Harvest for Strait of Gibraltar Species List Created 25 Dec 15:50

Stage: completed
Fetched: 25 Dec 15:50
Validated: 25 Dec 15:50
Deltas Created 25 Dec 15:50
Units Normalized: 25 Dec 15:54
Ancestry Built: 25 Dec 15:51
Nodes Matched: 25 Dec 15:54
Names Parsed: 25 Dec 15:51
New Models Stored: 25 Dec 15:50
Indexed: 25 Dec 15:54
Completed: 25 Dec 15:56
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 15:50:31 -0500 by logger.rb/56815
[START] [2019-12-25 15:50:31] logged process
[START] [2019-12-25 15:50:31] create_harvest_instance
[STOP] [2019-12-25 15:50:31] create_harvest_instance
[START] [2019-12-25 15:50:31] fetch_files
[STOP] [2019-12-25 15:50:31] fetch_files
[START] [2019-12-25 15:50:31] validate_each_file
[STOP] [2019-12-25 15:50:31] validate_each_file
[START] [2019-12-25 15:50:31] convert_to_csv
[CMD] [2019-12-25 15:50:31] /usr/bin/sort /app/public/converted_csv/strait_gibraltar_refs_19698.csv > /app/public/converted_csv/strait_gibraltar_refs_19698.csv_sorted
[CMD] [2019-12-25 15:50:32] /usr/bin/sort /app/public/converted_csv/strait_gibraltar_nodes_19699.csv > /app/public/converted_csv/strait_gibraltar_nodes_19699.csv_sorted
[CMD] [2019-12-25 15:50:33] /usr/bin/sort /app/public/converted_csv/strait_gibraltar_occurrences_19700.csv > /app/public/converted_csv/strait_gibraltar_occurrences_19700.csv_sorted
[CMD] [2019-12-25 15:50:33] /usr/bin/sort /app/public/converted_csv/strait_gibraltar_measurements_19701.csv > /app/public/converted_csv/strait_gibraltar_measurements_19701.csv_sorted
[STOP] [2019-12-25 15:50:34] convert_to_csv
[START] [2019-12-25 15:50:34] calculate_delta
[CMD] [2019-12-25 15:50:34] echo "0a" > /app/public/diff/strait_gibraltar_refs_19698.diff
[CMD] [2019-12-25 15:50:35] tail -n +1 /app/public/converted_csv/strait_gibraltar_refs_19698.csv >> /app/public/diff/strait_gibraltar_refs_19698.diff
[CMD] [2019-12-25 15:50:35] echo "." >> /app/public/diff/strait_gibraltar_refs_19698.diff
[CMD] [2019-12-25 15:50:36] echo "0a" > /app/public/diff/strait_gibraltar_nodes_19699.diff
[CMD] [2019-12-25 15:50:37] tail -n +1 /app/public/converted_csv/strait_gibraltar_nodes_19699.csv >> /app/public/diff/strait_gibraltar_nodes_19699.diff
[CMD] [2019-12-25 15:50:37] echo "." >> /app/public/diff/strait_gibraltar_nodes_19699.diff
[CMD] [2019-12-25 15:50:38] echo "0a" > /app/public/diff/strait_gibraltar_occurrences_19700.diff
[CMD] [2019-12-25 15:50:39] tail -n +1 /app/public/converted_csv/strait_gibraltar_occurrences_19700.csv >> /app/public/diff/strait_gibraltar_occurrences_19700.diff
[CMD] [2019-12-25 15:50:39] echo "." >> /app/public/diff/strait_gibraltar_occurrences_19700.diff
[CMD] [2019-12-25 15:50:40] echo "0a" > /app/public/diff/strait_gibraltar_measurements_19701.diff
[CMD] [2019-12-25 15:50:41] tail -n +1 /app/public/converted_csv/strait_gibraltar_measurements_19701.csv >> /app/public/diff/strait_gibraltar_measurements_19701.diff
[CMD] [2019-12-25 15:50:41] echo "." >> /app/public/diff/strait_gibraltar_measurements_19701.diff
[STOP] [2019-12-25 15:50:42] calculate_delta
[START] [2019-12-25 15:50:42] parse_diff_and_store
[INFO] [2019-12-25 15:50:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 15:50:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 15:50:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 15:50:45] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 15:50:48] Storing 2 References
[INFO] [2019-12-25 15:50:48] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 15:50:48] Average Time: 0.0
[INFO] [2019-12-25 15:50:48] Total Time: 1s
[INFO] [2019-12-25 15:50:48] Storing 1456 ScientificNames
[INFO] [2019-12-25 15:50:48] Processing group of 1456 in 2 groups of 1000
[INFO] [2019-12-25 15:50:49] Average Time: 0.32
[INFO] [2019-12-25 15:50:49] Total Time: 1s
[INFO] [2019-12-25 15:50:49] Storing 1456 Nodes
[INFO] [2019-12-25 15:50:49] Processing group of 1456 in 2 groups of 1000
[INFO] [2019-12-25 15:50:50] Average Time: 0.295
[INFO] [2019-12-25 15:50:50] Total Time: 1s
[INFO] [2019-12-25 15:50:50] Storing 609 Occurrences
[INFO] [2019-12-25 15:50:50] Processing group of 609 in 1 groups of 1000
[INFO] [2019-12-25 15:50:50] Average Time: 0.09
[INFO] [2019-12-25 15:50:50] Total Time: 1s
[INFO] [2019-12-25 15:50:50] Storing 1218 TraitsReferences
[INFO] [2019-12-25 15:50:50] Processing group of 1218 in 2 groups of 1000
[INFO] [2019-12-25 15:50:50] Average Time: 0.085
[INFO] [2019-12-25 15:50:50] Total Time: 1s
[INFO] [2019-12-25 15:50:50] Storing 1218 Traits
[INFO] [2019-12-25 15:50:50] Processing group of 1218 in 2 groups of 1000
[INFO] [2019-12-25 15:50:50] Average Time: 0.245
[INFO] [2019-12-25 15:50:50] Total Time: 1s
[INFO] [2019-12-25 15:50:50] Storing 1218 MetaTraits
[INFO] [2019-12-25 15:50:50] Processing group of 1218 in 2 groups of 1000
[INFO] [2019-12-25 15:50:51] Average Time: 0.095
[INFO] [2019-12-25 15:50:51] Total Time: 1s
[STOP] [2019-12-25 15:50:51] parse_diff_and_store
[START] [2019-12-25 15:50:51] resolve_keys
[INFO] [2019-12-25 15:50:59] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 15:51:00] traits to occurrences...
[INFO] [2019-12-25 15:51:01] traits to nodes (through occurrences)...
[INFO] [2019-12-25 15:51:01] Traits to sex term...
[INFO] [2019-12-25 15:51:01] Traits to lifestage term...
[INFO] [2019-12-25 15:51:02] MetaTraits to traits...
[INFO] [2019-12-25 15:51:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 15:51:02] Assocs to occurrences...
[INFO] [2019-12-25 15:51:02] Assocs to nodes...
[INFO] [2019-12-25 15:51:02] Assoc to sex term...
[INFO] [2019-12-25 15:51:02] Assoc to lifestage term...
[STOP] [2019-12-25 15:51:02] resolve_keys
[START] [2019-12-25 15:51:02] hold_for_later_1
[STOP] [2019-12-25 15:51:02] hold_for_later_1
[START] [2019-12-25 15:51:02] hold_for_later_2
[STOP] [2019-12-25 15:51:02] hold_for_later_2
[START] [2019-12-25 15:51:02] resolve_missing_parents
[STOP] [2019-12-25 15:51:04] resolve_missing_parents
[START] [2019-12-25 15:51:04] rebuild_nodes
[START] [2019-12-25 15:51:04] Flattener#flatten
[START] [2019-12-25 15:51:04] Flattener#study_resource
[START] [2019-12-25 15:51:04] Flattener#build_ancestry
[STOP] [2019-12-25 15:51:04] Flattener#build_ancestry
[INFO] [2019-12-25 15:51:04] 1456 ancestry keys
[START] [2019-12-25 15:51:04] build_node_ancestors
[INFO] [2019-12-25 15:51:04] old ancestors deleted.
[STOP] [2019-12-25 15:51:05] build_node_ancestors
[START] [2019-12-25 15:51:05] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 15:51:05] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 15:51:05] Flattener#flatten
[STOP] [2019-12-25 15:51:05] rebuild_nodes
[START] [2019-12-25 15:51:05] resolve_missing_media_owners
[STOP] [2019-12-25 15:51:05] resolve_missing_media_owners
[START] [2019-12-25 15:51:05] sanitize_media_verbatims
[STOP] [2019-12-25 15:51:05] sanitize_media_verbatims
[START] [2019-12-25 15:51:05] queue_downloads
[STOP] [2019-12-25 15:51:05] queue_downloads
[START] [2019-12-25 15:51:05] parse_names
[WARN] [2019-12-25 15:51:05] I see 1456 names which still need to be parsed.
[STOP] [2019-12-25 15:51:08] parse_names
[START] [2019-12-25 15:51:08] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 15:51:08] denormalize_canonical_names_to_nodes
[START] [2019-12-25 15:51:08] match_nodes
[START] [2019-12-25 15:51:08] map_all_nodes_to_pages
[STOP] [2019-12-25 15:54:16] map_all_nodes_to_pages
[INFO] [2019-12-25 15:54:16] 54 Unmatched nodes (of 1456)! That's too many to output. First 10: Larus audouinii (#62498809); Scorpaeniformes (#62499027); Pleurogona (#62499012); Dardanus calidus (#62498890); Calcinus tubularis (#62499325); Atyaephyra (#62499994); Atyaephyra desmarestii (#62499993); Atyaephyra desmaresti (#62500048); Maxillopoda (#62498714); Pectiniidae (#62499280)
[START] [2019-12-25 15:54:16] update_nodes
[STOP] [2019-12-25 15:54:16] update_nodes
[STOP] [2019-12-25 15:54:16] match_nodes
[START] [2019-12-25 15:54:16] reindex_search
[STOP] [2019-12-25 15:54:18] reindex_search
[START] [2019-12-25 15:54:18] normalize_units
[STOP] [2019-12-25 15:54:18] normalize_units
[START] [2019-12-25 15:54:18] calculate_statistics
[STOP] [2019-12-25 15:54:18] calculate_statistics
[START] [2019-12-25 15:54:18] complete_harvest_instance
[START] [2019-12-25 15:54:18] overall_tsv_creation
[INFO] [2019-12-25 15:54:18] Processing group of 1456 in 1 batches of 10000
[INFO] [2019-12-25 15:55:14] 609 Traits (unfiltered)...
[INFO] [2019-12-25 15:55:29] 609 Traits (filtered)...
[INFO] [2019-12-25 15:55:29] 0 Associations (filtered)...
[INFO] [2019-12-25 15:56:10] 3045 metadata added.
[INFO] [2019-12-25 15:56:10] 0 metadata added.
[INFO] [2019-12-25 15:56:10] Average Time: 84.82
[INFO] [2019-12-25 15:56:10] Total Time: 1m52s
[STOP] [2019-12-25 15:56:10] overall_tsv_creation
[INFO] [2019-12-25 15:56:10] Done. Check your files:
[INFO] [2019-12-25 15:56:10] (1456 lines) /app/public/data/strait_gibraltar/publish_nodes.tsv
[INFO] [2019-12-25 15:56:11] (6771 lines) /app/public/data/strait_gibraltar/publish_node_ancestors.tsv
[INFO] [2019-12-25 15:56:12] (1456 lines) /app/public/data/strait_gibraltar/publish_scientific_names.tsv
[INFO] [2019-12-25 15:56:12] (610 lines) /app/public/data/strait_gibraltar/publish_traits.tsv
[INFO] [2019-12-25 15:56:13] (3046 lines) /app/public/data/strait_gibraltar/publish_metadata.tsv
[STOP] [2019-12-25 15:56:13] complete_harvest_instance
[START] [2019-12-25 15:56:13] completed
[STOP] [2019-12-25 15:56:13] completed
[STOP] [2019-12-25 15:56:13] logged process, took 342.24
Latest Process

25 Dec 15:50 EXITED currently processing 0