Harvest for Kiribati Species List Created 14 Oct 00:34

Stage: completed
Fetched: 14 Oct 00:34
Validated: 14 Oct 00:34
Deltas Created 14 Oct 00:34
Units Normalized: 14 Oct 00:36
Ancestry Built: 14 Oct 00:34
Nodes Matched: 14 Oct 00:36
Names Parsed: 14 Oct 00:34
New Models Stored: 14 Oct 00:34
Indexed: 14 Oct 00:36
Completed: 14 Oct 00:37
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 00:34:31 -0400 by logger.rb/56815
[START] [2019-10-14 00:34:31] logged process
[START] [2019-10-14 00:34:31] create_harvest_instance
[STOP] [2019-10-14 00:34:32] create_harvest_instance
[START] [2019-10-14 00:34:32] fetch_files
[STOP] [2019-10-14 00:34:32] fetch_files
[START] [2019-10-14 00:34:32] validate_each_file
[STOP] [2019-10-14 00:34:32] validate_each_file
[START] [2019-10-14 00:34:32] convert_to_csv
[CMD] [2019-10-14 00:34:32] /usr/bin/sort /app/public/converted_csv/kiribati_sp_list_refs_16307.csv > /app/public/converted_csv/kiribati_sp_list_refs_16307.csv_sorted
[CMD] [2019-10-14 00:34:32] /usr/bin/sort /app/public/converted_csv/kiribati_sp_list_nodes_16308.csv > /app/public/converted_csv/kiribati_sp_list_nodes_16308.csv_sorted
[CMD] [2019-10-14 00:34:32] /usr/bin/sort /app/public/converted_csv/kiribati_sp_list_occurrences_16309.csv > /app/public/converted_csv/kiribati_sp_list_occurrences_16309.csv_sorted
[CMD] [2019-10-14 00:34:32] /usr/bin/sort /app/public/converted_csv/kiribati_sp_list_measurements_16310.csv > /app/public/converted_csv/kiribati_sp_list_measurements_16310.csv_sorted
[STOP] [2019-10-14 00:34:32] convert_to_csv
[START] [2019-10-14 00:34:32] calculate_delta
[CMD] [2019-10-14 00:34:32] echo "0a" > /app/public/diff/kiribati_sp_list_refs_16307.diff
[CMD] [2019-10-14 00:34:32] tail -n +1 /app/public/converted_csv/kiribati_sp_list_refs_16307.csv >> /app/public/diff/kiribati_sp_list_refs_16307.diff
[CMD] [2019-10-14 00:34:32] echo "." >> /app/public/diff/kiribati_sp_list_refs_16307.diff
[CMD] [2019-10-14 00:34:32] echo "0a" > /app/public/diff/kiribati_sp_list_nodes_16308.diff
[CMD] [2019-10-14 00:34:32] tail -n +1 /app/public/converted_csv/kiribati_sp_list_nodes_16308.csv >> /app/public/diff/kiribati_sp_list_nodes_16308.diff
[CMD] [2019-10-14 00:34:33] echo "." >> /app/public/diff/kiribati_sp_list_nodes_16308.diff
[CMD] [2019-10-14 00:34:33] echo "0a" > /app/public/diff/kiribati_sp_list_occurrences_16309.diff
[CMD] [2019-10-14 00:34:33] tail -n +1 /app/public/converted_csv/kiribati_sp_list_occurrences_16309.csv >> /app/public/diff/kiribati_sp_list_occurrences_16309.diff
[CMD] [2019-10-14 00:34:33] echo "." >> /app/public/diff/kiribati_sp_list_occurrences_16309.diff
[CMD] [2019-10-14 00:34:33] echo "0a" > /app/public/diff/kiribati_sp_list_measurements_16310.diff
[CMD] [2019-10-14 00:34:33] tail -n +1 /app/public/converted_csv/kiribati_sp_list_measurements_16310.csv >> /app/public/diff/kiribati_sp_list_measurements_16310.diff
[CMD] [2019-10-14 00:34:33] echo "." >> /app/public/diff/kiribati_sp_list_measurements_16310.diff
[STOP] [2019-10-14 00:34:33] calculate_delta
[START] [2019-10-14 00:34:33] parse_diff_and_store
[INFO] [2019-10-14 00:34:33] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 00:34:33] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 00:34:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 00:34:34] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 00:34:35] Storing 2 References
[INFO] [2019-10-14 00:34:35] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 00:34:36] Average Time: 0.0
[INFO] [2019-10-14 00:34:36] Total Time: 1s
[INFO] [2019-10-14 00:34:36] Storing 665 ScientificNames
[INFO] [2019-10-14 00:34:36] Processing group of 665 in 1 groups of 1000
[INFO] [2019-10-14 00:34:36] Average Time: 0.29
[INFO] [2019-10-14 00:34:36] Total Time: 1s
[INFO] [2019-10-14 00:34:36] Storing 665 Nodes
[INFO] [2019-10-14 00:34:36] Processing group of 665 in 1 groups of 1000
[INFO] [2019-10-14 00:34:36] Average Time: 0.21
[INFO] [2019-10-14 00:34:36] Total Time: 1s
[INFO] [2019-10-14 00:34:36] Storing 261 Occurrences
[INFO] [2019-10-14 00:34:36] Processing group of 261 in 1 groups of 1000
[INFO] [2019-10-14 00:34:36] Average Time: 0.04
[INFO] [2019-10-14 00:34:36] Total Time: 1s
[INFO] [2019-10-14 00:34:36] Storing 522 TraitsReferences
[INFO] [2019-10-14 00:34:36] Processing group of 522 in 1 groups of 1000
[INFO] [2019-10-14 00:34:36] Average Time: 0.19
[INFO] [2019-10-14 00:34:36] Total Time: 1s
[INFO] [2019-10-14 00:34:36] Storing 522 Traits
[INFO] [2019-10-14 00:34:36] Processing group of 522 in 1 groups of 1000
[INFO] [2019-10-14 00:34:37] Average Time: 0.22
[INFO] [2019-10-14 00:34:37] Total Time: 1s
[INFO] [2019-10-14 00:34:37] Storing 522 MetaTraits
[INFO] [2019-10-14 00:34:37] Processing group of 522 in 1 groups of 1000
[INFO] [2019-10-14 00:34:37] Average Time: 0.09
[INFO] [2019-10-14 00:34:37] Total Time: 1s
[STOP] [2019-10-14 00:34:37] parse_diff_and_store
[START] [2019-10-14 00:34:37] resolve_keys
[INFO] [2019-10-14 00:34:41] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 00:34:42] traits to occurrences...
[INFO] [2019-10-14 00:34:42] traits to nodes (through occurrences)...
[INFO] [2019-10-14 00:34:42] Traits to sex term...
[INFO] [2019-10-14 00:34:42] Traits to lifestage term...
[INFO] [2019-10-14 00:34:42] MetaTraits to traits...
[INFO] [2019-10-14 00:34:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 00:34:42] Assocs to occurrences...
[INFO] [2019-10-14 00:34:42] Assocs to nodes...
[INFO] [2019-10-14 00:34:42] Assoc to sex term...
[INFO] [2019-10-14 00:34:42] Assoc to lifestage term...
[STOP] [2019-10-14 00:34:42] resolve_keys
[START] [2019-10-14 00:34:42] hold_for_later_1
[STOP] [2019-10-14 00:34:42] hold_for_later_1
[START] [2019-10-14 00:34:42] hold_for_later_2
[STOP] [2019-10-14 00:34:42] hold_for_later_2
[START] [2019-10-14 00:34:42] resolve_missing_parents
[STOP] [2019-10-14 00:34:42] resolve_missing_parents
[START] [2019-10-14 00:34:42] rebuild_nodes
[START] [2019-10-14 00:34:42] Flattener#flatten
[START] [2019-10-14 00:34:42] Flattener#study_resource
[START] [2019-10-14 00:34:42] Flattener#build_ancestry
[STOP] [2019-10-14 00:34:42] Flattener#build_ancestry
[INFO] [2019-10-14 00:34:42] 665 ancestry keys
[START] [2019-10-14 00:34:42] build_node_ancestors
[INFO] [2019-10-14 00:34:42] old ancestors deleted.
[STOP] [2019-10-14 00:34:43] build_node_ancestors
[START] [2019-10-14 00:34:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:34:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:34:43] Flattener#flatten
[STOP] [2019-10-14 00:34:43] rebuild_nodes
[START] [2019-10-14 00:34:43] resolve_missing_media_owners
[STOP] [2019-10-14 00:34:43] resolve_missing_media_owners
[START] [2019-10-14 00:34:43] sanitize_media_verbatims
[STOP] [2019-10-14 00:34:43] sanitize_media_verbatims
[START] [2019-10-14 00:34:43] queue_downloads
[STOP] [2019-10-14 00:34:43] queue_downloads
[START] [2019-10-14 00:34:43] parse_names
[WARN] [2019-10-14 00:34:43] I see 665 names which still need to be parsed.
[STOP] [2019-10-14 00:34:45] parse_names
[START] [2019-10-14 00:34:45] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 00:34:45] denormalize_canonical_names_to_nodes
[START] [2019-10-14 00:34:45] match_nodes
[START] [2019-10-14 00:34:45] map_all_nodes_to_pages
[STOP] [2019-10-14 00:36:02] map_all_nodes_to_pages
[INFO] [2019-10-14 00:36:02] 26 Unmatched nodes (of 665)! That's too many to output. First 10: Procelsterna (#50505326); Procelsterna cerulea (#50505325); Thalaseus (#50505443); Thalaseus bergii (#50505442); Puffinus pacificus (#50505327); Pomacentrus micronesicus (#50505682); Scorpaeniformes (#50505453); Aspidochirotida (#50505494); Chlorodopsis (#50505740); Clibanarius corallinus (#50505601)
[START] [2019-10-14 00:36:02] update_nodes
[STOP] [2019-10-14 00:36:02] update_nodes
[STOP] [2019-10-14 00:36:02] match_nodes
[START] [2019-10-14 00:36:02] reindex_search
[STOP] [2019-10-14 00:36:04] reindex_search
[START] [2019-10-14 00:36:04] normalize_units
[STOP] [2019-10-14 00:36:04] normalize_units
[START] [2019-10-14 00:36:04] calculate_statistics
[STOP] [2019-10-14 00:36:04] calculate_statistics
[START] [2019-10-14 00:36:04] complete_harvest_instance
[START] [2019-10-14 00:36:04] overall_tsv_creation
[INFO] [2019-10-14 00:36:04] Processing group of 665 in 1 batches of 10000
[INFO] [2019-10-14 00:36:52] 261 Traits (unfiltered)...
[INFO] [2019-10-14 00:37:06] 261 Traits (filtered)...
[INFO] [2019-10-14 00:37:06] 0 Associations (filtered)...
[INFO] [2019-10-14 00:37:49] 1305 metadata added.
[INFO] [2019-10-14 00:37:49] 0 metadata added.
[INFO] [2019-10-14 00:37:49] Average Time: 82.36
[INFO] [2019-10-14 00:37:49] Total Time: 1m46s
[STOP] [2019-10-14 00:37:49] overall_tsv_creation
[INFO] [2019-10-14 00:37:49] Done. Check your files:
[INFO] [2019-10-14 00:37:49] (665 lines) /app/public/data/kiribati_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 00:37:49] (3166 lines) /app/public/data/kiribati_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 00:37:49] (665 lines) /app/public/data/kiribati_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 00:37:49] (262 lines) /app/public/data/kiribati_sp_list/publish_traits.tsv
[INFO] [2019-10-14 00:37:49] (1306 lines) /app/public/data/kiribati_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 00:37:49] complete_harvest_instance
[START] [2019-10-14 00:37:49] completed
[STOP] [2019-10-14 00:37:49] completed
[STOP] [2019-10-14 00:37:49] logged process, took 198.04
Latest Process

14 Oct 00:34 EXITED currently processing 0