Harvest for Red Sea Species List Created 25 Dec 09:53

Stage: completed
Fetched: 25 Dec 09:53
Validated: 25 Dec 09:53
Deltas Created 25 Dec 09:53
Units Normalized: 25 Dec 10:23
Ancestry Built: 25 Dec 09:54
Nodes Matched: 25 Dec 10:23
Names Parsed: 25 Dec 09:54
New Models Stored: 25 Dec 09:54
Indexed: 25 Dec 10:23
Completed: 25 Dec 10:25
Time to Harvest: 1 minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-25 09:53:31 -0500 by logger.rb/56815
[START] [2019-12-25 09:53:31] logged process
[START] [2019-12-25 09:53:31] create_harvest_instance
[STOP] [2019-12-25 09:53:32] create_harvest_instance
[START] [2019-12-25 09:53:32] fetch_files
[STOP] [2019-12-25 09:53:32] fetch_files
[START] [2019-12-25 09:53:32] validate_each_file
[STOP] [2019-12-25 09:53:33] validate_each_file
[START] [2019-12-25 09:53:33] convert_to_csv
[CMD] [2019-12-25 09:53:33] /usr/bin/sort /app/public/converted_csv/red_sea_sp_list_refs_19594.csv > /app/public/converted_csv/red_sea_sp_list_refs_19594.csv_sorted
[CMD] [2019-12-25 09:53:33] /usr/bin/sort /app/public/converted_csv/red_sea_sp_list_nodes_19595.csv > /app/public/converted_csv/red_sea_sp_list_nodes_19595.csv_sorted
[CMD] [2019-12-25 09:53:33] /usr/bin/sort /app/public/converted_csv/red_sea_sp_list_occurrences_19596.csv > /app/public/converted_csv/red_sea_sp_list_occurrences_19596.csv_sorted
[CMD] [2019-12-25 09:53:33] /usr/bin/sort /app/public/converted_csv/red_sea_sp_list_measurements_19597.csv > /app/public/converted_csv/red_sea_sp_list_measurements_19597.csv_sorted
[STOP] [2019-12-25 09:53:33] convert_to_csv
[START] [2019-12-25 09:53:33] calculate_delta
[CMD] [2019-12-25 09:53:33] echo "0a" > /app/public/diff/red_sea_sp_list_refs_19594.diff
[CMD] [2019-12-25 09:53:34] tail -n +1 /app/public/converted_csv/red_sea_sp_list_refs_19594.csv >> /app/public/diff/red_sea_sp_list_refs_19594.diff
[CMD] [2019-12-25 09:53:34] echo "." >> /app/public/diff/red_sea_sp_list_refs_19594.diff
[CMD] [2019-12-25 09:53:34] echo "0a" > /app/public/diff/red_sea_sp_list_nodes_19595.diff
[CMD] [2019-12-25 09:53:34] tail -n +1 /app/public/converted_csv/red_sea_sp_list_nodes_19595.csv >> /app/public/diff/red_sea_sp_list_nodes_19595.diff
[CMD] [2019-12-25 09:53:34] echo "." >> /app/public/diff/red_sea_sp_list_nodes_19595.diff
[CMD] [2019-12-25 09:53:34] echo "0a" > /app/public/diff/red_sea_sp_list_occurrences_19596.diff
[CMD] [2019-12-25 09:53:35] tail -n +1 /app/public/converted_csv/red_sea_sp_list_occurrences_19596.csv >> /app/public/diff/red_sea_sp_list_occurrences_19596.diff
[CMD] [2019-12-25 09:53:35] echo "." >> /app/public/diff/red_sea_sp_list_occurrences_19596.diff
[CMD] [2019-12-25 09:53:35] echo "0a" > /app/public/diff/red_sea_sp_list_measurements_19597.diff
[CMD] [2019-12-25 09:53:35] tail -n +1 /app/public/converted_csv/red_sea_sp_list_measurements_19597.csv >> /app/public/diff/red_sea_sp_list_measurements_19597.diff
[CMD] [2019-12-25 09:53:35] echo "." >> /app/public/diff/red_sea_sp_list_measurements_19597.diff
[STOP] [2019-12-25 09:53:35] calculate_delta
[START] [2019-12-25 09:53:36] parse_diff_and_store
[INFO] [2019-12-25 09:53:36] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-25 09:53:36] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-25 09:53:38] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-25 09:53:39] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-25 09:53:54] Storing 2 References
[INFO] [2019-12-25 09:53:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-25 09:53:54] Average Time: 0.0
[INFO] [2019-12-25 09:53:54] Total Time: 1s
[INFO] [2019-12-25 09:53:54] Storing 4554 ScientificNames
[INFO] [2019-12-25 09:53:54] Processing group of 4554 in 5 groups of 1000
[INFO] [2019-12-25 09:53:56] Average Time: 0.362
[INFO] [2019-12-25 09:53:56] Total Time: 2s
[INFO] [2019-12-25 09:53:56] Storing 4554 Nodes
[INFO] [2019-12-25 09:53:56] Processing group of 4554 in 5 groups of 1000
[INFO] [2019-12-25 09:53:58] Average Time: 0.394
[INFO] [2019-12-25 09:53:58] Total Time: 2s
[INFO] [2019-12-25 09:53:58] Storing 2422 Occurrences
[INFO] [2019-12-25 09:53:58] Processing group of 2422 in 3 groups of 1000
[INFO] [2019-12-25 09:53:58] Average Time: 0.09
[INFO] [2019-12-25 09:53:58] Total Time: 1s
[INFO] [2019-12-25 09:53:58] Storing 4844 TraitsReferences
[INFO] [2019-12-25 09:53:58] Processing group of 4844 in 5 groups of 1000
[INFO] [2019-12-25 09:53:58] Average Time: 0.102
[INFO] [2019-12-25 09:53:58] Total Time: 1s
[INFO] [2019-12-25 09:53:58] Storing 4844 Traits
[INFO] [2019-12-25 09:53:58] Processing group of 4844 in 5 groups of 1000
[INFO] [2019-12-25 09:54:00] Average Time: 0.33
[INFO] [2019-12-25 09:54:00] Total Time: 2s
[INFO] [2019-12-25 09:54:00] Storing 4844 MetaTraits
[INFO] [2019-12-25 09:54:00] Processing group of 4844 in 5 groups of 1000
[INFO] [2019-12-25 09:54:01] Average Time: 0.148
[INFO] [2019-12-25 09:54:01] Total Time: 1s
[STOP] [2019-12-25 09:54:01] parse_diff_and_store
[START] [2019-12-25 09:54:01] resolve_keys
[INFO] [2019-12-25 09:54:22] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-25 09:54:24] traits to occurrences...
[INFO] [2019-12-25 09:54:27] traits to nodes (through occurrences)...
[INFO] [2019-12-25 09:54:27] Traits to sex term...
[INFO] [2019-12-25 09:54:29] Traits to lifestage term...
[INFO] [2019-12-25 09:54:31] MetaTraits to traits...
[INFO] [2019-12-25 09:54:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-25 09:54:32] Assocs to occurrences...
[INFO] [2019-12-25 09:54:32] Assocs to nodes...
[INFO] [2019-12-25 09:54:32] Assoc to sex term...
[INFO] [2019-12-25 09:54:32] Assoc to lifestage term...
[STOP] [2019-12-25 09:54:32] resolve_keys
[START] [2019-12-25 09:54:32] hold_for_later_1
[STOP] [2019-12-25 09:54:32] hold_for_later_1
[START] [2019-12-25 09:54:32] hold_for_later_2
[STOP] [2019-12-25 09:54:32] hold_for_later_2
[START] [2019-12-25 09:54:32] resolve_missing_parents
[STOP] [2019-12-25 09:54:41] resolve_missing_parents
[START] [2019-12-25 09:54:41] rebuild_nodes
[START] [2019-12-25 09:54:41] Flattener#flatten
[START] [2019-12-25 09:54:41] Flattener#study_resource
[START] [2019-12-25 09:54:41] Flattener#build_ancestry
[STOP] [2019-12-25 09:54:41] Flattener#build_ancestry
[INFO] [2019-12-25 09:54:41] 4554 ancestry keys
[START] [2019-12-25 09:54:41] build_node_ancestors
[INFO] [2019-12-25 09:54:41] old ancestors deleted.
[STOP] [2019-12-25 09:54:43] build_node_ancestors
[START] [2019-12-25 09:54:45] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 09:54:45] Flattener#propagate_ancestor_ids
[STOP] [2019-12-25 09:54:45] Flattener#flatten
[STOP] [2019-12-25 09:54:45] rebuild_nodes
[START] [2019-12-25 09:54:45] resolve_missing_media_owners
[STOP] [2019-12-25 09:54:45] resolve_missing_media_owners
[START] [2019-12-25 09:54:45] sanitize_media_verbatims
[STOP] [2019-12-25 09:54:45] sanitize_media_verbatims
[START] [2019-12-25 09:54:45] queue_downloads
[STOP] [2019-12-25 09:54:45] queue_downloads
[START] [2019-12-25 09:54:45] parse_names
[WARN] [2019-12-25 09:54:45] I see 4554 names which still need to be parsed.
[STOP] [2019-12-25 09:54:50] parse_names
[START] [2019-12-25 09:54:50] denormalize_canonical_names_to_nodes
[STOP] [2019-12-25 09:54:50] denormalize_canonical_names_to_nodes
[START] [2019-12-25 09:54:50] match_nodes
[START] [2019-12-25 09:54:50] map_all_nodes_to_pages
[STOP] [2019-12-25 10:23:26] map_all_nodes_to_pages
[INFO] [2019-12-25 10:23:26] 228 Unmatched nodes (of 4554)! That's too many to output. First 10: Granuloreticulosea (#62423988); Globorotalia cultrata (#62424023); Globorotalia inflata (#62426464); Globorotalia acostaensis (#62426936); Dentagloborotalia (#62424348); Dentagloborotalia anfracta (#62424347); Usbekistania charoides (#62424045); Triloculina affinis (#62424132); Quinqueloculina pittensis (#62426046); Bolivina subspathulata (#62424201)
[START] [2019-12-25 10:23:26] update_nodes
[STOP] [2019-12-25 10:23:28] update_nodes
[STOP] [2019-12-25 10:23:28] match_nodes
[START] [2019-12-25 10:23:28] reindex_search
[STOP] [2019-12-25 10:23:47] reindex_search
[START] [2019-12-25 10:23:47] normalize_units
[STOP] [2019-12-25 10:23:47] normalize_units
[START] [2019-12-25 10:23:47] calculate_statistics
[STOP] [2019-12-25 10:23:47] calculate_statistics
[START] [2019-12-25 10:23:47] complete_harvest_instance
[START] [2019-12-25 10:23:47] overall_tsv_creation
[INFO] [2019-12-25 10:23:47] Processing group of 4554 in 1 batches of 10000
[INFO] [2019-12-25 10:24:54] 2422 Traits (unfiltered)...
[INFO] [2019-12-25 10:25:07] 2422 Traits (filtered)...
[INFO] [2019-12-25 10:25:07] 0 Associations (filtered)...
[INFO] [2019-12-25 10:25:49] 12110 metadata added.
[INFO] [2019-12-25 10:25:49] 0 metadata added.
[INFO] [2019-12-25 10:25:49] Average Time: 96.51
[INFO] [2019-12-25 10:25:49] Total Time: 2m3s
[STOP] [2019-12-25 10:25:49] overall_tsv_creation
[INFO] [2019-12-25 10:25:49] Done. Check your files:
[INFO] [2019-12-25 10:25:50] (4554 lines) /app/public/data/red_sea_sp_list/publish_nodes.tsv
[INFO] [2019-12-25 10:25:50] (23430 lines) /app/public/data/red_sea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-12-25 10:25:50] (4554 lines) /app/public/data/red_sea_sp_list/publish_scientific_names.tsv
[INFO] [2019-12-25 10:25:50] (2423 lines) /app/public/data/red_sea_sp_list/publish_traits.tsv
[INFO] [2019-12-25 10:25:50] (12111 lines) /app/public/data/red_sea_sp_list/publish_metadata.tsv
[STOP] [2019-12-25 10:25:50] complete_harvest_instance
[START] [2019-12-25 10:25:50] completed
[STOP] [2019-12-25 10:25:50] completed
[STOP] [2019-12-25 10:25:50] logged process, took 1939.17
Latest Process

25 Dec 09:53 EXITED currently processing 0