [2019-12-22 21:33:25] Total Time: 1s
[INFO] [2019-12-22 21:33:25] Storing 6135 ScientificNames
[INFO] [2019-12-22 21:33:25] Processing group of 6135 in 7 groups of 1000
[INFO] [2019-12-22 21:33:27] Average Time: 0.37
[INFO] [2019-12-22 21:33:27] Total Time: 3s
[INFO] [2019-12-22 21:33:27] last 3 / first 3: 0.69
[INFO] [2019-12-22 21:33:27] Std.Dev: 0.1414213562373095; Max: 0.46
[INFO] [2019-12-22 21:33:27] Storing 6135 Nodes
[INFO] [2019-12-22 21:33:27] Processing group of 6135 in 7 groups of 1000
[INFO] [2019-12-22 21:33:30] Average Time: 0.329
[INFO] [2019-12-22 21:33:30] Total Time: 3s
[INFO] [2019-12-22 21:33:30] last 3 / first 3: 0.61
[INFO] [2019-12-22 21:33:30] Std.Dev: 0.1414213562373095; Max: 0.52
[INFO] [2019-12-22 21:33:30] Storing 2975 Occurrences
[INFO] [2019-12-22 21:33:30] Processing group of 2975 in 3 groups of 1000
[INFO] [2019-12-22 21:33:30] Average Time: 0.127
[INFO] [2019-12-22 21:33:30] Total Time: 1s
[INFO] [2019-12-22 21:33:30] Storing 5950 TraitsReferences
[INFO] [2019-12-22 21:33:30] Processing group of 5950 in 6 groups of 1000
[INFO] [2019-12-22 21:33:31] Average Time: 0.098
[INFO] [2019-12-22 21:33:31] Total Time: 1s
[INFO] [2019-12-22 21:33:31] Storing 5950 Traits
[INFO] [2019-12-22 21:33:31] Processing group of 5950 in 6 groups of 1000
[INFO] [2019-12-22 21:33:33] Average Time: 0.397
[INFO] [2019-12-22 21:33:33] Total Time: 3s
[INFO] [2019-12-22 21:33:33] Storing 5948 MetaTraits
[INFO] [2019-12-22 21:33:33] Processing group of 5948 in 6 groups of 1000
[INFO] [2019-12-22 21:33:34] Average Time: 0.188
[INFO] [2019-12-22 21:33:34] Total Time: 2s
[STOP] [2019-12-22 21:33:34] parse_diff_and_store
[START] [2019-12-22 21:33:34] resolve_keys
[INFO] [2019-12-22 21:34:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-22 21:34:04] traits to occurrences...
[INFO] [2019-12-22 21:34:06] traits to nodes (through occurrences)...
[INFO] [2019-12-22 21:34:06] Traits to sex term...
[INFO] [2019-12-22 21:34:07] Traits to lifestage term...
[INFO] [2019-12-22 21:34:08] MetaTraits to traits...
[INFO] [2019-12-22 21:34:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-22 21:34:10] Assocs to occurrences...
[INFO] [2019-12-22 21:34:10] Assocs to nodes...
[INFO] [2019-12-22 21:34:10] Assoc to sex term...
[INFO] [2019-12-22 21:34:10] Assoc to lifestage term...
[STOP] [2019-12-22 21:34:10] resolve_keys
[START] [2019-12-22 21:34:10] hold_for_later_1
[STOP] [2019-12-22 21:34:10] hold_for_later_1
[START] [2019-12-22 21:34:10] hold_for_later_2
[STOP] [2019-12-22 21:34:10] hold_for_later_2
[START] [2019-12-22 21:34:10] resolve_missing_parents
[STOP] [2019-12-22 21:34:23] resolve_missing_parents
[START] [2019-12-22 21:34:23] rebuild_nodes
[START] [2019-12-22 21:34:23] Flattener#flatten
[START] [2019-12-22 21:34:23] Flattener#study_resource
[START] [2019-12-22 21:34:23] Flattener#build_ancestry
[STOP] [2019-12-22 21:34:23] Flattener#build_ancestry
[INFO] [2019-12-22 21:34:23] 6135 ancestry keys
[START] [2019-12-22 21:34:23] build_node_ancestors
[INFO] [2019-12-22 21:34:23] old ancestors deleted.
[STOP] [2019-12-22 21:34:25] build_node_ancestors
[START] [2019-12-22 21:34:28] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:34:29] Flattener#propagate_ancestor_ids
[STOP] [2019-12-22 21:34:29] Flattener#flatten
[STOP] [2019-12-22 21:34:29] rebuild_nodes
[START] [2019-12-22 21:34:29] resolve_missing_media_owners
[STOP] [2019-12-22 21:34:29] resolve_missing_media_owners
[START] [2019-12-22 21:34:29] sanitize_media_verbatims
[STOP] [2019-12-22 21:34:29] sanitize_media_verbatims
[START] [2019-12-22 21:34:29] queue_downloads
[STOP] [2019-12-22 21:34:29] queue_downloads
[START] [2019-12-22 21:34:29] parse_names
[WARN] [2019-12-22 21:34:29] I see 6135 names which still need to be parsed.
[STOP] [2019-12-22 21:34:35] parse_names
[START] [2019-12-22 21:34:35] denormalize_canonical_names_to_nodes
[STOP] [2019-12-22 21:34:35] denormalize_canonical_names_to_nodes
[START] [2019-12-22 21:34:35] match_nodes
[START] [2019-12-22 21:34:35] map_all_nodes_to_pages
[STOP] [2019-12-22 21:48:27] map_all_nodes_to_pages
[INFO] [2019-12-22 21:48:27] 283 Unmatched nodes (of 6135)! That's too many to output. First 10: Puffinus griseus (#61737680); Larus melanocephalus (#61737870); Philomachus (#61738148); Philomachus pugnax (#61738147); Anas clypeata (#61737323); Anas penelope (#61737336); Anas strepera (#61737385); Anas querquedula (#61737953); Anas discors (#61741750); Oxynotus salviani (#61742263)
[START] [2019-12-22 21:48:27] update_nodes
[STOP] [2019-12-22 21:48:29] update_nodes
[STOP] [2019-12-22 21:48:29] match_nodes
[START] [2019-12-22 21:48:29] reindex_search
[STOP] [2019-12-22 21:48:41] reindex_search
[START] [2019-12-22 21:48:41] normalize_units
[STOP] [2019-12-22 21:48:41] normalize_units
[START] [2019-12-22 21:48:41] calculate_statistics
[STOP] [2019-12-22 21:48:41] calculate_statistics
[START] [2019-12-22 21:48:41] complete_harvest_instance
[START] [2019-12-22 21:48:41] overall_tsv_creation
[INFO] [2019-12-22 21:48:41] Processing group of 6135 in 1 batches of 10000
[INFO] [2019-12-22 21:49:56] 2975 Traits (unfiltered)...
[INFO] [2019-12-22 21:50:09] 2975 Traits (filtered)...
[INFO] [2019-12-22 21:50:09] 0 Associations (filtered)...
[INFO] [2019-12-22 21:50:52] 14873 metadata added.
[INFO] [2019-12-22 21:50:52] 0 metadata added.
[INFO] [2019-12-22 21:50:52] Average Time: 104.15
[INFO] [2019-12-22 21:50:52] Total Time: 2m12s
[STOP] [2019-12-22 21:50:52] overall_tsv_creation
[INFO] [2019-12-22 21:50:52] Done. Check your files:
[INFO] [2019-12-22 21:50:53] (6135 lines) /app/public/data/bay_biscay_sp_li/publish_nodes.tsv
[INFO] [2019-12-22 21:50:54] (30220 lines) /app/public/data/bay_biscay_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-22 21:50:54] (6135 lines) /app/public/data/bay_biscay_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-22 21:50:55] (2976 lines) /app/public/data/bay_biscay_sp_li/publish_traits.tsv
[INFO] [2019-12-22 21:50:56] (14874 lines) /app/public/data/bay_biscay_sp_li/publish_metadata.tsv
[STOP] [2019-12-22 21:50:56] complete_harvest_instance
[START] [2019-12-22 21:50:56] completed
[STOP] [2019-12-22 21:50:56] completed
[STOP] [2019-12-22 21:50:56] logged process, took 1086.23
Latest Process

22 Dec 21:32 EXITED currently processing 0