Harvest for Rwanda Species List Created 15 Oct 16:03

Stage: completed
Fetched: 15 Oct 16:03
Validated: 15 Oct 16:03
Deltas Created 15 Oct 16:03
Units Normalized: 15 Oct 16:08
Ancestry Built: 15 Oct 16:04
Nodes Matched: 15 Oct 16:08
Names Parsed: 15 Oct 16:04
New Models Stored: 15 Oct 16:04
Indexed: 15 Oct 16:08
Completed: 15 Oct 16:10
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:03:32 -0400 by logger.rb/56815
[START] [2019-10-15 16:03:32] logged process
[START] [2019-10-15 16:03:32] create_harvest_instance
[STOP] [2019-10-15 16:03:32] create_harvest_instance
[START] [2019-10-15 16:03:32] fetch_files
[STOP] [2019-10-15 16:03:32] fetch_files
[START] [2019-10-15 16:03:32] validate_each_file
[STOP] [2019-10-15 16:03:33] validate_each_file
[START] [2019-10-15 16:03:33] convert_to_csv
[CMD] [2019-10-15 16:03:33] /usr/bin/sort /app/public/converted_csv/rwanda_sp_list_refs_17013.csv > /app/public/converted_csv/rwanda_sp_list_refs_17013.csv_sorted
[CMD] [2019-10-15 16:03:33] /usr/bin/sort /app/public/converted_csv/rwanda_sp_list_nodes_17014.csv > /app/public/converted_csv/rwanda_sp_list_nodes_17014.csv_sorted
[CMD] [2019-10-15 16:03:34] /usr/bin/sort /app/public/converted_csv/rwanda_sp_list_occurrences_17015.csv > /app/public/converted_csv/rwanda_sp_list_occurrences_17015.csv_sorted
[CMD] [2019-10-15 16:03:34] /usr/bin/sort /app/public/converted_csv/rwanda_sp_list_measurements_17016.csv > /app/public/converted_csv/rwanda_sp_list_measurements_17016.csv_sorted
[STOP] [2019-10-15 16:03:34] convert_to_csv
[START] [2019-10-15 16:03:34] calculate_delta
[CMD] [2019-10-15 16:03:34] echo "0a" > /app/public/diff/rwanda_sp_list_refs_17013.diff
[CMD] [2019-10-15 16:03:34] tail -n +1 /app/public/converted_csv/rwanda_sp_list_refs_17013.csv >> /app/public/diff/rwanda_sp_list_refs_17013.diff
[CMD] [2019-10-15 16:03:35] echo "." >> /app/public/diff/rwanda_sp_list_refs_17013.diff
[CMD] [2019-10-15 16:03:35] echo "0a" > /app/public/diff/rwanda_sp_list_nodes_17014.diff
[CMD] [2019-10-15 16:03:35] tail -n +1 /app/public/converted_csv/rwanda_sp_list_nodes_17014.csv >> /app/public/diff/rwanda_sp_list_nodes_17014.diff
[CMD] [2019-10-15 16:03:36] echo "." >> /app/public/diff/rwanda_sp_list_nodes_17014.diff
[CMD] [2019-10-15 16:03:36] echo "0a" > /app/public/diff/rwanda_sp_list_occurrences_17015.diff
[CMD] [2019-10-15 16:03:36] tail -n +1 /app/public/converted_csv/rwanda_sp_list_occurrences_17015.csv >> /app/public/diff/rwanda_sp_list_occurrences_17015.diff
[CMD] [2019-10-15 16:03:36] echo "." >> /app/public/diff/rwanda_sp_list_occurrences_17015.diff
[CMD] [2019-10-15 16:03:37] echo "0a" > /app/public/diff/rwanda_sp_list_measurements_17016.diff
[CMD] [2019-10-15 16:03:37] tail -n +1 /app/public/converted_csv/rwanda_sp_list_measurements_17016.csv >> /app/public/diff/rwanda_sp_list_measurements_17016.diff
[CMD] [2019-10-15 16:03:37] echo "." >> /app/public/diff/rwanda_sp_list_measurements_17016.diff
[STOP] [2019-10-15 16:03:38] calculate_delta
[START] [2019-10-15 16:03:38] parse_diff_and_store
[INFO] [2019-10-15 16:03:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:03:38] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:03:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:03:41] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:03:58] Storing 2 References
[INFO] [2019-10-15 16:03:58] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:03:58] Average Time: 0.0
[INFO] [2019-10-15 16:03:58] Total Time: 1s
[INFO] [2019-10-15 16:03:58] Storing 4411 ScientificNames
[INFO] [2019-10-15 16:03:58] Processing group of 4411 in 5 groups of 1000
[INFO] [2019-10-15 16:04:00] Average Time: 0.394
[INFO] [2019-10-15 16:04:00] Total Time: 3s
[INFO] [2019-10-15 16:04:00] Storing 4411 Nodes
[INFO] [2019-10-15 16:04:00] Processing group of 4411 in 5 groups of 1000
[INFO] [2019-10-15 16:04:01] Average Time: 0.272
[INFO] [2019-10-15 16:04:01] Total Time: 2s
[INFO] [2019-10-15 16:04:01] Storing 2410 Occurrences
[INFO] [2019-10-15 16:04:01] Processing group of 2410 in 3 groups of 1000
[INFO] [2019-10-15 16:04:02] Average Time: 0.08
[INFO] [2019-10-15 16:04:02] Total Time: 1s
[INFO] [2019-10-15 16:04:02] Storing 5330 TraitsReferences
[INFO] [2019-10-15 16:04:02] Processing group of 5330 in 6 groups of 1000
[INFO] [2019-10-15 16:04:02] Average Time: 0.07
[INFO] [2019-10-15 16:04:02] Total Time: 1s
[INFO] [2019-10-15 16:04:02] Storing 5329 Traits
[INFO] [2019-10-15 16:04:02] Processing group of 5329 in 6 groups of 1000
[INFO] [2019-10-15 16:04:04] Average Time: 0.287
[INFO] [2019-10-15 16:04:04] Total Time: 2s
[INFO] [2019-10-15 16:04:04] Storing 5327 MetaTraits
[INFO] [2019-10-15 16:04:04] Processing group of 5327 in 6 groups of 1000
[INFO] [2019-10-15 16:04:04] Average Time: 0.103
[INFO] [2019-10-15 16:04:04] Total Time: 1s
[STOP] [2019-10-15 16:04:04] parse_diff_and_store
[START] [2019-10-15 16:04:04] resolve_keys
[INFO] [2019-10-15 16:04:24] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:04:26] traits to occurrences...
[INFO] [2019-10-15 16:04:28] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:04:28] Traits to sex term...
[INFO] [2019-10-15 16:04:30] Traits to lifestage term...
[INFO] [2019-10-15 16:04:32] MetaTraits to traits...
[INFO] [2019-10-15 16:04:32] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:04:33] Assocs to occurrences...
[INFO] [2019-10-15 16:04:33] Assocs to nodes...
[INFO] [2019-10-15 16:04:33] Assoc to sex term...
[INFO] [2019-10-15 16:04:33] Assoc to lifestage term...
[STOP] [2019-10-15 16:04:33] resolve_keys
[START] [2019-10-15 16:04:33] hold_for_later_1
[STOP] [2019-10-15 16:04:33] hold_for_later_1
[START] [2019-10-15 16:04:33] hold_for_later_2
[STOP] [2019-10-15 16:04:33] hold_for_later_2
[START] [2019-10-15 16:04:33] resolve_missing_parents
[STOP] [2019-10-15 16:04:41] resolve_missing_parents
[START] [2019-10-15 16:04:41] rebuild_nodes
[START] [2019-10-15 16:04:41] Flattener#flatten
[START] [2019-10-15 16:04:41] Flattener#study_resource
[START] [2019-10-15 16:04:41] Flattener#build_ancestry
[STOP] [2019-10-15 16:04:41] Flattener#build_ancestry
[INFO] [2019-10-15 16:04:41] 4411 ancestry keys
[START] [2019-10-15 16:04:41] build_node_ancestors
[INFO] [2019-10-15 16:04:41] old ancestors deleted.
[STOP] [2019-10-15 16:04:42] build_node_ancestors
[START] [2019-10-15 16:04:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:04:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:04:43] Flattener#flatten
[STOP] [2019-10-15 16:04:43] rebuild_nodes
[START] [2019-10-15 16:04:43] resolve_missing_media_owners
[STOP] [2019-10-15 16:04:43] resolve_missing_media_owners
[START] [2019-10-15 16:04:43] sanitize_media_verbatims
[STOP] [2019-10-15 16:04:43] sanitize_media_verbatims
[START] [2019-10-15 16:04:43] queue_downloads
[STOP] [2019-10-15 16:04:43] queue_downloads
[START] [2019-10-15 16:04:43] parse_names
[WARN] [2019-10-15 16:04:43] I see 4411 names which still need to be parsed.
[STOP] [2019-10-15 16:04:47] parse_names
[START] [2019-10-15 16:04:47] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:04:47] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:04:47] match_nodes
[START] [2019-10-15 16:04:47] map_all_nodes_to_pages
[STOP] [2019-10-15 16:08:33] map_all_nodes_to_pages
[INFO] [2019-10-15 16:08:33] 232 Unmatched nodes (of 4411)! That's too many to output. First 10: Euplectes macrourus (#51748523); Nectarinia venusta (#51745489); Nectarinia verticalis (#51745620); Nectarinia afra (#51745623); Nectarinia regia (#51745657); Nectarinia cuprea (#51745700); Nectarinia preussi (#51745709); Nectarinia mariquensis (#51746571); Nectarinia batesi (#51747361); Nectarinia bifasciata (#51748146)
[START] [2019-10-15 16:08:33] update_nodes
[STOP] [2019-10-15 16:08:35] update_nodes
[STOP] [2019-10-15 16:08:35] match_nodes
[START] [2019-10-15 16:08:35] reindex_search
[STOP] [2019-10-15 16:08:45] reindex_search
[START] [2019-10-15 16:08:45] normalize_units
[STOP] [2019-10-15 16:08:45] normalize_units
[START] [2019-10-15 16:08:45] calculate_statistics
[STOP] [2019-10-15 16:08:45] calculate_statistics
[START] [2019-10-15 16:08:45] complete_harvest_instance
[START] [2019-10-15 16:08:45] overall_tsv_creation
[INFO] [2019-10-15 16:08:45] Processing group of 4411 in 1 batches of 10000
[INFO] [2019-10-15 16:09:51] 2410 Traits (unfiltered)...
[INFO] [2019-10-15 16:10:05] 2410 Traits (filtered)...
[INFO] [2019-10-15 16:10:05] 0 Associations (filtered)...
[INFO] [2019-10-15 16:10:47] 12047 metadata added.
[INFO] [2019-10-15 16:10:47] 0 metadata added.
[INFO] [2019-10-15 16:10:47] Average Time: 96.58
[INFO] [2019-10-15 16:10:47] Total Time: 2m3s
[STOP] [2019-10-15 16:10:47] overall_tsv_creation
[INFO] [2019-10-15 16:10:47] Done. Check your files:
[INFO] [2019-10-15 16:10:47] (4411 lines) /app/public/data/rwanda_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 16:10:47] (10722 lines) /app/public/data/rwanda_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:10:48] (4411 lines) /app/public/data/rwanda_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 16:10:48] (2411 lines) /app/public/data/rwanda_sp_list/publish_traits.tsv
[INFO] [2019-10-15 16:10:48] (12048 lines) /app/public/data/rwanda_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 16:10:48] complete_harvest_instance
[START] [2019-10-15 16:10:48] completed
[STOP] [2019-10-15 16:10:48] completed
[STOP] [2019-10-15 16:10:48] logged process, took 436.6
Latest Process

15 Oct 16:03 EXITED currently processing 0