Harvest for Gulf of Boni Species List Created 23 Dec 03:50

Stage: completed
Fetched: 23 Dec 03:50
Validated: 23 Dec 03:50
Deltas Created 23 Dec 03:50
Units Normalized: 23 Dec 03:53
Ancestry Built: 23 Dec 03:50
Nodes Matched: 23 Dec 03:53
Names Parsed: 23 Dec 03:50
New Models Stored: 23 Dec 03:50
Indexed: 23 Dec 03:53
Completed: 23 Dec 03:54
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 03:50:30 -0500 by logger.rb/56815
[START] [2019-12-23 03:50:30] logged process
[START] [2019-12-23 03:50:30] create_harvest_instance
[STOP] [2019-12-23 03:50:31] create_harvest_instance
[START] [2019-12-23 03:50:31] fetch_files
[STOP] [2019-12-23 03:50:31] fetch_files
[START] [2019-12-23 03:50:31] validate_each_file
[STOP] [2019-12-23 03:50:31] validate_each_file
[START] [2019-12-23 03:50:31] convert_to_csv
[CMD] [2019-12-23 03:50:31] /usr/bin/sort /app/public/converted_csv/gulf_boni_sp_lis_refs_19282.csv > /app/public/converted_csv/gulf_boni_sp_lis_refs_19282.csv_sorted
[CMD] [2019-12-23 03:50:31] /usr/bin/sort /app/public/converted_csv/gulf_boni_sp_lis_nodes_19283.csv > /app/public/converted_csv/gulf_boni_sp_lis_nodes_19283.csv_sorted
[CMD] [2019-12-23 03:50:32] /usr/bin/sort /app/public/converted_csv/gulf_boni_sp_lis_occurrences_19284.csv > /app/public/converted_csv/gulf_boni_sp_lis_occurrences_19284.csv_sorted
[CMD] [2019-12-23 03:50:33] /usr/bin/sort /app/public/converted_csv/gulf_boni_sp_lis_measurements_19285.csv > /app/public/converted_csv/gulf_boni_sp_lis_measurements_19285.csv_sorted
[STOP] [2019-12-23 03:50:33] convert_to_csv
[START] [2019-12-23 03:50:33] calculate_delta
[CMD] [2019-12-23 03:50:34] echo "0a" > /app/public/diff/gulf_boni_sp_lis_refs_19282.diff
[CMD] [2019-12-23 03:50:34] tail -n +1 /app/public/converted_csv/gulf_boni_sp_lis_refs_19282.csv >> /app/public/diff/gulf_boni_sp_lis_refs_19282.diff
[CMD] [2019-12-23 03:50:35] echo "." >> /app/public/diff/gulf_boni_sp_lis_refs_19282.diff
[CMD] [2019-12-23 03:50:36] echo "0a" > /app/public/diff/gulf_boni_sp_lis_nodes_19283.diff
[CMD] [2019-12-23 03:50:36] tail -n +1 /app/public/converted_csv/gulf_boni_sp_lis_nodes_19283.csv >> /app/public/diff/gulf_boni_sp_lis_nodes_19283.diff
[CMD] [2019-12-23 03:50:37] echo "." >> /app/public/diff/gulf_boni_sp_lis_nodes_19283.diff
[CMD] [2019-12-23 03:50:38] echo "0a" > /app/public/diff/gulf_boni_sp_lis_occurrences_19284.diff
[CMD] [2019-12-23 03:50:38] tail -n +1 /app/public/converted_csv/gulf_boni_sp_lis_occurrences_19284.csv >> /app/public/diff/gulf_boni_sp_lis_occurrences_19284.diff
[CMD] [2019-12-23 03:50:39] echo "." >> /app/public/diff/gulf_boni_sp_lis_occurrences_19284.diff
[CMD] [2019-12-23 03:50:40] echo "0a" > /app/public/diff/gulf_boni_sp_lis_measurements_19285.diff
[CMD] [2019-12-23 03:50:40] tail -n +1 /app/public/converted_csv/gulf_boni_sp_lis_measurements_19285.csv >> /app/public/diff/gulf_boni_sp_lis_measurements_19285.diff
[CMD] [2019-12-23 03:50:41] echo "." >> /app/public/diff/gulf_boni_sp_lis_measurements_19285.diff
[STOP] [2019-12-23 03:50:42] calculate_delta
[START] [2019-12-23 03:50:42] parse_diff_and_store
[INFO] [2019-12-23 03:50:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 03:50:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 03:50:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 03:50:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 03:50:46] Storing 2 References
[INFO] [2019-12-23 03:50:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 03:50:46] Average Time: 0.0
[INFO] [2019-12-23 03:50:46] Total Time: 1s
[INFO] [2019-12-23 03:50:46] Storing 496 ScientificNames
[INFO] [2019-12-23 03:50:46] Processing group of 496 in 1 groups of 1000
[INFO] [2019-12-23 03:50:46] Average Time: 0.28
[INFO] [2019-12-23 03:50:46] Total Time: 1s
[INFO] [2019-12-23 03:50:46] Storing 496 Nodes
[INFO] [2019-12-23 03:50:46] Processing group of 496 in 1 groups of 1000
[INFO] [2019-12-23 03:50:46] Average Time: 0.15
[INFO] [2019-12-23 03:50:46] Total Time: 1s
[INFO] [2019-12-23 03:50:46] Storing 167 Occurrences
[INFO] [2019-12-23 03:50:46] Processing group of 167 in 1 groups of 1000
[INFO] [2019-12-23 03:50:46] Average Time: 0.03
[INFO] [2019-12-23 03:50:46] Total Time: 1s
[INFO] [2019-12-23 03:50:46] Storing 334 TraitsReferences
[INFO] [2019-12-23 03:50:46] Processing group of 334 in 1 groups of 1000
[INFO] [2019-12-23 03:50:46] Average Time: 0.11
[INFO] [2019-12-23 03:50:46] Total Time: 1s
[INFO] [2019-12-23 03:50:46] Storing 334 Traits
[INFO] [2019-12-23 03:50:46] Processing group of 334 in 1 groups of 1000
[INFO] [2019-12-23 03:50:46] Average Time: 0.24
[INFO] [2019-12-23 03:50:46] Total Time: 1s
[INFO] [2019-12-23 03:50:46] Storing 334 MetaTraits
[INFO] [2019-12-23 03:50:46] Processing group of 334 in 1 groups of 1000
[INFO] [2019-12-23 03:50:47] Average Time: 0.08
[INFO] [2019-12-23 03:50:47] Total Time: 1s
[STOP] [2019-12-23 03:50:47] parse_diff_and_store
[START] [2019-12-23 03:50:47] resolve_keys
[INFO] [2019-12-23 03:50:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 03:50:52] traits to occurrences...
[INFO] [2019-12-23 03:50:52] traits to nodes (through occurrences)...
[INFO] [2019-12-23 03:50:52] Traits to sex term...
[INFO] [2019-12-23 03:50:52] Traits to lifestage term...
[INFO] [2019-12-23 03:50:52] MetaTraits to traits...
[INFO] [2019-12-23 03:50:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 03:50:52] Assocs to occurrences...
[INFO] [2019-12-23 03:50:52] Assocs to nodes...
[INFO] [2019-12-23 03:50:52] Assoc to sex term...
[INFO] [2019-12-23 03:50:52] Assoc to lifestage term...
[STOP] [2019-12-23 03:50:52] resolve_keys
[START] [2019-12-23 03:50:52] hold_for_later_1
[STOP] [2019-12-23 03:50:52] hold_for_later_1
[START] [2019-12-23 03:50:52] hold_for_later_2
[STOP] [2019-12-23 03:50:52] hold_for_later_2
[START] [2019-12-23 03:50:52] resolve_missing_parents
[STOP] [2019-12-23 03:50:52] resolve_missing_parents
[START] [2019-12-23 03:50:52] rebuild_nodes
[START] [2019-12-23 03:50:52] Flattener#flatten
[START] [2019-12-23 03:50:52] Flattener#study_resource
[START] [2019-12-23 03:50:52] Flattener#build_ancestry
[STOP] [2019-12-23 03:50:52] Flattener#build_ancestry
[INFO] [2019-12-23 03:50:52] 496 ancestry keys
[START] [2019-12-23 03:50:52] build_node_ancestors
[INFO] [2019-12-23 03:50:52] old ancestors deleted.
[STOP] [2019-12-23 03:50:53] build_node_ancestors
[START] [2019-12-23 03:50:53] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:50:53] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:50:53] Flattener#flatten
[STOP] [2019-12-23 03:50:53] rebuild_nodes
[START] [2019-12-23 03:50:53] resolve_missing_media_owners
[STOP] [2019-12-23 03:50:53] resolve_missing_media_owners
[START] [2019-12-23 03:50:53] sanitize_media_verbatims
[STOP] [2019-12-23 03:50:53] sanitize_media_verbatims
[START] [2019-12-23 03:50:53] queue_downloads
[STOP] [2019-12-23 03:50:53] queue_downloads
[START] [2019-12-23 03:50:53] parse_names
[WARN] [2019-12-23 03:50:53] I see 496 names which still need to be parsed.
[STOP] [2019-12-23 03:50:54] parse_names
[START] [2019-12-23 03:50:54] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 03:50:54] denormalize_canonical_names_to_nodes
[START] [2019-12-23 03:50:54] match_nodes
[START] [2019-12-23 03:50:54] map_all_nodes_to_pages
[STOP] [2019-12-23 03:53:03] map_all_nodes_to_pages
[INFO] [2019-12-23 03:53:03] 24 Unmatched nodes (of 496)! That's too many to output. First 10: Gasterosteiformes (#61907133); Nematocarcinus kaiensis (#61907101); Glyphocrangon sibogae (#61906767); Glyphocrangon unguiculata (#61907040); Sympagurus trispinosus (#61906886); Munidopsis andamanica (#61906900); Munida microps (#61906978); Paralomis ochthodes (#61906915); Maxillopoda (#61906766); Paracalanus parvus (#61907118)
[START] [2019-12-23 03:53:03] update_nodes
[STOP] [2019-12-23 03:53:04] update_nodes
[STOP] [2019-12-23 03:53:04] match_nodes
[START] [2019-12-23 03:53:04] reindex_search
[STOP] [2019-12-23 03:53:05] reindex_search
[START] [2019-12-23 03:53:05] normalize_units
[STOP] [2019-12-23 03:53:05] normalize_units
[START] [2019-12-23 03:53:05] calculate_statistics
[STOP] [2019-12-23 03:53:05] calculate_statistics
[START] [2019-12-23 03:53:05] complete_harvest_instance
[START] [2019-12-23 03:53:05] overall_tsv_creation
[INFO] [2019-12-23 03:53:05] Processing group of 496 in 1 batches of 10000
[INFO] [2019-12-23 03:53:51] 167 Traits (unfiltered)...
[INFO] [2019-12-23 03:54:04] 167 Traits (filtered)...
[INFO] [2019-12-23 03:54:04] 0 Associations (filtered)...
[INFO] [2019-12-23 03:54:42] 835 metadata added.
[INFO] [2019-12-23 03:54:42] 0 metadata added.
[INFO] [2019-12-23 03:54:42] Average Time: 74.33
[INFO] [2019-12-23 03:54:42] Total Time: 1m37s
[STOP] [2019-12-23 03:54:42] overall_tsv_creation
[INFO] [2019-12-23 03:54:42] Done. Check your files:
[INFO] [2019-12-23 03:54:42] (496 lines) /app/public/data/gulf_boni_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 03:54:43] (2251 lines) /app/public/data/gulf_boni_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:54:44] (496 lines) /app/public/data/gulf_boni_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 03:54:44] (168 lines) /app/public/data/gulf_boni_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 03:54:45] (836 lines) /app/public/data/gulf_boni_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 03:54:45] complete_harvest_instance
[START] [2019-12-23 03:54:45] completed
[STOP] [2019-12-23 03:54:45] completed
[STOP] [2019-12-23 03:54:45] logged process, took 254.98
Latest Process

23 Dec 03:50 EXITED currently processing 0