Harvest for Chad Species List Created 12 Oct 02:36

Stage: completed
Fetched: 12 Oct 02:36
Validated: 12 Oct 02:36
Deltas Created 12 Oct 02:36
Units Normalized: 12 Oct 02:38
Ancestry Built: 12 Oct 02:37
Nodes Matched: 12 Oct 02:38
Names Parsed: 12 Oct 02:37
New Models Stored: 12 Oct 02:37
Indexed: 12 Oct 02:38
Completed: 12 Oct 02:40
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 02:36:50 -0400 by logger.rb/56815
[START] [2019-10-12 02:36:50] logged process
[START] [2019-10-12 02:36:50] create_harvest_instance
[STOP] [2019-10-12 02:36:51] create_harvest_instance
[START] [2019-10-12 02:36:51] fetch_files
[STOP] [2019-10-12 02:36:51] fetch_files
[START] [2019-10-12 02:36:51] validate_each_file
[STOP] [2019-10-12 02:36:51] validate_each_file
[START] [2019-10-12 02:36:51] convert_to_csv
[CMD] [2019-10-12 02:36:51] /usr/bin/sort /app/public/converted_csv/chad_sp_list_refs_15411.csv > /app/public/converted_csv/chad_sp_list_refs_15411.csv_sorted
[CMD] [2019-10-12 02:36:51] /usr/bin/sort /app/public/converted_csv/chad_sp_list_nodes_15412.csv > /app/public/converted_csv/chad_sp_list_nodes_15412.csv_sorted
[CMD] [2019-10-12 02:36:51] /usr/bin/sort /app/public/converted_csv/chad_sp_list_occurrences_15413.csv > /app/public/converted_csv/chad_sp_list_occurrences_15413.csv_sorted
[CMD] [2019-10-12 02:36:51] /usr/bin/sort /app/public/converted_csv/chad_sp_list_measurements_15414.csv > /app/public/converted_csv/chad_sp_list_measurements_15414.csv_sorted
[STOP] [2019-10-12 02:36:51] convert_to_csv
[START] [2019-10-12 02:36:51] calculate_delta
[CMD] [2019-10-12 02:36:51] echo "0a" > /app/public/diff/chad_sp_list_refs_15411.diff
[CMD] [2019-10-12 02:36:52] tail -n +1 /app/public/converted_csv/chad_sp_list_refs_15411.csv >> /app/public/diff/chad_sp_list_refs_15411.diff
[CMD] [2019-10-12 02:36:52] echo "." >> /app/public/diff/chad_sp_list_refs_15411.diff
[CMD] [2019-10-12 02:36:52] echo "0a" > /app/public/diff/chad_sp_list_nodes_15412.diff
[CMD] [2019-10-12 02:36:52] tail -n +1 /app/public/converted_csv/chad_sp_list_nodes_15412.csv >> /app/public/diff/chad_sp_list_nodes_15412.diff
[CMD] [2019-10-12 02:36:52] echo "." >> /app/public/diff/chad_sp_list_nodes_15412.diff
[CMD] [2019-10-12 02:36:52] echo "0a" > /app/public/diff/chad_sp_list_occurrences_15413.diff
[CMD] [2019-10-12 02:36:52] tail -n +1 /app/public/converted_csv/chad_sp_list_occurrences_15413.csv >> /app/public/diff/chad_sp_list_occurrences_15413.diff
[CMD] [2019-10-12 02:36:52] echo "." >> /app/public/diff/chad_sp_list_occurrences_15413.diff
[CMD] [2019-10-12 02:36:52] echo "0a" > /app/public/diff/chad_sp_list_measurements_15414.diff
[CMD] [2019-10-12 02:36:52] tail -n +1 /app/public/converted_csv/chad_sp_list_measurements_15414.csv >> /app/public/diff/chad_sp_list_measurements_15414.diff
[CMD] [2019-10-12 02:36:52] echo "." >> /app/public/diff/chad_sp_list_measurements_15414.diff
[STOP] [2019-10-12 02:36:53] calculate_delta
[START] [2019-10-12 02:36:53] parse_diff_and_store
[INFO] [2019-10-12 02:36:53] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 02:36:53] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 02:36:54] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 02:36:54] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 02:37:00] Storing 2 References
[INFO] [2019-10-12 02:37:00] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 02:37:00] Average Time: 0.0
[INFO] [2019-10-12 02:37:00] Total Time: 1s
[INFO] [2019-10-12 02:37:00] Storing 1945 ScientificNames
[INFO] [2019-10-12 02:37:00] Processing group of 1945 in 2 groups of 1000
[INFO] [2019-10-12 02:37:01] Average Time: 0.41
[INFO] [2019-10-12 02:37:01] Total Time: 1s
[INFO] [2019-10-12 02:37:01] Storing 1945 Nodes
[INFO] [2019-10-12 02:37:01] Processing group of 1945 in 2 groups of 1000
[INFO] [2019-10-12 02:37:01] Average Time: 0.29
[INFO] [2019-10-12 02:37:01] Total Time: 1s
[INFO] [2019-10-12 02:37:01] Storing 964 Occurrences
[INFO] [2019-10-12 02:37:01] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-12 02:37:02] Average Time: 0.24
[INFO] [2019-10-12 02:37:02] Total Time: 1s
[INFO] [2019-10-12 02:37:02] Storing 2150 TraitsReferences
[INFO] [2019-10-12 02:37:02] Processing group of 2150 in 3 groups of 1000
[INFO] [2019-10-12 02:37:02] Average Time: 0.077
[INFO] [2019-10-12 02:37:02] Total Time: 1s
[INFO] [2019-10-12 02:37:02] Storing 2149 Traits
[INFO] [2019-10-12 02:37:02] Processing group of 2149 in 3 groups of 1000
[INFO] [2019-10-12 02:37:03] Average Time: 0.283
[INFO] [2019-10-12 02:37:03] Total Time: 1s
[INFO] [2019-10-12 02:37:03] Storing 2150 MetaTraits
[INFO] [2019-10-12 02:37:03] Processing group of 2150 in 3 groups of 1000
[INFO] [2019-10-12 02:37:03] Average Time: 0.13
[INFO] [2019-10-12 02:37:03] Total Time: 1s
[STOP] [2019-10-12 02:37:03] parse_diff_and_store
[START] [2019-10-12 02:37:03] resolve_keys
[INFO] [2019-10-12 02:37:13] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 02:37:14] traits to occurrences...
[INFO] [2019-10-12 02:37:15] traits to nodes (through occurrences)...
[INFO] [2019-10-12 02:37:15] Traits to sex term...
[INFO] [2019-10-12 02:37:15] Traits to lifestage term...
[INFO] [2019-10-12 02:37:15] MetaTraits to traits...
[INFO] [2019-10-12 02:37:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 02:37:16] Assocs to occurrences...
[INFO] [2019-10-12 02:37:16] Assocs to nodes...
[INFO] [2019-10-12 02:37:16] Assoc to sex term...
[INFO] [2019-10-12 02:37:16] Assoc to lifestage term...
[STOP] [2019-10-12 02:37:16] resolve_keys
[START] [2019-10-12 02:37:16] hold_for_later_1
[STOP] [2019-10-12 02:37:16] hold_for_later_1
[START] [2019-10-12 02:37:16] hold_for_later_2
[STOP] [2019-10-12 02:37:16] hold_for_later_2
[START] [2019-10-12 02:37:16] resolve_missing_parents
[STOP] [2019-10-12 02:37:19] resolve_missing_parents
[START] [2019-10-12 02:37:19] rebuild_nodes
[START] [2019-10-12 02:37:19] Flattener#flatten
[START] [2019-10-12 02:37:19] Flattener#study_resource
[START] [2019-10-12 02:37:19] Flattener#build_ancestry
[STOP] [2019-10-12 02:37:19] Flattener#build_ancestry
[INFO] [2019-10-12 02:37:19] 1945 ancestry keys
[START] [2019-10-12 02:37:19] build_node_ancestors
[INFO] [2019-10-12 02:37:19] old ancestors deleted.
[STOP] [2019-10-12 02:37:19] build_node_ancestors
[START] [2019-10-12 02:37:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:37:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:37:19] Flattener#flatten
[STOP] [2019-10-12 02:37:19] rebuild_nodes
[START] [2019-10-12 02:37:19] resolve_missing_media_owners
[STOP] [2019-10-12 02:37:19] resolve_missing_media_owners
[START] [2019-10-12 02:37:19] sanitize_media_verbatims
[STOP] [2019-10-12 02:37:19] sanitize_media_verbatims
[START] [2019-10-12 02:37:19] queue_downloads
[STOP] [2019-10-12 02:37:19] queue_downloads
[START] [2019-10-12 02:37:19] parse_names
[WARN] [2019-10-12 02:37:19] I see 1945 names which still need to be parsed.
[STOP] [2019-10-12 02:37:21] parse_names
[START] [2019-10-12 02:37:21] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 02:37:22] denormalize_canonical_names_to_nodes
[START] [2019-10-12 02:37:22] match_nodes
[START] [2019-10-12 02:37:22] map_all_nodes_to_pages
[STOP] [2019-10-12 02:38:53] map_all_nodes_to_pages
[INFO] [2019-10-12 02:38:53] 110 Unmatched nodes (of 1945)! That's too many to output. First 10: Pennisetum (#49097401); Pennisetum ramosum (#49099213); Andropogon fastigiata (#49098955); Chrysopogon nigritana (#49098440); Paspalidium (#49098949); Setaria pallidifusca (#49099019); Gerbilliscus robusta (#49098939); Gerbilliscus gambiana (#49099215); Egretta intermedia (#49098353); Butorides striatus (#49099241)
[START] [2019-10-12 02:38:53] update_nodes
[STOP] [2019-10-12 02:38:54] update_nodes
[STOP] [2019-10-12 02:38:54] match_nodes
[START] [2019-10-12 02:38:54] reindex_search
[STOP] [2019-10-12 02:38:57] reindex_search
[START] [2019-10-12 02:38:57] normalize_units
[STOP] [2019-10-12 02:38:57] normalize_units
[START] [2019-10-12 02:38:57] calculate_statistics
[STOP] [2019-10-12 02:38:57] calculate_statistics
[START] [2019-10-12 02:38:57] complete_harvest_instance
[START] [2019-10-12 02:38:57] overall_tsv_creation
[INFO] [2019-10-12 02:38:57] Processing group of 1945 in 1 batches of 10000
[INFO] [2019-10-12 02:39:52] 964 Traits (unfiltered)...
[INFO] [2019-10-12 02:40:05] 964 Traits (filtered)...
[INFO] [2019-10-12 02:40:05] 0 Associations (filtered)...
[INFO] [2019-10-12 02:40:44] 4820 metadata added.
[INFO] [2019-10-12 02:40:44] 0 metadata added.
[INFO] [2019-10-12 02:40:44] Average Time: 84.2
[INFO] [2019-10-12 02:40:44] Total Time: 1m48s
[STOP] [2019-10-12 02:40:44] overall_tsv_creation
[INFO] [2019-10-12 02:40:44] Done. Check your files:
[INFO] [2019-10-12 02:40:44] (1945 lines) /app/public/data/chad_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 02:40:44] (2604 lines) /app/public/data/chad_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 02:40:44] (1945 lines) /app/public/data/chad_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 02:40:45] (965 lines) /app/public/data/chad_sp_list/publish_traits.tsv
[INFO] [2019-10-12 02:40:45] (4821 lines) /app/public/data/chad_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 02:40:45] complete_harvest_instance
[START] [2019-10-12 02:40:45] completed
[STOP] [2019-10-12 02:40:45] completed
[STOP] [2019-10-12 02:40:45] logged process, took 234.36
Latest Process

12 Oct 02:36 EXITED currently processing 0