Harvest for Gulf of Aqaba Species List Created 23 Dec 03:37

Stage: completed
Fetched: 23 Dec 03:37
Validated: 23 Dec 03:37
Deltas Created 23 Dec 03:37
Units Normalized: 23 Dec 03:48
Ancestry Built: 23 Dec 03:38
Nodes Matched: 23 Dec 03:48
Names Parsed: 23 Dec 03:38
New Models Stored: 23 Dec 03:37
Indexed: 23 Dec 03:48
Completed: 23 Dec 03:50
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 03:37:27 -0500 by logger.rb/56815
[START] [2019-12-23 03:37:27] logged process
[START] [2019-12-23 03:37:27] create_harvest_instance
[STOP] [2019-12-23 03:37:28] create_harvest_instance
[START] [2019-12-23 03:37:28] fetch_files
[STOP] [2019-12-23 03:37:28] fetch_files
[START] [2019-12-23 03:37:28] validate_each_file
[STOP] [2019-12-23 03:37:28] validate_each_file
[START] [2019-12-23 03:37:28] convert_to_csv
[CMD] [2019-12-23 03:37:28] /usr/bin/sort /app/public/converted_csv/gulf_aqaba_sp_li_refs_19274.csv > /app/public/converted_csv/gulf_aqaba_sp_li_refs_19274.csv_sorted
[CMD] [2019-12-23 03:37:29] /usr/bin/sort /app/public/converted_csv/gulf_aqaba_sp_li_nodes_19275.csv > /app/public/converted_csv/gulf_aqaba_sp_li_nodes_19275.csv_sorted
[CMD] [2019-12-23 03:37:30] /usr/bin/sort /app/public/converted_csv/gulf_aqaba_sp_li_occurrences_19276.csv > /app/public/converted_csv/gulf_aqaba_sp_li_occurrences_19276.csv_sorted
[CMD] [2019-12-23 03:37:31] /usr/bin/sort /app/public/converted_csv/gulf_aqaba_sp_li_measurements_19277.csv > /app/public/converted_csv/gulf_aqaba_sp_li_measurements_19277.csv_sorted
[STOP] [2019-12-23 03:37:31] convert_to_csv
[START] [2019-12-23 03:37:31] calculate_delta
[CMD] [2019-12-23 03:37:31] echo "0a" > /app/public/diff/gulf_aqaba_sp_li_refs_19274.diff
[CMD] [2019-12-23 03:37:32] tail -n +1 /app/public/converted_csv/gulf_aqaba_sp_li_refs_19274.csv >> /app/public/diff/gulf_aqaba_sp_li_refs_19274.diff
[CMD] [2019-12-23 03:37:33] echo "." >> /app/public/diff/gulf_aqaba_sp_li_refs_19274.diff
[CMD] [2019-12-23 03:37:33] echo "0a" > /app/public/diff/gulf_aqaba_sp_li_nodes_19275.diff
[CMD] [2019-12-23 03:37:34] tail -n +1 /app/public/converted_csv/gulf_aqaba_sp_li_nodes_19275.csv >> /app/public/diff/gulf_aqaba_sp_li_nodes_19275.diff
[CMD] [2019-12-23 03:37:35] echo "." >> /app/public/diff/gulf_aqaba_sp_li_nodes_19275.diff
[CMD] [2019-12-23 03:37:35] echo "0a" > /app/public/diff/gulf_aqaba_sp_li_occurrences_19276.diff
[CMD] [2019-12-23 03:37:36] tail -n +1 /app/public/converted_csv/gulf_aqaba_sp_li_occurrences_19276.csv >> /app/public/diff/gulf_aqaba_sp_li_occurrences_19276.diff
[CMD] [2019-12-23 03:37:37] echo "." >> /app/public/diff/gulf_aqaba_sp_li_occurrences_19276.diff
[CMD] [2019-12-23 03:37:37] echo "0a" > /app/public/diff/gulf_aqaba_sp_li_measurements_19277.diff
[CMD] [2019-12-23 03:37:38] tail -n +1 /app/public/converted_csv/gulf_aqaba_sp_li_measurements_19277.csv >> /app/public/diff/gulf_aqaba_sp_li_measurements_19277.diff
[CMD] [2019-12-23 03:37:39] echo "." >> /app/public/diff/gulf_aqaba_sp_li_measurements_19277.diff
[STOP] [2019-12-23 03:37:39] calculate_delta
[START] [2019-12-23 03:37:39] parse_diff_and_store
[INFO] [2019-12-23 03:37:40] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 03:37:41] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 03:37:42] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 03:37:43] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 03:37:50] Storing 2 References
[INFO] [2019-12-23 03:37:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 03:37:50] Average Time: 0.0
[INFO] [2019-12-23 03:37:50] Total Time: 1s
[INFO] [2019-12-23 03:37:50] Storing 2310 ScientificNames
[INFO] [2019-12-23 03:37:50] Processing group of 2310 in 3 groups of 1000
[INFO] [2019-12-23 03:37:51] Average Time: 0.33
[INFO] [2019-12-23 03:37:51] Total Time: 2s
[INFO] [2019-12-23 03:37:51] Storing 2310 Nodes
[INFO] [2019-12-23 03:37:51] Processing group of 2310 in 3 groups of 1000
[INFO] [2019-12-23 03:37:53] Average Time: 0.313
[INFO] [2019-12-23 03:37:53] Total Time: 2s
[INFO] [2019-12-23 03:37:53] Storing 1147 Occurrences
[INFO] [2019-12-23 03:37:53] Processing group of 1147 in 2 groups of 1000
[INFO] [2019-12-23 03:37:53] Average Time: 0.07
[INFO] [2019-12-23 03:37:53] Total Time: 1s
[INFO] [2019-12-23 03:37:53] Storing 2294 TraitsReferences
[INFO] [2019-12-23 03:37:53] Processing group of 2294 in 3 groups of 1000
[INFO] [2019-12-23 03:37:53] Average Time: 0.063
[INFO] [2019-12-23 03:37:53] Total Time: 1s
[INFO] [2019-12-23 03:37:53] Storing 2294 Traits
[INFO] [2019-12-23 03:37:53] Processing group of 2294 in 3 groups of 1000
[INFO] [2019-12-23 03:37:54] Average Time: 0.3
[INFO] [2019-12-23 03:37:54] Total Time: 1s
[INFO] [2019-12-23 03:37:54] Storing 2294 MetaTraits
[INFO] [2019-12-23 03:37:54] Processing group of 2294 in 3 groups of 1000
[INFO] [2019-12-23 03:37:55] Average Time: 0.107
[INFO] [2019-12-23 03:37:55] Total Time: 1s
[STOP] [2019-12-23 03:37:55] parse_diff_and_store
[START] [2019-12-23 03:37:55] resolve_keys
[INFO] [2019-12-23 03:38:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 03:38:07] traits to occurrences...
[INFO] [2019-12-23 03:38:08] traits to nodes (through occurrences)...
[INFO] [2019-12-23 03:38:08] Traits to sex term...
[INFO] [2019-12-23 03:38:08] Traits to lifestage term...
[INFO] [2019-12-23 03:38:08] MetaTraits to traits...
[INFO] [2019-12-23 03:38:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 03:38:09] Assocs to occurrences...
[INFO] [2019-12-23 03:38:09] Assocs to nodes...
[INFO] [2019-12-23 03:38:09] Assoc to sex term...
[INFO] [2019-12-23 03:38:09] Assoc to lifestage term...
[STOP] [2019-12-23 03:38:09] resolve_keys
[START] [2019-12-23 03:38:09] hold_for_later_1
[STOP] [2019-12-23 03:38:09] hold_for_later_1
[START] [2019-12-23 03:38:09] hold_for_later_2
[STOP] [2019-12-23 03:38:09] hold_for_later_2
[START] [2019-12-23 03:38:09] resolve_missing_parents
[STOP] [2019-12-23 03:38:12] resolve_missing_parents
[START] [2019-12-23 03:38:12] rebuild_nodes
[START] [2019-12-23 03:38:12] Flattener#flatten
[START] [2019-12-23 03:38:12] Flattener#study_resource
[START] [2019-12-23 03:38:12] Flattener#build_ancestry
[STOP] [2019-12-23 03:38:13] Flattener#build_ancestry
[INFO] [2019-12-23 03:38:13] 2310 ancestry keys
[START] [2019-12-23 03:38:13] build_node_ancestors
[INFO] [2019-12-23 03:38:13] old ancestors deleted.
[STOP] [2019-12-23 03:38:13] build_node_ancestors
[START] [2019-12-23 03:38:14] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:38:15] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 03:38:15] Flattener#flatten
[STOP] [2019-12-23 03:38:15] rebuild_nodes
[START] [2019-12-23 03:38:15] resolve_missing_media_owners
[STOP] [2019-12-23 03:38:15] resolve_missing_media_owners
[START] [2019-12-23 03:38:15] sanitize_media_verbatims
[STOP] [2019-12-23 03:38:15] sanitize_media_verbatims
[START] [2019-12-23 03:38:15] queue_downloads
[STOP] [2019-12-23 03:38:15] queue_downloads
[START] [2019-12-23 03:38:15] parse_names
[WARN] [2019-12-23 03:38:15] I see 2310 names which still need to be parsed.
[STOP] [2019-12-23 03:38:18] parse_names
[START] [2019-12-23 03:38:18] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 03:38:18] denormalize_canonical_names_to_nodes
[START] [2019-12-23 03:38:18] match_nodes
[START] [2019-12-23 03:38:18] map_all_nodes_to_pages
[STOP] [2019-12-23 03:48:21] map_all_nodes_to_pages
[INFO] [2019-12-23 03:48:21] 81 Unmatched nodes (of 2310)! That's too many to output. First 10: Cheilodipterus lineatus (#61906196); Ptereleotridae (#61906296); Scorpaeniformes (#61904380); Trachinocephalus (#61906590); Gasterosteiformes (#61904775); Manta (#61905218); Larus leucophthalmus (#61906544); Philomachus (#61906143); Philomachus pugnax (#61906142); Anas querquedula (#61906517)
[START] [2019-12-23 03:48:21] update_nodes
[STOP] [2019-12-23 03:48:22] update_nodes
[STOP] [2019-12-23 03:48:22] match_nodes
[START] [2019-12-23 03:48:22] reindex_search
[STOP] [2019-12-23 03:48:28] reindex_search
[START] [2019-12-23 03:48:28] normalize_units
[STOP] [2019-12-23 03:48:28] normalize_units
[START] [2019-12-23 03:48:28] calculate_statistics
[STOP] [2019-12-23 03:48:28] calculate_statistics
[START] [2019-12-23 03:48:28] complete_harvest_instance
[START] [2019-12-23 03:48:28] overall_tsv_creation
[INFO] [2019-12-23 03:48:28] Processing group of 2310 in 1 batches of 10000
[INFO] [2019-12-23 03:49:25] 1147 Traits (unfiltered)...
[INFO] [2019-12-23 03:49:38] 1147 Traits (filtered)...
[INFO] [2019-12-23 03:49:38] 0 Associations (filtered)...
[INFO] [2019-12-23 03:50:17] 5735 metadata added.
[INFO] [2019-12-23 03:50:17] 0 metadata added.
[INFO] [2019-12-23 03:50:17] Average Time: 84.88
[INFO] [2019-12-23 03:50:17] Total Time: 1m49s
[STOP] [2019-12-23 03:50:17] overall_tsv_creation
[INFO] [2019-12-23 03:50:17] Done. Check your files:
[INFO] [2019-12-23 03:50:17] (2310 lines) /app/public/data/gulf_aqaba_sp_li/publish_nodes.tsv
[INFO] [2019-12-23 03:50:18] (11748 lines) /app/public/data/gulf_aqaba_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:50:19] (2310 lines) /app/public/data/gulf_aqaba_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-23 03:50:19] (1148 lines) /app/public/data/gulf_aqaba_sp_li/publish_traits.tsv
[INFO] [2019-12-23 03:50:20] (5736 lines) /app/public/data/gulf_aqaba_sp_li/publish_metadata.tsv
[STOP] [2019-12-23 03:50:20] complete_harvest_instance
[START] [2019-12-23 03:50:20] completed
[STOP] [2019-12-23 03:50:20] completed
[STOP] [2019-12-23 03:50:20] logged process, took 772.91
Latest Process

23 Dec 03:37 EXITED currently processing 0