Harvest for Davis Strait Species List Created 23 Dec 00:34

Stage: completed
Fetched: 23 Dec 00:34
Validated: 23 Dec 00:34
Deltas Created 23 Dec 00:34
Units Normalized: 23 Dec 00:42
Ancestry Built: 23 Dec 00:34
Nodes Matched: 23 Dec 00:42
Names Parsed: 23 Dec 00:34
New Models Stored: 23 Dec 00:34
Indexed: 23 Dec 00:42
Completed: 23 Dec 00:44
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 00:34:14 -0500 by logger.rb/56815
[START] [2019-12-23 00:34:14] logged process
[START] [2019-12-23 00:34:14] create_harvest_instance
[STOP] [2019-12-23 00:34:15] create_harvest_instance
[START] [2019-12-23 00:34:15] fetch_files
[STOP] [2019-12-23 00:34:15] fetch_files
[START] [2019-12-23 00:34:15] validate_each_file
[STOP] [2019-12-23 00:34:15] validate_each_file
[START] [2019-12-23 00:34:15] convert_to_csv
[CMD] [2019-12-23 00:34:15] /usr/bin/sort /app/public/converted_csv/davis_strait_sp__refs_19202.csv > /app/public/converted_csv/davis_strait_sp__refs_19202.csv_sorted
[CMD] [2019-12-23 00:34:15] /usr/bin/sort /app/public/converted_csv/davis_strait_sp__nodes_19203.csv > /app/public/converted_csv/davis_strait_sp__nodes_19203.csv_sorted
[CMD] [2019-12-23 00:34:16] /usr/bin/sort /app/public/converted_csv/davis_strait_sp__occurrences_19204.csv > /app/public/converted_csv/davis_strait_sp__occurrences_19204.csv_sorted
[CMD] [2019-12-23 00:34:16] /usr/bin/sort /app/public/converted_csv/davis_strait_sp__measurements_19205.csv > /app/public/converted_csv/davis_strait_sp__measurements_19205.csv_sorted
[STOP] [2019-12-23 00:34:16] convert_to_csv
[START] [2019-12-23 00:34:16] calculate_delta
[CMD] [2019-12-23 00:34:16] echo "0a" > /app/public/diff/davis_strait_sp__refs_19202.diff
[CMD] [2019-12-23 00:34:16] tail -n +1 /app/public/converted_csv/davis_strait_sp__refs_19202.csv >> /app/public/diff/davis_strait_sp__refs_19202.diff
[CMD] [2019-12-23 00:34:16] echo "." >> /app/public/diff/davis_strait_sp__refs_19202.diff
[CMD] [2019-12-23 00:34:16] echo "0a" > /app/public/diff/davis_strait_sp__nodes_19203.diff
[CMD] [2019-12-23 00:34:16] tail -n +1 /app/public/converted_csv/davis_strait_sp__nodes_19203.csv >> /app/public/diff/davis_strait_sp__nodes_19203.diff
[CMD] [2019-12-23 00:34:16] echo "." >> /app/public/diff/davis_strait_sp__nodes_19203.diff
[CMD] [2019-12-23 00:34:16] echo "0a" > /app/public/diff/davis_strait_sp__occurrences_19204.diff
[CMD] [2019-12-23 00:34:16] tail -n +1 /app/public/converted_csv/davis_strait_sp__occurrences_19204.csv >> /app/public/diff/davis_strait_sp__occurrences_19204.diff
[CMD] [2019-12-23 00:34:16] echo "." >> /app/public/diff/davis_strait_sp__occurrences_19204.diff
[CMD] [2019-12-23 00:34:16] echo "0a" > /app/public/diff/davis_strait_sp__measurements_19205.diff
[CMD] [2019-12-23 00:34:16] tail -n +1 /app/public/converted_csv/davis_strait_sp__measurements_19205.csv >> /app/public/diff/davis_strait_sp__measurements_19205.diff
[CMD] [2019-12-23 00:34:16] echo "." >> /app/public/diff/davis_strait_sp__measurements_19205.diff
[STOP] [2019-12-23 00:34:16] calculate_delta
[START] [2019-12-23 00:34:16] parse_diff_and_store
[INFO] [2019-12-23 00:34:16] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 00:34:16] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 00:34:17] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 00:34:17] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 00:34:24] Storing 2 References
[INFO] [2019-12-23 00:34:24] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 00:34:24] Average Time: 0.0
[INFO] [2019-12-23 00:34:24] Total Time: 1s
[INFO] [2019-12-23 00:34:24] Storing 2790 ScientificNames
[INFO] [2019-12-23 00:34:24] Processing group of 2790 in 3 groups of 1000
[INFO] [2019-12-23 00:34:25] Average Time: 0.333
[INFO] [2019-12-23 00:34:25] Total Time: 2s
[INFO] [2019-12-23 00:34:25] Storing 2790 Nodes
[INFO] [2019-12-23 00:34:25] Processing group of 2790 in 3 groups of 1000
[INFO] [2019-12-23 00:34:26] Average Time: 0.287
[INFO] [2019-12-23 00:34:26] Total Time: 1s
[INFO] [2019-12-23 00:34:26] Storing 1202 Occurrences
[INFO] [2019-12-23 00:34:26] Processing group of 1202 in 2 groups of 1000
[INFO] [2019-12-23 00:34:26] Average Time: 0.06
[INFO] [2019-12-23 00:34:26] Total Time: 1s
[INFO] [2019-12-23 00:34:26] Storing 2404 TraitsReferences
[INFO] [2019-12-23 00:34:26] Processing group of 2404 in 3 groups of 1000
[INFO] [2019-12-23 00:34:26] Average Time: 0.083
[INFO] [2019-12-23 00:34:26] Total Time: 1s
[INFO] [2019-12-23 00:34:26] Storing 2404 Traits
[INFO] [2019-12-23 00:34:26] Processing group of 2404 in 3 groups of 1000
[INFO] [2019-12-23 00:34:27] Average Time: 0.307
[INFO] [2019-12-23 00:34:27] Total Time: 1s
[INFO] [2019-12-23 00:34:27] Storing 2404 MetaTraits
[INFO] [2019-12-23 00:34:27] Processing group of 2404 in 3 groups of 1000
[INFO] [2019-12-23 00:34:27] Average Time: 0.127
[INFO] [2019-12-23 00:34:27] Total Time: 1s
[STOP] [2019-12-23 00:34:27] parse_diff_and_store
[START] [2019-12-23 00:34:27] resolve_keys
[INFO] [2019-12-23 00:34:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 00:34:41] traits to occurrences...
[INFO] [2019-12-23 00:34:42] traits to nodes (through occurrences)...
[INFO] [2019-12-23 00:34:42] Traits to sex term...
[INFO] [2019-12-23 00:34:43] Traits to lifestage term...
[INFO] [2019-12-23 00:34:43] MetaTraits to traits...
[INFO] [2019-12-23 00:34:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 00:34:44] Assocs to occurrences...
[INFO] [2019-12-23 00:34:44] Assocs to nodes...
[INFO] [2019-12-23 00:34:44] Assoc to sex term...
[INFO] [2019-12-23 00:34:44] Assoc to lifestage term...
[STOP] [2019-12-23 00:34:44] resolve_keys
[START] [2019-12-23 00:34:44] hold_for_later_1
[STOP] [2019-12-23 00:34:44] hold_for_later_1
[START] [2019-12-23 00:34:44] hold_for_later_2
[STOP] [2019-12-23 00:34:44] hold_for_later_2
[START] [2019-12-23 00:34:44] resolve_missing_parents
[STOP] [2019-12-23 00:34:48] resolve_missing_parents
[START] [2019-12-23 00:34:48] rebuild_nodes
[START] [2019-12-23 00:34:48] Flattener#flatten
[START] [2019-12-23 00:34:48] Flattener#study_resource
[START] [2019-12-23 00:34:48] Flattener#build_ancestry
[STOP] [2019-12-23 00:34:48] Flattener#build_ancestry
[INFO] [2019-12-23 00:34:48] 2790 ancestry keys
[START] [2019-12-23 00:34:48] build_node_ancestors
[INFO] [2019-12-23 00:34:48] old ancestors deleted.
[STOP] [2019-12-23 00:34:49] build_node_ancestors
[START] [2019-12-23 00:34:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:34:50] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:34:50] Flattener#flatten
[STOP] [2019-12-23 00:34:50] rebuild_nodes
[START] [2019-12-23 00:34:50] resolve_missing_media_owners
[STOP] [2019-12-23 00:34:50] resolve_missing_media_owners
[START] [2019-12-23 00:34:50] sanitize_media_verbatims
[STOP] [2019-12-23 00:34:50] sanitize_media_verbatims
[START] [2019-12-23 00:34:50] queue_downloads
[STOP] [2019-12-23 00:34:50] queue_downloads
[START] [2019-12-23 00:34:50] parse_names
[WARN] [2019-12-23 00:34:50] I see 2790 names which still need to be parsed.
[STOP] [2019-12-23 00:34:53] parse_names
[START] [2019-12-23 00:34:53] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 00:34:53] denormalize_canonical_names_to_nodes
[START] [2019-12-23 00:34:53] match_nodes
[START] [2019-12-23 00:34:53] map_all_nodes_to_pages
[STOP] [2019-12-23 00:42:27] map_all_nodes_to_pages
[INFO] [2019-12-23 00:42:27] 138 Unmatched nodes (of 2790)! That's too many to output. First 10: Larus thayeri (#61857103); Puffinus griseus (#61857413); Chen (#61857509); Chen caerulescens (#61857508); Scorpaeniformes (#61856695); Ulcina (#61856958); Gasterosteiformes (#61856889); Anotopteridae (#61857953); Stephanoberyciformes (#61858456); Pleurogona (#61858060)
[START] [2019-12-23 00:42:27] update_nodes
[STOP] [2019-12-23 00:42:28] update_nodes
[STOP] [2019-12-23 00:42:28] match_nodes
[START] [2019-12-23 00:42:28] reindex_search
[STOP] [2019-12-23 00:42:35] reindex_search
[START] [2019-12-23 00:42:35] normalize_units
[STOP] [2019-12-23 00:42:35] normalize_units
[START] [2019-12-23 00:42:35] calculate_statistics
[STOP] [2019-12-23 00:42:35] calculate_statistics
[START] [2019-12-23 00:42:35] complete_harvest_instance
[START] [2019-12-23 00:42:35] overall_tsv_creation
[INFO] [2019-12-23 00:42:35] Processing group of 2790 in 1 batches of 10000
[INFO] [2019-12-23 00:43:33] 1202 Traits (unfiltered)...
[INFO] [2019-12-23 00:43:47] 1202 Traits (filtered)...
[INFO] [2019-12-23 00:43:47] 0 Associations (filtered)...
[INFO] [2019-12-23 00:44:27] 6010 metadata added.
[INFO] [2019-12-23 00:44:27] 0 metadata added.
[INFO] [2019-12-23 00:44:27] Average Time: 87.62
[INFO] [2019-12-23 00:44:27] Total Time: 1m53s
[STOP] [2019-12-23 00:44:27] overall_tsv_creation
[INFO] [2019-12-23 00:44:27] Done. Check your files:
[INFO] [2019-12-23 00:44:27] (2790 lines) /app/public/data/davis_strait_sp_/publish_nodes.tsv
[INFO] [2019-12-23 00:44:27] (13242 lines) /app/public/data/davis_strait_sp_/publish_node_ancestors.tsv
[INFO] [2019-12-23 00:44:27] (2790 lines) /app/public/data/davis_strait_sp_/publish_scientific_names.tsv
[INFO] [2019-12-23 00:44:27] (1203 lines) /app/public/data/davis_strait_sp_/publish_traits.tsv
[INFO] [2019-12-23 00:44:27] (6011 lines) /app/public/data/davis_strait_sp_/publish_metadata.tsv
[STOP] [2019-12-23 00:44:27] complete_harvest_instance
[START] [2019-12-23 00:44:27] completed
[STOP] [2019-12-23 00:44:27] completed
[STOP] [2019-12-23 00:44:27] logged process, took 613.27
Latest Process

23 Dec 00:34 EXITED currently processing 0