Harvest for Gulf of Suez Species List Created 23 Dec 09:56

Stage: completed
Fetched: 23 Dec 09:56
Validated: 23 Dec 09:56
Deltas Created 23 Dec 09:57
Units Normalized: 23 Dec 10:02
Ancestry Built: 23 Dec 09:57
Nodes Matched: 23 Dec 10:02
Names Parsed: 23 Dec 09:57
New Models Stored: 23 Dec 09:57
Indexed: 23 Dec 10:02
Completed: 23 Dec 10:04
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 09:56:54 -0500 by logger.rb/56815
[START] [2019-12-23 09:56:54] logged process
[START] [2019-12-23 09:56:54] create_harvest_instance
[STOP] [2019-12-23 09:56:55] create_harvest_instance
[START] [2019-12-23 09:56:55] fetch_files
[STOP] [2019-12-23 09:56:55] fetch_files
[START] [2019-12-23 09:56:55] validate_each_file
[STOP] [2019-12-23 09:56:55] validate_each_file
[START] [2019-12-23 09:56:55] convert_to_csv
[CMD] [2019-12-23 09:56:55] /usr/bin/sort /app/public/converted_csv/gulf_suez_sp_lis_refs_19354.csv > /app/public/converted_csv/gulf_suez_sp_lis_refs_19354.csv_sorted
[CMD] [2019-12-23 09:56:56] /usr/bin/sort /app/public/converted_csv/gulf_suez_sp_lis_nodes_19355.csv > /app/public/converted_csv/gulf_suez_sp_lis_nodes_19355.csv_sorted
[CMD] [2019-12-23 09:56:57] /usr/bin/sort /app/public/converted_csv/gulf_suez_sp_lis_occurrences_19356.csv > /app/public/converted_csv/gulf_suez_sp_lis_occurrences_19356.csv_sorted
[CMD] [2019-12-23 09:56:57] /usr/bin/sort /app/public/converted_csv/gulf_suez_sp_lis_measurements_19357.csv > /app/public/converted_csv/gulf_suez_sp_lis_measurements_19357.csv_sorted
[STOP] [2019-12-23 09:56:58] convert_to_csv
[START] [2019-12-23 09:56:58] calculate_delta
[CMD] [2019-12-23 09:56:58] echo "0a" > /app/public/diff/gulf_suez_sp_lis_refs_19354.diff
[CMD] [2019-12-23 09:56:59] tail -n +1 /app/public/converted_csv/gulf_suez_sp_lis_refs_19354.csv >> /app/public/diff/gulf_suez_sp_lis_refs_19354.diff
[CMD] [2019-12-23 09:56:59] echo "." >> /app/public/diff/gulf_suez_sp_lis_refs_19354.diff
[CMD] [2019-12-23 09:57:00] echo "0a" > /app/public/diff/gulf_suez_sp_lis_nodes_19355.diff
[CMD] [2019-12-23 09:57:01] tail -n +1 /app/public/converted_csv/gulf_suez_sp_lis_nodes_19355.csv >> /app/public/diff/gulf_suez_sp_lis_nodes_19355.diff
[CMD] [2019-12-23 09:57:01] echo "." >> /app/public/diff/gulf_suez_sp_lis_nodes_19355.diff
[CMD] [2019-12-23 09:57:02] echo "0a" > /app/public/diff/gulf_suez_sp_lis_occurrences_19356.diff
[CMD] [2019-12-23 09:57:03] tail -n +1 /app/public/converted_csv/gulf_suez_sp_lis_occurrences_19356.csv >> /app/public/diff/gulf_suez_sp_lis_occurrences_19356.diff
[CMD] [2019-12-23 09:57:03] echo "." >> /app/public/diff/gulf_suez_sp_lis_occurrences_19356.diff
[CMD] [2019-12-23 09:57:04] echo "0a" > /app/public/diff/gulf_suez_sp_lis_measurements_19357.diff
[CMD] [2019-12-23 09:57:05] tail -n +1 /app/public/converted_csv/gulf_suez_sp_lis_measurements_19357.csv >> /app/public/diff/gulf_suez_sp_lis_measurements_19357.diff
[CMD] [2019-12-23 09:57:05] echo "." >> /app/public/diff/gulf_suez_sp_lis_measurements_19357.diff
[STOP] [2019-12-23 09:57:06] calculate_delta
[START] [2019-12-23 09:57:06] parse_diff_and_store
[INFO] [2019-12-23 09:57:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 09:57:07] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 09:57:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 09:57:09] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 09:57:11] Storing 2 References
[INFO] [2019-12-23 09:57:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 09:57:11] Average Time: 0.0
[INFO] [2019-12-23 09:57:11] Total Time: 1s
[INFO] [2019-12-23 09:57:11] Storing 895 ScientificNames
[INFO] [2019-12-23 09:57:11] Processing group of 895 in 1 groups of 1000
[INFO] [2019-12-23 09:57:12] Average Time: 0.42
[INFO] [2019-12-23 09:57:12] Total Time: 1s
[INFO] [2019-12-23 09:57:12] Storing 895 Nodes
[INFO] [2019-12-23 09:57:12] Processing group of 895 in 1 groups of 1000
[INFO] [2019-12-23 09:57:12] Average Time: 0.31
[INFO] [2019-12-23 09:57:12] Total Time: 1s
[INFO] [2019-12-23 09:57:12] Storing 364 Occurrences
[INFO] [2019-12-23 09:57:12] Processing group of 364 in 1 groups of 1000
[INFO] [2019-12-23 09:57:12] Average Time: 0.05
[INFO] [2019-12-23 09:57:12] Total Time: 1s
[INFO] [2019-12-23 09:57:12] Storing 728 TraitsReferences
[INFO] [2019-12-23 09:57:12] Processing group of 728 in 1 groups of 1000
[INFO] [2019-12-23 09:57:12] Average Time: 0.14
[INFO] [2019-12-23 09:57:12] Total Time: 1s
[INFO] [2019-12-23 09:57:12] Storing 728 Traits
[INFO] [2019-12-23 09:57:12] Processing group of 728 in 1 groups of 1000
[INFO] [2019-12-23 09:57:13] Average Time: 0.37
[INFO] [2019-12-23 09:57:13] Total Time: 1s
[INFO] [2019-12-23 09:57:13] Storing 728 MetaTraits
[INFO] [2019-12-23 09:57:13] Processing group of 728 in 1 groups of 1000
[INFO] [2019-12-23 09:57:13] Average Time: 0.13
[INFO] [2019-12-23 09:57:13] Total Time: 1s
[STOP] [2019-12-23 09:57:13] parse_diff_and_store
[START] [2019-12-23 09:57:13] resolve_keys
[INFO] [2019-12-23 09:57:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 09:57:19] traits to occurrences...
[INFO] [2019-12-23 09:57:19] traits to nodes (through occurrences)...
[INFO] [2019-12-23 09:57:19] Traits to sex term...
[INFO] [2019-12-23 09:57:20] Traits to lifestage term...
[INFO] [2019-12-23 09:57:20] MetaTraits to traits...
[INFO] [2019-12-23 09:57:20] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 09:57:20] Assocs to occurrences...
[INFO] [2019-12-23 09:57:20] Assocs to nodes...
[INFO] [2019-12-23 09:57:20] Assoc to sex term...
[INFO] [2019-12-23 09:57:20] Assoc to lifestage term...
[STOP] [2019-12-23 09:57:20] resolve_keys
[START] [2019-12-23 09:57:20] hold_for_later_1
[STOP] [2019-12-23 09:57:20] hold_for_later_1
[START] [2019-12-23 09:57:20] hold_for_later_2
[STOP] [2019-12-23 09:57:20] hold_for_later_2
[START] [2019-12-23 09:57:20] resolve_missing_parents
[STOP] [2019-12-23 09:57:20] resolve_missing_parents
[START] [2019-12-23 09:57:20] rebuild_nodes
[START] [2019-12-23 09:57:20] Flattener#flatten
[START] [2019-12-23 09:57:20] Flattener#study_resource
[START] [2019-12-23 09:57:20] Flattener#build_ancestry
[STOP] [2019-12-23 09:57:20] Flattener#build_ancestry
[INFO] [2019-12-23 09:57:20] 895 ancestry keys
[START] [2019-12-23 09:57:20] build_node_ancestors
[INFO] [2019-12-23 09:57:20] old ancestors deleted.
[STOP] [2019-12-23 09:57:21] build_node_ancestors
[START] [2019-12-23 09:57:21] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:57:21] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:57:21] Flattener#flatten
[STOP] [2019-12-23 09:57:21] rebuild_nodes
[START] [2019-12-23 09:57:21] resolve_missing_media_owners
[STOP] [2019-12-23 09:57:21] resolve_missing_media_owners
[START] [2019-12-23 09:57:21] sanitize_media_verbatims
[STOP] [2019-12-23 09:57:21] sanitize_media_verbatims
[START] [2019-12-23 09:57:21] queue_downloads
[STOP] [2019-12-23 09:57:21] queue_downloads
[START] [2019-12-23 09:57:21] parse_names
[WARN] [2019-12-23 09:57:21] I see 895 names which still need to be parsed.
[STOP] [2019-12-23 09:57:23] parse_names
[START] [2019-12-23 09:57:23] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 09:57:23] denormalize_canonical_names_to_nodes
[START] [2019-12-23 09:57:23] match_nodes
[START] [2019-12-23 09:57:23] map_all_nodes_to_pages
[STOP] [2019-12-23 10:02:28] map_all_nodes_to_pages
[INFO] [2019-12-23 10:02:28] 26 Unmatched nodes (of 895)! That's too many to output. First 10: Scorpaeniformes (#61960896); Trachinocephalus (#61961003); Polyceratidae (#61961549); Pleurobranchomorpha (#61961299); Neotaenioglossa (#61961416); Cycloneritimorpha (#61961639); Archaeogastropoda (#61961695); Trubinidae (#61961694); Mytiloida (#61961125); Veneroida (#61961178)
[START] [2019-12-23 10:02:28] update_nodes
[STOP] [2019-12-23 10:02:28] update_nodes
[STOP] [2019-12-23 10:02:28] match_nodes
[START] [2019-12-23 10:02:28] reindex_search
[STOP] [2019-12-23 10:02:31] reindex_search
[START] [2019-12-23 10:02:31] normalize_units
[STOP] [2019-12-23 10:02:31] normalize_units
[START] [2019-12-23 10:02:31] calculate_statistics
[STOP] [2019-12-23 10:02:31] calculate_statistics
[START] [2019-12-23 10:02:31] complete_harvest_instance
[START] [2019-12-23 10:02:31] overall_tsv_creation
[INFO] [2019-12-23 10:02:31] Processing group of 895 in 1 batches of 10000
[INFO] [2019-12-23 10:03:19] 364 Traits (unfiltered)...
[INFO] [2019-12-23 10:03:32] 364 Traits (filtered)...
[INFO] [2019-12-23 10:03:32] 0 Associations (filtered)...
[INFO] [2019-12-23 10:04:10] 1820 metadata added.
[INFO] [2019-12-23 10:04:10] 0 metadata added.
[INFO] [2019-12-23 10:04:10] Average Time: 76.8
[INFO] [2019-12-23 10:04:10] Total Time: 1m40s
[STOP] [2019-12-23 10:04:10] overall_tsv_creation
[INFO] [2019-12-23 10:04:10] Done. Check your files:
[INFO] [2019-12-23 10:04:11] (895 lines) /app/public/data/gulf_suez_sp_lis/publish_nodes.tsv
[INFO] [2019-12-23 10:04:12] (4332 lines) /app/public/data/gulf_suez_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-12-23 10:04:12] (895 lines) /app/public/data/gulf_suez_sp_lis/publish_scientific_names.tsv
[INFO] [2019-12-23 10:04:13] (365 lines) /app/public/data/gulf_suez_sp_lis/publish_traits.tsv
[INFO] [2019-12-23 10:04:14] (1821 lines) /app/public/data/gulf_suez_sp_lis/publish_metadata.tsv
[STOP] [2019-12-23 10:04:14] complete_harvest_instance
[START] [2019-12-23 10:04:14] completed
[STOP] [2019-12-23 10:04:14] completed
[STOP] [2019-12-23 10:04:14] logged process, took 439.22
Latest Process

23 Dec 09:56 EXITED currently processing 0