Harvest for Ligurian Sea Species List Created 23 Dec 18:07

Stage: completed
Fetched: 23 Dec 18:07
Validated: 23 Dec 18:07
Deltas Created 23 Dec 18:07
Units Normalized: 23 Dec 18:10
Ancestry Built: 23 Dec 18:08
Nodes Matched: 23 Dec 18:10
Names Parsed: 23 Dec 18:08
New Models Stored: 23 Dec 18:08
Indexed: 23 Dec 18:10
Completed: 23 Dec 18:12
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 18:07:48 -0500 by logger.rb/56815
[START] [2019-12-23 18:07:48] logged process
[START] [2019-12-23 18:07:48] create_harvest_instance
[STOP] [2019-12-23 18:07:48] create_harvest_instance
[START] [2019-12-23 18:07:48] fetch_files
[STOP] [2019-12-23 18:07:48] fetch_files
[START] [2019-12-23 18:07:48] validate_each_file
[STOP] [2019-12-23 18:07:48] validate_each_file
[START] [2019-12-23 18:07:48] convert_to_csv
[CMD] [2019-12-23 18:07:48] /usr/bin/sort /app/public/converted_csv/ligurian_sea_sp__refs_19458.csv > /app/public/converted_csv/ligurian_sea_sp__refs_19458.csv_sorted
[CMD] [2019-12-23 18:07:49] /usr/bin/sort /app/public/converted_csv/ligurian_sea_sp__nodes_19459.csv > /app/public/converted_csv/ligurian_sea_sp__nodes_19459.csv_sorted
[CMD] [2019-12-23 18:07:50] /usr/bin/sort /app/public/converted_csv/ligurian_sea_sp__occurrences_19460.csv > /app/public/converted_csv/ligurian_sea_sp__occurrences_19460.csv_sorted
[CMD] [2019-12-23 18:07:50] /usr/bin/sort /app/public/converted_csv/ligurian_sea_sp__measurements_19461.csv > /app/public/converted_csv/ligurian_sea_sp__measurements_19461.csv_sorted
[STOP] [2019-12-23 18:07:51] convert_to_csv
[START] [2019-12-23 18:07:51] calculate_delta
[CMD] [2019-12-23 18:07:51] echo "0a" > /app/public/diff/ligurian_sea_sp__refs_19458.diff
[CMD] [2019-12-23 18:07:52] tail -n +1 /app/public/converted_csv/ligurian_sea_sp__refs_19458.csv >> /app/public/diff/ligurian_sea_sp__refs_19458.diff
[CMD] [2019-12-23 18:07:52] echo "." >> /app/public/diff/ligurian_sea_sp__refs_19458.diff
[CMD] [2019-12-23 18:07:53] echo "0a" > /app/public/diff/ligurian_sea_sp__nodes_19459.diff
[CMD] [2019-12-23 18:07:53] tail -n +1 /app/public/converted_csv/ligurian_sea_sp__nodes_19459.csv >> /app/public/diff/ligurian_sea_sp__nodes_19459.diff
[CMD] [2019-12-23 18:07:54] echo "." >> /app/public/diff/ligurian_sea_sp__nodes_19459.diff
[CMD] [2019-12-23 18:07:55] echo "0a" > /app/public/diff/ligurian_sea_sp__occurrences_19460.diff
[CMD] [2019-12-23 18:07:55] tail -n +1 /app/public/converted_csv/ligurian_sea_sp__occurrences_19460.csv >> /app/public/diff/ligurian_sea_sp__occurrences_19460.diff
[CMD] [2019-12-23 18:07:56] echo "." >> /app/public/diff/ligurian_sea_sp__occurrences_19460.diff
[CMD] [2019-12-23 18:07:57] echo "0a" > /app/public/diff/ligurian_sea_sp__measurements_19461.diff
[CMD] [2019-12-23 18:07:57] tail -n +1 /app/public/converted_csv/ligurian_sea_sp__measurements_19461.csv >> /app/public/diff/ligurian_sea_sp__measurements_19461.diff
[CMD] [2019-12-23 18:07:58] echo "." >> /app/public/diff/ligurian_sea_sp__measurements_19461.diff
[STOP] [2019-12-23 18:07:59] calculate_delta
[START] [2019-12-23 18:07:59] parse_diff_and_store
[INFO] [2019-12-23 18:07:59] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 18:08:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 18:08:01] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 18:08:02] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 18:08:04] Storing 2 References
[INFO] [2019-12-23 18:08:04] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 18:08:04] Average Time: 0.0
[INFO] [2019-12-23 18:08:04] Total Time: 1s
[INFO] [2019-12-23 18:08:04] Storing 973 ScientificNames
[INFO] [2019-12-23 18:08:04] Processing group of 973 in 1 groups of 1000
[INFO] [2019-12-23 18:08:04] Average Time: 0.43
[INFO] [2019-12-23 18:08:04] Total Time: 1s
[INFO] [2019-12-23 18:08:04] Storing 973 Nodes
[INFO] [2019-12-23 18:08:04] Processing group of 973 in 1 groups of 1000
[INFO] [2019-12-23 18:08:05] Average Time: 0.33
[INFO] [2019-12-23 18:08:05] Total Time: 1s
[INFO] [2019-12-23 18:08:05] Storing 372 Occurrences
[INFO] [2019-12-23 18:08:05] Processing group of 372 in 1 groups of 1000
[INFO] [2019-12-23 18:08:05] Average Time: 0.06
[INFO] [2019-12-23 18:08:05] Total Time: 1s
[INFO] [2019-12-23 18:08:05] Storing 744 TraitsReferences
[INFO] [2019-12-23 18:08:05] Processing group of 744 in 1 groups of 1000
[INFO] [2019-12-23 18:08:05] Average Time: 0.12
[INFO] [2019-12-23 18:08:05] Total Time: 1s
[INFO] [2019-12-23 18:08:05] Storing 744 Traits
[INFO] [2019-12-23 18:08:05] Processing group of 744 in 1 groups of 1000
[INFO] [2019-12-23 18:08:05] Average Time: 0.44
[INFO] [2019-12-23 18:08:05] Total Time: 1s
[INFO] [2019-12-23 18:08:05] Storing 744 MetaTraits
[INFO] [2019-12-23 18:08:05] Processing group of 744 in 1 groups of 1000
[INFO] [2019-12-23 18:08:05] Average Time: 0.14
[INFO] [2019-12-23 18:08:05] Total Time: 1s
[STOP] [2019-12-23 18:08:05] parse_diff_and_store
[START] [2019-12-23 18:08:05] resolve_keys
[INFO] [2019-12-23 18:08:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 18:08:12] traits to occurrences...
[INFO] [2019-12-23 18:08:13] traits to nodes (through occurrences)...
[INFO] [2019-12-23 18:08:13] Traits to sex term...
[INFO] [2019-12-23 18:08:13] Traits to lifestage term...
[INFO] [2019-12-23 18:08:13] MetaTraits to traits...
[INFO] [2019-12-23 18:08:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 18:08:13] Assocs to occurrences...
[INFO] [2019-12-23 18:08:13] Assocs to nodes...
[INFO] [2019-12-23 18:08:13] Assoc to sex term...
[INFO] [2019-12-23 18:08:13] Assoc to lifestage term...
[STOP] [2019-12-23 18:08:13] resolve_keys
[START] [2019-12-23 18:08:13] hold_for_later_1
[STOP] [2019-12-23 18:08:13] hold_for_later_1
[START] [2019-12-23 18:08:13] hold_for_later_2
[STOP] [2019-12-23 18:08:13] hold_for_later_2
[START] [2019-12-23 18:08:13] resolve_missing_parents
[STOP] [2019-12-23 18:08:13] resolve_missing_parents
[START] [2019-12-23 18:08:13] rebuild_nodes
[START] [2019-12-23 18:08:13] Flattener#flatten
[START] [2019-12-23 18:08:13] Flattener#study_resource
[START] [2019-12-23 18:08:13] Flattener#build_ancestry
[STOP] [2019-12-23 18:08:13] Flattener#build_ancestry
[INFO] [2019-12-23 18:08:13] 973 ancestry keys
[START] [2019-12-23 18:08:13] build_node_ancestors
[INFO] [2019-12-23 18:08:13] old ancestors deleted.
[STOP] [2019-12-23 18:08:14] build_node_ancestors
[START] [2019-12-23 18:08:14] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 18:08:14] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 18:08:14] Flattener#flatten
[STOP] [2019-12-23 18:08:14] rebuild_nodes
[START] [2019-12-23 18:08:14] resolve_missing_media_owners
[STOP] [2019-12-23 18:08:14] resolve_missing_media_owners
[START] [2019-12-23 18:08:14] sanitize_media_verbatims
[STOP] [2019-12-23 18:08:14] sanitize_media_verbatims
[START] [2019-12-23 18:08:14] queue_downloads
[STOP] [2019-12-23 18:08:14] queue_downloads
[START] [2019-12-23 18:08:14] parse_names
[WARN] [2019-12-23 18:08:14] I see 973 names which still need to be parsed.
[STOP] [2019-12-23 18:08:16] parse_names
[START] [2019-12-23 18:08:16] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 18:08:16] denormalize_canonical_names_to_nodes
[START] [2019-12-23 18:08:16] match_nodes
[START] [2019-12-23 18:08:16] map_all_nodes_to_pages
[STOP] [2019-12-23 18:10:38] map_all_nodes_to_pages
[INFO] [2019-12-23 18:10:38] 36 Unmatched nodes (of 973)! That's too many to output. First 10: Larus melanocephalus (#62101820); Philomachus (#62102125); Philomachus pugnax (#62102124); Trachinotus glaucus (#62102747); Scorpaeniformes (#62101942); Gasterosteiformes (#62102332); Maja verrucosa (#62102529); Maxillopoda (#62101847); Pedunculata (#62102100); Chrysolina haemoptera (#62102264)
[START] [2019-12-23 18:10:38] update_nodes
[STOP] [2019-12-23 18:10:38] update_nodes
[STOP] [2019-12-23 18:10:38] match_nodes
[START] [2019-12-23 18:10:38] reindex_search
[STOP] [2019-12-23 18:10:40] reindex_search
[START] [2019-12-23 18:10:40] normalize_units
[STOP] [2019-12-23 18:10:40] normalize_units
[START] [2019-12-23 18:10:40] calculate_statistics
[STOP] [2019-12-23 18:10:40] calculate_statistics
[START] [2019-12-23 18:10:40] complete_harvest_instance
[START] [2019-12-23 18:10:40] overall_tsv_creation
[INFO] [2019-12-23 18:10:40] Processing group of 973 in 1 batches of 10000
[INFO] [2019-12-23 18:11:31] 372 Traits (unfiltered)...
[INFO] [2019-12-23 18:11:45] 372 Traits (filtered)...
[INFO] [2019-12-23 18:11:45] 0 Associations (filtered)...
[INFO] [2019-12-23 18:12:26] 1860 metadata added.
[INFO] [2019-12-23 18:12:26] 0 metadata added.
[INFO] [2019-12-23 18:12:26] Average Time: 82.22
[INFO] [2019-12-23 18:12:26] Total Time: 1m46s
[STOP] [2019-12-23 18:12:26] overall_tsv_creation
[INFO] [2019-12-23 18:12:26] Done. Check your files:
[INFO] [2019-12-23 18:12:26] (973 lines) /app/public/data/ligurian_sea_sp_/publish_nodes.tsv
[INFO] [2019-12-23 18:12:27] (4544 lines) /app/public/data/ligurian_sea_sp_/publish_node_ancestors.tsv
[INFO] [2019-12-23 18:12:27] (973 lines) /app/public/data/ligurian_sea_sp_/publish_scientific_names.tsv
[INFO] [2019-12-23 18:12:28] (373 lines) /app/public/data/ligurian_sea_sp_/publish_traits.tsv
[INFO] [2019-12-23 18:12:29] (1861 lines) /app/public/data/ligurian_sea_sp_/publish_metadata.tsv
[STOP] [2019-12-23 18:12:29] complete_harvest_instance
[START] [2019-12-23 18:12:29] completed
[STOP] [2019-12-23 18:12:29] completed
[STOP] [2019-12-23 18:12:29] logged process, took 281.13
Latest Process

23 Dec 18:07 EXITED currently processing 0