Harvest for Dominica Species List Created 12 Oct 14:26

Stage: completed
Fetched: 12 Oct 14:26
Validated: 12 Oct 14:26
Deltas Created 12 Oct 14:26
Units Normalized: 12 Oct 14:31
Ancestry Built: 12 Oct 14:27
Nodes Matched: 12 Oct 14:31
Names Parsed: 12 Oct 14:27
New Models Stored: 12 Oct 14:27
Indexed: 12 Oct 14:31
Completed: 12 Oct 14:33
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 14:26:54 -0400 by logger.rb/56815
[START] [2019-10-12 14:26:54] logged process
[START] [2019-10-12 14:26:54] create_harvest_instance
[STOP] [2019-10-12 14:26:55] create_harvest_instance
[START] [2019-10-12 14:26:55] fetch_files
[STOP] [2019-10-12 14:26:55] fetch_files
[START] [2019-10-12 14:26:55] validate_each_file
[STOP] [2019-10-12 14:26:55] validate_each_file
[START] [2019-10-12 14:26:55] convert_to_csv
[CMD] [2019-10-12 14:26:55] /usr/bin/sort /app/public/converted_csv/dominica_sp_list_refs_15603.csv > /app/public/converted_csv/dominica_sp_list_refs_15603.csv_sorted
[CMD] [2019-10-12 14:26:55] /usr/bin/sort /app/public/converted_csv/dominica_sp_list_nodes_15604.csv > /app/public/converted_csv/dominica_sp_list_nodes_15604.csv_sorted
[CMD] [2019-10-12 14:26:56] /usr/bin/sort /app/public/converted_csv/dominica_sp_list_occurrences_15605.csv > /app/public/converted_csv/dominica_sp_list_occurrences_15605.csv_sorted
[CMD] [2019-10-12 14:26:56] /usr/bin/sort /app/public/converted_csv/dominica_sp_list_measurements_15606.csv > /app/public/converted_csv/dominica_sp_list_measurements_15606.csv_sorted
[STOP] [2019-10-12 14:26:56] convert_to_csv
[START] [2019-10-12 14:26:56] calculate_delta
[CMD] [2019-10-12 14:26:56] echo "0a" > /app/public/diff/dominica_sp_list_refs_15603.diff
[CMD] [2019-10-12 14:26:56] tail -n +1 /app/public/converted_csv/dominica_sp_list_refs_15603.csv >> /app/public/diff/dominica_sp_list_refs_15603.diff
[CMD] [2019-10-12 14:26:56] echo "." >> /app/public/diff/dominica_sp_list_refs_15603.diff
[CMD] [2019-10-12 14:26:56] echo "0a" > /app/public/diff/dominica_sp_list_nodes_15604.diff
[CMD] [2019-10-12 14:26:56] tail -n +1 /app/public/converted_csv/dominica_sp_list_nodes_15604.csv >> /app/public/diff/dominica_sp_list_nodes_15604.diff
[CMD] [2019-10-12 14:26:56] echo "." >> /app/public/diff/dominica_sp_list_nodes_15604.diff
[CMD] [2019-10-12 14:26:56] echo "0a" > /app/public/diff/dominica_sp_list_occurrences_15605.diff
[CMD] [2019-10-12 14:26:56] tail -n +1 /app/public/converted_csv/dominica_sp_list_occurrences_15605.csv >> /app/public/diff/dominica_sp_list_occurrences_15605.diff
[CMD] [2019-10-12 14:26:56] echo "." >> /app/public/diff/dominica_sp_list_occurrences_15605.diff
[CMD] [2019-10-12 14:26:57] echo "0a" > /app/public/diff/dominica_sp_list_measurements_15606.diff
[CMD] [2019-10-12 14:26:57] tail -n +1 /app/public/converted_csv/dominica_sp_list_measurements_15606.csv >> /app/public/diff/dominica_sp_list_measurements_15606.diff
[CMD] [2019-10-12 14:26:57] echo "." >> /app/public/diff/dominica_sp_list_measurements_15606.diff
[STOP] [2019-10-12 14:26:57] calculate_delta
[START] [2019-10-12 14:26:57] parse_diff_and_store
[INFO] [2019-10-12 14:26:57] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 14:26:57] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 14:26:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 14:26:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 14:27:08] Storing 2 References
[INFO] [2019-10-12 14:27:08] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 14:27:08] Average Time: 0.0
[INFO] [2019-10-12 14:27:08] Total Time: 1s
[INFO] [2019-10-12 14:27:08] Storing 3493 ScientificNames
[INFO] [2019-10-12 14:27:08] Processing group of 3493 in 4 groups of 1000
[INFO] [2019-10-12 14:27:10] Average Time: 0.342
[INFO] [2019-10-12 14:27:10] Total Time: 2s
[INFO] [2019-10-12 14:27:10] Storing 3493 Nodes
[INFO] [2019-10-12 14:27:10] Processing group of 3493 in 4 groups of 1000
[INFO] [2019-10-12 14:27:11] Average Time: 0.265
[INFO] [2019-10-12 14:27:11] Total Time: 2s
[INFO] [2019-10-12 14:27:11] Storing 1446 Occurrences
[INFO] [2019-10-12 14:27:11] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-12 14:27:11] Average Time: 0.075
[INFO] [2019-10-12 14:27:11] Total Time: 1s
[INFO] [2019-10-12 14:27:11] Storing 3496 TraitsReferences
[INFO] [2019-10-12 14:27:11] Processing group of 3496 in 4 groups of 1000
[INFO] [2019-10-12 14:27:11] Average Time: 0.07
[INFO] [2019-10-12 14:27:11] Total Time: 1s
[INFO] [2019-10-12 14:27:11] Storing 3495 Traits
[INFO] [2019-10-12 14:27:11] Processing group of 3495 in 4 groups of 1000
[INFO] [2019-10-12 14:27:13] Average Time: 0.293
[INFO] [2019-10-12 14:27:13] Total Time: 2s
[INFO] [2019-10-12 14:27:13] Storing 3496 MetaTraits
[INFO] [2019-10-12 14:27:13] Processing group of 3496 in 4 groups of 1000
[INFO] [2019-10-12 14:27:13] Average Time: 0.11
[INFO] [2019-10-12 14:27:13] Total Time: 1s
[STOP] [2019-10-12 14:27:13] parse_diff_and_store
[START] [2019-10-12 14:27:13] resolve_keys
[INFO] [2019-10-12 14:27:30] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 14:27:31] traits to occurrences...
[INFO] [2019-10-12 14:27:32] traits to nodes (through occurrences)...
[INFO] [2019-10-12 14:27:32] Traits to sex term...
[INFO] [2019-10-12 14:27:33] Traits to lifestage term...
[INFO] [2019-10-12 14:27:33] MetaTraits to traits...
[INFO] [2019-10-12 14:27:33] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 14:27:34] Assocs to occurrences...
[INFO] [2019-10-12 14:27:34] Assocs to nodes...
[INFO] [2019-10-12 14:27:34] Assoc to sex term...
[INFO] [2019-10-12 14:27:34] Assoc to lifestage term...
[STOP] [2019-10-12 14:27:34] resolve_keys
[START] [2019-10-12 14:27:34] hold_for_later_1
[STOP] [2019-10-12 14:27:34] hold_for_later_1
[START] [2019-10-12 14:27:34] hold_for_later_2
[STOP] [2019-10-12 14:27:34] hold_for_later_2
[START] [2019-10-12 14:27:34] resolve_missing_parents
[STOP] [2019-10-12 14:27:41] resolve_missing_parents
[START] [2019-10-12 14:27:41] rebuild_nodes
[START] [2019-10-12 14:27:41] Flattener#flatten
[START] [2019-10-12 14:27:41] Flattener#study_resource
[START] [2019-10-12 14:27:41] Flattener#build_ancestry
[STOP] [2019-10-12 14:27:41] Flattener#build_ancestry
[INFO] [2019-10-12 14:27:41] 3493 ancestry keys
[START] [2019-10-12 14:27:41] build_node_ancestors
[INFO] [2019-10-12 14:27:41] old ancestors deleted.
[STOP] [2019-10-12 14:27:42] build_node_ancestors
[START] [2019-10-12 14:27:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 14:27:44] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 14:27:44] Flattener#flatten
[STOP] [2019-10-12 14:27:44] rebuild_nodes
[START] [2019-10-12 14:27:44] resolve_missing_media_owners
[STOP] [2019-10-12 14:27:44] resolve_missing_media_owners
[START] [2019-10-12 14:27:44] sanitize_media_verbatims
[STOP] [2019-10-12 14:27:44] sanitize_media_verbatims
[START] [2019-10-12 14:27:44] queue_downloads
[STOP] [2019-10-12 14:27:44] queue_downloads
[START] [2019-10-12 14:27:44] parse_names
[WARN] [2019-10-12 14:27:44] I see 3493 names which still need to be parsed.
[STOP] [2019-10-12 14:27:47] parse_names
[START] [2019-10-12 14:27:47] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 14:27:47] denormalize_canonical_names_to_nodes
[START] [2019-10-12 14:27:47] match_nodes
[START] [2019-10-12 14:27:47] map_all_nodes_to_pages
[STOP] [2019-10-12 14:31:25] map_all_nodes_to_pages
[INFO] [2019-10-12 14:31:25] 126 Unmatched nodes (of 3493)! That's too many to output. First 10: Coerebidae (#49451975); Dendroica (#49452851); Dendroica petechia (#49452850); Limnodromus (#49453165); Thalaseus (#49452135); Thalaseus maximus (#49452134); Thalaseus maxima (#49455325); Thalasseus maxima (#49454851); Onychoprion fuscata (#49454134); Anas discors (#49453159)
[START] [2019-10-12 14:31:25] update_nodes
[STOP] [2019-10-12 14:31:26] update_nodes
[STOP] [2019-10-12 14:31:26] match_nodes
[START] [2019-10-12 14:31:26] reindex_search
[STOP] [2019-10-12 14:31:33] reindex_search
[START] [2019-10-12 14:31:33] normalize_units
[STOP] [2019-10-12 14:31:33] normalize_units
[START] [2019-10-12 14:31:33] calculate_statistics
[STOP] [2019-10-12 14:31:33] calculate_statistics
[START] [2019-10-12 14:31:33] complete_harvest_instance
[START] [2019-10-12 14:31:33] overall_tsv_creation
[INFO] [2019-10-12 14:31:33] Processing group of 3493 in 1 batches of 10000
[INFO] [2019-10-12 14:32:35] 1446 Traits (unfiltered)...
[INFO] [2019-10-12 14:32:49] 1446 Traits (filtered)...
[INFO] [2019-10-12 14:32:49] 0 Associations (filtered)...
[INFO] [2019-10-12 14:33:29] 7230 metadata added.
[INFO] [2019-10-12 14:33:29] 0 metadata added.
[INFO] [2019-10-12 14:33:29] Average Time: 91.92
[INFO] [2019-10-12 14:33:29] Total Time: 1m56s
[STOP] [2019-10-12 14:33:29] overall_tsv_creation
[INFO] [2019-10-12 14:33:29] Done. Check your files:
[INFO] [2019-10-12 14:33:29] (3493 lines) /app/public/data/dominica_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 14:33:29] (18018 lines) /app/public/data/dominica_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 14:33:29] (3493 lines) /app/public/data/dominica_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 14:33:29] (1447 lines) /app/public/data/dominica_sp_list/publish_traits.tsv
[INFO] [2019-10-12 14:33:29] (7231 lines) /app/public/data/dominica_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 14:33:30] complete_harvest_instance
[START] [2019-10-12 14:33:30] completed
[STOP] [2019-10-12 14:33:30] completed
[STOP] [2019-10-12 14:33:30] logged process, took 395.19
Latest Process

12 Oct 14:26 EXITED currently processing 0