Harvest for Niger Species List Created 14 Oct 13:51

Stage: completed
Fetched: 14 Oct 13:51
Validated: 14 Oct 13:51
Deltas Created 14 Oct 13:51
Units Normalized: 14 Oct 13:54
Ancestry Built: 14 Oct 13:52
Nodes Matched: 14 Oct 13:54
Names Parsed: 14 Oct 13:52
New Models Stored: 14 Oct 13:51
Indexed: 14 Oct 13:54
Completed: 14 Oct 13:55
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 13:51:24 -0400 by logger.rb/56815
[START] [2019-10-14 13:51:24] logged process
[START] [2019-10-14 13:51:24] create_harvest_instance
[STOP] [2019-10-14 13:51:25] create_harvest_instance
[START] [2019-10-14 13:51:25] fetch_files
[STOP] [2019-10-14 13:51:25] fetch_files
[START] [2019-10-14 13:51:25] validate_each_file
[STOP] [2019-10-14 13:51:25] validate_each_file
[START] [2019-10-14 13:51:25] convert_to_csv
[CMD] [2019-10-14 13:51:25] /usr/bin/sort /app/public/converted_csv/niger_sp_list_refs_16715.csv > /app/public/converted_csv/niger_sp_list_refs_16715.csv_sorted
[CMD] [2019-10-14 13:51:25] /usr/bin/sort /app/public/converted_csv/niger_sp_list_nodes_16716.csv > /app/public/converted_csv/niger_sp_list_nodes_16716.csv_sorted
[CMD] [2019-10-14 13:51:25] /usr/bin/sort /app/public/converted_csv/niger_sp_list_occurrences_16717.csv > /app/public/converted_csv/niger_sp_list_occurrences_16717.csv_sorted
[CMD] [2019-10-14 13:51:26] /usr/bin/sort /app/public/converted_csv/niger_sp_list_measurements_16718.csv > /app/public/converted_csv/niger_sp_list_measurements_16718.csv_sorted
[STOP] [2019-10-14 13:51:26] convert_to_csv
[START] [2019-10-14 13:51:26] calculate_delta
[CMD] [2019-10-14 13:51:26] echo "0a" > /app/public/diff/niger_sp_list_refs_16715.diff
[CMD] [2019-10-14 13:51:26] tail -n +1 /app/public/converted_csv/niger_sp_list_refs_16715.csv >> /app/public/diff/niger_sp_list_refs_16715.diff
[CMD] [2019-10-14 13:51:26] echo "." >> /app/public/diff/niger_sp_list_refs_16715.diff
[CMD] [2019-10-14 13:51:26] echo "0a" > /app/public/diff/niger_sp_list_nodes_16716.diff
[CMD] [2019-10-14 13:51:26] tail -n +1 /app/public/converted_csv/niger_sp_list_nodes_16716.csv >> /app/public/diff/niger_sp_list_nodes_16716.diff
[CMD] [2019-10-14 13:51:26] echo "." >> /app/public/diff/niger_sp_list_nodes_16716.diff
[CMD] [2019-10-14 13:51:26] echo "0a" > /app/public/diff/niger_sp_list_occurrences_16717.diff
[CMD] [2019-10-14 13:51:26] tail -n +1 /app/public/converted_csv/niger_sp_list_occurrences_16717.csv >> /app/public/diff/niger_sp_list_occurrences_16717.diff
[CMD] [2019-10-14 13:51:26] echo "." >> /app/public/diff/niger_sp_list_occurrences_16717.diff
[CMD] [2019-10-14 13:51:27] echo "0a" > /app/public/diff/niger_sp_list_measurements_16718.diff
[CMD] [2019-10-14 13:51:27] tail -n +1 /app/public/converted_csv/niger_sp_list_measurements_16718.csv >> /app/public/diff/niger_sp_list_measurements_16718.diff
[CMD] [2019-10-14 13:51:27] echo "." >> /app/public/diff/niger_sp_list_measurements_16718.diff
[STOP] [2019-10-14 13:51:27] calculate_delta
[START] [2019-10-14 13:51:27] parse_diff_and_store
[INFO] [2019-10-14 13:51:27] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 13:51:27] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 13:51:28] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 13:51:28] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 13:51:36] Storing 2 References
[INFO] [2019-10-14 13:51:36] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 13:51:36] Average Time: 0.0
[INFO] [2019-10-14 13:51:36] Total Time: 1s
[INFO] [2019-10-14 13:51:36] Storing 2615 ScientificNames
[INFO] [2019-10-14 13:51:36] Processing group of 2615 in 3 groups of 1000
[INFO] [2019-10-14 13:51:37] Average Time: 0.323
[INFO] [2019-10-14 13:51:37] Total Time: 1s
[INFO] [2019-10-14 13:51:37] Storing 2615 Nodes
[INFO] [2019-10-14 13:51:37] Processing group of 2615 in 3 groups of 1000
[INFO] [2019-10-14 13:51:38] Average Time: 0.25
[INFO] [2019-10-14 13:51:38] Total Time: 1s
[INFO] [2019-10-14 13:51:38] Storing 964 Occurrences
[INFO] [2019-10-14 13:51:38] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-14 13:51:38] Average Time: 0.11
[INFO] [2019-10-14 13:51:38] Total Time: 1s
[INFO] [2019-10-14 13:51:38] Storing 2730 TraitsReferences
[INFO] [2019-10-14 13:51:38] Processing group of 2730 in 3 groups of 1000
[INFO] [2019-10-14 13:51:38] Average Time: 0.083
[INFO] [2019-10-14 13:51:38] Total Time: 1s
[INFO] [2019-10-14 13:51:38] Storing 2729 Traits
[INFO] [2019-10-14 13:51:38] Processing group of 2729 in 3 groups of 1000
[INFO] [2019-10-14 13:51:39] Average Time: 0.3
[INFO] [2019-10-14 13:51:39] Total Time: 1s
[INFO] [2019-10-14 13:51:39] Storing 2729 MetaTraits
[INFO] [2019-10-14 13:51:39] Processing group of 2729 in 3 groups of 1000
[INFO] [2019-10-14 13:51:40] Average Time: 0.11
[INFO] [2019-10-14 13:51:40] Total Time: 1s
[STOP] [2019-10-14 13:51:40] parse_diff_and_store
[START] [2019-10-14 13:51:40] resolve_keys
[INFO] [2019-10-14 13:51:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 13:51:53] traits to occurrences...
[INFO] [2019-10-14 13:51:54] traits to nodes (through occurrences)...
[INFO] [2019-10-14 13:51:54] Traits to sex term...
[INFO] [2019-10-14 13:51:55] Traits to lifestage term...
[INFO] [2019-10-14 13:51:56] MetaTraits to traits...
[INFO] [2019-10-14 13:51:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 13:51:56] Assocs to occurrences...
[INFO] [2019-10-14 13:51:56] Assocs to nodes...
[INFO] [2019-10-14 13:51:56] Assoc to sex term...
[INFO] [2019-10-14 13:51:56] Assoc to lifestage term...
[STOP] [2019-10-14 13:51:56] resolve_keys
[START] [2019-10-14 13:51:56] hold_for_later_1
[STOP] [2019-10-14 13:51:56] hold_for_later_1
[START] [2019-10-14 13:51:56] hold_for_later_2
[STOP] [2019-10-14 13:51:56] hold_for_later_2
[START] [2019-10-14 13:51:56] resolve_missing_parents
[STOP] [2019-10-14 13:52:01] resolve_missing_parents
[START] [2019-10-14 13:52:01] rebuild_nodes
[START] [2019-10-14 13:52:01] Flattener#flatten
[START] [2019-10-14 13:52:01] Flattener#study_resource
[START] [2019-10-14 13:52:01] Flattener#build_ancestry
[STOP] [2019-10-14 13:52:01] Flattener#build_ancestry
[INFO] [2019-10-14 13:52:01] 2615 ancestry keys
[START] [2019-10-14 13:52:01] build_node_ancestors
[INFO] [2019-10-14 13:52:01] old ancestors deleted.
[STOP] [2019-10-14 13:52:01] build_node_ancestors
[START] [2019-10-14 13:52:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 13:52:02] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 13:52:02] Flattener#flatten
[STOP] [2019-10-14 13:52:02] rebuild_nodes
[START] [2019-10-14 13:52:02] resolve_missing_media_owners
[STOP] [2019-10-14 13:52:02] resolve_missing_media_owners
[START] [2019-10-14 13:52:02] sanitize_media_verbatims
[STOP] [2019-10-14 13:52:02] sanitize_media_verbatims
[START] [2019-10-14 13:52:02] queue_downloads
[STOP] [2019-10-14 13:52:02] queue_downloads
[START] [2019-10-14 13:52:02] parse_names
[WARN] [2019-10-14 13:52:02] I see 2615 names which still need to be parsed.
[STOP] [2019-10-14 13:52:05] parse_names
[START] [2019-10-14 13:52:05] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 13:52:05] denormalize_canonical_names_to_nodes
[START] [2019-10-14 13:52:05] match_nodes
[START] [2019-10-14 13:52:05] map_all_nodes_to_pages
[STOP] [2019-10-14 13:54:04] map_all_nodes_to_pages
[INFO] [2019-10-14 13:54:04] 127 Unmatched nodes (of 2615)! That's too many to output. First 10: Diplostomida (#50941219); Strigeatida (#50941231); Schistosoma (#50941217); Schistosoma haematobium (#50941216); Schistosoma bovis (#50941284); Schistosoma mansoni (#50941631); Apharyngostrigea ibis (#50943703); Plagiorchiida (#50943074); Bulinus senegalensis (#50943656); Basommatophora (#50941244)
[START] [2019-10-14 13:54:04] update_nodes
[STOP] [2019-10-14 13:54:04] update_nodes
[STOP] [2019-10-14 13:54:04] match_nodes
[START] [2019-10-14 13:54:04] reindex_search
[STOP] [2019-10-14 13:54:09] reindex_search
[START] [2019-10-14 13:54:09] normalize_units
[STOP] [2019-10-14 13:54:09] normalize_units
[START] [2019-10-14 13:54:09] calculate_statistics
[STOP] [2019-10-14 13:54:09] calculate_statistics
[START] [2019-10-14 13:54:09] complete_harvest_instance
[START] [2019-10-14 13:54:09] overall_tsv_creation
[INFO] [2019-10-14 13:54:09] Processing group of 2615 in 1 batches of 10000
[INFO] [2019-10-14 13:55:06] 964 Traits (unfiltered)...
[INFO] [2019-10-14 13:55:19] 964 Traits (filtered)...
[INFO] [2019-10-14 13:55:19] 0 Associations (filtered)...
[INFO] [2019-10-14 13:55:58] 4819 metadata added.
[INFO] [2019-10-14 13:55:58] 0 metadata added.
[INFO] [2019-10-14 13:55:58] Average Time: 86.1
[INFO] [2019-10-14 13:55:58] Total Time: 1m49s
[STOP] [2019-10-14 13:55:58] overall_tsv_creation
[INFO] [2019-10-14 13:55:58] Done. Check your files:
[INFO] [2019-10-14 13:55:58] (2615 lines) /app/public/data/niger_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 13:55:58] (6849 lines) /app/public/data/niger_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 13:55:58] (2615 lines) /app/public/data/niger_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 13:55:58] (965 lines) /app/public/data/niger_sp_list/publish_traits.tsv
[INFO] [2019-10-14 13:55:58] (4820 lines) /app/public/data/niger_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 13:55:59] complete_harvest_instance
[START] [2019-10-14 13:55:59] completed
[STOP] [2019-10-14 13:55:59] completed
[STOP] [2019-10-14 13:55:59] logged process, took 274.44
Latest Process

14 Oct 13:51 EXITED currently processing 0