Harvest for Samoa Species List Created 15 Oct 16:33

Stage: completed
Fetched: 15 Oct 16:33
Validated: 15 Oct 16:33
Deltas Created 15 Oct 16:33
Units Normalized: 15 Oct 16:37
Ancestry Built: 15 Oct 16:34
Nodes Matched: 15 Oct 16:37
Names Parsed: 15 Oct 16:34
New Models Stored: 15 Oct 16:34
Indexed: 15 Oct 16:37
Completed: 15 Oct 16:39
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 16:33:47 -0400 by logger.rb/56815
[START] [2019-10-15 16:33:47] logged process
[START] [2019-10-15 16:33:47] create_harvest_instance
[STOP] [2019-10-15 16:33:47] create_harvest_instance
[START] [2019-10-15 16:33:47] fetch_files
[STOP] [2019-10-15 16:33:47] fetch_files
[START] [2019-10-15 16:33:47] validate_each_file
[STOP] [2019-10-15 16:33:47] validate_each_file
[START] [2019-10-15 16:33:47] convert_to_csv
[CMD] [2019-10-15 16:33:47] /usr/bin/sort /app/public/converted_csv/samoa_sp_list_refs_17077.csv > /app/public/converted_csv/samoa_sp_list_refs_17077.csv_sorted
[CMD] [2019-10-15 16:33:48] /usr/bin/sort /app/public/converted_csv/samoa_sp_list_nodes_17078.csv > /app/public/converted_csv/samoa_sp_list_nodes_17078.csv_sorted
[CMD] [2019-10-15 16:33:48] /usr/bin/sort /app/public/converted_csv/samoa_sp_list_occurrences_17079.csv > /app/public/converted_csv/samoa_sp_list_occurrences_17079.csv_sorted
[CMD] [2019-10-15 16:33:48] /usr/bin/sort /app/public/converted_csv/samoa_sp_list_measurements_17080.csv > /app/public/converted_csv/samoa_sp_list_measurements_17080.csv_sorted
[STOP] [2019-10-15 16:33:49] convert_to_csv
[START] [2019-10-15 16:33:49] calculate_delta
[CMD] [2019-10-15 16:33:49] echo "0a" > /app/public/diff/samoa_sp_list_refs_17077.diff
[CMD] [2019-10-15 16:33:49] tail -n +1 /app/public/converted_csv/samoa_sp_list_refs_17077.csv >> /app/public/diff/samoa_sp_list_refs_17077.diff
[CMD] [2019-10-15 16:33:49] echo "." >> /app/public/diff/samoa_sp_list_refs_17077.diff
[CMD] [2019-10-15 16:33:49] echo "0a" > /app/public/diff/samoa_sp_list_nodes_17078.diff
[CMD] [2019-10-15 16:33:50] tail -n +1 /app/public/converted_csv/samoa_sp_list_nodes_17078.csv >> /app/public/diff/samoa_sp_list_nodes_17078.diff
[CMD] [2019-10-15 16:33:50] echo "." >> /app/public/diff/samoa_sp_list_nodes_17078.diff
[CMD] [2019-10-15 16:33:50] echo "0a" > /app/public/diff/samoa_sp_list_occurrences_17079.diff
[CMD] [2019-10-15 16:33:50] tail -n +1 /app/public/converted_csv/samoa_sp_list_occurrences_17079.csv >> /app/public/diff/samoa_sp_list_occurrences_17079.diff
[CMD] [2019-10-15 16:33:51] echo "." >> /app/public/diff/samoa_sp_list_occurrences_17079.diff
[CMD] [2019-10-15 16:33:51] echo "0a" > /app/public/diff/samoa_sp_list_measurements_17080.diff
[CMD] [2019-10-15 16:33:51] tail -n +1 /app/public/converted_csv/samoa_sp_list_measurements_17080.csv >> /app/public/diff/samoa_sp_list_measurements_17080.diff
[CMD] [2019-10-15 16:33:52] echo "." >> /app/public/diff/samoa_sp_list_measurements_17080.diff
[STOP] [2019-10-15 16:33:52] calculate_delta
[START] [2019-10-15 16:33:52] parse_diff_and_store
[INFO] [2019-10-15 16:33:52] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 16:33:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 16:33:54] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 16:33:54] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 16:34:03] Storing 2 References
[INFO] [2019-10-15 16:34:03] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 16:34:03] Average Time: 0.0
[INFO] [2019-10-15 16:34:03] Total Time: 1s
[INFO] [2019-10-15 16:34:03] Storing 2809 ScientificNames
[INFO] [2019-10-15 16:34:03] Processing group of 2809 in 3 groups of 1000
[INFO] [2019-10-15 16:34:04] Average Time: 0.377
[INFO] [2019-10-15 16:34:04] Total Time: 2s
[INFO] [2019-10-15 16:34:04] Storing 2809 Nodes
[INFO] [2019-10-15 16:34:04] Processing group of 2809 in 3 groups of 1000
[INFO] [2019-10-15 16:34:05] Average Time: 0.287
[INFO] [2019-10-15 16:34:05] Total Time: 1s
[INFO] [2019-10-15 16:34:05] Storing 1446 Occurrences
[INFO] [2019-10-15 16:34:05] Processing group of 1446 in 2 groups of 1000
[INFO] [2019-10-15 16:34:05] Average Time: 0.09
[INFO] [2019-10-15 16:34:05] Total Time: 1s
[INFO] [2019-10-15 16:34:05] Storing 2990 TraitsReferences
[INFO] [2019-10-15 16:34:05] Processing group of 2990 in 3 groups of 1000
[INFO] [2019-10-15 16:34:05] Average Time: 0.103
[INFO] [2019-10-15 16:34:05] Total Time: 1s
[INFO] [2019-10-15 16:34:05] Storing 2989 Traits
[INFO] [2019-10-15 16:34:05] Processing group of 2989 in 3 groups of 1000
[INFO] [2019-10-15 16:34:06] Average Time: 0.357
[INFO] [2019-10-15 16:34:06] Total Time: 2s
[INFO] [2019-10-15 16:34:06] Storing 2988 MetaTraits
[INFO] [2019-10-15 16:34:06] Processing group of 2988 in 3 groups of 1000
[INFO] [2019-10-15 16:34:07] Average Time: 0.173
[INFO] [2019-10-15 16:34:07] Total Time: 1s
[STOP] [2019-10-15 16:34:07] parse_diff_and_store
[START] [2019-10-15 16:34:07] resolve_keys
[INFO] [2019-10-15 16:34:19] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 16:34:21] traits to occurrences...
[INFO] [2019-10-15 16:34:21] traits to nodes (through occurrences)...
[INFO] [2019-10-15 16:34:21] Traits to sex term...
[INFO] [2019-10-15 16:34:22] Traits to lifestage term...
[INFO] [2019-10-15 16:34:22] MetaTraits to traits...
[INFO] [2019-10-15 16:34:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 16:34:23] Assocs to occurrences...
[INFO] [2019-10-15 16:34:23] Assocs to nodes...
[INFO] [2019-10-15 16:34:23] Assoc to sex term...
[INFO] [2019-10-15 16:34:23] Assoc to lifestage term...
[STOP] [2019-10-15 16:34:23] resolve_keys
[START] [2019-10-15 16:34:23] hold_for_later_1
[STOP] [2019-10-15 16:34:23] hold_for_later_1
[START] [2019-10-15 16:34:23] hold_for_later_2
[STOP] [2019-10-15 16:34:23] hold_for_later_2
[START] [2019-10-15 16:34:23] resolve_missing_parents
[STOP] [2019-10-15 16:34:28] resolve_missing_parents
[START] [2019-10-15 16:34:28] rebuild_nodes
[START] [2019-10-15 16:34:28] Flattener#flatten
[START] [2019-10-15 16:34:28] Flattener#study_resource
[START] [2019-10-15 16:34:28] Flattener#build_ancestry
[STOP] [2019-10-15 16:34:28] Flattener#build_ancestry
[INFO] [2019-10-15 16:34:28] 2809 ancestry keys
[START] [2019-10-15 16:34:28] build_node_ancestors
[INFO] [2019-10-15 16:34:28] old ancestors deleted.
[STOP] [2019-10-15 16:34:29] build_node_ancestors
[START] [2019-10-15 16:34:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:34:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 16:34:29] Flattener#flatten
[STOP] [2019-10-15 16:34:29] rebuild_nodes
[START] [2019-10-15 16:34:29] resolve_missing_media_owners
[STOP] [2019-10-15 16:34:29] resolve_missing_media_owners
[START] [2019-10-15 16:34:29] sanitize_media_verbatims
[STOP] [2019-10-15 16:34:29] sanitize_media_verbatims
[START] [2019-10-15 16:34:29] queue_downloads
[STOP] [2019-10-15 16:34:29] queue_downloads
[START] [2019-10-15 16:34:29] parse_names
[WARN] [2019-10-15 16:34:29] I see 2809 names which still need to be parsed.
[STOP] [2019-10-15 16:34:33] parse_names
[START] [2019-10-15 16:34:33] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 16:34:33] denormalize_canonical_names_to_nodes
[START] [2019-10-15 16:34:33] match_nodes
[START] [2019-10-15 16:34:33] map_all_nodes_to_pages
[STOP] [2019-10-15 16:37:19] map_all_nodes_to_pages
[INFO] [2019-10-15 16:37:19] 142 Unmatched nodes (of 2809)! That's too many to output. First 10: Foulehaio carunculata (#51758911); Collocalia spodiopygia (#51759179); Procelsterna (#51759236); Procelsterna cerulea (#51759235); Thalaseus (#51759258); Thalaseus bergii (#51759257); Tringa incanus (#51758302); Puffinus pacificus (#51757507); Puffinus tenuirostris (#51757552); Puffinus griseus (#51757571)
[START] [2019-10-15 16:37:19] update_nodes
[STOP] [2019-10-15 16:37:20] update_nodes
[STOP] [2019-10-15 16:37:20] match_nodes
[START] [2019-10-15 16:37:20] reindex_search
[STOP] [2019-10-15 16:37:27] reindex_search
[START] [2019-10-15 16:37:27] normalize_units
[STOP] [2019-10-15 16:37:27] normalize_units
[START] [2019-10-15 16:37:27] calculate_statistics
[STOP] [2019-10-15 16:37:27] calculate_statistics
[START] [2019-10-15 16:37:27] complete_harvest_instance
[START] [2019-10-15 16:37:27] overall_tsv_creation
[INFO] [2019-10-15 16:37:27] Processing group of 2809 in 1 batches of 10000
[INFO] [2019-10-15 16:38:24] 1446 Traits (unfiltered)...
[INFO] [2019-10-15 16:38:38] 1446 Traits (filtered)...
[INFO] [2019-10-15 16:38:38] 0 Associations (filtered)...
[INFO] [2019-10-15 16:39:19] 7228 metadata added.
[INFO] [2019-10-15 16:39:19] 0 metadata added.
[INFO] [2019-10-15 16:39:19] Average Time: 89.75
[INFO] [2019-10-15 16:39:19] Total Time: 1m53s
[STOP] [2019-10-15 16:39:19] overall_tsv_creation
[INFO] [2019-10-15 16:39:19] Done. Check your files:
[INFO] [2019-10-15 16:39:20] (2809 lines) /app/public/data/samoa_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 16:39:20] (9108 lines) /app/public/data/samoa_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 16:39:20] (2809 lines) /app/public/data/samoa_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 16:39:21] (1447 lines) /app/public/data/samoa_sp_list/publish_traits.tsv
[INFO] [2019-10-15 16:39:21] (7229 lines) /app/public/data/samoa_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 16:39:21] complete_harvest_instance
[START] [2019-10-15 16:39:21] completed
[STOP] [2019-10-15 16:39:21] completed
[STOP] [2019-10-15 16:39:21] logged process, took 334.5
Latest Process

15 Oct 16:33 EXITED currently processing 0