Harvest for Bad Frog Created 08 Aug 15:19

Harvesting Log

# Logfile created on 2019-08-08 15:19:55 -0400 by logger.rb/56815
[START] [2019-08-08 15:19:55] logged process
[START] [2019-08-08 15:19:55] create_harvest_instance
[STOP] [2019-08-08 15:19:55] create_harvest_instance
[START] [2019-08-08 15:19:55] fetch_files
[STOP] [2019-08-08 15:19:55] fetch_files
[START] [2019-08-08 15:19:55] validate_each_file
[STOP] [2019-08-08 15:19:57] validate_each_file
[START] [2019-08-08 15:19:57] convert_to_csv
[CMD] [2019-08-08 15:19:57] /usr/bin/sort /app/public/converted_csv/bad_frog_refs_14409.csv > /app/public/converted_csv/bad_frog_refs_14409.csv_sorted
[CMD] [2019-08-08 15:19:57] /usr/bin/sort /app/public/converted_csv/bad_frog_nodes_14410.csv > /app/public/converted_csv/bad_frog_nodes_14410.csv_sorted
[STOP] [2019-08-08 15:19:57] convert_to_csv
[START] [2019-08-08 15:19:57] calculate_delta
[CMD] [2019-08-08 15:19:57] echo "0a" > /app/public/diff/bad_frog_refs_14409.diff
[CMD] [2019-08-08 15:19:57] tail -n +1 /app/public/converted_csv/bad_frog_refs_14409.csv >> /app/public/diff/bad_frog_refs_14409.diff
[CMD] [2019-08-08 15:19:57] echo "." >> /app/public/diff/bad_frog_refs_14409.diff
[CMD] [2019-08-08 15:19:57] echo "0a" > /app/public/diff/bad_frog_nodes_14410.diff
[CMD] [2019-08-08 15:19:57] tail -n +1 /app/public/converted_csv/bad_frog_nodes_14410.csv >> /app/public/diff/bad_frog_nodes_14410.diff
[CMD] [2019-08-08 15:19:57] echo "." >> /app/public/diff/bad_frog_nodes_14410.diff
[STOP] [2019-08-08 15:19:57] calculate_delta
[START] [2019-08-08 15:19:57] parse_diff_and_store
[INFO] [2019-08-08 15:19:57] Loading refs diff file into memory (true lines)...
[INFO] [2019-08-08 15:19:58] Loading nodes diff file into memory (true lines)...
[INFO] [2019-08-08 15:20:09] Storing 4775 References
[INFO] [2019-08-08 15:20:09] Processing group of 4775 in 5 groups of 1000
[INFO] [2019-08-08 15:20:10] Average Time: 0.204
[INFO] [2019-08-08 15:20:10] Total Time: 2s
[INFO] [2019-08-08 15:20:10] Storing 31030 ScientificNames
[INFO] [2019-08-08 15:20:10] Processing group of 31030 in 32 groups of 1000
[INFO] [2019-08-08 15:20:24] Average Time: 0.44
[INFO] [2019-08-08 15:20:24] Total Time: 15s
[INFO] [2019-08-08 15:20:24] last 3 / first 3: 0.46
[INFO] [2019-08-08 15:20:24] Std.Dev: 0.12649110640673517; Max: 0.75
[INFO] [2019-08-08 15:20:24] Storing 8733 Nodes
[INFO] [2019-08-08 15:20:24] Processing group of 8733 in 9 groups of 1000
[INFO] [2019-08-08 15:20:28] Average Time: 0.432
[INFO] [2019-08-08 15:20:28] Total Time: 4s
[INFO] [2019-08-08 15:20:28] last 3 / first 3: 0.86
[INFO] [2019-08-08 15:20:28] Std.Dev: 0.05477225575051661; Max: 0.52
[STOP] [2019-08-08 15:20:28] parse_diff_and_store
[START] [2019-08-08 15:20:28] resolve_keys
[INFO] [2019-08-08 15:20:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-08-08 15:20:37] traits to occurrences...
[INFO] [2019-08-08 15:20:37] traits to nodes (through occurrences)...
[INFO] [2019-08-08 15:20:37] Traits to sex term...
[INFO] [2019-08-08 15:20:37] Traits to lifestage term...
[INFO] [2019-08-08 15:20:37] MetaTraits to traits...
[INFO] [2019-08-08 15:20:37] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-08-08 15:20:37] Assocs to occurrences...
[INFO] [2019-08-08 15:20:37] Assocs to nodes...
[INFO] [2019-08-08 15:20:37] Assoc to sex term...
[INFO] [2019-08-08 15:20:37] Assoc to lifestage term...
[STOP] [2019-08-08 15:20:37] resolve_keys
[START] [2019-08-08 15:20:37] hold_for_later_1
[STOP] [2019-08-08 15:20:37] hold_for_later_1
[START] [2019-08-08 15:20:37] hold_for_later_2
[STOP] [2019-08-08 15:20:37] hold_for_later_2
[START] [2019-08-08 15:20:37] resolve_missing_parents
[STOP] [2019-08-08 15:20:37] resolve_missing_parents
[START] [2019-08-08 15:20:37] rebuild_nodes
[START] [2019-08-08 15:20:37] Flattener#flatten
[START] [2019-08-08 15:20:37] Flattener#study_resource
[START] [2019-08-08 15:20:37] Flattener#build_ancestry
[STOP] [2019-08-08 15:20:38] Flattener#build_ancestry
[INFO] [2019-08-08 15:20:38] 8733 ancestry keys
[START] [2019-08-08 15:20:38] build_node_ancestors
[INFO] [2019-08-08 15:20:38] old ancestors deleted.
[STOP] [2019-08-08 15:20:40] build_node_ancestors
[START] [2019-08-08 15:20:43] Flattener#propagate_ancestor_ids
[STOP] [2019-08-08 15:20:44] Flattener#propagate_ancestor_ids
[STOP] [2019-08-08 15:20:44] Flattener#flatten
[STOP] [2019-08-08 15:20:44] rebuild_nodes
[START] [2019-08-08 15:20:44] resolve_missing_media_owners
[STOP] [2019-08-08 15:20:44] resolve_missing_media_owners
[START] [2019-08-08 15:20:44] sanitize_media_verbatims
[STOP] [2019-08-08 15:20:44] sanitize_media_verbatims
[START] [2019-08-08 15:20:44] queue_downloads
[STOP] [2019-08-08 15:20:44] queue_downloads
[START] [2019-08-08 15:20:44] parse_names
[WARN] [2019-08-08 15:20:44] I see 31030 names which still need to be parsed.
[STOP] [2019-08-08 15:21:11] parse_names
[START] [2019-08-08 15:21:11] denormalize_canonical_names_to_nodes
[STOP] [2019-08-08 15:21:11] denormalize_canonical_names_to_nodes
[START] [2019-08-08 15:21:11] match_nodes
[START] [2019-08-08 15:21:11] map_all_nodes_to_pages
[STOP] [2019-08-08 15:23:32] map_all_nodes_to_pages
[INFO] [2019-08-08 15:23:32] ZERO unmatched nodes (of 8733)! Nicely done.
[START] [2019-08-08 15:23:32] update_nodes
[STOP] [2019-08-08 15:23:36] update_nodes
[STOP] [2019-08-08 15:23:36] match_nodes
[START] [2019-08-08 15:23:36] reindex_search
[STOP] [2019-08-08 15:23:53] reindex_search
[START] [2019-08-08 15:23:53] normalize_units
[STOP] [2019-08-08 15:23:53] normalize_units
[START] [2019-08-08 15:23:53] calculate_statistics
[STOP] [2019-08-08 15:23:53] calculate_statistics
[START] [2019-08-08 15:23:53] complete_harvest_instance
[START] [2019-08-08 15:23:53] overall_tsv_creation
[INFO] [2019-08-08 15:23:53] Processing group of 8733 in 1 batches of 10000
[2019-08-08 15:24:25] Encountered new taxonomic status, please assign set its alternative/preferred/problematic/mergeable: valid
[2019-08-08 15:24:25] Encountered new taxonomic status, please assign set its alternative/preferred/problematic/mergeable: invalid
[INFO] [2019-08-08 15:25:38] Average Time: 73.58
[INFO] [2019-08-08 15:25:38] Total Time: 1m45s
[STOP] [2019-08-08 15:25:38] overall_tsv_creation
[INFO] [2019-08-08 15:25:38] Done. Check your files:
[INFO] [2019-08-08 15:25:38] (8733 lines) /app/public/data/bad_frog/publish_nodes.tsv
[INFO] [2019-08-08 15:25:38] (38174 lines) /app/public/data/bad_frog/publish_node_ancestors.tsv
[INFO] [2019-08-08 15:25:38] (31027 lines) /app/public/data/bad_frog/publish_scientific_names.tsv
[STOP] [2019-08-08 15:25:38] complete_harvest_instance
[START] [2019-08-08 15:25:38] completed
[STOP] [2019-08-08 15:25:38] completed
[STOP] [2019-08-08 15:25:38] logged process, took 343.6

Latest Process

08 Aug 15:19 EXITED currently processing 0